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Inyang KE, Evans CM, Heussner M, Petroff M, Reimers M, Vermeer PD, Tykocki N, Folger JK, Laumet G. HPV+ head and neck cancer-derived small extracellular vesicles communicate with TRPV1+ neurons to mediate cancer pain. Pain 2024; 165:608-620. [PMID: 37678566 PMCID: PMC10915104 DOI: 10.1097/j.pain.0000000000003045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
ABSTRACT Severe pain is often experienced by patients with head and neck cancer and is associated with a poor prognosis. Despite its frequency and severity, current treatments fail to adequately control cancer-associated pain because of our lack of mechanistic understanding. Although recent works have shed some light of the biology underlying pain in HPV-negative oral cancers, the mechanisms mediating pain in HPV+ cancers remain unknown. Cancer-derived small extracellular vesicles (cancer-sEVs) are well positioned to function as mediators of communication between cancer cells and neurons. Inhibition of cancer-sEV release attenuated pain in tumor-bearing mice. Injection of purified cancer-sEVs is sufficient to induce pain hypersensitivity in naive mice that is prevented by QX-314 treatment and in Trpv1-/- mice. Cancer-sEVs triggered calcium influx in nociceptors, and inhibition or ablation of nociceptors protects against cancer pain. Interrogation of published sequencing data of human sensory neurons exposed to human cancer-sEVs suggested a stimulation of protein translation in neurons. Induction of translation by cancer-sEVs was validated in our mouse model, and its inhibition alleviated cancer pain in mice. In summary, our work reveals that HPV+ head and neck squamous cell carcinoma-derived sEVs alter TRPV1+ neurons by promoting nascent translation to mediate cancer pain and identified several promising therapeutic targets to interfere with this pathway.
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Affiliation(s)
| | - Christine M. Evans
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Matthew Heussner
- Department of Physiology, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI
| | - Margaret Petroff
- Department of Pathology Michigan State University College of Veterinary Medicine, East Lansing, MI
| | - Mark Reimers
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Paola D. Vermeer
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
| | - Nathan Tykocki
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
| | - Joseph K. Folger
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Geoffroy Laumet
- Department of Physiology, Michigan State University, East Lansing, MI, USA
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2
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Sirois J, Reddy S, Nguyen T, Walker H, Rendall J, Bergen G, Reimers M, Cermak E, Tiwary A, Helmes E, Palmer J, Teo S, Mackle T, Park M, Wang C. Safety considerations for dietary supplement manufacturers in the United States. Regul Toxicol Pharmacol 2024; 147:105544. [PMID: 38158034 DOI: 10.1016/j.yrtph.2023.105544] [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] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Due to significant dietary supplement use in the US, product manufacturers must understand the importance of implementing a robust approach to establishing safety for all ingredients, including dietary ingredients, components, and finished dietary supplement products. Different regulatory pathways exist by which the safety of dietary ingredients can be established, and thus allowed to be marketed in a dietary supplement. For individual dietary ingredients, safety information may come from a variety of sources including history of safe use, presence of the ingredient in foods, and/or non-clinical and clinical data. On occasion safety data gaps are identified for a specific ingredient, particularly those of botanical origin. Modern toxicological methods and models can prove helpful in satisfying data gaps and are presented in this review. For finished dietary supplement products, issues potentially impacting safety to consider include claims, product labeling, overages, contaminants, residual solvents, heavy metals, packaging, and product stability. In addition, a safety assessment does not end once a product is marketed. It is important that manufacturers actively monitor and record the occurrence of adverse events reported in association with the use of their products, in accordance with the law. Herein, we provide a comprehensive overview of considerations for assessing dietary supplement safety.
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Affiliation(s)
- Jay Sirois
- Consumer Healthcare Products Association, Washington, DC, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | - Mimi Park
- Nestle Health Science, Bridgewater, NJ, USA
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3
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Baumann BC, Laugeman E, Kohlmyer S, Levine L, Russell K, Smith Z, Reimers M, Michalski JM, Picus J, Pachynski R, Sivaraman A, Thomas L, Smelser W, Sands K, Kim E, Frankel J, Moravan MJ, Gay HA, Price AT. ARTIA-Bladder: Daily Online Adaptive Short-Course Radiation Therapy (RT) and Concurrent Chemotherapy for Muscle-Invasive Bladder Cancer (MIBC): A Prospective Trial of an Individualized Approach for Reducing Bowel and Bladder Toxicity. Int J Radiat Oncol Biol Phys 2023; 117:e366. [PMID: 37785254 DOI: 10.1016/j.ijrobp.2023.06.2461] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Concurrent chemo-radiotherapy is commonly prescribed for muscle-invasive bladder cancer (MIBC). Post hoc analysis of two large, randomized trials found that hypofractionation improves loco-regional control (LRC) vs. standard fractionation in this population. A challenge in traditional image-guided radiotherapy of the bladder is that daily changes in bladder position and size requires large margins to ensure target coverage. This makes it difficult to spare uninvolved bladder from high-dose treatment, increases the risk of bowel toxicity, and results in historical rates of acute G3+ toxicity exceeding 20-30%. Daily online adaptive RT (ART) may enable reduced, personalized margins that maintain target coverage while reducing dose to OARs. This prospective clinical trial will test whether: 1) participants undergoing ART for MIBC have a lower rate of acute G3+ GI/GU toxicity compared with the 31% historical control rate (Stage III BC2001 trial), and 2) 2-year LRC with ART will be non-inferior to historical controls (75%). MATERIALS/METHODS This multi-national trial will enroll 165 adult subjects with stage cT2-T4aN0M0 urothelial MIBC. Subjects will have undergone an attempt at maximal transurethral resection of bladder tumor. Patients with clinically involved nodes or G2+ GI or G3+ GU symptoms/conditions at baseline are ineligible. Concurrent with chemotherapy, participants will receive (at the discretion of the investigator) either 55 Gy in 20 fx to whole-bladder or 46 Gy in 20 fx to whole-bladder plus simultaneous in-field boost of 55 Gy in 20 fx to tumor bed. A personalized ITV will be derived for each subject based on bladder expansion, as assessed on two CT simulations separated by 30 min. Daily ART will be attempted for all subjects. The primary endpoint is acute G3+ GI/GU toxicity. Secondary endpoints are LRC; quality of life (EORTC QLQ-BLM30, EPIC 26 bowel and urinary); global function (EQ-5D-5L ); 2-year disease-free, bladder intact event-free, and overall survival; 2-year bladder cancer-specific mortality; NTCP model of acute GI toxicity for hypofractionated bladder RT; workflow feasibility of ART; improved target coverage ± reduced dose to critical OARs vs. non-ART dosimetry; acute G3+ GI/GU toxicity rate in subjects with ≥75% of their treatments as ART; and acute G3+ GI/GU toxicity in the cohort treated with partial bladder boost. Exploratory translational and correlative endpoints will also be examined. RESULTS This trial opened to enrollment on Feb 2, 2023; the study duration is expected to be 4-5 years. CONCLUSION This prospective clinical trial will provide robust clinical data to inform healthcare providers' decisions on the use of daily online ART and hypofractionation as a bladder preservation strategy for this population.
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Affiliation(s)
- B C Baumann
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - E Laugeman
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | | | - L Levine
- Varian Medical Systems, A Siemens Healthineers Company, Palo Alto, CA
| | - K Russell
- Varian Medical Systems, Palo Alto, CA
| | - Z Smith
- Department of Surgery, Division of Urology, Washington University School of Medicine, St. Louis, MO
| | - M Reimers
- Washington University School of Medicine, Department of Medicine, Division of Medical Oncology, St. Louis, MO
| | - J M Michalski
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - J Picus
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO
| | - R Pachynski
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO
| | - A Sivaraman
- Washington University in St. Louis, St. Louis, MO
| | - L Thomas
- Washington University in St. Louis, St. Louis, MO
| | - W Smelser
- Washington University in St. Louis, St Louis, MO
| | - K Sands
- Washington University in St. Louis, St. Louis, MO
| | - E Kim
- Department of Surgery, Division of Urology, Washington University School of Medicine, St. Louis, MO
| | - J Frankel
- Washington University in St. Louis, St. Louis, MO
| | - M J Moravan
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO
| | - H A Gay
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - A T Price
- University Hospitals, Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH
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Cai NA, Bigdeli TB, Kretzschmar W, Li Y, Liang J, Song L, Hu J, Li Q, Jin W, Hu Z, Wang G, Wang L, Qian P, Liu Y, Jiang T, Lu Y, Zhang X, Yin Y, Li Y, Xu X, Gao J, Reimers M, Webb T, Riley B, Bacanu S, Peterson RE, Chen Y, Zhong H, Liu Z, Wang G, Sun J, Sang H, Jiang G, Zhou X, Li Y, Li Y, Zhang W, Wang X, Fang X, Pan R, Miao G, Zhang Q, Hu J, Yu F, Du B, Sang W, Li K, Chen G, Cai M, Yang L, Yang D, Ha B, Hong X, Deng H, Li G, Li K, Song Y, Gao S, Zhang J, Gan Z, Meng H, Pan J, Gao C, Zhang K, Sun N, Li Y, Niu Q, Zhang Y, Liu T, Hu C, Zhang Z, Lv L, Dong J, Wang X, Tao M, Wang X, Xia J, Rong H, He Q, Liu T, Huang G, Mei Q, Shen Z, Liu Y, Shen J, Tian T, Liu X, Wu W, Gu D, Fu G, Shi J, Chen Y, Gan X, Liu L, Wang L, Yang F, Cong E, Marchini J, Yang H, Wang J, Shi S, Mott R, Xu Q, Wang J, Kendler KS, Flint J. Author Correction: Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 2023; 620:E28. [PMID: 37567929 DOI: 10.1038/s41586-023-06276-1] [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: 08/13/2023]
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5
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Andruska N, Fischer-Valuck B, Efstathiou J, Smith Z, Kim E, Brenneman R, Reimers M, Gay H, Patel S, Michalski J, Delacroix S, Baumann B. Does Chemo-Radiotherapy Improve Survival Outcomes vs. Radiotherapy Alone for High-Grade cT1 Urothelial Carcinoma of the Bladder? Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1126] [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: 10/31/2022]
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6
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Wang Z, Belecciu T, Eaves J, Reimers M, Bachmann MH, Woldring D. Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction. J Biomol Struct Dyn 2022:1-21. [PMID: 35993534 DOI: 10.1080/07391102.2022.2112976] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but in-silico screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zirui Wang
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Theodore Belecciu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Joelle Eaves
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Mark Reimers
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Michael H Bachmann
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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7
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Laumet G, Inyang KE, Evans CM, Heussner M, Petroff M, Reimers M, Tykocki N, Vermeer P, Folger JK. Head and Neck Cancer‐derived Small Extracellular Vesicles Activate TRPV1+ neurons to Mediate Cancer Pain. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7547] [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)
| | | | | | | | | | - Mark Reimers
- PhysiologyMichigan State UniversityEast LansingMI
| | - Nathan Tykocki
- Pharmacology and ToxicologyMichigan State UniversityEast LansingMI
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8
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Chen K, Chauhan P, Babbra R, Feng W, Pejovic N, Harris P, Dienstbach K, Atkocius A, Maguire L, Qaium F, Huang Y, Szymanski J, Baumann B, Ding L, Cao D, Reimers M, Kim E, Smith Z, Arora V, Chaudhuri A. Urine- and Plasma-Based Detection of Minimal Residual Disease in Localized Bladder Cancer Patients. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.854] [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: 11/28/2022]
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9
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Hunt RD, Ashbaugh RC, Reimers M, Udpa L, Saldana De Jimenez G, Moore M, Gilad AA, Pelled G. Swimming direction of the glass catfish is responsive to magnetic stimulation. PLoS One 2021; 16:e0248141. [PMID: 33667278 PMCID: PMC7935302 DOI: 10.1371/journal.pone.0248141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/21/2021] [Indexed: 12/19/2022] Open
Abstract
Several marine species have developed a magnetic perception that is essential for navigation and detection of prey and predators. One of these species is the transparent glass catfish that contains an ampullary organ dedicated to sense magnetic fields. Here we examine the behavior of the glass catfish in response to static magnetic fields which will provide valuable insight on function of this magnetic response. By utilizing state of the art animal tracking software and artificial intelligence approaches, we quantified the effects of magnetic fields on the swimming direction of glass catfish. The results demonstrate that glass catfish placed in a radial arm maze, consistently swim away from magnetic fields over 20 μT and show adaptability to changing magnetic field direction and location.
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Affiliation(s)
- Ryan D. Hunt
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Ryan C. Ashbaugh
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Mark Reimers
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Physiology and Neuroscience Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Lalita Udpa
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Gabriela Saldana De Jimenez
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Michael Moore
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Physiology and Neuroscience Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Assaf A. Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Radiology, Michigan State University, East Lansing, Michigan, United States of America
- Synthetic Biology Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Galit Pelled
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Neuroengineering Division, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Radiology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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10
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Dozmorov MG, Cresswell KG, Bacanu SA, Craver C, Reimers M, Kendler KS. A method for estimating coherence of molecular mechanisms in major human disease and traits. BMC Bioinformatics 2020; 21:473. [PMID: 33087046 PMCID: PMC7579960 DOI: 10.1186/s12859-020-03821-x] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Phenotypes such as height and intelligence, are thought to be a product of the collective effects of multiple phenotype-associated genes and interactions among their protein products. High/low degree of interactions is suggestive of coherent/random molecular mechanisms, respectively. Comparing the degree of interactions may help to better understand the coherence of phenotype-specific molecular mechanisms and the potential for therapeutic intervention. However, direct comparison of the degree of interactions is difficult due to different sizes and configurations of phenotype-associated gene networks. METHODS We introduce a metric for measuring coherence of molecular-interaction networks as a slope of internal versus external distributions of the degree of interactions. The internal degree distribution is defined by interaction counts within a phenotype-specific gene network, while the external degree distribution counts interactions with other genes in the whole protein-protein interaction (PPI) network. We present a novel method for normalizing the coherence estimates, making them directly comparable. RESULTS Using STRING and BioGrid PPI databases, we compared the coherence of 116 phenotype-associated gene sets from GWAScatalog against size-matched KEGG pathways (the reference for high coherence) and random networks (the lower limit of coherence). We observed a range of coherence estimates for each category of phenotypes. Metabolic traits and diseases were the most coherent, while psychiatric disorders and intelligence-related traits were the least coherent. We demonstrate that coherence and modularity measures capture distinct network properties. CONCLUSIONS We present a general-purpose method for estimating and comparing the coherence of molecular-interaction gene networks that accounts for the network size and shape differences. Our results highlight gaps in our current knowledge of genetics and molecular mechanisms of complex phenotypes and suggest priorities for future GWASs.
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Affiliation(s)
- Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA USA
| | - Kellen G. Cresswell
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavior Genetics and the Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
| | - Carl Craver
- Philosophy-Neuroscience-Psychology Program, Washington University in St. Louis, St. Louis, MO USA
| | - Mark Reimers
- Department Physiology, Michigan State University, East Lansing, MI USA
- Department Biomedical Engineering, Michigan State University, East Lansing, MI USA
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavior Genetics and the Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
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11
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Cywiak C, Ashbaugh RC, Metto AC, Udpa L, Qian C, Gilad AA, Reimers M, Zhong M, Pelled G. Non-invasive neuromodulation using rTMS and the electromagnetic-perceptive gene (EPG) facilitates plasticity after nerve injury. Brain Stimul 2020; 13:1774-1783. [PMID: 33068795 DOI: 10.1016/j.brs.2020.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Twenty million Americans suffer from peripheral nerve injury. These patients often develop chronic pain and sensory dysfunctions. In the past decade, neuroimaging studies showed that these changes are associated with altered cortical excitation-inhibition balance and maladaptive plasticity. We tested if neuromodulation of the deprived sensory cortex could restore the cortical balance, and whether it would be effective in alleviating sensory complications. OBJECTIVE We tested if non-invasive repetitive transcranial magnetic stimulation (rTMS) which induces neuronal excitability, and cell-specific magnetic activation via the Electromagnetic-perceptive gene (EPG) which is a novel gene that was identified and cloned from glass catfish and demonstrated to evoke neural responses when magnetically stimulated, can restore cortical excitability. METHODS A rat model of forepaw denervation was used. rTMS was delivered every other day for 30 days, starting at the acute or at the chronic post-injury phase. A minimally-invasive neuromodulation via EPG was performed every day for 30 days starting at the chronic phase. A battery of behavioral tests was performed in the days and weeks following limb denervation in EPG-treated rats, and behavioral tests, fMRI and immunochemistry were performed in rTMS-treated rats. RESULTS The results demonstrate that neuromodulation significantly improved long-term mobility, decreased anxiety and enhanced neuroplasticity. The results identify that both acute and delayed rTMS intervention facilitated rehabilitation. Moreover, the results implicate EPG as an effective cell-specific neuromodulation approach. CONCLUSION Together, these results reinforce the growing amount of evidence from human and animal studies that are establishing neuromodulation as an effective strategy to promote plasticity and rehabilitation.
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Affiliation(s)
- Carolina Cywiak
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA; The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Ryan C Ashbaugh
- The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA
| | - Abigael C Metto
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA; The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Lalita Udpa
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA
| | - Chunqi Qian
- Department of Radiology, Michigan State University, East Lansing, MI, USA
| | - Assaf A Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA; The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Radiology, Michigan State University, East Lansing, MI, USA
| | - Mark Reimers
- The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Physiology and Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Ming Zhong
- The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Galit Pelled
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA; The Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Radiology, Michigan State University, East Lansing, MI, USA.
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12
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Valley MT, Moore MG, Zhuang J, Mesa N, Castelli D, Sullivan D, Reimers M, Waters J. Separation of hemodynamic signals from GCaMP fluorescence measured with wide-field imaging. J Neurophysiol 2020; 123:356-366. [DOI: 10.1152/jn.00304.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Wide-field calcium imaging is often used to measure brain dynamics in behaving mice. With a large field of view and a high sampling rate, wide-field imaging can monitor activity from several distant cortical areas simultaneously, revealing cortical interactions. Interpretation of wide-field images is complicated, however, by the absorption of light by hemoglobin, which can substantially affect the measured fluorescence. One approach to separating hemodynamics and calcium signals is to use multiwavelength backscatter recordings to measure light absorption by hemoglobin. Following this approach, we develop a spatially detailed regression-based method to estimate hemodynamics. This Spatial Model is based on a linear form of the Beer–Lambert relationship but is fit at every pixel in the image and does not rely on the estimation of physical parameters. In awake mice of three transgenic lines, the Spatial Model offers improved separation of hemodynamics and changes in GCaMP fluorescence. The improvement is pronounced near blood vessels and, in contrast with the Beer–Lambert equations, can remove vascular artifacts along the sagittal midline and in general permits more accurate fluorescence-based determination of neuronal activity across the cortex. NEW & NOTEWORTHY This paper addresses a well-known and strong source of contamination in wide-field calcium-imaging data: hemodynamics. To guide researchers toward the best method to separate calcium signals from hemodynamics, we compare the performance of several methods in three commonly used mouse lines and present a novel regression model that outperforms the other techniques we consider.
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Affiliation(s)
- M. T. Valley
- Allen Institute for Brain Science, Seattle, Washington
| | - M. G. Moore
- Neuroscience Program and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan
| | - J. Zhuang
- Allen Institute for Brain Science, Seattle, Washington
| | - N. Mesa
- Allen Institute for Brain Science, Seattle, Washington
| | - D. Castelli
- Allen Institute for Brain Science, Seattle, Washington
| | - D. Sullivan
- Allen Institute for Brain Science, Seattle, Washington
| | - M. Reimers
- Neuroscience Program and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan
| | - J. Waters
- Allen Institute for Brain Science, Seattle, Washington
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13
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Krishnan VS, Shin SS, Belegu V, Celnik P, Reimers M, Smith KR, Pelled G. Multimodal Evaluation of TMS - Induced Somatosensory Plasticity and Behavioral Recovery in Rats With Contusion Spinal Cord Injury. Front Neurosci 2019; 13:387. [PMID: 31068784 PMCID: PMC6491761 DOI: 10.3389/fnins.2019.00387] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
Introduction: Spinal cord injury (SCI) causes partial or complete damage to sensory and motor pathways and induces immediate changes in cortical function. Current rehabilitative strategies do not address this early alteration, therefore impacting the degree of neuroplasticity and subsequent recovery. The following study aims to test if a non-invasive brain stimulation technique such as repetitive transcranial magnetic stimulation (rTMS) is effective in promoting plasticity and rehabilitation, and can be used as an early intervention strategy in a rat model of SCI. Methods: A contusion SCI was induced at segment T9 in adult rats. An rTMS coil was positioned over the brain to deliver high frequency stimulation. Behavior, motor and sensory functions were tested in three groups: SCI rats that received high-frequency (20 Hz) rTMS within 10 min post-injury (acute-TMS; n = 7); SCI rats that received TMS starting 2 weeks post-injury (chronic-TMS; n = 5), and SCI rats that received sham TMS (no-TMS, n = 5). Locomotion was evaluated by the Basso, Beattie, and Bresnahan (BBB) and gridwalk tests. Motor evoked potentials (MEP) were recorded from the forepaw across all groups to measure integrity of motor pathways. Functional MRI (fMRI) responses to contralateral tactile hindlimb stimulation were measured in an 11.7T horizontal bore small-animal scanner. Results: The acute-TMS group demonstrated the fastest improvements in locomotor performance in both the BBB and gridwalk tests compared to chronic and no-TMS groups. MEP responses from forepaw showed significantly greater difference in the inter-peak latency between acute-TMS and no-TMS groups, suggesting increases in motor function. Finally, the acute-TMS group showed increased fMRI-evoked responses to hindlimb stimulation over the right and left hindlimb (LHL) primary somatosensory representations (S1), respectively; the chronic-TMS group showed moderate sensory responses in comparison, and the no-TMS group exhibited the lowest sensory responses to both hindlimbs. Conclusion: The results suggest that rTMS therapy beginning in the acute phase after SCI promotes neuroplasticity and is an effective rehabilitative approach in a rat model of SCI.
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Affiliation(s)
- Vijai S Krishnan
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States.,The Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States.,Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Samuel S Shin
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States
| | - Visar Belegu
- Department of Neurology and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,International Center for Spinal Cord Injury, Kennedy Krieger Institute, Baltimore, MD, United States
| | - Pablo Celnik
- Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mark Reimers
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States.,The Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Kylie R Smith
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States.,The Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Galit Pelled
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States.,The Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States.,Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Radiology, Michigan State University, East Lansing, MI, United States
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14
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Guelfi S, Botia JA, Thom M, Ramasamy A, Perona M, Stanyer L, Martinian L, Trabzuni D, Smith C, Walker R, Ryten M, Reimers M, Weale ME, Hardy J, Matarin M. Transcriptomic and genetic analyses reveal potential causal drivers for intractable partial epilepsy. Brain 2019; 142:1616-1630. [DOI: 10.1093/brain/awz074] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 12/10/2018] [Accepted: 01/31/2019] [Indexed: 01/05/2023] Open
Affiliation(s)
- Sebastian Guelfi
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
| | - Juan A. Botia
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Maria Thom
- Division of Neuropathology, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
| | | | - Marina Perona
- Department of Radiobiology (CAC), National Atomic Energy Commission (CNEA), National Scientific and Technical Research Council (CONICET), Argentina
| | - Lee Stanyer
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
| | - Lillian Martinian
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Daniah Trabzuni
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Colin Smith
- Academic Department of Neuropathology, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert Walker
- Academic Department of Neuropathology, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
| | - Mark Reimers
- Neuroscience Program and Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Michael E. Weale
- Department Medical and Molecular Genetics, King’s College London, London, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
| | - Mar Matarin
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, UK
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, Queen Square, London, WC1N 3, UK
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15
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Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Molecular and cellular reorganization of neural circuits in the human lineage. Science 2018; 358:1027-1032. [PMID: 29170230 DOI: 10.1126/science.aan3456] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/17/2017] [Indexed: 01/06/2023]
Abstract
To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. Integration with human single-cell transcriptomic data revealed global, regional, and cell-type-specific species expression differences in genes representing distinct functional categories. We validated and further characterized the human specificity of genes enriched in distinct cell types through histological and functional analyses, including rare subpallial-derived interneurons expressing dopamine biosynthesis genes enriched in the human striatum and absent in the nonhuman African ape neocortex. Our integrated analysis of the generated data revealed diverse molecular and cellular features of the phylogenetic reorganization of the human brain across multiple levels, with relevance for brain function and disease.
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Affiliation(s)
- André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Marco Onorati
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Biology, Unit of Cell and Developmental Biology, University of Pisa, Pisa, Italy
| | - Andrew T N Tebbenkamp
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Bernardo Stutz
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Yuka Imamura Kawasawa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Departments of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Raquel Garcia Perez
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Marta Mele
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Tiago Carvalho
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Mario Skarica
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Akemi Shibata
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alexa R Stephenson
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Melissa K Edler
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, NM, USA
| | - John D Elsworth
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Tamas L Horvath
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Mark Reimers
- Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Matthew W State
- Department of Psychiatry and Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - James A Knowles
- Department of Psychiatry and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.,Centro Nacional de Analisis Genomico, Barcelona, Catalonia, Spain
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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16
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Kass RE, Amari SI, Arai K, Brown EN, Diekman CO, Diesmann M, Doiron B, Eden UT, Fairhall AL, Fiddyment GM, Fukai T, Grün S, Harrison MT, Helias M, Nakahara H, Teramae JN, Thomas PJ, Reimers M, Rodu J, Rotstein HG, Shea-Brown E, Shimazaki H, Shinomoto S, Yu BM, Kramer MA. Computational Neuroscience: Mathematical and Statistical Perspectives. Annu Rev Stat Appl 2018; 5:183-214. [PMID: 30976604 PMCID: PMC6454918 DOI: 10.1146/annurev-statistics-041715-033733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Mathematical and statistical models have played important roles in neuroscience, especially by describing the electrical activity of neurons recorded individually, or collectively across large networks. As the field moves forward rapidly, new challenges are emerging. For maximal effectiveness, those working to advance computational neuroscience will need to appreciate and exploit the complementary strengths of mechanistic theory and the statistical paradigm.
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Affiliation(s)
- Robert E Kass
- Carnegie Mellon University, Pittsburgh, PA, USA, 15213;
| | - Shun-Ichi Amari
- RIKEN Brain Science Institute, Wako, Saitama Prefecture, Japan, 351-0198
| | | | - Emery N Brown
- Massachusetts Institute of Technology, Cambridge, MA, USA, 02139
- Harvard Medical School, Boston, MA, USA, 02115
| | | | - Markus Diesmann
- Jülich Research Centre, Jülich, Germany, 52428
- RWTH Aachen University, Aachen, Germany, 52062
| | - Brent Doiron
- University of Pittsburgh, Pittsburgh, PA, USA, 15260
| | - Uri T Eden
- Boston University, Boston, MA, USA, 02215
| | | | | | - Tomoki Fukai
- RIKEN Brain Science Institute, Wako, Saitama Prefecture, Japan, 351-0198
| | - Sonja Grün
- Jülich Research Centre, Jülich, Germany, 52428
- RWTH Aachen University, Aachen, Germany, 52062
| | | | - Moritz Helias
- Jülich Research Centre, Jülich, Germany, 52428
- RWTH Aachen University, Aachen, Germany, 52062
| | - Hiroyuki Nakahara
- RIKEN Brain Science Institute, Wako, Saitama Prefecture, Japan, 351-0198
| | | | - Peter J Thomas
- Case Western Reserve University, Cleveland, OH, USA, 44106
| | - Mark Reimers
- Michigan State University, East Lansing, MI, USA, 48824
| | - Jordan Rodu
- Carnegie Mellon University, Pittsburgh, PA, USA, 15213;
| | | | | | - Hideaki Shimazaki
- Honda Research Institute Japan, Wako, Saitama Prefecture, Japan, 351-0188
- Kyoto University, Kyoto, Kyoto Prefecture, Japan, 606-8502
| | | | - Byron M Yu
- Carnegie Mellon University, Pittsburgh, PA, USA, 15213;
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17
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Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS. The Genetic Architecture of Major Depressive Disorder in Han Chinese Women. JAMA Psychiatry 2017; 74:162-168. [PMID: 28002544 PMCID: PMC5319866 DOI: 10.1001/jamapsychiatry.2016.3578] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
IMPORTANCE Despite the moderate, well-demonstrated heritability of major depressive disorder (MDD), there has been limited success in identifying replicable genetic risk loci, suggesting a complex genetic architecture. Research is needed to quantify the relative contribution of classes of genetic variation across the genome to inform future genetic studies of MDD. OBJECTIVES To apply aggregate genetic risk methods to clarify the genetic architecture of MDD by estimating and partitioning heritability by chromosome, minor allele frequency, and functional annotations and to test for enrichment of rare deleterious variants. DESIGN, SETTING, AND PARTICIPANTS The CONVERGE (China, Oxford, and Virginia Commonwealth University Experimental Research on Genetic Epidemiology) study collected data on 5278 patients with recurrent MDD from 58 provincial mental health centers and psychiatric departments of general medical hospitals in 45 cities and 23 provinces of China. Screened controls (n = 5196) were recruited from a range of locations, including general hospitals and local community centers. Data were collected from August 1, 2008, to October 31, 2012. MAIN OUTCOMES AND MEASURES Genetic risk for liability to recurrent MDD was partitioned using sparse whole-genome sequencing. RESULTS In aggregate, common single-nucleotide polymorphisms (SNPs) explained between 20% and 29% of the variance in MDD risk, and the heritability in MDD explained by each chromosome was proportional to its length (r = 0.680; P = .0003), supporting a common polygenic etiology. Partitioning heritability by minor allele frequency indicated that the variance explained was distributed across the allelic frequency spectrum, although relatively common SNPs accounted for a disproportionate fraction of risk. Partitioning by genic annotation indicated a greater contribution of SNPs in protein-coding regions and within 3'-UTR regions of genes. Enrichment of SNPs associated with DNase I-hypersensitive sites was also found in many tissue types, including brain tissue. Examining burden scores from singleton exonic SNPs predicted to be deleterious indicated that cases had significantly more mutations than controls (odds ratio, 1.009; 95% CI, 1.003-1.014; P = .003), including those occurring in genes expressed in the brain (odds ratio, 1.011; 95% CI, 1.003-1.018; P = .004) and within nuclear-encoded genes with mitochondrial gene products (odds ratio, 1.075; 95% CI, 1.018-1.135; P = .009). CONCLUSIONS AND RELEVANCE Results support a complex etiology for MDD and highlight the value of analyzing components of heritability to clarify genetic architecture.
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Affiliation(s)
- Roseann E. Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
| | - Na Cai
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom3European Bioinformatics Institute, Hinxton, United Kingdom
| | - Tim B. Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
| | - Yihan Li
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England
| | - Mark Reimers
- Neuroscience Program, Michigan State University, East Lansing
| | - Anna Nikulova
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Bradley T. Webb
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California–Los Angeles
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond
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18
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Cai N, Bigdeli T, Kretzschmar W, Li Y, Liang J, Song L, Hu J, Li Q, Jin W, Hu Z, Wang G, Wang L, Qian P, Liu Y, Jiang T, Lu Y, Zhang X, Yin Y, Li Y, Xu X, Gan X, Reimers M, Webb T, Riley B, Bacanu S, Peterson RE, Chen Y, Zhong H, Liu Z, Wang G, Sun J, Sang H, Jiang G, Zhou X, Li Y, Zhang W, Wang X, Fang X, Pan R, Miao G, Zhang Q, Hu J, Yu F, Du B, Sang W, Li K, Chen G, Cai M, Yang L, Yang D, Ha B, Hong X, Deng H, Li G, Li K, Song Y, Gao S, Zhang J, Gan Z, Meng H, Pan J, Gao C, Zhang K, Sun N, Li Y, Niu Q, Zhang Y, Liu T, Hu C, Zhang Z, Lv L, Dong J, Wang X, Tao M, Wang X, Xia J, Rong H, He Q, Liu T, Huang G, Mei Q, Shen Z, Liu Y, Shen J, Tian T, Liu X, Wu W, Gu D, Fu G, Li Y, Shi J, Chen Y, Gao J, Liu L, Wang L, Yang F, Cong E, Marchini J, Yang H, Wang J, Shi S, Mott R, Wang J, Kendler KS, Flint J. CONVERGE dataset: 12,000 whole-genome sequences representative of the Han Chinese population. Gigascience 2016. [DOI: 10.1186/s13742-016-0123-8] [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: 11/10/2022] Open
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19
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Reimers M, Fastbom J. P-419: Changes in drug prescribing during a care episode in a geriatric clinic. Eur Geriatr Med 2015. [DOI: 10.1016/s1878-7649(15)30516-7] [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: 10/23/2022]
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20
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Zhao Z, Xu J, Chen J, Kim S, Reimers M, Bacanu SA, Yu H, Liu C, Sun J, Wang Q, Jia P, Xu F, Zhang Y, Kendler KS, Peng Z, Chen X. Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. Mol Psychiatry 2015; 20:563-572. [PMID: 25113377 PMCID: PMC4326626 DOI: 10.1038/mp.2014.82] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 05/23/2014] [Accepted: 06/17/2014] [Indexed: 12/20/2022]
Abstract
Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental disorders with high heritability. Clinicians have long noticed the similarities of clinic symptoms between these disorders. In recent years, accumulating evidence indicates some shared genetic liabilities. However, what is shared remains elusive. In this study, we conducted whole transcriptome analysis of post-mortem brain tissues (cingulate cortex) from SCZ, BPD and control subjects, and identified differentially expressed genes in these disorders. We found 105 and 153 genes differentially expressed in SCZ and BPD, respectively. By comparing the t-test scores, we found that many of the genes differentially expressed in SCZ and BPD are concordant in their expression level (q⩽0.01, 53 genes; q⩽0.05, 213 genes; q⩽0.1, 885 genes). Using genome-wide association data from the Psychiatric Genomics Consortium, we found that these differentially and concordantly expressed genes were enriched in association signals for both SCZ (P<10(-7)) and BPD (P=0.029). To our knowledge, this is the first time that a substantially large number of genes show concordant expression and association for both SCZ and BPD. Pathway analyses of these genes indicated that they are involved in the lysosome, Fc gamma receptor-mediated phagocytosis, regulation of actin cytoskeleton pathways, along with several cancer pathways. Functional analyses of these genes revealed an interconnected pathway network centered on lysosomal function and the regulation of actin cytoskeleton. These pathways and their interacting network were principally confirmed by an independent transcriptome sequencing data set of the hippocampus. Dysregulation of lysosomal function and cytoskeleton remodeling has direct impacts on endocytosis, phagocytosis, exocytosis, vesicle trafficking, neuronal maturation and migration, neurite outgrowth and synaptic density and plasticity, and different aspects of these processes have been implicated in SCZ and BPD.
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Affiliation(s)
- Zhongming Zhao
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jiabao Xu
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, 518083, China
| | - Jingchun Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Sanghyeon Kim
- Stanley Laboratory of Brain Research, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Mark Reimers
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Hui Yu
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chunyu Liu
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60637, USA
| | - Jingchun Sun
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Quan Wang
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Peilin Jia
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Fengping Xu
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, 518083, China
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Zhiyu Peng
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, 518083, China
| | - Xiangning Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
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21
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Hauser S, Reimers M. Network dynamics contribute to a gamma rhythm highly robust to synaptic variation. BMC Neurosci 2014. [PMCID: PMC4126525 DOI: 10.1186/1471-2202-15-s1-p62] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Mohajerani MH, Chan AW, Mohsenvand M, LeDue J, Liu R, McVea DA, Boyd JD, Wang YT, Reimers M, Murphy TH. Spontaneous cortical activity alternates between motifs defined by regional axonal projections. Nat Neurosci 2013; 16:1426-35. [PMID: 23974708 DOI: 10.1038/nn.3499] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/17/2013] [Indexed: 12/20/2022]
Abstract
Using millisecond-timescale voltage-sensitive dye imaging in lightly anesthetized or awake adult mice, we show that a palette of sensory-evoked and hemisphere-wide activity motifs are represented in spontaneous activity. These motifs can reflect multiple modes of sensory processing, including vision, audition and touch. We found similar cortical networks with direct cortical activation using channelrhodopsin-2. Regional analysis of activity spread indicated modality-specific sources, such as primary sensory areas, a common posterior-medial cortical sink where sensory activity was extinguished within the parietal association area and a secondary anterior medial sink within the cingulate and secondary motor cortices for visual stimuli. Correlation analysis between functional circuits and intracortical axonal projections indicated a common framework corresponding to long-range monosynaptic connections between cortical regions. Maps of intracortical monosynaptic structural connections predicted hemisphere-wide patterns of spontaneous and sensory-evoked depolarization. We suggest that an intracortical monosynaptic connectome shapes the ebb and flow of spontaneous cortical activity.
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Affiliation(s)
- Majid H Mohajerani
- 1] Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada. [2] Brain Research Centre, University of British Columbia, Vancouver, British Columbia, Canada. [3] [4]
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23
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Reimers M, Mohajerani M, Murphy TH. A model for delta rhythm fit to high-frequency cortical activity data. BMC Neurosci 2013. [PMCID: PMC3704529 DOI: 10.1186/1471-2202-14-s1-p287] [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: 11/11/2022] Open
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24
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Behnke MK, Reimers M, Fisher RA. Stem cell and hepatocyte proliferation in hepatitis C cirrhosis and hepatocellular carcinoma: transplant implications. Ann Hepatol 2013; 13:45-53. [PMID: 24378265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND. The liver possesses two distinct mechanisms for healing. Wound healing via hepatic stem cells recapitulates early development (hepatoblast proliferation), while liver regeneration resembles late embryonic growth (hepatocyte proliferation). Loss of control over both of these processes have been proposed as mechanisms that may contribute to poor outcomes in HCC. MATERIAL AND METHODS. We used microarray gene expression profiles to examine the involvement of hepatic stem cell and hepatocyte proliferation markers and regulators in HCV-induced cirrhosis and HCC. We compared 30 cirrhosis and 49 HCC samples to 12 disease-free control livers. RESULTS. Cirrhosis and HCC expressed markers of stem cell. Inhibitors of hepatocyte proliferation (HP) were highly expressed in cirrhosis. Loss of these HP inhibitors in HCC patients was associated poor prognosis (94 vs. 38% 2-year recurrence- free survival, p = 0.0003). Principal Components Analysis discriminated cirrhotic and HCC tissues, and HCC patients with poor (< 2 year) vs. good (> 2 year) recurrence-free survival. Loss of CDH1 expression correlated with up-regulation of hepatocyte proliferation promoters MET and YAP1. CDH1, MET, and YAP1 were independent predictors of recurrence-free survival by Cox regression when corrected for tumor stage (p < 0.0001). CONCLUSION. HCV-cirrhosis is characterized by proliferation of liver stem cells and inhibition of hepatocyte proliferation. HCC tumors in which this pattern persists have superior outcomes to those which acquire a hepatocyte proliferation signature. Genes in this signature should be studied further for potential as tissue or serum biomarkers for patient risk stratification. CDH1 and MET are candidates for personalized therapies with targeted pharmaceutical agents.
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Affiliation(s)
- Martha K Behnke
- Transplant Program Administration, Virginia Commonwealth University Health System, 1200 E. Broad St., Richmond, VA 23298, USA
| | - Mark Reimers
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, 800 E Leigh St., Richmond, VA 23298, USA
| | - Robert A Fisher
- Department of Surgery, Virginia Commonwealth University, 1200 E. Broad St., Richmond, VA 23298, USA
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25
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Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AMM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N. Spatio-temporal transcriptome of the human brain. Nature 2011; 478:483-9. [PMID: 22031440 PMCID: PMC3566780 DOI: 10.1038/nature10523] [Citation(s) in RCA: 1384] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 08/30/2011] [Indexed: 12/14/2022]
Abstract
Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.
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Affiliation(s)
- Hyo Jung Kang
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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26
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Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 2011; 118:3559-69. [PMID: 21828137 PMCID: PMC3186332 DOI: 10.1182/blood-2011-06-357996] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [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: 06/03/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression affecting most notably genes of the NFkB and MAP kinase signaling pathways. GC B cells were predominantly hypomethylated compared with naive B cells and AICDA binding sites were highly overrepresented among hypomethylated loci. GC B cells also exhibited greater DNA methylation heterogeneity than naive B cells. Among DNA methyltransferases (DNMTs), only DNMT1 was significantly up-regulated in GC B cells. Dnmt1 hypomorphic mice displayed deficient GC formation and treatment of mice with the DNA methyltransferase inhibitor decitabine resulted in failure to form GCs after immune stimulation. Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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27
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Kim AH, Reimers M, Maher B, Williamson V, McMichael O, McClay JL, van den Oord EJ, Riley BP, Kendler KS, Vladimirov VI. MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders. Schizophr Res 2010; 124:183-91. [PMID: 20675101 PMCID: PMC4373420 DOI: 10.1016/j.schres.2010.07.002] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/01/2010] [Accepted: 07/06/2010] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are a large family of small non-coding RNAs which negatively control gene expression at both the mRNA and protein levels. The number of miRNAs identified is growing rapidly and approximately one-third is expressed in the brain where they have been shown to affect neuronal differentiation, synaptosomal complex localization and synapse plasticity, all functions thought to be disrupted in schizophrenia. Here we investigated the expression of 667 miRNAs (miRBase v.13) in the prefrontal cortex of individuals with schizophrenia (SZ, N = 35) and bipolar disorder (BP, N = 35) using a real-time PCR-based Taqman Low Density Array (TLDA). After extensive QC steps, 441 miRNAs were included in the final analyses. At a FDR of 10%, 22 miRNAs were identified as being differentially expressed between cases and controls, 7 dysregulated in SZ and 15 in BP. Using in silico target gene prediction programs, the 22miRNAs were found to target brain specific genes contained within networks overrepresented for neurodevelopment, behavior, and SZ and BP disease development. In an initial attempt to corroborate some of these predictions, we investigated the extent of correlation between the expressions of hsa-mir-34a, -132 and -212 and their predicted gene targets. mRNA expression of tyrosine hydroxylase (TH), phosphogluconate dehydrogenase (PGD) and metabotropic glutamate receptor 3 (GRM3) was measured in the SMRI sample. Hsa-miR-132 and -212 were negatively correlated with TH (p = 0.0001 and 0.0017) and with PGD (p = 0.0054 and 0.017, respectively).
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Affiliation(s)
- Albert H. Kim
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
| | - Mark Reimers
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Brion Maher
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Vernell Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Department of Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Omari McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
| | - Joseph L. McClay
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
| | - Edwin J.C.G. van den Oord
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
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Buck G, Fettweis J, Alves J, Borzelleca J, Brooks J, Friedline C, Gao Y, Gao X, Girerd P, Harwich M, Hendricks S, Jefferson K, Lee V, Mo H, Neale M, Puma F, Reimers M, Rivera M, Roberts S, Serrano M, Sheth N, Silbert J, Voegtly L, Prom-Wormley E, Xie B, York T, Cornelissen C, Strauss J, Eaves L, Buck G. The Vaginal Microbiome: Disease, Genetics and the Environment. ACTA ACUST UNITED AC 2010. [DOI: 10.1038/npre.2010.5150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer ELL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, Höög C, Agarwal P, Wasserman WW. Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp Funct Genomics 2010; 5:584-95. [PMID: 18629180 PMCID: PMC2447472 DOI: 10.1002/cfg.443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2004] [Indexed: 02/02/2023] Open
Abstract
In this paper we aim to create a reference data collection of Northern blot results
and demonstrate how such a collection can enable a quantitative comparison of
modern expression profiling techniques, a central component of functional genomics
studies. Historically, Northern blots were the de facto standard for determining RNA
transcript levels. However, driven by the demand for analysis of large sets of genes in
parallel, high-throughput methods, such as microarrays, dominate modern profiling
efforts. To facilitate assessment of these methods, in comparison to Northern blots,
we created a database of published Northern results obtained with a standardized
commercial multiple tissue blot (dbMTN). In order to demonstrate the utility of the
dbMTN collection for technology comparison, we also generated expression profiles
for genes across a set of human tissues, using multiple profiling techniques. No method
produced profiles that were strongly correlated with the Northern blot data. The
highest correlations to the Northern blot data were determined with microarrays
for the subset of genes observed to be specifically expressed in a single tissue in
the Northern analyses. The database and expression profiling data are available
via the project website (http://www.cisreg.ca). We believe that emphasis on multitechnique
validation of expression profiles is justified, as the correlation results
between platforms are not encouraging on the whole. Supplementary material for this
article can be found at: http://www.interscience.wiley.com/jpages/1531-6912/suppmat
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Affiliation(s)
- Danielle Kemmer
- Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
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30
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Affiliation(s)
- Mark Reimers
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America.
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31
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Mathé EA, Nguyen GH, Bowman ED, Zhao Y, Budhu A, Schetter AJ, Braun R, Reimers M, Kumamoto K, Hughes D, Altorki NK, Casson AG, Liu CG, Wang XW, Yanaihara N, Hagiwara N, Dannenberg AJ, Miyashita M, Croce CM, Harris CC. MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res 2009; 15:6192-200. [PMID: 19789312 DOI: 10.1158/1078-0432.ccr-09-1467] [Citation(s) in RCA: 304] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE The dismal outcome of esophageal cancer patients highlights the need for novel prognostic biomarkers, such as microRNAs (miRNA). Although recent studies have established the role of miRNAs in esophageal carcinoma, a comprehensive multicenter study investigating different histologic types, including squamous cell carcinoma (SCC) and adenocarcinoma with or without Barrett's, is still lacking. EXPERIMENTAL DESIGN miRNA expression was measured in cancerous and adjacent noncancerous tissue pairs collected from 100 adenocarcinoma and 70 SCC patients enrolled at four clinical centers from the United States, Canada, and Japan. Microarray-based expression was measured in a subset of samples in two cohorts and was validated in all available samples. RESULTS In adenocarcinoma patients, miR-21, miR-223, miR-192, and miR-194 expression was elevated, whereas miR-203 expression was reduced in cancerous compared with noncancerous tissue. In SCC patients, we found elevated miR-21 and reduced miR-375 expression levels in cancerous compared with noncancerous tissue. When comparing cancerous tissue expression between adenocarcinoma and SCC patients, miR-194 and miR-375 were elevated in adenocarcinoma patients. Significantly, elevated miR-21 expression in noncancerous tissue of SCC patients and reduced levels of miR-375 in cancerous tissue of adenocarcinoma patients with Barrett's were strongly associated with worse prognosis. Associations with prognosis were independent of tumor stage or nodal status, cohort type, and chemoradiation therapy. CONCLUSIONS Our multicenter-based results highlight miRNAs involved in major histologic types of esophageal carcinoma and uncover significant associations with prognosis. Elucidating miRNAs relevant to esophageal carcinogenesis is potentially clinically useful for developing prognostic biomarkers and identifying novel drug targets and therapies.
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Affiliation(s)
- Ewy A Mathé
- Laboratory of Human Carcinogenesis, National Cancer Institute/NIH, Bethesda, Maryland 20892, USA
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32
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Ikediobi ON, Reimers M, Durinck S, Blower PE, Futreal AP, Stratton MR, Weinstein JN. In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation. Mol Cancer Ther 2008; 7:1337-46. [PMID: 18524847 DOI: 10.1158/1535-7163.mct-07-2308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [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
The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. We previously sequenced 24 cancer genes in those cell lines. Eleven of the genes were found to be mutated in three or more of the lines. Using a pharmacogenomic approach, we analyzed the relationship between drug activity and mutations in those 11 genes (APC, RB1, KRAS, NRAS, BRAF, PIK3CA, PTEN, STK11, MADH4, TP53, and CDKN2A). That analysis identified an association between mutation in BRAF and the antiproliferative potential of phenothiazine compounds. Phenothiazines have been used as antipsychotics and as adjunct antiemetics during cancer chemotherapy and more recently have been reported to have anticancer properties. However, to date, the anticancer mechanism of action of phenothiazines has not been elucidated. To follow up on the initial pharmacologic observations in the NCI-60 screen, we did pharmacologic experiments on 11 of the NCI-60 cell lines and, prospectively, on an additional 24 lines. The studies provide evidence that BRAF mutation (codon 600) in melanoma as opposed to RAS mutation is predictive of an increase in sensitivity to phenothiazines as determined by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt assay (Wilcoxon P = 0.007). That pattern of increased sensitivity to phenothiazines based on the presence of codon 600 BRAF mutation may be unique to melanomas, as we do not observe it in a panel of colorectal cancers. The findings reported here have potential implications for the use of phenothiazines in the treatment of V600E BRAF mutant melanoma.
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Affiliation(s)
- Ogechi N Ikediobi
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, USA.
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33
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Boersma BJ, Reimers M, Yi M, Ludwig JA, Luke BT, Stephens RM, Yfantis HG, Lee DH, Weinstein JN, Ambs S. A stromal gene signature associated with inflammatory breast cancer. Int J Cancer 2008; 122:1324-32. [PMID: 17999412 DOI: 10.1002/ijc.23237] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The factors that determine whether a breast carcinoma will develop into inflammatory breast cancer (IBC) remain poorly understood. Recent evidence indicates that the tumor stroma influences cancer phenotypes. We tested the hypotheses that the gene expression signature of the tumor stroma is a distinctive feature of IBC. We used laser capture microdissection to obtain enriched populations of tumor epithelial cells and adjacent stromal cells from 15 patients with IBC and 35 patients with invasive, noninflammatory breast cancer (non-IBC). Their mRNA expression profiles were assessed using Affymetrix GeneChips. In addition, a previously established classifier for IBC was evaluated for the resulting data sets. The gene expression profile of the tumor stroma distinguished IBC from non-IBC, and a previously established IBC prediction signature performed better in classifying IBC using the gene expression profile of the tumor stroma than it did using the profile of the tumor epithelium. In a pathway analysis, the genes differentially expressed between IBC and non-IBC tumors clustered in distinct pathways. We identified multiple pathways related to the endoplasmic stress response that could be functionally significant in IBC. Our findings suggest that the gene expression in the tumor stroma may play a role in determining the IBC phenotype.
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Affiliation(s)
- Brenda J Boersma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4258, USA
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Figueroa ME, Reimers M, Thompson RF, Ye K, Li Y, Selzer RR, Fridriksson J, Paietta E, Wiernik P, Green RD, Greally JM, Melnick A. An integrative genomic and epigenomic approach for the study of transcriptional regulation. PLoS One 2008; 3:e1882. [PMID: 18365023 PMCID: PMC2266992 DOI: 10.1371/journal.pone.0001882] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 02/19/2008] [Indexed: 12/31/2022] Open
Abstract
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation is a hallmark of cancer and plays a central role in determining tumor phenotype. We predicted that integration of different genome-wide epigenetic regulatory marks along with gene expression levels would provide greater power in capturing biological differences between leukemia subtypes. Gene expression, cytosine methylation and histone H3 lysine 9 (H3K9) acetylation were measured using high-density oligonucleotide microarrays in primary human acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) specimens. We found that DNA methylation and H3K9 acetylation distinguished these leukemias of distinct cell lineage, as expected, but that an integrative analysis combining the information from each platform revealed hundreds of additional differentially expressed genes that were missed by gene expression arrays alone. This integrated analysis also enhanced the detection and statistical significance of biological pathways dysregulated in AML and ALL. Integrative epigenomic studies are thus feasible using clinical samples and provide superior detection of aberrant transcriptional programming than single-platform microarray studies.
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Affiliation(s)
- Maria E. Figueroa
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Mark Reimers
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Reid F. Thompson
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yushan Li
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | | | - Elisabeth Paietta
- Our Lady of Mercy Comprehensive Cancer Center, Bronx, New York, United States of America
| | - Peter Wiernik
- Our Lady of Mercy Comprehensive Cancer Center, Bronx, New York, United States of America
| | - Roland D. Green
- Roche NimbleGen, Inc. Madison, Wisconsin, United States of America
| | - John M. Greally
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (JG); (AM)
| | - Ari Melnick
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (JG); (AM)
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Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM. An analytical pipeline for genomic representations used for cytosine methylation studies. ACTA ACUST UNITED AC 2008; 24:1161-7. [PMID: 18353789 DOI: 10.1093/bioinformatics/btn096] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Representations of the genome can be generated by the selection of a subpopulation of restriction fragments using ligation-mediated PCR. Such representations form the basis for a number of high-throughput assays, including the HELP assay to study cytosine methylation. We find that HELP data analysis is complicated not only by PCR amplification heterogeneity but also by a complex and variable distribution of cytosine methylation. To address this, we created an analytical pipeline and novel normalization approach that improves concordance between microarray-derived data and single locus validation results, demonstrating the value of the analytical approach. A major influence on the PCR amplification is the size of the restriction fragment, requiring a quantile normalization approach that reduces the influence of fragment length on signal intensity. Here we describe all of the components of the pipeline, which can also be applied to data derived from other assays based on genomic representations.
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Affiliation(s)
- Reid F Thompson
- Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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36
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Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, Trent JM, Bittner ML, Meltzer PS, Fornace AJ. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res 2008; 68:415-24. [PMID: 18199535 DOI: 10.1158/0008-5472.can-07-2120] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [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
The 60 cell lines of the National Cancer Institute Anticancer Drug Screen (NCI-60) constitute the most extensively characterized in vitro cancer cell model. They have been tested for sensitivity to more than 100,000 potential chemotherapy agents and have been profiled extensively at the DNA, RNA, protein, functional, and pharmacologic levels. We have used the NCI-60 cell lines and three additional lines to develop a database of responses of cancer cells to ionizing radiation. We compared clonogenic survival, apoptosis, and gene expression response by microarray. Although several studies have profiled relative basal gene expression in the NCI-60, this is the first comparison of large-scale gene expression changes in response to genotoxic stress. Twenty-two genes were differentially regulated in cells with low survival after 2-Gy gamma-rays; 14 genes identified lines more sensitive to 8 Gy. Unlike reported basal gene expression patterns, changes in expression in response to radiation showed little tissue-of-origin effect, except for differentiating the lymphoblastoid cell lines from other cell types. Basal expression patterns, however, discriminated well between radiosensitive and more resistant lines, possibly being more informative than radiation response signatures. The most striking patterns in the radiation data were a set of genes up-regulated preferentially in the p53 wild-type lines and a set of cell cycle regulatory genes down-regulated across the entire NCI-60 panel. The response of those genes to gamma-rays seems to be unaffected by the myriad of genetic differences across this diverse cell set; it represents the most penetrant gene expression response to ionizing radiation yet observed.
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Affiliation(s)
- Sally A Amundson
- Center for Radiological Research, Columbia University Medical Center, New York, New York 10032, USA.
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Stevens EV, Nishizuka S, Antony S, Reimers M, Varma S, Young L, Munson PJ, Weinstein JN, Kohn EC, Pommier Y. Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers. Mol Cancer Ther 2008; 7:10-8. [PMID: 18187810 DOI: 10.1158/1535-7163.mct-07-0192] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [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
Molecular profiling of markers involved in the activity of chemotherapeutic agents can shed light on the successes and failures of treatment in patients and can also provide a basis for individualization of therapy. Toward those ends, we have used reverse-phase protein lysate microarrays to evaluate expression of protein components of the nucleotide excision repair (NER) pathways. Those pathways strongly influence the anticancer activities of numerous drugs, including those that are the focus here, cisplatin and ecteinascidin 743 (Et-743; Yondelis, Trabectedin). Cisplatin is generally more active in cell types deficient in NER, whereas Et-743 tends to be less active in those cells. We measured protein expression and sensitivity to those drugs in 17 human ovarian and colon cancer cell lines (13 of them from the NCI-60 panel) and five xeroderma pigmentosum (XP) patient cell types, each containing a different NER defect. Of the NER proteins giving reliable signals, XPF and XPG showed the highest correlations of protein expression with drug activity across all three tissue-of-origin groups. When we compared protein expression data with mRNA expression data from Affymetrix U133A chips, we found no consistent correlation between the two across the cell lines studied, which reinforces the conclusion that protein measurements can give more interpretable mechanistic information than can transcript measurements. The work reported here provides motivation for larger proteomic studies with more cell types focused on potential biomarkers in additional pharmacologically pertinent pathways.
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Affiliation(s)
- Ellen V Stevens
- National Cancer Institute, Building 37, Room 5068, Bethesda, MD 20892, USA
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Eichler GS, Reimers M, Kane D, Weinstein JN. The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data. Genome Biol 2007; 8:R187. [PMID: 17845722 PMCID: PMC2375025 DOI: 10.1186/gb-2007-8-9-r187] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 06/29/2007] [Accepted: 09/10/2007] [Indexed: 11/10/2022] Open
Abstract
Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce Learner of Functional Enrichment (LeFE), a statistical/machine learning algorithm based on Random Forest, and demonstrate it on several diverse datasets: smoker/never smoker, breast cancer classification, and cancer drug sensitivity. We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant functional themes consistent with known biology.
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Affiliation(s)
- Gabriel S Eichler
- Genomics and Bioinformatics Groups, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Bioinformatics Program, Boston University, Cummington St, Boston, Massachusetts 02215, USA
| | - Mark Reimers
- Genomics and Bioinformatics Groups, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Virginia Commonwealth University, Biostatistics Department, E Marshall St, Richmond, Virginia 23284, USA
| | - David Kane
- Genomics and Bioinformatics Groups, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- SRA International, Fair Lakes Court, Fairfax, Virginia 22033, USA
| | - John N Weinstein
- Genomics and Bioinformatics Groups, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological experiments. Particular attention is paid to concepts of container and workflow design, connections of biological metadata to statistical analysis products, support for statistical quality assessment, and calibration of inference uncertainty measures when tens of thousands of simultaneous statistical tests are performed.
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Affiliation(s)
- Mark Reimers
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Huber J, Löffler M, Bilban M, Reimers M, Kadl A, Todoric J, Zeyda M, Geyeregger R, Schreiner M, Weichhart T, Leitinger N, Waldhäusl W, Stulnig TM. Prevention of high-fat diet-induced adipose tissue remodeling in obese diabetic mice by n-3 polyunsaturated fatty acids. Int J Obes (Lond) 2006; 31:1004-13. [PMID: 17130847 DOI: 10.1038/sj.ijo.0803511] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Obesity is associated with reduced insulin sensitivity and extensive reorganization of adipose tissue. As polyunsaturated fatty acids (PUFA) appear to inhibit diabetes development, we investigated PUFA effects on markers of matrix remodeling in white adipose tissue. METHODS AND PROCEDURE Male obese diabetic (db/db) mice were treated with either a low-fat standard diet (LF), or high-fat diets rich in saturated and monounsaturated fatty acids (HF/S), n-6 PUFA (HF/6) or the latter including marine n-3 PUFA (HF/3). White adipose tissue was analyzed for gene expression, fatty acid composition and by immunofluorescence. RESULTS HF/S treatment increased adipose tissue expression of a number of genes involved in matrix degradation including matrix metalloproteinase (MMP)-12, -14 and cathepsin K, L and S compared with LF. MMP-12 gene was expressed in macrophages and adipocytes, and MMP-12 protein colocalized with both cell types. In addition, mean adipocyte area increased by 1.6-fold in HF/S-treated mice. Genes essential for collagen production, such as procollagen I, III, VI, tenascin C and biglycan were upregulated in HF/S-treated animals as well. N-3 PUFA supplementation resulted in enrichment of these fatty acids in adipose tissue. Moreover, n-3 PUFA inhibited the HF/S-induced upregulation of genes involved in matrix degradation and production I restored mean adipocyte area and prevented MMP-12 expression in macrophages and adipocytes. CONCLUSION N-3 PUFA prevent high-fat diet-induced matrix remodeling and adipocyte enlargement in adipose tissue of obese diabetic mice. Such changes could contribute to diabetes prevention by n-3 PUFA in obese patients.
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MESH Headings
- Adipocytes/physiology
- Adipose Tissue, White/metabolism
- Adipose Tissue, White/physiopathology
- Animals
- Biomarkers/analysis
- Cathepsins/genetics
- Cell Size
- Collagenases/genetics
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/physiopathology
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/physiopathology
- Dietary Fats/administration & dosage
- Fatty Acids/administration & dosage
- Fatty Acids/analysis
- Fatty Acids, Omega-3/administration & dosage
- Gene Expression Regulation/physiology
- Gonads/metabolism
- Gonads/physiopathology
- Liver/metabolism
- Male
- Matrix Metalloproteinase 12/analysis
- Mice
- Mice, Inbred C3H
- Obesity/complications
- Obesity/genetics
- Obesity/physiopathology
- Tissue Inhibitor of Metalloproteinases/genetics
- Triglycerides/analysis
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Affiliation(s)
- J Huber
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria
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Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 2006; 5:853-67. [PMID: 16648555 DOI: 10.1158/1535-7163.mct-05-0155] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromosome rearrangement, a hallmark of cancer, has profound effects on carcinogenesis and tumor phenotype. We used a panel of 60 human cancer cell lines (the NCI-60) as a model system to identify relationships among DNA copy number, mRNA expression level, and drug sensitivity. For each of 64 cancer-relevant genes, we calculated all 4,096 possible Pearson's correlation coefficients relating DNA copy number (assessed by comparative genomic hybridization using bacterial artificial chromosome microarrays) and mRNA expression level (determined using both cDNA and Affymetrix oligonucleotide microarrays). The analysis identified an association of ERBB2 overexpression with 3p copy number, a finding supported by data from human tumors and a mouse model of ERBB2-induced carcinogenesis. When we examined the correlation between DNA copy number for all 353 unique loci on the bacterial artificial chromosome microarray and drug sensitivity for 118 drugs with putatively known mechanisms of action, we found a striking negative correlation (-0.983; 95% bootstrap confidence interval, -0.999 to -0.899) between activity of the enzyme drug L-asparaginase and DNA copy number of genes near asparagine synthetase in the ovarian cancer cells. Previous analysis of drug sensitivity and mRNA expression had suggested an inverse relationship between mRNA levels of asparagine synthetase and L-asparaginase sensitivity in the NCI-60. The concordance of pharmacogenomic findings at the DNA and mRNA levels strongly suggests further study of L-asparaginase for possible treatment of a low-synthetase subset of clinical ovarian cancers. The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus.
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Affiliation(s)
- Kimberly J Bussey
- Laboratory of Molecular Pharmacology, National Cancer Institute, Building 37, Room 5056, NIH, MSC 4255, 9000 Rockville Pike, Bethesda, MD 20892-4255, USA
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42
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Björk K, Saarikoski ST, Arlinde C, Kovanen L, Osei-Hyiaman D, Ubaldi M, Reimers M, Hyytiä P, Heilig M, Sommer WH. Glutathione-S-transferase expression in the brain: possible role in ethanol preference and longevity. FASEB J 2006; 20:1826-35. [PMID: 16940154 DOI: 10.1096/fj.06-5896com] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [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] [Indexed: 01/12/2023]
Abstract
Identification of genes that are differentially expressed in rats bidirectionally selected for alcohol preference might reveal biological mechanisms underlying alcoholism or related phenotypes. Microarray analysis from medial prefrontal cortex (mPFC), a key brain region for drug reward, indicated increased expression of glutathione-S-transferases of the alpha (Gsta4) and mu (Gstm1-5) classes in ethanol-preferring AA rats compared with nonpreferring ANA rats. Real-time RT polymerase chain reaction (RT-PCR) analysis demonstrated approximately 2-fold higher Gsta4 transcript levels in several brain regions of ethanol-naive AA compared with ANA rats. Differences in mRNA levels were accompanied by differential levels of GSTA4 protein. We identified a novel haplotype variant in the rat Gsta4 gene, defined here as var3. Allele frequencies of var3 were markedly different between AA and ANA rats, 52% and 100%, respectively. Gsta4 expression was strongly correlated with the gene dose of var3, with approximately 60% of the variance in expression accounted for by genotype at this locus. The contribution of glutathione S-transferase expression to the ethanol-preferring phenotype is presently unclear. It could, however, underlie observed differences in life span between AA and ANA lines, prompting a utility of this animal model in aging research.
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Affiliation(s)
- K Björk
- Laboratory of Clinical and Translational Studies, NCI, National Institutes of Health, Bethesda, USA
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43
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Todoric J, Löffler M, Huber J, Bilban M, Reimers M, Kadl A, Zeyda M, Waldhäusl W, Stulnig TM. Adipose tissue inflammation induced by high-fat diet in obese diabetic mice is prevented by n-3 polyunsaturated fatty acids. Diabetologia 2006; 49:2109-19. [PMID: 16783472 DOI: 10.1007/s00125-006-0300-x] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 05/22/2006] [Indexed: 01/22/2023]
Abstract
AIMS/HYPOTHESIS Inflammatory alterations in white adipose tissue appear to underlie complications of obesity including diabetes mellitus. Polyunsaturated fatty acids (PUFA), particularly those of the n-3 series, modulate immune responses and may ameliorate insulin sensitivity. In this study, we investigated how PUFA affect white adipose tissue inflammation and gene expression in obese diabetic animals. MATERIALS AND METHODS We treated db/db mice as well as lean non-diabetic mice (db/+) with either low-fat standard diet (LF) or high-fat diets rich in (1) saturated/monounsaturated fatty acids (HF/S), (2) n-6 PUFA (HF/6) and (3) the latter including purified marine n-3 PUFA (HF/3). RESULTS Many genes involved in inflammatory alterations were upregulated in db/db mice on HF/S compared with LF in parallel with phosphorylation of c-Jun N-terminal kinase (JNK). In parallel, adipose tissue infiltration with macrophages was markedly enhanced by HF/S. When compared with HF/S, HF/6 showed only marginal effects on adipose tissue inflammation. However, inclusion of n-3 PUFA in the diet (HF/3) completely prevented macrophage infiltration induced by high-fat diet and changes in inflammatory gene expression, also tending to reduce JNK phosphorylation (p<0.1) in diabetic mice despite unreduced body weight. Moreover, high-fat diets (HF/S, HF/6) downregulated expression and reduced serum concentrations of adiponectin, but this was not the case with n-3 PUFA. CONCLUSIONS/INTERPRETATION n-3 PUFA prevent adipose tissue inflammation induced by high-fat diet in obese diabetic mice, thereby dissecting obesity from adipose tissue inflammation. These data suggest that beneficial effects of n-3 PUFA on diabetes development could be mediated by their effect on adipose tissue inflammation.
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Affiliation(s)
- J Todoric
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
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44
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Reimers M, Heilig M, Sommer WH. Gene discovery in neuropharmacological and behavioral studies using Affymetrix microarray data. Methods 2006; 37:219-28. [PMID: 16308151 DOI: 10.1016/j.ymeth.2005.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Accepted: 03/15/2005] [Indexed: 01/13/2023] Open
Abstract
We describe methods and software tools for doing data analysis based on Affymetrix microarray data, emphasizing often neglected issues. In our experience with neuroscience studies, experimental design and quality assessment are vital. We also describe in detail the pre-processing methods we have found useful for Affymetrix data. Finally, we summarize the statistical literature and describe some pitfalls in the post-processing analysis.
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Affiliation(s)
- Mark Reimers
- Laboratory of Molecular Pharmacology, NCI, National Institutes of Health, Bethesda, USA.
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45
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46
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Loffler M, Bilban M, Reimers M, Waldhäusl W, Stulnig TM. Blood glucose-lowering nuclear receptor agonists only partially normalize hepatic gene expression in db/db mice. J Pharmacol Exp Ther 2005; 316:797-804. [PMID: 16260581 DOI: 10.1124/jpet.105.093831] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Agonists of the nuclear receptors peroxisome proliferator-activated receptor (PPAR) gamma, PPARalpha, and liver X receptors (LXRs) reduce blood glucose in type 2 diabetic patients and comparable mouse models. Since the capacity of these drugs to normalize hepatic gene expression is not known, we compared groups of obese diabetic db/db mice treated with agonists for PPARgamma [rosiglitazone (Rosi); 10 mg/kg/day], PPARalpha [Wy 14643 (Wy; 4-chloro-6-(2,3-xylidino)-2-pyrimidinyl)thioacetic acid); 30 mg/kg/day], and LXR [T0901317 (T09; N-(2,2,2-trifluoroethyl)-N-[4-[2,2,2-trifluoro-1-hydroxy-1(trifluoromethyl)-ethyl]phenyl]-benzenesulfonamide); 40 mg/kg/day] and from untreated nondiabetic litter mates (db/+) by oligonucleotide microarrays and quantitative reverse transcriptase-polymerase chain reaction. The 10-day treatment period of db/db mice with Rosi, Wy, and T09 altered expression of 300, 620, and 735 genes including agonist-specific target genes, respectively. However, from the 337 genes differentially regulated in untreated db/+ versus db/db animals, only 34 (10%), 51 (15%), and 82 (24%) were regulated in the direction of the db/+ group by Rosi, Wy, and T09, respectively. Gene expression normalization by drug treatment involved glucose homeostasis, lipid homeostasis, and local glucocorticoid activation. In addition, our data pointed to hitherto unknown interference of these nuclear receptors with growth hormone receptor gene expression and endoplasmic reticulum stress. However, many diabetes-associated gene alterations remained unaffected or were even aggravated by nuclear receptor agonist treatment. These results suggest that diabetes-induced gene expression is minimally reversed by potent blood glucose-lowering nuclear receptor agonists.
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Affiliation(s)
- Michael Loffler
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University Vienna, Austria
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47
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Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN. High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 2005; 6:168. [PMID: 15998470 PMCID: PMC1190154 DOI: 10.1186/1471-2105-6-168] [Citation(s) in RCA: 236] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 07/05/2005] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations. RESULTS We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories. CONCLUSION High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.
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Affiliation(s)
- Barry R Zeeberg
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haiying Qin
- Metabolism Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Margot Sunshine
- SRA International, 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Hong Cao
- SRA International, 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - David W Kane
- SRA International, 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Mark Reimers
- SRA International, 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Robert M Stephens
- Advanced Biomedical Computing Center, National Cancer Institute at Frederick, SAIC Frederick, PO Box B, Frederick, MD, 21702, USA
| | - David Bryant
- Advanced Biomedical Computing Center, National Cancer Institute at Frederick, SAIC Frederick, PO Box B, Frederick, MD, 21702, USA
| | - Stanley K Burt
- Advanced Biomedical Computing Center, National Cancer Institute at Frederick, SAIC Frederick, PO Box B, Frederick, MD, 21702, USA
| | - Eldad Elnekave
- Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle M Hari
- Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas A Wynn
- Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Donn M Stewart
- Metabolism Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Nelson
- Metabolism Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John N Weinstein
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Reimers M, Weinstein JN. Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics 2005; 6:166. [PMID: 15992406 PMCID: PMC1189079 DOI: 10.1186/1471-2105-6-166] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 07/01/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios in a two-channel array) relative to the majority of the chip. Current practice in quality assessment for microarrays does not address regional biases. RESULTS We present methods implemented in R for visualizing regional biases and other spatial artifacts on spotted microarrays and Affymetrix chips. We also propose a statistical index to quantify regional bias and investigate its typical distribution on spotted and Affymetrix arrays. We demonstrate that notable regional biases occur on both Affymetrix and spotted arrays and that they can make a significant difference in the case of spotted microarray results. Although strong biases are also seen at the level of individual probes on Affymetrix chips, the gene expression measures are less affected, especially when the RMA method is used to summarize intensities for the probe sets. A web application program for visualization and quantitation of regional bias is provided at http://www.discover.nci.nih.gov/affytools. CONCLUSION Researchers should visualize and measure the regional biases and should estimate their impact on gene expression measurements obtained. Here, we (i) introduce pictorial visualizations of the spatial biases; (ii) present for Affymetrix chips a useful resolution of the biases into two components, one related to background, the other to intensity scale factor; (iii) introduce a single parameter to reflect the global bias present across an array. We also examine the pattern distribution of such biases and conclude that algorithms based on smoothing are unlikely to compensate adequately for them.
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Affiliation(s)
- Mark Reimers
- Genomics & Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda Maryland, 20892 USA
| | - John N Weinstein
- Genomics & Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda Maryland, 20892 USA
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Kleven M, Melaaen M, Reimers M, Røtnes J, Aurdal L, Djupesland P. Using Computational Fluid Dynamics (CFD) to Improve the Bi-Directional Nasal Drug Delivery Concept. Food and Bioproducts Processing 2005. [DOI: 10.1205/fbp.04403] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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50
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Reimers M. [Sonographical differential diagnosis of cervical lumps]. Praxis (Bern 1994) 2005; 94:427-430. [PMID: 15822440 DOI: 10.1024/0369-8394.94.11.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A brief synopsis for a practical approach in the clinical and sonographical evaluation of cervical lumps except for lymph node diseases is presented.
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Affiliation(s)
- M Reimers
- Hirslandengruppe Bern, Klinik Permanence.
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