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Chan JC, Alenina N, Cunningham AM, Ramakrishnan A, Shen L, Bader M, Maze I. Serotonin Transporter-dependent Histone Serotonylation in Placenta Contributes to the Neurodevelopmental Transcriptome. J Mol Biol 2024; 436:168454. [PMID: 38266980 PMCID: PMC10957302 DOI: 10.1016/j.jmb.2024.168454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Brain development requires appropriate regulation of serotonin (5-HT) signaling from distinct tissue sources across embryogenesis. At the maternal-fetal interface, the placenta is thought to be an important contributor of offspring brain 5-HT and is critical to overall fetal health. Yet, how placental 5-HT is acquired, and the mechanisms through which 5-HT influences placental functions, are not well understood. Recently, our group identified a novel epigenetic role for 5-HT, in which 5-HT can be added to histone proteins to regulate transcription, a process called H3 serotonylation. Here, we show that H3 serotonylation undergoes dynamic regulation during placental development, corresponding to gene expression changes that are known to influence key metabolic processes. Using transgenic mice, we demonstrate that placental H3 serotonylation is dependent on 5-HT uptake by the serotonin transporter (SERT/SLC6A4). SERT deletion robustly reduces enrichment of H3 serotonylation across the placental genome, and disrupts neurodevelopmental gene networks in early embryonic brain tissues. Thus, these findings suggest a novel role for H3 serotonylation in coordinating placental transcription at the intersection of maternal physiology and offspring brain development.
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Affiliation(s)
- Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Alenina
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Ashley M Cunningham
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Charité Universitätsmedizin Berlin, Berlin, Germany; Institute for Biology, University of Lübeck, Germany
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Liu N, Bhuva DD, Mohamed A, Bokelund M, Kulasinghe A, Tan C, Davis M. standR: spatial transcriptomic analysis for GeoMx DSP data. Nucleic Acids Res 2024; 52:e2. [PMID: 37953397 PMCID: PMC10783521 DOI: 10.1093/nar/gkad1026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/08/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of the subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here, we present standR, an R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how the application of standR enables scientists to develop in-depth insights into the biology of interest.
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Affiliation(s)
- Ning Liu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Dharmesh D Bhuva
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ahmed Mohamed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Micah Bokelund
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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3
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Szabelska-Beresewicz A, Zyprych-Walczak J, Siatkowski I, Okoniewski M. Ambiguous genes due to aligners and their impact on RNA-seq data analysis. Sci Rep 2023; 13:21770. [PMID: 38066001 PMCID: PMC10709571 DOI: 10.1038/s41598-023-41085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023] Open
Abstract
The main scope of the study is ambiguous genes, i.e. genes whose expression is difficult to estimate from the data produced by next-generation sequencing technologies. We focused on the RNA sequencing (RNA-Seq) type of experiment performed on the Illumina platform. It is crucial to identify such genes and understand the cause of their difficulty, as these genes may be involved in some diseases. By giving misleading results, they could contribute to a misunderstanding of the cause of certain diseases, which could lead to inappropriate treatment. We thought that the ambiguous genes would be difficult to map because of their complex structure. So we looked at RNA-seq analysis using different mappers to find genes that would have different measurements from the aligners. We were able to identify such genes using a generalized linear model with two factors: mappers and groups introduced by the experiment. A large proportion of ambiguous genes are pseudogenes. High sequence similarity of pseudogenes to functional genes may indicate problems in alignment procedures. In addition, predictive analysis verified the performance of difficult genes in classification. The effectiveness of classifying samples into specific groups was compared, including the expression of difficult and not difficult genes as covariates. In almost all cases considered, ambiguous genes have less predictive power.
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Affiliation(s)
- Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Michał Okoniewski
- Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
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4
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Ford K, Zuin E, Righelli D, Medina E, Schoch H, Singletary K, Muheim C, Frank MG, Hicks SC, Risso D, Peixoto L. A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569011. [PMID: 38076891 PMCID: PMC10705260 DOI: 10.1101/2023.11.28.569011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Sleep deprivation (SD) has negative effects on brain function. Sleep problems are prevalent in neurodevelopmental, neurodegenerative and psychiatric disorders. Thus, understanding the molecular consequences of SD is of fundamental importance in neuroscience. In this study, we present the first simultaneous bulk and single-nuclear (sn)RNA sequencing characterization of the effects of SD in the mouse frontal cortex. We show that SD predominantly affects glutamatergic neurons, specifically in layers 4 and 5, and produces isoform switching of thousands of transcripts. At both the global and cell-type specific level, SD has a large repressive effect on transcription, down-regulating thousands of genes and transcripts; underscoring the importance of accounting for the effects of sleep loss in transcriptome studies of brain function. As a resource we provide extensive characterizations of cell types, genes, transcripts and pathways affected by SD; as well as tutorials for data analysis.
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Affiliation(s)
- Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Elena Zuin
- Department of Biology, University of Padova, Italy
- Department of Statistical Sciences, University of Padova, Italy
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Italy
| | - Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Hannah Schoch
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Christine Muheim
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Marcos G Frank
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, MD, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Italy
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
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5
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Chan JC, Alenina N, Cunningham AM, Ramakrishnan A, Shen L, Bader M, Maze I. Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567020. [PMID: 38014301 PMCID: PMC10680709 DOI: 10.1101/2023.11.14.567020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Brain development requires appropriate regulation of serotonin (5-HT) signaling from distinct tissue sources across embryogenesis. At the maternal-fetal interface, the placenta is thought to be an important contributor of offspring brain 5-HT and is critical to overall fetal health. Yet, how placental 5-HT is acquired, and the mechanisms through which 5-HT influences placental functions, are not well understood. Recently, our group identified a novel epigenetic role for 5-HT, in which 5-HT can be added to histone proteins to regulate transcription, a process called H3 serotonylation. Here, we show that H3 serotonylation undergoes dynamic regulation during placental development, corresponding to gene expression changes that are known to influence key metabolic processes. Using transgenic mice, we demonstrate that placental H3 serotonylation largely depends on 5-HT uptake by the serotonin transporter (SERT/SLC6A4). SERT deletion robustly reduces enrichment of H3 serotonylation across the placental genome, and disrupts neurodevelopmental gene networks in early embryonic brain tissues. Thus, these findings suggest a novel role for H3 serotonylation in coordinating placental transcription at the intersection of maternal physiology and offspring brain development.
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Affiliation(s)
- Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Alenina
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Ashley M Cunningham
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Institute for Biology, University of Lübeck, Germany
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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6
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Chatterjee S, Park BJ, Vanrobaeys Y, Heiney SA, Rhone AE, Nourski KV, Langmack L, Mukherjee U, Kovach CK, Kocsis Z, Kikuchi Y, Petkov CI, Hefti MM, Bahl E, Michaelson JJ, Kawasaki H, Oya H, Howard MA, Nickl-Jockschat T, Lin LC, Abel T. Activity-induced gene expression in the human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558812. [PMID: 37790527 PMCID: PMC10542502 DOI: 10.1101/2023.09.21.558812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Activity-induced gene expression underlies synaptic plasticity and brain function. Here, using molecular sequencing techniques, we define activity-dependent transcriptomic and epigenomic changes at the tissue and single-cell level in the human brain following direct electrical stimulation of the anterior temporal lobe in patients undergoing neurosurgery. Genes related to transcriptional regulation and microglia-specific cytokine activity displayed the greatest induction pattern, revealing a precise molecular signature of neuronal activation in the human brain.
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Affiliation(s)
- Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Brian J. Park
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Shane A. Heiney
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Neural Circuits and Behavior Core, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ariane E. Rhone
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Kirill V. Nourski
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Lucy Langmack
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Christopher K. Kovach
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Zsuzsanna Kocsis
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Yukiko Kikuchi
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Christopher I. Petkov
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Marco M. Hefti
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Ethan Bahl
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Hiroyuki Oya
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Matthew A. Howard
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Thomas Nickl-Jockschat
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Li-Chun Lin
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Iowa NeuroBank Core, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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7
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Schwartz PB, Nukaya M, Berres ME, Rubinstein CD, Wu G, Hogenesch JB, Bradfield CA, Ronnekleiv-Kelly SM. The circadian clock is disrupted in pancreatic cancer. PLoS Genet 2023; 19:e1010770. [PMID: 37262074 DOI: 10.1371/journal.pgen.1010770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/01/2023] [Indexed: 06/03/2023] Open
Abstract
Disruption of the circadian clock is linked to cancer development and progression. Establishing this connection has proven beneficial for understanding cancer pathogenesis, determining prognosis, and uncovering novel therapeutic targets. However, barriers to characterizing the circadian clock in human pancreas and human pancreatic cancer-one of the deadliest malignancies-have hindered an appreciation of its role in this cancer. Here, we employed normalized coefficient of variation (nCV) and clock correlation analysis in human population-level data to determine the functioning of the circadian clock in pancreas cancer and adjacent normal tissue. We found a substantially attenuated clock in the pancreatic cancer tissue. Then we exploited our existing mouse pancreatic transcriptome data to perform an analysis of the human normal and pancreas cancer samples using a machine learning method, cyclic ordering by periodic structure (CYCLOPS). Through CYCLOPS ordering, we confirmed the nCV and clock correlation findings of an intact circadian clock in normal pancreas with robust cycling of several core clock genes. However, in pancreas cancer, there was a loss of rhythmicity of many core clock genes with an inability to effectively order the cancer samples, providing substantive evidence of a dysregulated clock. The implications of clock disruption were further assessed with a Bmal1 knockout pancreas cancer model, which revealed that an arrhythmic clock caused accelerated cancer growth and worse survival, accompanied by chemoresistance and enrichment of key cancer-related pathways. These findings provide strong evidence for clock disruption in human pancreas cancer and demonstrate a link between circadian disruption and pancreas cancer progression.
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Affiliation(s)
- Patrick B Schwartz
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Mark E Berres
- Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Clifford D Rubinstein
- Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Gang Wu
- Division of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - John B Hogenesch
- Division of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Christopher A Bradfield
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Sean M Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
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8
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Jung J, Popella L, Do PT, Pfau P, Vogel J, Barquist L. Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server. RNA (NEW YORK, N.Y.) 2023; 29:570-583. [PMID: 36750372 PMCID: PMC10158992 DOI: 10.1261/rna.079263.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/10/2023] [Indexed: 05/06/2023]
Abstract
Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10-mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq data set from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed that our findings are not unique to Salmonella We believe that MASON's off-target assessment will improve the design of specific PNAs and other ASOs.
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Affiliation(s)
- Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Linda Popella
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Phuong Thao Do
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Patrick Pfau
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
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9
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Pérez-Rodríguez D, Agís-Balboa RC, López-Fernández H. MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders. Biomedicines 2023; 11:biomedicines11041230. [PMID: 37189848 DOI: 10.3390/biomedicines11041230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
High-throughput sequencing of small RNA molecules such as microRNAs (miRNAs) has become a widely used approach for studying gene expression and regulation. However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and pathway-enrichment analyses, with many tools and databases available for each step. Furthermore, reproducibility of the analysis pipeline is crucial to ensure that the results are accurate and reliable. Here, we present myBrain-Seq, a comprehensive and reproducible pipeline for analyzing miRNA-Seq data that incorporates miRNA-specific solutions at each step of the analysis. The pipeline was designed to be flexible and user-friendly, allowing researchers with different levels of expertise to perform the analysis in a standardized and reproducible manner, using the most common and widely used tools for each step. In this work, we describe the implementation of myBrain-Seq and demonstrate its capacity to consistently and reproducibly identify differentially expressed miRNAs and enriched pathways by applying it to a real case study in which we compared schizophrenia patients who responded to medication with treatment-resistant schizophrenia patients to obtain a 16-miRNA treatment-resistant schizophrenia profile.
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Affiliation(s)
- Daniel Pérez-Rodríguez
- Neuro Epigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
| | - Roberto Carlos Agís-Balboa
- Neuro Epigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Translational Research in Neurological Diseases Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Hugo López-Fernández
- CINBIO, Department of Computer Science, ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
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10
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Kelley DP, Albrechet‐Souza L, Cruise S, Maiya R, Destouni A, Sakamuri SSVP, Duplooy A, Hibicke M, Nichols C, Katakam PVG, Gilpin NW, Francis J. Conditioned place avoidance is associated with a distinct hippocampal phenotype, partly preserved pattern separation, and reduced reactive oxygen species production after stress. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12840. [PMID: 36807494 PMCID: PMC10067435 DOI: 10.1111/gbb.12840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/20/2023]
Abstract
Stress is associated with contextual memory deficits, which may mediate avoidance of trauma-associated contexts in posttraumatic stress disorder. These deficits may emerge from impaired pattern separation, the independent representation of similar experiences by the dentate gyrus-Cornu Ammonis 3 (DG-CA3) circuit of the dorsal hippocampus, which allows for appropriate behavioral responses to specific environmental stimuli. Neurogenesis in the DG is controlled by mitochondrial reactive oxygen species (ROS) production, and may contribute to pattern separation. In Experiment 1, we performed RNA sequencing of the dorsal hippocampus 16 days after stress in rats that either develop conditioned place avoidance to a predator urine-associated context (Avoiders), or do not (Non-Avoiders). Weighted genome correlational network analysis showed that increased expression of oxidative phosphorylation-associated gene transcripts and decreased expression of gene transcripts for axon guidance and insulin signaling were associated with avoidance behavior. Based on these data, in Experiment 2, we hypothesized that Avoiders would exhibit elevated hippocampal (HPC) ROS production and degraded object pattern separation (OPS) compared with Nonavoiders. Stress impaired pattern separation performance in Non-Avoider and Avoider rats compared with nonstressed Controls, but surprisingly, Avoiders exhibited partly preserved pattern separation performance and significantly lower ROS production compared with Non-Avoiders. Lower ROS production was associated with better OPS performance in Stressed rats, but ROS production was not associated with OPS performance in Controls. These results suggest a strong negative association between HPC ROS production and pattern separation after stress, and that stress effects on these outcome variables may be associated with avoidance of a stress-paired context.
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Affiliation(s)
- D. Parker Kelley
- Comparative Biomedical SciencesLouisiana State University School of Veterinary MedicineBaton RougeLouisianaUSA
- Department of PhysiologyLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Lucas Albrechet‐Souza
- Department of Cell Biology & AnatomyLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
- Alcohol & Drug Abuse Center of ExcellenceLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Shealan Cruise
- Department of PhysiologyLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Rajani Maiya
- Department of PhysiologyLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Aspasia Destouni
- Comparative Biomedical SciencesLouisiana State University School of Veterinary MedicineBaton RougeLouisianaUSA
| | | | - Alexander Duplooy
- Comparative Biomedical SciencesLouisiana State University School of Veterinary MedicineBaton RougeLouisianaUSA
| | - Meghan Hibicke
- Department of Pharmacology and Experimental TherapeuticsLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Charles Nichols
- Alcohol & Drug Abuse Center of ExcellenceLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
- Department of Pharmacology and Experimental TherapeuticsLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
| | - Prasad V. G. Katakam
- Department of PharmacologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Nicholas W. Gilpin
- Department of PhysiologyLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
- Alcohol & Drug Abuse Center of ExcellenceLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
- Neuroscience Center of ExcellenceLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA
- Southeast Louisiana VA Healthcare System (SLVHCS)New OrleansLouisianaUSA
| | - Joseph Francis
- Comparative Biomedical SciencesLouisiana State University School of Veterinary MedicineBaton RougeLouisianaUSA
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11
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Wu Y, Yuen BWY, Wei Y, Qin LX. On data normalization and batch-effect correction for tumor subtyping with microRNA data. NAR Genom Bioinform 2023; 5:lqac100. [PMID: 36632610 PMCID: PMC9830544 DOI: 10.1093/nargab/lqac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
The discovery of new tumor subtypes has been aided by transcriptomics profiling. However, some new subtypes can be irreproducible due to data artifacts that arise from disparate experimental handling. To deal with these artifacts, methods for data normalization and batch-effect correction have been utilized before performing sample clustering for disease subtyping, despite that these methods were primarily developed for group comparison. It remains to be elucidated whether they are effective for sample clustering. We examined this issue with a re-sampling-based simulation study that leverages a pair of microRNA microarray data sets. Our study showed that (i) normalization generally benefited the discovery of sample clusters and quantile normalization tended to be the best performer, (ii) batch-effect correction was harmful when data artifacts confounded with biological signals, and (iii) their performance can be influenced by the choice of clustering method with the Prediction Around Medoid method based on Pearson correlation being consistently a best performer. Our study provides important insights on the use of data normalization and batch-effect correction in connection with the design of array-to-sample assignment and the choice of clustering method for facilitating accurate and reproducible discovery of tumor subtypes with microRNAs.
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Affiliation(s)
- Yilin Wu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Becky Wing-Yan Yuen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingying Wei
- Department of Statistics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
| | - Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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12
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. Neurobiol Sleep Circadian Rhythms 2023; 14:100092. [PMID: 37020466 PMCID: PMC10068260 DOI: 10.1016/j.nbscr.2023.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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13
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524266. [PMID: 36712085 PMCID: PMC9882159 DOI: 10.1101/2023.01.16.524266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages in adults. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Affiliation(s)
- Christine M. Muheim
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Kaitlyn Ford
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Elizabeth Medina
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Kristan Singletary
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Lucia Peixoto
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
| | - Marcos G. Frank
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
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14
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Molania R, Foroutan M, Gagnon-Bartsch JA, Gandolfo LC, Jain A, Sinha A, Olshansky G, Dobrovic A, Papenfuss AT, Speed TP. Removing unwanted variation from large-scale RNA sequencing data with PRPS. Nat Biotechnol 2023; 41:82-95. [PMID: 36109686 PMCID: PMC9849124 DOI: 10.1038/s41587-022-01440-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data come from large and complex studies. Using RNA-seq data from The Cancer Genome Atlas (TCGA), we examined several sources of unwanted variation and demonstrate here how these can significantly compromise various downstream analyses, including cancer subtype identification, association between gene expression and survival outcomes and gene co-expression analysis. We propose a strategy, called pseudo-replicates of pseudo-samples (PRPS), for deploying our recently developed normalization method, called removing unwanted variation III (RUV-III), to remove the variation caused by library size, tumor purity and batch effects in TCGA RNA-seq data. We illustrate the value of our approach by comparing it to the standard TCGA normalizations on several TCGA RNA-seq datasets. RUV-III with PRPS can be used to integrate and normalize other large transcriptomic datasets coming from multiple laboratories or platforms.
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Affiliation(s)
- Ramyar Molania
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | | | - Luke C Gandolfo
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aryan Jain
- Department of Economics and Statistics, Monash University, Melbourne, Victoria, Australia
| | - Abhishek Sinha
- Department of Economics and Statistics, Monash University, Melbourne, Victoria, Australia
| | - Gavriel Olshansky
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Terence P Speed
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia.
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15
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Koduru L, Lakshmanan M, Lee YQ, Ho PL, Lim PY, Ler WX, Ng SK, Kim D, Park DS, Banu M, Ow DSW, Lee DY. Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet- and strain-specific probiotic idiosyncrasies. Cell Rep 2022; 41:111735. [PMID: 36476869 DOI: 10.1016/j.celrep.2022.111735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/24/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Lactic acid bacteria (LAB) are well known to elicit health benefits in humans, but their functional metabolic landscapes remain unexplored. Here, we analyze differences in growth, intestinal persistence, and postbiotic biosynthesis of six representative LAB and their interactions with 15 gut bacteria under 11 dietary regimes by combining multi-omics and in silico modeling. We confirmed predictions on short-term persistence of LAB and their interactions with commensals using cecal microbiome abundance and spent-medium experiments. Our analyses indicate that probiotic attributes are both diet and species specific and cannot be solely explained using genomics. For example, although both Lacticaseibacillus casei and Lactiplantibacillus plantarum encode similarly sized genomes with diverse capabilities, L. casei exhibits a more desirable phenotype. In addition, "high-fat/low-carb" diets more likely lead to detrimental outcomes for most LAB. Collectively, our results highlight that probiotics are not "one size fits all" health supplements and lay the foundation for personalized probiotic design.
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Affiliation(s)
- Lokanand Koduru
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Yi Qing Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Pooi-Leng Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Pei-Yu Lim
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Wei Xuan Ler
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Dongseok Kim
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Doo-Sang Park
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup 56212, Republic of Korea
| | - Mazlina Banu
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
| | - Dave Siak Wei Ow
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore.
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.
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16
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Gonsioroski A, Laws M, Mourikes VE, Neff A, Drnevich J, Plewa MJ, Flaws JA. Iodoacetic acid exposure alters the transcriptome in mouse ovarian antral follicles. J Environ Sci (China) 2022; 117:46-57. [PMID: 35725088 PMCID: PMC9972181 DOI: 10.1016/j.jes.2022.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 05/20/2023]
Abstract
Iodoacetic acid (IAA) is an unregulated water disinfection byproduct that is an ovarian toxicant. However, the mechanisms of action underlying IAA toxicity in ovarian follicles remain unclear. Thus, we determined whether IAA alters gene expression in ovarian follicles in mice. Adult female mice were dosed with water or IAA (10 or 500 mg/L) in the water for 35-40 days. Antral follicles were collected for RNA-sequencing analysis and sera were collected to measure estradiol. RNA-sequencing analysis identified 1063 differentially expressed genes (DEGs) in the 10 and 500 mg/L IAA groups (false discovery rate FDR < 0.1), respectively, compared to controls. Gene Ontology Enrichment analysis showed that DEGs were involved with RNA processing and regulation of angiogenesis (10 mg/L) and the cell cycle and cell division (500 mg/L). Pathway Enrichment analysis showed that DEGs were involved in the phosphatidylinositol 3-kinase and protein kinase B (PI3K-Akt), gonadotropin-releasing hormone (GnRH), estrogen, and insulin signaling pathways (10 mg/L). Pathway Enrichment analysis showed that DEGs were involved in the oocyte meiosis, GnRH, and oxytocin signaling pathways (500 mg/L). RNA-sequencing analysis identified 809 DEGs when comparing the 500 and 10 mg/L IAA groups (FDR < 0.1). DEGs were related to ribosome, translation, mRNA processing, oxidative phosphorylation, chromosome, cell cycle, cell division, protein folding, and the oxytocin signaling pathway. Moreover, IAA exposure significantly decreased estradiol levels (500 mg/L) compared to control. This study identified key candidate genes and pathways involved in IAA toxicity and can help to further understand the molecular mechanisms of IAA toxicity in ovarian follicles.
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Affiliation(s)
- Andressa Gonsioroski
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mary Laws
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Vasiliki E Mourikes
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Alison Neff
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jenny Drnevich
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA; Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Michael J Plewa
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA; Department of Crop Sciences and the Safe Global Water Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
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17
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Saremi B, Gusmag F, Distl O, Schaarschmidt F, Metzger J, Becker S, Jung K. A comparison of strategies for generating artificial replicates in RNA-seq experiments. Sci Rep 2022; 12:7170. [PMID: 35505053 PMCID: PMC9065086 DOI: 10.1038/s41598-022-11302-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
Due to the overall high costs, technical replicates are usually omitted in RNA-seq experiments, but several methods exist to generate them artificially. Bootstrapping reads from FASTQ-files has recently been used in the context of other NGS analyses and can be used to generate artificial technical replicates. Bootstrapping samples from the columns of the expression matrix has already been used for DNA microarray data and generates a new artificial replicate of the whole experiment. Mixing data of individual samples has been used for data augmentation in machine learning. The aim of this comparison is to evaluate which of these strategies are best suited to study the reproducibility of differential expression and gene-set enrichment analysis in an RNA-seq experiment. To study the approaches under controlled conditions, we performed a new RNA-seq experiment on gene expression changes upon virus infection compared to untreated control samples. In order to compare the approaches for artificial replicates, each of the samples was sequenced twice, i.e. as true technical replicates, and differential expression analysis and GO term enrichment analysis was conducted separately for the two resulting data sets. Although we observed a high correlation between the results from the two replicates, there are still many genes and GO terms that would be selected from one replicate but not from the other. Cluster analyses showed that artificial replicates generated by bootstrapping reads produce it p values and fold changes that are close to those obtained from the true data sets. Results generated from artificial replicates with the approaches of column bootstrap or mixing observations were less similar to the results from the true replicates. Furthermore, the overlap of results among replicates generated by column bootstrap or mixing observations was much stronger than among the true replicates. Artificial technical replicates generated by bootstrapping sequencing reads from FASTQ-files are better suited to study the reproducibility of results from differential expression and GO term enrichment analysis in RNA-seq experiments than column bootstrap or mixing observations. However, FASTQ-bootstrapping is computationally more expensive than the other two approaches. The FASTQ-bootstrapping may be applicable to other applications of high-throughput sequencing.
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Affiliation(s)
- Babak Saremi
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Frederic Gusmag
- Institute for Parasitology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Frank Schaarschmidt
- Biostatistics Department, Institute for Cell Biology, Leibniz University Hannover, Hannover, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.,RG Development and Disease, Veterinary Functional Genomics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Stefanie Becker
- Institute for Parasitology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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18
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Chatterjee S, Bahl E, Mukherjee U, Walsh EN, Shetty MS, Yan AL, Vanrobaeys Y, Lederman JD, Giese KP, Michaelson J, Abel T. Endoplasmic reticulum chaperone genes encode effectors of long-term memory. SCIENCE ADVANCES 2022; 8:eabm6063. [PMID: 35319980 PMCID: PMC8942353 DOI: 10.1126/sciadv.abm6063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/28/2022] [Indexed: 06/10/2023]
Abstract
The mechanisms underlying memory loss associated with Alzheimer's disease and related dementias (ADRD) remain unclear, and no effective treatments exist. Fundamental studies have shown that a set of transcriptional regulatory proteins of the nuclear receptor 4a (Nr4a) family serve as molecular switches for long-term memory. Here, we show that Nr4a proteins regulate the transcription of genes encoding chaperones that localize to the endoplasmic reticulum (ER). These chaperones fold and traffic plasticity-related proteins to the cell surface during long-lasting forms of synaptic plasticity and memory. Dysregulation of Nr4a transcription factors and ER chaperones is linked to ADRD, and overexpressing Nr4a1 or the chaperone Hspa5 ameliorates long-term memory deficits in a tau-based mouse model of ADRD, pointing toward innovative therapeutic approaches for treating memory loss. Our findings establish a unique molecular concept underlying long-term memory and provide insights into the mechanistic basis of cognitive deficits in dementia.
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Affiliation(s)
- Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Ethan Bahl
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
| | - Emily N. Walsh
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
| | - Mahesh Shivarama Shetty
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Amy L. Yan
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Joseph D. Lederman
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - K. Peter Giese
- Department of Basic and Clinical Neuroscience, King’s College London, London, UK
| | - Jacob Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA
- Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
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19
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Gallego-Paez LM, Mauer J. DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization. FRONTIERS IN BIOINFORMATICS 2022; 2:786898. [PMID: 36304260 PMCID: PMC9580925 DOI: 10.3389/fbinf.2022.786898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
RNA-seq analysis of alternative pre-mRNA splicing has facilitated an unprecedented understanding of transcriptome complexity in health and disease. However, despite the availability of countless bioinformatic pipelines for transcriptome-wide splicing analysis, the use of these tools is often limited to expert bioinformaticians. The need for high computational power, combined with computational outputs that are complicated to visualize and interpret present obstacles to the broader research community. Here we introduce DJExpress, an R package for differential expression analysis of transcriptomic features and expression-trait associations. To determine gene-level differential junction usage as well as associations between junction expression and molecular/clinical features, DJExpress uses raw splice junction counts as input data. Importantly, DJExpress runs on an average laptop computer and provides a set of interactive and intuitive visualization formats. In contrast to most existing pipelines, DJExpress can handle both annotated and de novo identified splice junctions, thereby allowing the quantification of novel splice events. Moreover, DJExpress offers a web-compatible graphical interface allowing the analysis of user-provided data as well as the visualization of splice events within our custom database of differential junction expression in cancer (DJEC DB). DJEC DB includes not only healthy and tumor tissue junction expression data from TCGA and GTEx repositories but also cancer cell line data from the DepMap project. The integration of DepMap functional genomics data sets allows association of junction expression with molecular features such as gene dependencies and drug response profiles. This facilitates identification of cancer cell models for specific splicing alterations that can then be used for functional characterization in the lab. Thus, DJExpress represents a powerful and user-friendly tool for exploration of alternative splicing alterations in RNA-seq data, including multi-level data integration of alternative splicing signatures in healthy tissue, tumors and cancer cell lines.
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Affiliation(s)
| | - Jan Mauer
- *Correspondence: Lina Marcela Gallego-Paez, ; Jan Mauer,
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20
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Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med 2022; 3:100525. [PMID: 35243422 PMCID: PMC8861971 DOI: 10.1016/j.xcrm.2022.100525] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/15/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms in individual people, here we present an omic and multidimensional spatial (OMS) atlas generated from four serial biopsies of an individual with metastatic breast cancer during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata that includes treatment times and doses, anatomic imaging, and blood-based response measurements to clinical and exploratory analyses, which includes comprehensive DNA, RNA, and protein profiles; images of multiplexed immunostaining; and 2- and 3-dimensional scanning electron micrographs. These data report aspects of heterogeneity and evolution of the cancer genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples of how integrative analyses of these data reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.
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Affiliation(s)
- Brett E. Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Allison L. Creason
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jayne M. Stommel
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jamie M. Keck
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Swapnil Parmar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Courtney B. Betts
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Boniface
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erik Burlingame
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Todd Camp
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Koei Chin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer Eng
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Heidi S. Feiler
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael B. Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zhi Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ben L. Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jinho Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Souraya Mitri
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Janice Patterson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica L. Riesterer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR 97239, USA
| | - Shamilene Sivagnanam
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Guillaume Thibault
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin R. Weeder
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina Zheng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F. Thompson
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR 97239, USA
| | - Laura M. Heiser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T. Spellman
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lisa M. Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexander R. Guimaraes
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Corless
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jeremy Goecks
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Raymond Bergan
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zahi Mitri
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W. Gray
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
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21
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Kelley DP, Venable K, Destouni A, Billac G, Ebenezer P, Stadler K, Nichols C, Barker S, Francis J. Pharmahuasca and DMT Rescue ROS Production and Differentially Expressed Genes Observed after Predator and Psychosocial Stress: Relevance to Human PTSD. ACS Chem Neurosci 2022; 13:257-274. [PMID: 34990116 DOI: 10.1021/acschemneuro.1c00660] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Post-traumatic stress disorder (PTSD) is associated with cognitive deficits, oxidative stress, and inflammation. Animal models have recapitulated features of PTSD, but no comparative RNA sequencing analysis of differentially expressed genes (DEGs) in the brain between PTSD and animal models of traumatic stress has been carried out. We compared DEGs from the prefrontal cortex (PFC) of an established stress model to DEGs from the dorsolateral PFC (dlPFC) of humans. We observed a significant enrichment of rat DEGs in human PTSD and identified 20 overlapping DEGs, of which 17 (85%) are directionally concordant. N,N-dimethyltryptamine (DMT) is a known indirect antioxidant, anti-inflammatory, and neuroprotective compound with antidepressant and plasticity-facilitating effects. We tested the capacity of DMT, the monoamine oxidase inhibitor (MAOI) harmaline, and "pharmahuasca" (DMT + harmaline) to reduce reactive oxygen species (ROS) production and inflammatory gene expression and to modulate neuroplasticity-related gene expression in the model. We administered DMT (2 mg/kg IP), harmaline (1.5 mg/kg IP), pharmahuasca, or vehicle every other day for 5 days, following a 30 day stress regiment. We measured ROS production in the PFC and hippocampus (HC) by electron paramagnetic resonance spectroscopy and sequenced total mRNA in the PFC. We also performed in vitro assays to measure the affinity and efficacy of DMT and harmaline at 5HT2AR compared to 5-HT. DMT and pharmahuasca reduced ROS production in the PFC and HC, while harmaline had mixed effects. Treatments normalized 9, 12, and 14 overlapping DEGs, and pathway analysis implicated that genes were involved in ROS production, inflammation, growth factor signaling, neurotransmission, and neuroplasticity.
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Affiliation(s)
- D. Parker Kelley
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
| | - Katy Venable
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
| | - Aspasia Destouni
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
| | - Gerald Billac
- Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, United States
| | - Philip Ebenezer
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
| | - Krisztian Stadler
- Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Charles Nichols
- Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, United States
| | - Steven Barker
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
| | - Joseph Francis
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana 70803, United States
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22
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McKennan C, Nicolae D. Estimating and accounting for unobserved covariates in high-dimensional correlated data. J Am Stat Assoc 2022; 117:225-236. [PMID: 35615339 PMCID: PMC9126075 DOI: 10.1080/01621459.2020.1769635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput 'omic' data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high dimensional data with correlated or nonexchangeable residuals. We demonstrate each method's superior performance compared to other state of the art methods by analyzing simulated multi-tissue gene expression data and identifying sex-associated DNA methylation sites in a real, longitudinal twin study.
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Affiliation(s)
| | - Dan Nicolae
- Department of Statistics, University of Chicago
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23
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Tran DT, Might M. cdev: a ground-truth based measure to evaluate RNA-seq normalization performance. PeerJ 2021; 9:e12233. [PMID: 34707933 PMCID: PMC8496462 DOI: 10.7717/peerj.12233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022] Open
Abstract
Normalization of RNA-seq data has been an active area of research since the problem was first recognized a decade ago. Despite the active development of new normalizers, their performance measures have been given little attention. To evaluate normalizers, researchers have been relying on ad hoc measures, most of which are either qualitative, potentially biased, or easily confounded by parametric choices of downstream analysis. We propose a metric called condition-number based deviation, or cdev, to quantify normalization success. cdev measures how much an expression matrix differs from another. If a ground truth normalization is given, cdev can then be used to evaluate the performance of normalizers. To establish experimental ground truth, we compiled an extensive set of public RNA-seq assays with external spike-ins. This data collection, together with cdev, provides a valuable toolset for benchmarking new and existing normalization methods.
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Affiliation(s)
- Diem-Trang Tran
- School of Computing, University of Utah, Salt Lake City, UT, United States of America
| | - Matthew Might
- Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, United States of America
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24
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Pérez-Rodríguez D, López-Fernández H, Agís-Balboa RC. Application of miRNA-seq in neuropsychiatry: A methodological perspective. Comput Biol Med 2021; 135:104603. [PMID: 34216893 DOI: 10.1016/j.compbiomed.2021.104603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
MiRNAs are emerging as key molecules to study neuropsychiatric diseases. However, despite the large number of methodologies and software for miRNA-seq analyses, there is little supporting literature for researchers in this area. This review focuses on evaluating how miRNA-seq has been used to study neuropsychiatric diseases to date, analyzing both the main findings discovered and the bioinformatics workflows and tools used from a methodological perspective. The objective of this review is two-fold: first, to evaluate current miRNA-seq procedures used in neuropsychiatry; and second, to offer comprehensive information that can serve as a guide to new researchers in bioinformatics. After conducting a systematic search (from 2016 to June 30, 2020) of articles using miRNA-seq in neuropsychiatry, we have seen that it has already been used for different types of studies in three main categories: diagnosis, prognosis, and mechanism. We carefully analyzed the bioinformatics workflows of each study, observing a high degree of variability with respect to the tools and methods used and several methodological complexities that are identified and discussed in this review.
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Affiliation(s)
- Daniel Pérez-Rodríguez
- Translational Neuroscience Group-CIBERSAM, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, 36213, Vigo, Spain; NeuroEpigenetics Lab. University Hospital Complex of Vigo, SERGAS-UVIGO, 36213, Vigo, Spain
| | - Hugo López-Fernández
- Instituto de Investigação e Inovação Em Saúde (I3S), Universidade Do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; CINBIO, Universidade de Vigo, Department of Computer Science, ESEI - Escuela Superior de Ingeniería Informática, 32004, Ourense, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain.
| | - Roberto C Agís-Balboa
- Translational Neuroscience Group-CIBERSAM, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, 36213, Vigo, Spain; NeuroEpigenetics Lab. University Hospital Complex of Vigo, SERGAS-UVIGO, 36213, Vigo, Spain.
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25
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Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
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26
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MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis. Nat Commun 2021; 12:3353. [PMID: 34099673 PMCID: PMC8184769 DOI: 10.1038/s41467-021-23608-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 05/07/2021] [Indexed: 11/09/2022] Open
Abstract
The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a lack of equivalent analysis and tools for RNA splicing. Here we first assess the effect of confounders on both expression and splicing quantifications in two large public RNA-Seq datasets (TARGET, ENCODE). We show quantification of splicing variations are affected at least as much as those of gene expression, revealing unwanted sources of variations in both datasets. Next, we develop MOCCASIN, a method to correct the effect of both known and unknown confounders on RNA splicing quantification and demonstrate MOCCASIN's effectiveness on both synthetic and real data. Code, synthetic and corrected datasets are all made available as resources.
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27
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Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - José F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
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28
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A gene expression atlas for different kinds of stress in the mouse brain. Sci Data 2020; 7:437. [PMID: 33328476 PMCID: PMC7744580 DOI: 10.1038/s41597-020-00772-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
Abstract
Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”.
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29
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Chatterjee S, Angelakos CC, Bahl E, Hawk JD, Gaine ME, Poplawski SG, Schneider-Anthony A, Yadav M, Porcari GS, Cassel JC, Giese KP, Michaelson JJ, Lyons LC, Boutillier AL, Abel T. The CBP KIX domain regulates long-term memory and circadian activity. BMC Biol 2020; 18:155. [PMID: 33121486 PMCID: PMC7597000 DOI: 10.1186/s12915-020-00886-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Background CREB-dependent transcription necessary for long-term memory is driven by interactions with CREB-binding protein (CBP), a multi-domain protein that binds numerous transcription factors potentially affecting expression of thousands of genes. Identifying specific domain functions for multi-domain proteins is essential to understand processes such as cognitive function and circadian clocks. We investigated the function of the CBP KIX domain in hippocampal memory and gene expression using CBPKIX/KIX mice with mutations that prevent phospho-CREB (Ser133) binding. Results We found that CBPKIX/KIX mice were impaired in long-term memory, but not learning acquisition or short-term memory for the Morris water maze. Using an unbiased analysis of gene expression in the dorsal hippocampus after training in the Morris water maze or contextual fear conditioning, we discovered dysregulation of CREB, CLOCK, and BMAL1 target genes and downregulation of circadian genes in CBPKIX/KIX mice. Given our finding that the CBP KIX domain was important for transcription of circadian genes, we profiled circadian activity and phase resetting in CBPKIX/KIX mice. CBPKIX/KIX mice exhibited delayed activity peaks after light offset and longer free-running periods in constant dark. Interestingly, CBPKIX/KIX mice displayed phase delays and advances in response to photic stimulation comparable to wildtype littermates. Thus, this work delineates site-specific regulation of the circadian clock by a multi-domain protein. Conclusions These studies provide insight into the significance of the CBP KIX domain by defining targets of CBP transcriptional co-activation in memory and the role of the CBP KIX domain in vivo on circadian rhythms. Graphical abstract ![]()
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Affiliation(s)
- Snehajyoti Chatterjee
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France.,Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Christopher C Angelakos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Joshua D Hawk
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shane G Poplawski
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, USA
| | - Anne Schneider-Anthony
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France
| | - Manish Yadav
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Giulia S Porcari
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Christophe Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, Iowa, USA.,Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France. .,LNCA, CNRS UMR 7364, Strasbourg, France.
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
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30
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Tong L, Wu PY, Phan JH, Hassazadeh HR, Tong W, Wang MD. Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction. Sci Rep 2020; 10:17925. [PMID: 33087762 PMCID: PMC7578822 DOI: 10.1038/s41598-020-74567-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline's performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.
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Affiliation(s)
- Li Tong
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Po-Yen Wu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - John H Phan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hamid R Hassazadeh
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - May D Wang
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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31
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Xie J, Xu Y, Chen H, Chi M, He J, Li M, Liu H, Xia J, Guan Q, Guo Z, Yan H. Identification of population-level differentially expressed genes in one-phenotype data. Bioinformatics 2020; 36:4283-4290. [PMID: 32428201 PMCID: PMC7520039 DOI: 10.1093/bioinformatics/btaa523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/15/2020] [Accepted: 05/14/2020] [Indexed: 01/01/2023] Open
Abstract
Motivation For some specific tissues, such as the heart and brain, normal controls are difficult to obtain. Thus, studies with only a particular type of disease samples (one phenotype) cannot be analyzed using common methods, such as significance analysis of microarrays, edgeR and limma. The RankComp algorithm, which was mainly developed to identify individual-level differentially expressed genes (DEGs), can be applied to identify population-level DEGs for the one-phenotype data but cannot identify the dysregulation directions of DEGs. Results Here, we optimized the RankComp algorithm, termed PhenoComp. Compared with RankComp, PhenoComp provided the dysregulation directions of DEGs and had more robust detection power in both simulated and real one-phenotype data. Moreover, using the DEGs detected by common methods as the ‘gold standard’, the results showed that the DEGs detected by PhenoComp using only one-phenotype data were comparable to those identified by common methods using case-control samples, independent of the measurement platform. PhenoComp also exhibited good performance for weakly differential expression signal data. Availability and implementation The PhenoComp algorithm is available on the web at https://github.com/XJJ-student/PhenoComp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiajing Xie
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Yang Xu
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Haifeng Chen
- Department of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou 350007, China
| | - Meirong Chi
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Jun He
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Meifeng Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Hui Liu
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Jie Xia
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Qingzhou Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Zheng Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
| | - Haidan Yan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou 350122, China
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32
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Vila-Sanjurjo A, Juarez D, Loyola S, Torres M, Leguia M. Minority Gene Expression Profiling: Probing the Genetic Signatures of Pathogenesis Using Ribosome Profiling. J Infect Dis 2020; 221:S341-S357. [PMID: 32221545 DOI: 10.1093/infdis/jiz565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Minority Gene Expression Profiling (MGEP) refers to a scenario where the expression profiles of specific genes of interest are concentrated in a small cellular pool that is embedded within a larger, non-expressive pool. An example of this is the analysis of disease-related genes within sub-populations of blood or biopsied tissues. These systems are characterized by low signal-to-noise ratios that make it difficult, if not impossible, to uncover the desired signatures of pathogenesis in the absence of lengthy, and often problematic, technical manipulations. We have adapted ribosome profiling (RP) workflows from the Illumina to the Ion Proton platform and used them to analyze signatures of pathogenesis in an MGEP model system consisting of human cells eliciting <3% productive dengue infection. We find that RP is powerful enough to identify relevant responses of differentially expressed genes, even in the presence of significant noise. We discuss how to deal with sources of unwanted variation, and propose ways to further improve this powerful approach to the study of pathogenic signatures within MGEP systems.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Diana Juarez
- Genomics Laboratory, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.,Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Steev Loyola
- Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Michael Torres
- Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.,Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
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33
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DeVera C, Tosini G. Circadian analysis of the mouse retinal pigment epithelium transcriptome. Exp Eye Res 2020; 193:107988. [PMID: 32105725 DOI: 10.1016/j.exer.2020.107988] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
The presence of a phagocytic peak of photoreceptor outer segments by the retinal pigment epithelium (RPE) one or 2 h after the onset of light has been reported for several diurnal and nocturnal species. This peak in phagocytic activity also persists under constant lighting conditions (i.e., constant light or dark) thus demonstrating that the timing of this peak is driven by a circadian clock. The aim of this study was to investigate the change in RPE whole transcriptome at two different circadian times (CT; 1 h before (CT23) and 1 h after (CT1) subjective light onset). C57BL/6J male mice were maintained in constant dark conditions for three days and euthanized under red light (<1 lux) at CT23 and CT1. RPE was isolated from whole eyes for RNA library preparation and sequencing on an Illumina HiSeq4000 platform. 14,083 mouse RPE transcripts were detected in common between CT23 and CT1. 12,005 were protein coding transcripts and 2078 were non-protein coding transcripts. 2421 protein coding transcripts were significantly upregulated whereas only 3 transcripts were significantly downregulated and 12 non-protein coding transcripts were significantly upregulated and 31 non-protein coding transcripts were significantly downregulated at CT1 when compared to CT23 (p < 0.05, fold change ≥ ±2.0). Of the protein coding transcripts, most of them were characterized as: enzymes, kinases, and transcriptional regulators with a large majority of activity in the cytoplasm, nucleus, and plasma membrane. Non-protein coding transcripts included biotypes such as long-non coding RNAs and pseudogenes. Gene ontology analysis and ingenuity pathway analysis revealed that differentially expressed transcripts were associated with integrin signaling, oxidative phosphorylation, protein phosphorylation, and actin cytoskeleton remodeling suggesting that these previously identified phagocytic pathways are under circadian control. Our analysis identified new pathways (e.g., increased mitochondrial respiration via increased oxidative phosphorylation) that may be involved in the circadian control of phagocytic activity. In addition, our dataset suggests a possible regulatory role for the identified non-protein coding transcripts in mediating the complex function of RPE phagocytosis. Finally, our results also indicate, as seen in other tissues, about 20% of the whole RPE transcriptome may be under circadian clock regulation.
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Affiliation(s)
- Christopher DeVera
- Department of Pharmacology and Toxicology, Atlanta, GA, USA, 30310; Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, USA, 30310
| | - Gianluca Tosini
- Department of Pharmacology and Toxicology, Atlanta, GA, USA, 30310; Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, USA, 30310.
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34
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Gulinello M, Mitchell HA, Chang Q, Timothy O'Brien W, Zhou Z, Abel T, Wang L, Corbin JG, Veeraragavan S, Samaco RC, Andrews NA, Fagiolini M, Cole TB, Burbacher TM, Crawley JN. Rigor and reproducibility in rodent behavioral research. Neurobiol Learn Mem 2019; 165:106780. [PMID: 29307548 PMCID: PMC6034984 DOI: 10.1016/j.nlm.2018.01.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023]
Abstract
Behavioral neuroscience research incorporates the identical high level of meticulous methodologies and exacting attention to detail as all other scientific disciplines. To achieve maximal rigor and reproducibility of findings, well-trained investigators employ a variety of established best practices. Here we explicate some of the requirements for rigorous experimental design and accurate data analysis in conducting mouse and rat behavioral tests. Novel object recognition is used as an example of a cognitive assay which has been conducted successfully with a range of methods, all based on common principles of appropriate procedures, controls, and statistics. Directors of Rodent Core facilities within Intellectual and Developmental Disabilities Research Centers contribute key aspects of their own novel object recognition protocols, offering insights into essential similarities and less-critical differences. Literature cited in this review article will lead the interested reader to source papers that provide step-by-step protocols which illustrate optimized methods for many standard rodent behavioral assays. Adhering to best practices in behavioral neuroscience will enhance the value of animal models for the multiple goals of understanding biological mechanisms, evaluating consequences of genetic mutations, and discovering efficacious therapeutics.
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Affiliation(s)
- Maria Gulinello
- IDDRC Behavioral Core Facility, Neuroscience Department, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Heather A Mitchell
- IDD Models Core, Waisman Center, University of Wisconsin Madison, Madison, WI 53705, USA
| | - Qiang Chang
- IDD Models Core, Waisman Center, University of Wisconsin Madison, Madison, WI 53705, USA
| | - W Timothy O'Brien
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhaolan Zhou
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ted Abel
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current affiliation: Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Li Wang
- IDDRC Neurobehavioral Core, Center for Neuroscience Research, Children's National Health System, Washington, DC 20010, USA
| | - Joshua G Corbin
- IDDRC Neurobehavioral Core, Center for Neuroscience Research, Children's National Health System, Washington, DC 20010, USA
| | - Surabi Veeraragavan
- IDDRC Neurobehavioral Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rodney C Samaco
- IDDRC Neurobehavioral Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nick A Andrews
- IDDRC Neurodevelopmental Behavior Core, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michela Fagiolini
- IDDRC Neurodevelopmental Behavior Core, Boston Children's Hospital, Boston, MA 02115, USA
| | - Toby B Cole
- IDDRC Rodent Behavior Laboratory, Center on Human Development and Disability, University of Washington, Seattle, WA 98195, USA
| | - Thomas M Burbacher
- IDDRC Rodent Behavior Laboratory, Center on Human Development and Disability, University of Washington, Seattle, WA 98195, USA
| | - Jacqueline N Crawley
- IDDRC Rodent Behavior Core, MIND Institute, University of California Davis School of Medicine, Sacramento, CA 95817, USA.
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35
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Short AK, Baram TZ. Early-life adversity and neurological disease: age-old questions and novel answers. Nat Rev Neurol 2019; 15:657-669. [PMID: 31530940 PMCID: PMC7261498 DOI: 10.1038/s41582-019-0246-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2019] [Indexed: 12/24/2022]
Abstract
Neurological illnesses, including cognitive impairment, memory decline and dementia, affect over 50 million people worldwide, imposing a substantial burden on individuals and society. These disorders arise from a combination of genetic, environmental and experiential factors, with the latter two factors having the greatest impact during sensitive periods in development. In this Review, we focus on the contribution of adverse early-life experiences to aberrant brain maturation, which might underlie vulnerability to cognitive brain disorders. Specifically, we draw on recent robust discoveries from diverse disciplines, encompassing human studies and experimental models. These discoveries suggest that early-life adversity, especially in the perinatal period, influences the maturation of brain circuits involved in cognition. Importantly, new findings suggest that fragmented and unpredictable environmental and parental signals comprise a novel potent type of adversity, which contributes to subsequent vulnerabilities to cognitive illnesses via mechanisms involving disordered maturation of brain 'wiring'.
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Affiliation(s)
- Annabel K Short
- Departments of Anatomy and Neruobiology, University of California-Irvine, Irvine, CA, USA
- Departments of Pediatrics, University of California-Irvine, Irvine, CA, USA
| | - Tallie Z Baram
- Departments of Anatomy and Neruobiology, University of California-Irvine, Irvine, CA, USA.
- Departments of Pediatrics, University of California-Irvine, Irvine, CA, USA.
- Departments of Neurology, University of California-Irvine, Irvine, CA, USA.
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36
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Muheim CM, Spinnler A, Sartorius T, Dürr R, Huber R, Kabagema C, Ruth P, Brown SA. Dynamic- and Frequency-Specific Regulation of Sleep Oscillations by Cortical Potassium Channels. Curr Biol 2019; 29:2983-2992.e3. [PMID: 31474531 DOI: 10.1016/j.cub.2019.07.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 06/15/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
Primary electroencephalographic (EEG) features of sleep arise in part from thalamocortical neural assemblies, and cortical potassium channels have long been thought to play a critical role. We have exploited the regionally dynamic nature of sleep EEG to develop a novel screening strategy and used it to conduct an adeno-associated virus (AAV)-mediated RNAi screen for cellular roles of 31 different voltage-gated potassium channels in modulating cortical EEG features across the circadian sleep-wake cycle. Surprisingly, a majority of channels modified only electroencephalographic frequency bands characteristic of sleep, sometimes diurnally or even in specific vigilance states. Confirming our screen for one channel, we show that depletion of the KCa1.1 (or "BK") channel reduces EEG power in slow-wave sleep by slowing neuronal repolarization. Strikingly, this reduction completely abolishes transcriptomic changes between sleep and wake. Thus, our data establish an unexpected connection between transcription and EEG power controlled by specific potassium channels. We postulate that additive dynamic roles of individual potassium channels could integrate different influences upon sleep and wake within single neurons.
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Affiliation(s)
- Christine M Muheim
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Andrea Spinnler
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Tina Sartorius
- Institute of Pharmacy, Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Roland Dürr
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Reto Huber
- University Children's Hospital Zurich, University of Zürich, Steinwiesstrasse 75, Zürich 8032, Switzerland
| | - Clement Kabagema
- Institute of Pharmacy, Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Peter Ruth
- Institute of Pharmacy, Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland.
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37
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Everson TM, Marsit CJ. Integrating -Omics Approaches into Human Population-Based Studies of Prenatal and Early-Life Exposures. Curr Environ Health Rep 2019; 5:328-337. [PMID: 30054820 DOI: 10.1007/s40572-018-0204-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We present the study design and methodological suggestions for population-based studies that integrate molecular -omics data and highlight recent studies that have used such data to examine the potential impacts of prenatal environmental exposures on fetal health. RECENT FINDINGS Epidemiologic studies have observed numerous relationships between prenatal exposures (smoking, toxic metals, endocrine disruptors) and fetal and early-life molecular profiles, though such investigations have so far been dominated by epigenomic association studies. However, recent transcriptomic, proteomic, and metabolomic studies have demonstrated their promise for the identification of exposure and response biomarkers. Molecular -omics have opened new avenues of research in environmental health that can improve our understanding of disease etiology and contribute to the development of exposure and response biomarkers. Studies that incorporate multiple -omics data from different molecular domains in longitudinally collected samples hold particular promise.
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Affiliation(s)
- Todd M Everson
- Departments of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA
| | - Carmen J Marsit
- Departments of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA. .,Departments of Environmental Health and Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA.
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38
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Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, Medina E, Risso D, Frank MG, Peixoto L. Shank3 modulates sleep and expression of circadian transcription factors. eLife 2019; 8:e42819. [PMID: 30973326 PMCID: PMC6488297 DOI: 10.7554/elife.42819] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/10/2019] [Indexed: 12/30/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States and often co-presents with sleep problems. Sleep problems in ASD predict the severity of ASD core diagnostic symptoms and have a considerable impact on the quality of life of caregivers. Little is known, however, about the underlying molecular mechanisms of sleep problems in ASD. We investigated the role of Shank3, a high confidence ASD gene candidate, in sleep architecture and regulation. We show that mice lacking exon 21 of Shank3 have problems falling asleep even when sleepy. Using RNA-seq we show that sleep deprivation increases the differences in prefrontal cortex gene expression between mutants and wild types, downregulating circadian transcription factors Per3, Bhlhe41, Hlf, Tef, and Nr1d1. Shank3 mutants also have trouble regulating wheel-running activity in constant darkness. Overall, our study shows that Shank3 is an important modulator of sleep and clock gene expression.
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Affiliation(s)
- Ashley M Ingiosi
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Hannah Schoch
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Taylor Wintler
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Kristan G Singletary
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Dario Righelli
- Istituto per le Applicazioni del Calcolo “M. Picone”Consiglio Nazionale della RicercheNapoliItaly
- Dipartimento di Scienze Aziendali Management & Innovation SystemsUniversity of FuscianoFiscianoItaly
| | - Leandro G Roser
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Elizabeth Medina
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Davide Risso
- Department of Statistical SciencesUniversity of PadovaPadovaItaly
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and ResearchWeill Cornell MedicineNew YorkUnited States
| | - Marcos G Frank
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
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Athanasiadou R, Neymotin B, Brandt N, Wang W, Christiaen L, Gresham D, Tranchina D. A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. PLoS Comput Biol 2019; 15:e1006794. [PMID: 30856174 PMCID: PMC6428340 DOI: 10.1371/journal.pcbi.1006794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/21/2019] [Accepted: 01/16/2019] [Indexed: 01/09/2023] Open
Abstract
A fundamental assumption, common to the vast majority of high-throughput transcriptome analyses, is that the expression of most genes is unchanged among samples and that total cellular RNA remains constant. As the number of analyzed experimental systems increases however, different independent studies demonstrate that this assumption is often violated. We present a calibration method using RNA spike-ins that allows for the measurement of absolute cellular abundance of RNA molecules. We apply the method to pooled RNA from cell populations of known sizes. For each transcript, we compute a nominal abundance that can be converted to absolute by dividing by a scale factor determined in separate experiments: the yield coefficient of the transcript relative to that of a reference spike-in measured with the same protocol. The method is derived by maximum likelihood theory in the context of a complete statistical model for sequencing counts contributed by cellular RNA and spike-ins. The counts are based on a sample from a fixed number of cells to which a fixed population of spike-in molecules has been added. We illustrate and evaluate the method with applications to two global expression data sets, one from the model eukaryote Saccharomyces cerevisiae, proliferating at different growth rates, and differentiating cardiopharyngeal cell lineages in the chordate Ciona robusta. We tested the method in a technical replicate dilution study, and in a k-fold validation study.
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Affiliation(s)
- Rodoniki Athanasiadou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Wei Wang
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniel Tranchina
- Department of Biology, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
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Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition. Sci Rep 2019; 9:848. [PMID: 30696862 PMCID: PMC6351599 DOI: 10.1038/s41598-018-36649-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/26/2018] [Indexed: 12/29/2022] Open
Abstract
Development of maternal blood transcriptomic markers to monitor placental function and risk of obstetrical complications throughout pregnancy requires accurate quantification of gene expression. Herein, we benchmark three state-of-the-art expression profiling techniques to assess in maternal circulation the expression of cell type-specific gene sets previously discovered by single-cell genomics studies of the placenta. We compared Affymetrix Human Transcriptome Arrays, Illumina RNA-Seq, and sequencing-based targeted expression profiling (DriverMapTM) to assess transcriptomic changes with gestational age and labor status at term, and tested 86 candidate genes by qRT-PCR. DriverMap identified twice as many significant genes (q < 0.1) than RNA-Seq and five times more than microarrays. The gap in the number of significant genes remained when testing only protein-coding genes detected by all platforms. qRT-PCR validation statistics (PPV and AUC) were high and similar among platforms, yet dynamic ranges were higher for sequencing based platforms than microarrays. DriverMap provided the strongest evidence for the association of B-cell and T-cell gene signatures with gestational age, while the T-cell expression was increased with spontaneous labor at term according to all three platforms. We concluded that sequencing-based techniques are more suitable to quantify whole-blood gene expression compared to microarrays, as they have an expanded dynamic range and identify more true positives. Targeted expression profiling achieved higher coverage of protein-coding genes with fewer total sequenced reads, and it is especially suited to track cell type-specific signatures discovered in the placenta. The T-cell gene expression signature was increased in women who underwent spontaneous labor at term, mimicking immunological processes at the maternal-fetal interface and placenta.
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41
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Wang L, Felts SJ, Van Keulen VP, Pease LR, Zhang Y. Exploring the effect of library preparation on RNA sequencing experiments. Genomics 2018; 111:1752-1759. [PMID: 30529531 DOI: 10.1016/j.ygeno.2018.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
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Affiliation(s)
- Lei Wang
- Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, United States; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
| | - Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Larry R Pease
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Yuji Zhang
- Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, United States; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
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42
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Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nat Neurosci 2018; 21:1717-1727. [DOI: 10.1038/s41593-018-0266-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022]
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Rigaill G, Balzergue S, Brunaud V, Blondet E, Rau A, Rogier O, Caius J, Maugis-Rabusseau C, Soubigou-Taconnat L, Aubourg S, Lurin C, Martin-Magniette ML, Delannoy E. Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief Bioinform 2018; 19:65-76. [PMID: 27742662 DOI: 10.1093/bib/bbw092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 12/16/2022] Open
Abstract
Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets. This framework is based on real data sets and allows the exploration of various scenarios differing in the proportion of non-differentially expressed genes. Hence, it provides an evaluation of the key ingredients of the differential analysis, free of the biases associated with the simulation of data using parametric models. Our results show the relevance of a proper modeling of the mean by using linear or generalized linear modeling. Once the mean is properly modeled, the impact of the other parameters on the performance of the test is much less important. Finally, we propose to use the simple visualization of the raw P-value histogram as a practical evaluation criterion of the performance of differential analysis methods on real data sets.
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44
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Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures. Sci Rep 2018; 8:13537. [PMID: 30202034 PMCID: PMC6131140 DOI: 10.1038/s41598-018-31659-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/21/2022] Open
Abstract
Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Aggressive disease was further characterised by transcriptional evidence of increased PRC2 activity, stemness and epithelial-to-mesenchymal transition. Our analyses discern biologically distinct variants of anaplastic meningioma with prognostic and therapeutic significance.
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Affiliation(s)
- Grace Collord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Patrick Tarpey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Natalja Kurbatova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Manuel Castro
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Tibor Nagy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Graham Bignell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Francesco Maura
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jorge Berna
- Mobile Genomes and Disease, Molecular Medicine and Chronic diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, 15706, Spain
| | - Jose M C Tubio
- Mobile Genomes and Disease, Molecular Medicine and Chronic diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, 15706, Spain
| | - Chris E McMurran
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Adam M H Young
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Mathijs Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Erasmus University Medical Center, Department of Hematology, Rotterdam, The Netherlands
| | - Imran Noorani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Stephen J Price
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Colin Watts
- Department of Neurosurgery, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elke Leipnitz
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Matthias Kirsch
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Gabriele Schackert
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Danita Pearson
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Abel Devadass
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Zvi Ram
- Department of Neurosurgery, Tel-Aviv Medical Center, Tel-Aviv, Israel
| | - V Peter Collins
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Kieren Allinson
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Michael D Jenkinson
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Translational Medicine, University of Liverpool, Liverpool, L9 7LJ, UK
| | - Rasheed Zakaria
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L9 7LJ, UK
| | - Khaja Syed
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L9 7LJ, UK
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, Devon, PL4 8AA, UK
| | - Jemma Dunn
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, Devon, PL4 8AA, UK
| | - Michael W McDermott
- Department of Neurosurgery, UCSF Medical Center, San Francisco, CA, 94143-0112, USA
| | - Ramez W Kirollos
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0QQ, UK
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Thomas Santarius
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - Ultan McDermott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Institute of Translational Medicine, University of Liverpool, Liverpool, L9 7LJ, UK.
- AstraZeneca, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
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45
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Recent Developments in Single-Cell RNA-Seq of Microorganisms. Biophys J 2018; 115:173-180. [PMID: 29958658 DOI: 10.1016/j.bpj.2018.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/29/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022] Open
Abstract
Single-cell transcriptome analysis through next-generation sequencing (single-cell RNA-seq) has been used broadly to address important biological questions. It has proved to be very powerful, and many exciting new biological discoveries have been achieved in the last decade. Its application has greatly improved our understanding of diverse biological processes and the underlying molecular mechanisms, an understanding that would not have been achievable by conventional analysis based on bulk populations. However, so far, single-cell RNA-seq analysis has been used mostly for higher organisms. For microorganisms, single-cell RNA-seq has not been widely used, mainly because the stiff cell wall prevents effective lysis, much less starting RNA material is obtained, and the RNA lacks polyadenylated tails for universal priming of mRNA molecules. In general, the detection efficiency of current single-cell RNA-seq technologies is very low, and further development or improvement of these technologies is required for exploring the microbial world at single-cell resolution. Here, we briefly review recent developments in single-cell RNA-seq of microorganisms and discuss current challenges and future directions.
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46
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Narrandes S, Xu W. Gene Expression Detection Assay for Cancer Clinical Use. J Cancer 2018; 9:2249-2265. [PMID: 30026820 PMCID: PMC6036716 DOI: 10.7150/jca.24744] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/15/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.
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Affiliation(s)
- Shavira Narrandes
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Wayne Xu
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada.,College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Cai H, Li X, Li J, Liang Q, Zheng W, Guan Q, Guo Z, Wang X. Identifying differentially expressed genes from cross-site integrated data based on relative expression orderings. Int J Biol Sci 2018; 14:892-900. [PMID: 29989020 PMCID: PMC6036750 DOI: 10.7150/ijbs.24548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
It is a basic task in high-throughput gene expression profiling studies to identify differentially expressed genes (DEGs) between two phenotypes. But the weakly differential expression signals between two phenotypes are hardly detectable with limited sample sizes. To solve this problem, many researchers tried to combine multiple independent datasets using meta-analysis or batch effect adjustment algorithms. However, these algorithms may distort true biological differences between two phenotypes and introduce unacceptable high false rates, as demonstrated in this study. These problems pose critical obstacles for analyzing the transcriptional data in The Cancer Genome Atlas where there are many small-scale batches of data. Previously, we developed RankComp to detect DEGs for individual disease samples through exploiting the incongruous relative expression orderings between two phenotypes and further improved it here to identify DEGs using multiple independent datasets. We demonstrated the improved RankComp can directly analyze integrated cross-site data to detect DEGs between two phenotypes without the need of batch effect adjustments. Its usage was illustrated in detecting weak differential expression signals of breast cancer drug-response data using combined datasets from multiple experiments.
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Affiliation(s)
- Hao Cai
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Xiangyu Li
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Jing Li
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Qirui Liang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Weicheng Zheng
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.,Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Qingzhou Guan
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Zheng Guo
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou 350122, China.,Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Xianlong Wang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
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48
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Koberstein JN, Poplawski SG, Wimmer ME, Porcari G, Kao C, Gomes B, Risso D, Hakonarson H, Zhang NR, Schultz RT, Abel T, Peixoto L. Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism. Sci Signal 2018; 11:11/513/eaan6500. [PMID: 29339533 DOI: 10.1126/scisignal.aan6500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder that is associated with genetic risk factors. Most human disease-associated single-nucleotide polymorphisms (SNPs) are not located in genes but rather are in regulatory regions that control gene expression. The function of regulatory regions is determined through epigenetic mechanisms. Parallels between the cellular basis of development and the formation of long-term memory have long been recognized, particularly the role of epigenetic mechanisms in both processes. We analyzed how learning alters chromatin accessibility in the mouse hippocampus using a new high-throughput sequencing bioinformatics strategy we call DEScan (differential enrichment scan). DEScan, which enabled the analysis of data from epigenomic experiments containing multiple replicates, revealed changes in chromatin accessibility at 2365 regulatory regions-most of which were promoters. Learning-regulated promoters were active during forebrain development in mice and were enriched in epigenetic modifications indicative of bivalent promoters. These promoters were disproportionally intronic, showed a complex relationship with gene expression and alternative splicing during memory consolidation and retrieval, and were enriched in the data set relative to known ASD risk genes. Genotyping in a clinical cohort within one of these promoters (SHANK3 promoter 6) revealed that the SNP rs6010065 was associated with ASD. Our data support the idea that learning recapitulates development at the epigenetic level and demonstrate that behaviorally induced epigenetic changes in mice can highlight regulatory regions relevant to brain disorders in patients.
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Affiliation(s)
- John N Koberstein
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA
| | | | - Mathieu E Wimmer
- Department of Psychology and Program in Neuroscience, College of Liberal Arts, Temple University, Philadelphia, PA 19122, USA
| | - Giulia Porcari
- Vanderbilt University Medical School, Nashville, TN 37232, USA
| | - Charlly Kao
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY 10065, USA
| | - Bruce Gomes
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA
| | - Davide Risso
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nancy R Zhang
- Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert T Schultz
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ted Abel
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA.
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Best MG, Sol N, In 't Veld SGJG, Vancura A, Muller M, Niemeijer ALN, Fejes AV, Tjon Kon Fat LA, Huis In 't Veld AE, Leurs C, Le Large TY, Meijer LL, Kooi IE, Rustenburg F, Schellen P, Verschueren H, Post E, Wedekind LE, Bracht J, Esenkbrink M, Wils L, Favaro F, Schoonhoven JD, Tannous J, Meijers-Heijboer H, Kazemier G, Giovannetti E, Reijneveld JC, Idema S, Killestein J, Heger M, de Jager SC, Urbanus RT, Hoefer IE, Pasterkamp G, Mannhalter C, Gomez-Arroyo J, Bogaard HJ, Noske DP, Vandertop WP, van den Broek D, Ylstra B, Nilsson RJA, Wesseling P, Karachaliou N, Rosell R, Lee-Lewandrowski E, Lewandrowski KB, Tannous BA, de Langen AJ, Smit EF, van den Heuvel MM, Wurdinger T. Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets. Cancer Cell 2017; 32:238-252.e9. [PMID: 28810146 PMCID: PMC6381325 DOI: 10.1016/j.ccell.2017.07.004] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/17/2017] [Accepted: 07/13/2017] [Indexed: 01/01/2023]
Abstract
Blood-based liquid biopsies, including tumor-educated blood platelets (TEPs), have emerged as promising biomarker sources for non-invasive detection of cancer. Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779). This resulted in accurate TEP-based detection of early- and late-stage non-small-cell lung cancer (n = 518 late-stage validation cohort, accuracy, 88%; AUC, 0.94; 95% CI, 0.92-0.96; p < 0.001; n = 106 early-stage validation cohort, accuracy, 81%; AUC, 0.89; 95% CI, 0.83-0.95; p < 0.001), independent of age of the individuals, smoking habits, whole-blood storage time, and various inflammatory conditions. PSO enabled selection of gene panels to diagnose cancer from TEPs, suggesting that swarm intelligence may also benefit the optimization of diagnostics readout of other liquid biopsy biosources.
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Affiliation(s)
- Myron G Best
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.
| | - Nik Sol
- Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Sjors G J G In 't Veld
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Adrienne Vancura
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Mirte Muller
- Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Anna-Larissa N Niemeijer
- Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Aniko V Fejes
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Clinical Institute of Laboratory Medicine, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | | | - Anna E Huis In 't Veld
- Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Cyra Leurs
- Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; MS Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Tessa Y Le Large
- Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Laura L Meijer
- Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Irsan E Kooi
- Department of Clinical Genetics, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - François Rustenburg
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Pepijn Schellen
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Heleen Verschueren
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; thromboDx B.V., 1098 EA Amsterdam, the Netherlands
| | - Edward Post
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; thromboDx B.V., 1098 EA Amsterdam, the Netherlands
| | - Laurine E Wedekind
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Jillian Bracht
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Michelle Esenkbrink
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Leon Wils
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Francesca Favaro
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Jilian D Schoonhoven
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Jihane Tannous
- Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Geert Kazemier
- Department of Surgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Jaap C Reijneveld
- Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Sander Idema
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Joep Killestein
- Department of Neurology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; MS Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Michal Heger
- Department of Surgery, Amsterdam Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Saskia C de Jager
- Department of Experimental Cardiology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Rolf T Urbanus
- Laboratory of Clinical Chemistry and Hematology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Imo E Hoefer
- Laboratory of Clinical Chemistry and Hematology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Gerard Pasterkamp
- Department of Experimental Cardiology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Christine Mannhalter
- Clinical Institute of Laboratory Medicine, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Jose Gomez-Arroyo
- Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Harm-Jan Bogaard
- Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - David P Noske
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - W Peter Vandertop
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Daan van den Broek
- Department of Clinical Chemistry, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - R Jonas A Nilsson
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Radiation Sciences, Oncology, Umeå University, 90185 Umeå, Sweden
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Niki Karachaliou
- Translational Research Unit, Dr. Rosell Oncology Institute, Quirón Dexeus University Hospital, Calle Sabine Arana 5-19, 08028 Barcelona, Spain
| | - Rafael Rosell
- Translational Research Unit, Dr. Rosell Oncology Institute, Quirón Dexeus University Hospital, Calle Sabine Arana 5-19, 08028 Barcelona, Spain; Pangaea Biotech SL, Calle Sabine Arana 5-19, 08028 Barcelona, Spain; Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Carretera de Canyet, 08916 Barcelona, Spain; Molecular Oncology Research (MORe) Foundation, Calle Sabine Arana 5-19, 08028 Barcelona, Spain
| | - Elizabeth Lee-Lewandrowski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA
| | - Kent B Lewandrowski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA
| | - Bakhos A Tannous
- Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA
| | - Adrianus J de Langen
- Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Egbert F Smit
- Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pulmonary Diseases, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Michel M van den Heuvel
- Department of Thoracic Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Respiratory Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA.
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Siangphoe U, Archer KJ. Estimation of random effects and identifying heterogeneous genes in meta-analysis of gene expression studies. Brief Bioinform 2017; 18:602-618. [PMID: 27345525 DOI: 10.1093/bib/bbw050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/12/2022] Open
Abstract
Combining effect sizes from individual studies using random-effects meta-analysis models are commonly applied in high-dimensional gene expression data. However, unknown study heterogeneity can arise from inconsistencies in sample quality and experimental conditions. High heterogeneity of effect sizes can reduce statistical power of the models. In this study, we describe three hypothesis-testing frameworks for meta-analysis of microarray data, and review several existing meta-analytic techniques that have been used in the genomic setting. These include P-value-based methods, rank-based methods and effect-size-based methods. We then discuss limitations of some of these methods and describe random-effects-based methods in detail. We introduce two methods for estimating the inter-study variance in random-effects meta-analytic models and another method for identifying heterogeneous genes for gene expression data. We compared various methods with the standard and existing meta-analytic techniques in the genomic framework. We demonstrate our results through a series of simulations and application in Alzheimer's gene expression data.
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