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Brooks TG, Lahens NF, Mrčela A, Grant GR. Challenges and best practices in omics benchmarking. Nat Rev Genet 2024; 25:326-339. [PMID: 38216661 DOI: 10.1038/s41576-023-00679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 01/14/2024]
Abstract
Technological advances enabling massively parallel measurement of biological features - such as microarrays, high-throughput sequencing and mass spectrometry - have ushered in the omics era, now in its third decade. The resulting complex landscape of analytical methods has naturally fostered the growth of an omics benchmarking industry. Benchmarking refers to the process of objectively comparing and evaluating the performance of different computational or analytical techniques when processing and analysing large-scale biological data sets, such as transcriptomics, proteomics and metabolomics. With thousands of omics benchmarking studies published over the past 25 years, the field has matured to the point where the foundations of benchmarking have been established and well described. However, generating meaningful benchmarking data and properly evaluating performance in this complex domain remains challenging. In this Review, we highlight some common oversights and pitfalls in omics benchmarking. We also establish a methodology to bring the issues that can be addressed into focus and to be transparent about those that cannot: this takes the form of a spreadsheet template of guidelines for comprehensive reporting, intended to accompany publications. In addition, a survey of recent developments in benchmarking is provided as well as specific guidance for commonly encountered difficulties.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Tang SY, Lordan R, Meng H, Auerbach BJ, Hennessy EJ, Sengupta A, Das US, Joshi R, Marcos-Contreras OA, McConnell R, Grant GR, Ricciotti E, Muzykantov VR, Grosser T, Weiljie AM, FitzGerald GA. Differential Impact In Vivo of Pf4-ΔCre-Mediated and Gp1ba-ΔCre-Mediated Depletion of Cyclooxygenase-1 in Platelets in Mice. Arterioscler Thromb Vasc Biol 2024. [PMID: 38660804 DOI: 10.1161/atvbaha.123.320295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Low-dose aspirin is widely used for the secondary prevention of cardiovascular disease. The beneficial effects of low-dose aspirin are attributable to its inhibition of platelet Cox (cyclooxygenase)-1-derived thromboxane A2. Until recently, the use of the Pf4 (platelet factor 4) Cre has been the only genetic approach to generating megakaryocyte/platelet ablation of Cox-1 in mice. However, Pf4-ΔCre displays ectopic expression outside the megakaryocyte/platelet lineage, especially during inflammation. The use of the Gp1ba (glycoprotein 1bα) Cre promises a more specific, targeted approach. METHODS To evaluate the role of Cox-1 in platelets, we crossed Pf4-ΔCre or Gp1ba-ΔCre mice with Cox-1flox/flox mice to generate platelet Cox-1-/- mice on normolipidemic and hyperlipidemic (Ldlr-/-) backgrounds. RESULTS Ex vivo platelet aggregation induced by arachidonic acid or adenosine diphosphate in platelet-rich plasma was inhibited to a similar extent in Pf4-ΔCre Cox-1-/-/Ldlr-/- and Gp1ba-ΔCre Cox-1-/-/Ldlr-/- mice. In a mouse model of tail injury, Pf4-ΔCre-mediated and Gp1ba-ΔCre-mediated deletions of Cox-1 were similarly efficient in suppressing platelet prostanoid biosynthesis. Experimental thrombogenesis and attendant blood loss were similar in both models. However, the impact on atherogenesis was divergent, being accelerated in the Pf4-ΔCre mice while restrained in the Gp1ba-ΔCres. In the former, accelerated atherogenesis was associated with greater suppression of PGI2 biosynthesis, a reduction in the lipopolysaccharide-evoked capacity to produce PGE2 and PGD2, activation of the inflammasome, elevated plasma levels of IL-1β, reduced plasma levels of HDL-C, and a reduction in the capacity for reverse cholesterol transport. By contrast, in the latter, plasma HDL-C and α-tocopherol were elevated, and MIP-1α (macrophage inflammatory protein-1α) and MCP-1 (monocyte chemoattractant protein 1) were reduced. CONCLUSIONS Both approaches to Cox-1 deletion similarly restrain thrombogenesis, but a differential impact on Cox-1-dependent prostanoid formation by the vasculature may contribute to an inflammatory phenotype and accelerated atherogenesis in Pf4-ΔCre mice.
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Affiliation(s)
- Soon Yew Tang
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Hu Meng
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Benjamin J Auerbach
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Elizabeth J Hennessy
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Arjun Sengupta
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Ujjalkumar S Das
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Robin Joshi
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Oscar A Marcos-Contreras
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia. (O.A.M.-C., E.R., V.R.M., A.M.W.)
| | - Ryan McConnell
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
- Department of Genetics, University of Pennsylvania, Philadelphia. (G.R.G., G.A.F.)
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia. (O.A.M.-C., E.R., V.R.M., A.M.W.)
| | - Vladimir R Muzykantov
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia. (O.A.M.-C., E.R., V.R.M., A.M.W.)
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (T.G.)
- Now with Department of Translational Pharmacology, Bielefeld University, Germany (T.G.)
| | - Aalim M Weiljie
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia. (O.A.M.-C., E.R., V.R.M., A.M.W.)
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (S.Y.T., R.L., H.M., B.J.A., E.J.H., A.S., U.S.D., R.J., R.M., G.R.G., E.R., T.G., A.M.W., G.A.F.)
- Department of Genetics, University of Pennsylvania, Philadelphia. (G.R.G., G.A.F.)
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight 2024; 9:e179745. [PMID: 38456509 PMCID: PMC10972589 DOI: 10.1172/jci.insight.179745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
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Abstract
To assess the consistency of biological rhythms across studies, 57 public mouse liver tissue timeseries totaling 1096 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies. Overlap of genes identified as rhythmic across studies was generally low, with no pair of studies having over 60% overlap. Distributions of phases of significant genes were remarkably inconsistent across studies, but the genes that consistently identified as rhythmic had acrophase clustering near ZT0 and ZT12. Despite the discrepancies between single-study analyses, cross-study analyses found substantial consistency. Running compareRhythms on each pair of studies identified a median of only 11% of the identified rhythmic genes as rhythmic in only 1 of the 2 studies. Data were integrated across studies in a joint and individual variance estimate (JIVE) analysis, which showed that the top 2 components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies, including identifying 72 genes with consistently multiple peaks.
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Affiliation(s)
- Thomas G. Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aditi Manjrekar
- Department of Neuroscience, The University of Texas at Dallas, Richardson, Texas
| | - Antonijo Mrcˇela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
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Brooks TG, Lahens NF, Grant GR, Sheline YI, FitzGerald GA, Skarke C. Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank. Nat Commun 2023; 14:5172. [PMID: 37620332 PMCID: PMC10449859 DOI: 10.1038/s41467-023-40977-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as sleep-wake behavior/environmental evoked components. Here, we investigated the association of wrist temperature amplitudes with a future onset of disease in the UK Biobank one year after actigraphy. Among 425 disease conditions (range n = 200-6728) compared to controls (range n = 62,107-91,134), a total of 73 (17%) disease phenotypes were significantly associated with decreased amplitudes of wrist temperature (Benjamini-Hochberg FDR q < 0.05) and 26 (6.1%) PheCODEs passed a more stringent significance level (Bonferroni-correction α < 0.05). A two-standard deviation (1.8° Celsius) lower wrist temperature amplitude corresponded to hazard ratios of 1.91 (1.58-2.31 95% CI) for NAFLD, 1.69 (1.53-1.88) for type 2 diabetes, 1.25 (1.14-1.37) for renal failure, 1.23 (1.17-1.3) for hypertension, and 1.22 (1.11-1.33) for pneumonia (phenome-wide atlas available at http://bioinf.itmat.upenn.edu/biorhythm_atlas/ ). This work suggests peripheral thermoregulation as a digital biomarker.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yvette I Sheline
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight 2023; 8:e164720. [PMID: 37463053 PMCID: PMC10543710 DOI: 10.1172/jci.insight.164720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Optimal lung repair and regeneration are essential for recovery from viral infections, including influenza A virus (IAV). We have previously demonstrated that acute inflammation and mortality induced by IAV is under circadian control. However, it is not known whether the influence of the circadian clock persists beyond the acute outcomes. Here, we utilize the UK Biobank to demonstrate an association between poor circadian rhythms and morbidity from lower respiratory tract infections, including the need for hospitalization and mortality after discharge; this persists even after adjusting for common confounding factors. Furthermore, we use a combination of lung organoid assays, single-cell RNA sequencing, and IAV infection in different models of clock disruption to investigate the role of the circadian clock in lung repair and regeneration. We show that lung organoids have a functional circadian clock and the disruption of this clock impairs regenerative capacity. Finally, we find that the circadian clock acts through distinct pathways in mediating lung regeneration - in tracheal cells via the Wnt/β-catenin pathway and through IL-1β in alveolar epithelial cells. We speculate that adding a circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes.
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Affiliation(s)
- Amruta Naik
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Oindrila Paul
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yasmine Issah
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Utham K. Valekunja
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Soon Y. Tang
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Akhilesh B. Reddy
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Thomas G. Brooks
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Fatima Chaudhry
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Department of Genetics
| | - Garret A. FitzGerald
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amita Sehgal
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, and
| | - G. Scott Worthen
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David B. Frank
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Edward E. Morrisey
- Penn-CHOP Lung Biology Institute
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn-CHOP Lung Biology Institute
- Department of Pediatrics
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Anderson ST, Meng H, Brooks TG, Tang SY, Lordan R, Sengupta A, Nayak S, Mřela A, Sarantopoulou D, Lahens NF, Weljie A, Grant GR, Bushman FD, FitzGerald GA. Sexual dimorphism in the response to chronic circadian misalignment on a high-fat diet. Sci Transl Med 2023; 15:eabo2022. [PMID: 37196066 DOI: 10.1126/scitranslmed.abo2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
Longitudinal studies associate shiftwork with cardiometabolic disorders but do not establish causation or elucidate mechanisms of disease. We developed a mouse model based on shiftwork schedules to study circadian misalignment in both sexes. Behavioral and transcriptional rhythmicity were preserved in female mice despite exposure to misalignment. Females were protected from the cardiometabolic impact of circadian misalignment on a high-fat diet seen in males. The liver transcriptome and proteome revealed discordant pathway perturbations between the sexes. Tissue-level changes were accompanied by gut microbiome dysbiosis only in male mice, biasing toward increased potential for diabetogenic branched chain amino acid production. Antibiotic ablation of the gut microbiota diminished the impact of misalignment. In the United Kingdom Biobank, females showed stronger circadian rhythmicity in activity and a lower incidence of metabolic syndrome than males among job-matched shiftworkers. Thus, we show that female mice are more resilient than males to chronic circadian misalignment and that these differences are conserved in humans.
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Affiliation(s)
- Seán T Anderson
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hu Meng
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Soon Yew Tang
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Sengupta
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Antonijo Mřela
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aalim Weljie
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Skarke C, Lordan R, Barekat K, Naik A, Mathew D, Ohtani T, Greenplate AR, Grant GR, Lahens NF, Gouma S, Troisi E, Sengupta A, Weljie AM, Meng W, Luning Prak ET, Lundgreen K, Bates P, Meng H, FitzGerald GA. Modulation of the immune response to SARS-CoV-2 vaccination by NSAIDs. J Pharmacol Exp Ther 2023:jpet.122.001415. [PMID: 37105582 PMCID: PMC10353078 DOI: 10.1124/jpet.122.001415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/13/2023] [Accepted: 02/09/2023] [Indexed: 04/29/2023] Open
Abstract
Evidence is scarce to guide the use of nonsteroidal anti-inflammatory drugs (NSAIDs) to mitigate SARS-CoV-2 vaccine related adverse effects, given the possibility of blunting the desired immune response. In this pilot study, we deeply phenotyped a small number of volunteers who did or did not take NSAIDs concomitant with SARS-CoV-2 immunizations to seek initial information on the immune response. A SARS-CoV-2 vaccine specific RBD-IgG antibody response and efficacy in the evoked neutralization titers were evident irrespective of concomitant NSAID consumption. Given the sample size, only a large and consistent signal of immunomodulation would have been detectable, and this was not apparent. However, the information gathered may inform the design of a definitive clinical trial. Here, we report a series of divergent omics signals that invite additional hypotheses testing. Significance Statement A SARS-CoV-2 vaccine specific immune response was evident irrespective of concomitant NSAID consumption in a clinical pilot study of small sample size.
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Affiliation(s)
- Carsten Skarke
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Ronan Lordan
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Kayla Barekat
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Amruta Naik
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Divij Mathew
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Takuya Ohtani
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Allison R Greenplate
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Gregory R Grant
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Nicholas F Lahens
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Sigrid Gouma
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Elizabeth Troisi
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Arjun Sengupta
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Aalim M Weljie
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Wenzhao Meng
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Eline T Luning Prak
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Kendall Lundgreen
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Paul Bates
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Hu Meng
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, United States
| | - Garret A FitzGerald
- Center for Experimental Therapeutics, University of Pennsylvania, United States
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10
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. bioRxiv 2023:2023.04.21.537847. [PMID: 37162982 PMCID: PMC10168222 DOI: 10.1101/2023.04.21.537847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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11
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Vaquero-Garcia J, Aicher JK, Jewell S, Gazzara MR, Radens CM, Jha A, Norton SS, Lahens NF, Grant GR, Barash Y. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nat Commun 2023; 14:1230. [PMID: 36869033 PMCID: PMC9984406 DOI: 10.1038/s41467-023-36585-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023] Open
Abstract
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
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Affiliation(s)
| | - Joseph K Aicher
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - San Jewell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew R Gazzara
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Anupama Jha
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott S Norton
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Kelly DE, Ramdas S, Ma R, Rawlings-Goss RA, Grant GR, Ranciaro A, Hirbo JB, Beggs W, Yeager M, Chanock S, Nyambo TB, Omar SA, Woldemeskel D, Belay G, Li H, Brown CD, Tishkoff SA. The genetic and evolutionary basis of gene expression variation in East Africans. Genome Biol 2023; 24:35. [PMID: 36829244 PMCID: PMC9951478 DOI: 10.1186/s13059-023-02874-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies have focused on individuals of European descent. While important progress has been made to study a greater diversity of human populations, many groups remain unstudied, particularly among indigenous populations within Africa. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations. RESULTS We find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine-mapping of causal variation. Integrating our QTL scans with signatures of natural selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation. CONCLUSION Extending QTL mapping studies beyond European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.
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Affiliation(s)
- Derek E Kelly
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Ramdas
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rong Ma
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Jibril B Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Beggs
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meredith Yeager
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Institutes of Health, Rockville, MD, USA
| | - Thomas B Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar Es Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dawit Woldemeskel
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hongzhe Li
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher D Brown
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, USA.
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13
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Lahens NF, Rahman M, Cohen JB, Cohen DL, Chen J, Weir MR, Feldman HI, Grant GR, Townsend RR, Skarke C, Study Investigators* ATCRIC. Time-specific associations of wearable sensor-based cardiovascular and behavioral readouts with disease phenotypes in the outpatient setting of the Chronic Renal Insufficiency Cohort. Digit Health 2022; 8:20552076221107903. [PMID: 35746950 PMCID: PMC9210076 DOI: 10.1177/20552076221107903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/30/2022] [Indexed: 11/15/2022] Open
Abstract
Patients with chronic kidney disease are at risk of developing cardiovascular disease. To facilitate out-of-clinic evaluation, we piloted wearable device-based analysis of heart rate variability and behavioral readouts in patients with chronic kidney disease from the Chronic Renal Insufficiency Cohort and controls (n = 49). Time-specific partitioning of heart rate variability readouts confirm higher parasympathetic nervous activity during the night (mean RR at night 14.4 ± 1.9 ms vs. 12.8 ± 2.1 ms during active hours; n = 47, analysis of variance (ANOVA) q = 0.001). The α2 long-term fluctuations in the detrended fluctuation analysis, a parameter predictive of cardiovascular mortality, significantly differentiated between diabetic and nondiabetic patients (prominent at night with 0.58 ± 0.2 vs. 0.45 ± 0.12, respectively, adj. p = 0.004). Both diabetic and nondiabetic chronic kidney disease patients showed loss of rhythmic organization compared to controls, with diabetic chronic kidney disease patients exhibiting deconsolidation of peak phases between their activity and standard deviation of interbeat intervals rhythms (mean phase difference chronic kidney disease 8.3 h, chronic kidney disease/type 2 diabetes mellitus 4 h, controls 6.8 h). This work provides a roadmap toward deriving actionable clinical insights from the data collected by wearable devices outside of highly controlled clinical environments.
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Affiliation(s)
- Nicholas F. Lahens
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia,
PA, USA
| | - Mahboob Rahman
- University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jordana B. Cohen
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Debbie L. Cohen
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jing Chen
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Matthew R. Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Harold I. Feldman
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Raymond R. Townsend
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia,
PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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14
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Abstract
Circadian omics analyses present investigators with large amounts of data to consider and many choices for methods of analysis. Visualization is crucial as rhythmicity can take many forms and p-values offer an incomplete picture. Yet statically viewing the entirety of high-throughput datasets is impractical, and there is often limited ability to assess the impact of choices, such as significance threshold cutoffs. Nitecap provides an intuitive and unified web-based solution to these problems. Through highly responsive visualizations, Nitecap enables investigators to see dataset-wide behavior. It supports deep analyses, including comparisons of two conditions. Moreover, it focuses upon ease-of-use and enables collaboration through dataset sharing. As an application, we investigated cross talk between peripheral clocks in adipose and liver tissues and determined that adipocyte clock disruption does not substantially modulate the transcriptional rhythmicity of liver but does advance the phase of core clock gene Bmal1 (Arntl) expression in the liver. Nitecap is available at nitecap.org and is free-to-use.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Georgios K Paschos
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania.,Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
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15
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Lahens NF, Brooks TG, Sarantopoulou D, Nayak S, Lawrence C, Mrčela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, Grant GR. CAMPAREE: a robust and configurable RNA expression simulator. BMC Genomics 2021; 22:692. [PMID: 34563123 PMCID: PMC8467241 DOI: 10.1186/s12864-021-07934-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/17/2021] [Indexed: 11/10/2022] Open
Abstract
Background The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accurately assess the performance of RNA-Seq analysis methods. However, existing RNA-Seq simulators focus on modeling the technical biases and artifacts of sequencing, rather than on simulating the original RNA samples. A first step in simulating RNA-Seq is to simulate RNA. Results To fill this need, we developed the Configurable And Modular Program Allowing RNA Expression Emulation (CAMPAREE), a simulator using empirical data to simulate diploid RNA samples at the level of individual molecules. We demonstrated CAMPAREE’s use for generating idealized coverage plots from real data, and for adding the ability to generate allele-specific data to existing RNA-Seq simulators that do not natively support this feature. Conclusions Separating input sample modeling from library preparation/sequencing offers added flexibility for both users and developers to mix-and-match different sample and sequencing simulators to suit their specific needs. Furthermore, the ability to maintain sample and sequencing simulators independently provides greater agility to incorporate new biological findings about transcriptomics and new developments in sequencing technologies. Additionally, by simulating at the level of individual molecules, CAMPAREE has the potential to model molecules transcribed from the same genes as a heterogeneous population of transcripts with different states of degradation and processing (splicing, editing, etc.). CAMPAREE was developed in Python, is open source, and freely available at https://github.com/itmat/CAMPAREE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07934-2.
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Affiliation(s)
- Nicholas F Lahens
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas G Brooks
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitra Sarantopoulou
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Present address: National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Soumyashant Nayak
- Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Cris Lawrence
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Antonijo Mrčela
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anand Srinivasan
- Perelman School of Medicine, Enterprise Research Applications and High Performance Computing, Penn Medicine Academic Computing Services, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan Schug
- The Institute for Diabetes, Obesity and Metabolism, The Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John B Hogenesch
- Division of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Yoseph Barash
- The Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA. .,The Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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16
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Tang SY, Meng H, Anderson ST, Sarantopoulou D, Ghosh S, Lahens NF, Theken KN, Ricciotti E, Hennessy EJ, Tu V, Bittinger K, Weiljie AM, Grant GR, FitzGerald GA. Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor-deficient mice. J Clin Invest 2021; 131:e136310. [PMID: 34101620 DOI: 10.1172/jci136310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/03/2021] [Indexed: 11/17/2022] Open
Abstract
Inhibitors of microsomal prostaglandin E synthase 1 (mPGES-1) are in the early phase of clinical development. Deletion of mPges-1 in mice confers analgesia, restrains atherogenesis, and fails to accelerate thrombogenesis, while suppressing prostaglandin E2 (PGE2), but increasing the biosynthesis of prostacyclin (PGI2). In low-density lipoprotein receptor-deficient (Ldlr-/-) mice, this last effect represents the dominant mechanism by which mPges-1 deletion restrains thrombogenesis, while suppression of PGE2 accounts for its antiatherogenic effect. However, the effect of mPges-1 depletion on blood pressure (BP) in this setting remains unknown. Here, we show that mPges-1 depletion significantly increased the BP response to salt loading in male Ldlr-/- mice, whereas, despite the direct vasodilator properties of PGI2, deletion of the I prostanoid receptor (Ipr) suppressed this response. Furthermore, combined deletion of the Ipr abrogated the exaggerated BP response in male mPges-1-/- mice. Interestingly, these unexpected BP phenotypes were not observed in female mice fed a high-salt diet (HSD). This is attributable to the protective effect of estrogen in Ldlr-/- mice and in Ipr-/- Ldlr-/- mice. Thus, estrogen compensates for a deficiency in PGI2 to maintain BP homeostasis in response to high salt in hyperlipidemic female mice. In male mice, by contrast, the augmented formation of atrial natriuretic peptide (ANP) plays a similar compensatory role, restraining hypertension and oxidant stress in the setting of Ipr depletion. Hence, men with hyperlipidemia on a HSD might be at risk of a hypertensive response to mPGES-1 inhibitors.
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Affiliation(s)
- Soon Y Tang
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hu Meng
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seán T Anderson
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Soumita Ghosh
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine N Theken
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth J Hennessy
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Aalim M Weiljie
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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17
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Sarantopoulou D, Brooks TG, Nayak S, Mrčela A, Lahens NF, Grant GR. Comparative evaluation of full-length isoform quantification from RNA-Seq. BMC Bioinformatics 2021; 22:266. [PMID: 34034652 PMCID: PMC8145802 DOI: 10.1186/s12859-021-04198-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 05/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short. Results Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control. Conclusions Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04198-1.
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Affiliation(s)
- Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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18
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Abstract
The COVID-19 pandemic has necessitated novel approaches and collaborative efforts across multiple disciplines. It is known that various aspects of our physiology and response to pathogens are under tight clock control. However, the assimilation of circadian biology into our clinical and research practices is still evolving. Using a focused review of the literature and original analyses of the UK Biobank, we discuss how circadian biology may inform our diagnostic and therapeutic strategies in this pandemic.
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Affiliation(s)
- Shaon Sengupta
- Department of Pediatrics, University of
Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Division of Neonatology, The Children’s
Hospital of Philadelphia, Philadelphia, Pennsylvania
- Institute of Translational Medicine and
Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, Pennsylvania
- Chronobiology and Sleep Institute,
University of Pennsylvania, Philadelphia, Pennsylvania
| | - Thomas G. Brooks
- Institute of Translational Medicine and
Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory R. Grant
- Institute of Translational Medicine and
Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of
Pennsylvania Perelman School of Medicine, Philadelphia
| | - Garret A. FitzGerald
- Institute of Translational Medicine and
Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, Pennsylvania
- Chronobiology and Sleep Institute,
University of Pennsylvania, Philadelphia, Pennsylvania
- Systems Pharmacology University of
Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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19
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Guo X, Gao X, Keenan BT, Zhu J, Sarantopoulou D, Lian J, Galante RJ, Grant GR, Pack AI. RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake. BMC Genomics 2020; 21:633. [PMID: 32928100 PMCID: PMC7491139 DOI: 10.1186/s12864-020-07050-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by comparing their transcriptional responses between sleeping mice and those kept awake, sacrificed at the same diurnal time. RESULTS RNA-sequencing (RNA-seq) analysis was performed on eGFP(+) galanin neurons isolated using laser captured microdissection (LCM) from VLPO. Expression of Gal was assessed in our LCM eGFP(+) neurons via real time qPCR and showed marked enrichment when compared to LCM eGFP(-) cells and to bulk VLPO samples. Gene set enrichment analysis utilizing data from a recent single-cell RNA-seq study of the preoptic area demonstrated that our VLPO-Gal samples were highly enriched with galanin-expressing inhibitory neurons, but not galanin-expressing excitatory neurons. A total of 263 genes were differentially expressed between sleep and wake in VLPO-Gal neurons. When comparing differentially expressed genes in VLPO-Gal neurons to differentially expressed genes in a wake-active neuronal region (the medial prefrontal cortex), evidence indicates that both systemic and cell-specific mechanisms contribute to the transcriptional regulation in VLPO-Gal neurons. In both wake-active and sleep-active neurons, ER stress pathways are activated by wake and cold-inducible RNA-binding proteins are activated by sleep. In contrast, expression of DNA repair genes is increased in VLPO-Gal during wakefulness, but increased in wake-active cells during sleep. CONCLUSION Our study identified transcriptomic responses of the galanin neurons in the ventrolateral preoptic nucleus during sleep and sleep deprivation. Data indicate that VLPO contains mainly sleep-active inhibitory galaninergic neurons. The VLPO galanin neurons show responses to sleep and wake similar to wake-active regions, indicating these responses, such as ER stress and cold-inducible RNA-binding proteins, are systemic affecting all neuronal populations. Region-specific differences in sleep/wake responses were also identified, in particular DNA repair. Our study expands knowledge about the transcriptional response of a distinct group of neurons essential for sleep.
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Affiliation(s)
- Xiaofeng Guo
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Xiaoling Gao
- Department of Respiratory and Critical Care Medicine, Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Brendan T Keenan
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Jingxu Zhu
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, 19104, USA.,Present address at National Institute on Aging, National Institutes of Health, Baltimore, 21224, USA
| | - Jie Lian
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Raymond J Galante
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, 19104, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine/Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, USA.
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20
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Guo X, Keenan BT, Sarantopoulou D, Lim DC, Lian J, Grant GR, Pack AI. Age attenuates the transcriptional changes that occur with sleep in the medial prefrontal cortex. Aging Cell 2019; 18:e13021. [PMID: 31549781 PMCID: PMC6826131 DOI: 10.1111/acel.13021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 07/14/2019] [Indexed: 12/29/2022] Open
Abstract
Sleep abnormalities are common with aging. Studies show that sleep plays important roles in brain functions, and loss of sleep is associated with increased risks for neurological diseases. Here, we used RNA sequencing to explore effects of age on transcriptome changes between sleep and sleep deprivation (SD) in medial prefrontal cortex and found that transcriptional changes with sleep are attenuated in old. In particular, old mice showed a 30% reduction in the number of genes significantly altered between sleep/wake and, in general, had smaller magnitudes of changes in differentially expressed genes compared to young mice. Gene ontology analysis revealed differential age effects on certain pathways. Compared to young mice, many of the wake‐active functions were similarly induced by SD in old mice, whereas many of the sleep‐active pathways were attenuated in old mice. We found similar magnitude of changes in synaptic homeostasis genes (Fos, Arc, and Bdnf) induced by SD, suggesting intact synaptic upscaling on the transcript level during extended wakefulness with aging. However, sleep‐activated processes, such as DNA repair, synaptogenesis, and axon guidance, were sensitive to the effect of aging. Old mice expressed elevated levels of immune response genes when compared to young mice, and enrichment analysis using cell‐type‐specific markers indicated upregulation of microglia and oligodendrocyte genes in old mice. Moreover, gene sets of the two cell types showed age‐specific sleep/wake regulation. Ultimately, this study enhances understanding of the transcriptional changes with sleep and aging, providing potential molecular targets for future studies of age‐related sleep abnormalities and neurological disorders.
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Affiliation(s)
- Xiaofeng Guo
- Division of Sleep Medicine Department of Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Brendan T. Keenan
- Division of Sleep Medicine Department of Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics University of Pennsylvania Philadelphia Pennsylvania
| | - Diane C. Lim
- Division of Sleep Medicine Department of Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Jie Lian
- Division of Sleep Medicine Department of Medicine University of Pennsylvania Philadelphia Pennsylvania
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics University of Pennsylvania Philadelphia Pennsylvania
- Department of Genetics University of Pennsylvania Philadelphia Pennsylvania
| | - Allan I. Pack
- Division of Sleep Medicine Department of Medicine University of Pennsylvania Philadelphia Pennsylvania
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21
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Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Grant GR, López CB. Correction: A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog 2019; 15:e1008099. [PMID: 31581268 PMCID: PMC6776294 DOI: 10.1371/journal.ppat.1008099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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22
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Grant GR, Naish TR, Dunbar GB, Stocchi P, Kominz MA, Kamp PJJ, Tapia CA, McKay RM, Levy RH, Patterson MO. The amplitude and origin of sea-level variability during the Pliocene epoch. Nature 2019; 574:237-241. [PMID: 31578526 DOI: 10.1038/s41586-019-1619-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/16/2019] [Indexed: 11/09/2022]
Abstract
Earth is heading towards a climate that last existed more than three million years ago (Ma) during the 'mid-Pliocene warm period'1, when atmospheric carbon dioxide concentrations were about 400 parts per million, global sea level oscillated in response to orbital forcing2,3 and peak global-mean sea level (GMSL) may have reached about 20 metres above the present-day value4,5. For sea-level rise of this magnitude, extensive retreat or collapse of the Greenland, West Antarctic and marine-based sectors of the East Antarctic ice sheets is required. Yet the relative amplitude of sea-level variations within glacial-interglacial cycles remains poorly constrained. To address this, we calibrate a theoretical relationship between modern sediment transport by waves and water depth, and then apply the technique to grain size in a continuous 800-metre-thick Pliocene sequence of shallow-marine sediments from Whanganui Basin, New Zealand. Water-depth variations obtained in this way, after corrections for tectonic subsidence, yield cyclic relative sea-level (RSL) variations. Here we show that sea level varied on average by 13 ± 5 metres over glacial-interglacial cycles during the middle-to-late Pliocene (about 3.3-2.5 Ma). The resulting record is independent of the global ice volume proxy3 (as derived from the deep-ocean oxygen isotope record) and sea-level cycles are in phase with 20-thousand-year (kyr) periodic changes in insolation over Antarctica, paced by eccentricity-modulated orbital precession6 between 3.3 and 2.7 Ma. Thereafter, sea-level fluctuations are paced by the 41-kyr period of cycles in Earth's axial tilt as ice sheets stabilize on Antarctica and intensify in the Northern Hemisphere3,6. Strictly, we provide the amplitude of RSL change, rather than absolute GMSL change. However, simulations of RSL change based on glacio-isostatic adjustment show that our record approximates eustatic sea level, defined here as GMSL unregistered to the centre of the Earth. Nonetheless, under conservative assumptions, our estimates limit maximum Pliocene sea-level rise to less than 25 metres and provide new constraints on polar ice-volume variability under the climate conditions predicted for this century.
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Affiliation(s)
- G R Grant
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand. .,GNS Science, Lower Hutt, New Zealand.
| | - T R Naish
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand
| | - G B Dunbar
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand
| | - P Stocchi
- Coastal Systems Department, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, The Netherlands
| | - M A Kominz
- Department of Geological and Environmental Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - P J J Kamp
- School of Science, University of Waikato, Hamilton, New Zealand
| | - C A Tapia
- Departamento de Obras Civiles y Geologia, Facultad de Ingenieria, Universidad Catolica de Temuco, Temuco, Chile
| | - R M McKay
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand
| | - R H Levy
- Antarctic Research Centre, Victoria University of Wellington, Wellington, New Zealand.,GNS Science, Lower Hutt, New Zealand
| | - M O Patterson
- Binghamton University, State University of New York, Binghamton, NY, USA
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23
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Sengupta S, Tang SY, Devine JC, Anderson ST, Nayak S, Zhang SL, Valenzuela A, Fisher DG, Grant GR, López CB, FitzGerald GA. Circadian control of lung inflammation in influenza infection. Nat Commun 2019; 10:4107. [PMID: 31511530 PMCID: PMC6739310 DOI: 10.1038/s41467-019-11400-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/10/2019] [Indexed: 12/13/2022] Open
Abstract
Influenza is a leading cause of respiratory mortality and morbidity. While inflammation is essential for fighting infection, a balance of anti-viral defense and host tolerance is necessary for recovery. Circadian rhythms have been shown to modulate inflammation. However, the importance of diurnal variability in the timing of influenza infection is not well understood. Here we demonstrate that endogenous rhythms affect survival in influenza infection. Circadian control of influenza infection is mediated by enhanced inflammation as proven by increased cellularity in bronchoalveolar lavage (BAL), pulmonary transcriptomic profile and histology and is not attributable to viral burden. Better survival is associated with a time dependent preponderance of NK and NKT cells and lower proportion of inflammatory monocytes in the lung. Further, using a series of genetic mouse mutants, we elucidate cellular mechanisms underlying circadian gating of influenza infection.
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Affiliation(s)
- Shaon Sengupta
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Soon Y Tang
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Systems Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jill C Devine
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Seán T Anderson
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Systems Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Soumyashant Nayak
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Shirley L Zhang
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Alex Valenzuela
- University of Pennsylvania Veterinary School, Philadelphia, PA, 19104, USA
| | - Devin G Fisher
- University of Pennsylvania Veterinary School, Philadelphia, PA, 19104, USA
| | - Gregory R Grant
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Carolina B López
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- University of Pennsylvania Veterinary School, Philadelphia, PA, 19104, USA
| | - Garret A FitzGerald
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Systems Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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24
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Theken KN, Hersh EV, Lahens NF, Lee HM, Li X, Granquist EJ, Giannakopoulos HE, Levin LM, Secreto SA, Grant GR, Detre JA, FitzGerald GA, Grosser T, Farrar JT. Variability in the Analgesic Response to Ibuprofen Is Associated With Cyclooxygenase Activation in Inflammatory Pain. Clin Pharmacol Ther 2019; 106:632-641. [PMID: 30929268 PMCID: PMC6753944 DOI: 10.1002/cpt.1446] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/22/2019] [Indexed: 01/31/2023]
Abstract
The mechanisms underlying interindividual variability in analgesic efficacy of nonsteroidal anti‐inflammatory drugs (NSAIDs) are not well understood. Therefore, we performed pain phenotyping, functional neuroimaging, pharmacokinetic/pharmacodynamic assessments, inflammation biomarkers, and gene expression profiling in healthy subjects who underwent surgical extraction of bony impacted third molars and were treated with ibuprofen (400 mg; N = 19) or placebo (N = 10). Analgesic efficacy was not associated with demographic or clinical characteristics, ibuprofen pharmacokinetics, or the degree of cyclooxygenase inhibition by ibuprofen. Compared with partial responders to ibuprofen (N = 9, required rescue medication within the dosing interval), complete responders (N = 10, no rescue medication) exhibited greater induction of urinary prostaglandin metabolites and serum tumor necrosis factor‐α and interleukin 8. Differentially expressed genes in peripheral blood mononuclear cells were enriched for inflammation‐related pathways. These findings suggest that a less pronounced activation of the inflammatory prostanoid system is associated with insufficient pain relief on ibuprofen alone and the need for additional therapeutic intervention.
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Affiliation(s)
- Katherine N Theken
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elliot V Hersh
- Oral Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hyo Min Lee
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Quebec, Canada
| | - Xuanwen Li
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Eric J Granquist
- Oral Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Helen E Giannakopoulos
- Oral Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lawrence M Levin
- Oral Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stacey A Secreto
- Oral Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John A Detre
- Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John T Farrar
- Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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25
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Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Grant GR, López CB. A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog 2019; 15:e1007707. [PMID: 30995283 PMCID: PMC6504078 DOI: 10.1371/journal.ppat.1007707] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/07/2019] [Accepted: 03/15/2019] [Indexed: 01/12/2023] Open
Abstract
Defective viral genomes of the copy-back type (cbDVGs) are the primary initiators of the antiviral immune response during infection with respiratory syncytial virus (RSV) both in vitro and in vivo. However, the mechanism governing cbDVG generation remains unknown, thereby limiting our ability to manipulate cbDVG content in order to modulate the host response to infection. Here we report a specific genomic signal that mediates the generation of a subset of RSV cbDVG species. Using a customized bioinformatics tool, we identified regions in the RSV genome frequently used to generate cbDVGs during infection. We then created a minigenome system to validate the function of one of these sequences and to determine if specific nucleotides were essential for cbDVG generation at that position. Further, we created a recombinant virus unable to produce a subset of cbDVGs due to mutations introduced in this sequence. The identified sequence was also found as a site for cbDVG generation during natural RSV infections, and common cbDVGs originated at this sequence were found among samples from various infected patients. These data demonstrate that sequences encoded in the viral genome determine the location of cbDVG formation and, therefore, the generation of cbDVGs is not a stochastic process. These findings open the possibility of genetically manipulating cbDVG formation to modulate infection outcome.
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Affiliation(s)
- Yan Sun
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eun Ji Kim
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sébastien A. Felt
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Louis J. Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Divyansh Agarwal
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Carolina B. López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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26
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Ricciotti E, Sarantopoulou D, Grant GR, Sanzari JK, Krigsfeld GS, Kiliti AJ, Kennedy AR, Grosser T. Distinct vascular genomic response of proton and gamma radiation-A pilot investigation. PLoS One 2019; 14:e0207503. [PMID: 30742630 PMCID: PMC6370185 DOI: 10.1371/journal.pone.0207503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/15/2019] [Indexed: 12/16/2022] Open
Abstract
The cardiovascular biology of proton radiotherapy is not well understood. We aimed to compare the genomic dose-response to proton and gamma radiation of the mouse aorta to assess whether their vascular effects may diverge. We performed comparative RNA sequencing of the aorta following (4 hrs) total-body proton and gamma irradiation (0.5–200 cGy whole body dose, 10 dose levels) of conscious mice. A trend analysis identified genes that showed a dose response. While fewer genes were dose-responsive to proton than gamma radiation (29 vs. 194 genes; q-value ≤ 0.1), the magnitude of the effect was greater. Highly responsive genes were enriched for radiation response pathways (DNA damage, apoptosis, cellular stress and inflammation; p-value ≤ 0.01). Gamma, but not proton radiation induced additionally genes in vasculature specific pathways. Genes responsive to both radiation types showed almost perfectly superimposable dose-response relationships. Despite the activation of canonical radiation response pathways by both radiation types, we detected marked differences in the genomic response of the murine aorta. Models of cardiovascular risk based on photon radiation may not accurately predict the risk associated with proton radiation.
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Affiliation(s)
- Emanuela Ricciotti
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jenine K. Sanzari
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gabriel S. Krigsfeld
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amber J. Kiliti
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ann R. Kennedy
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tilo Grosser
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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27
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Shakhmantsir I, Nayak S, Grant GR, Sehgal A. Spliceosome factors target timeless ( tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila. eLife 2018; 7:39821. [PMID: 30516472 PMCID: PMC6281371 DOI: 10.7554/elife.39821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
Transcription-translation feedback loops that comprise eukaryotic circadian clocks rely upon temporal delays that separate the phase of active transcription of clock genes, such as Drosophila period (per) and timeless (tim), from negative feedback by the two proteins. However, our understanding of the mechanisms involved is incomplete. Through an RNA interference screen, we found that pre-mRNA processing 4 (PRP4) kinase, a component of the U4/U5.U6 triple small nuclear ribonucleoprotein (tri-snRNP) spliceosome, and other tri-snRNP components regulate cycling of the molecular clock as well as rest:activity rhythms. Unbiased RNA-Sequencing uncovered an alternatively spliced intron in tim whose increased retention upon prp4 downregulation leads to decreased TIM levels. We demonstrate that the splicing of tim is rhythmic with a phase that parallels delayed accumulation of the protein in a 24 hr cycle. We propose that alternative splicing constitutes an important clock mechanism for delaying the daily accumulation of clock proteins, and thereby negative feedback by them. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Iryna Shakhmantsir
- Chronobiology Program at Penn, Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Soumyashant Nayak
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Amita Sehgal
- Chronobiology Program at Penn, Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
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Song WL, Ricciotti E, Liang X, Grosser T, Grant GR, FitzGerald GA. Lipocalin-Like Prostaglandin D Synthase but Not Hemopoietic Prostaglandin D Synthase Deletion Causes Hypertension and Accelerates Thrombogenesis in Mice. J Pharmacol Exp Ther 2018; 367:425-432. [PMID: 30305427 PMCID: PMC6226547 DOI: 10.1124/jpet.118.250936] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
Prostaglandin (PG) D2 is formed by two distinct PGD synthases (PGDS): lipocalin-type PGDS (L-PGDS), which acts as a PGD2-producing enzyme and as extracellular lipophilic transporter, and hematopoietic PGDS (H-PGDS), a σ glutathione-S-transferase. PGD2 plays an important role in the maintenance of vascular function; however, the relative contribution of L-PGDS– and H-PGDS–dependent formation of PGD2 in this setting is unknown. To gain insight into the function played by these distinct PGDS, we assessed systemic blood pressure (BP) and thrombogenesis in L-Pgds and H-Pgds knockout (KO) mice. Deletion of L-Pgds depresses urinary PGD2 metabolite (PGDM) by ∼35%, whereas deletion of H-Pgds does so by ∼90%. Deletion of L-Pgds, but not H-Pgds, elevates BP and accelerates the thrombogenic occlusive response to a photochemical injury to the carotid artery. HQL-79, a H-PGDS inhibitor, further depresses PGDM in L-Pgds KO mice, but has no effect on BP or on the thrombogenic response. Gene expression profiling reveals that pathways relevant to vascular function are dysregulated in the aorta of L-Pgds KOs. These results indicate that the functional impact of L-Pgds deletion on vascular homeostasis may result from an autocrine effect of L-PGDS–dependent PGD2 on the vasculature and/or the L-PGDS function as lipophilic carrier protein.
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Affiliation(s)
- Wen-Liang Song
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Emanuela Ricciotti
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xue Liang
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tilo Grosser
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory R Grant
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics (W.-L.S., E.R., X.L., T.G., G.A.F.), Institute for Translational Medicine and Therapeutics (W.-L.S., E.R., X.L., T.G., G.R.G., G.A.F.), and Perelman School of Medicine and Department of Genetics (G.R.G.), University of Pennsylvania, Philadelphia, Pennsylvania
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29
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Gupta P, Uner OE, Nayak S, Grant GR, Kalb RG. SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus. PLoS One 2018; 13:e0200477. [PMID: 29995933 PMCID: PMC6040763 DOI: 10.1371/journal.pone.0200477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/27/2018] [Indexed: 01/10/2023] Open
Abstract
Synapse associated protein of 97KDa (SAP97) belongs to a family of scaffolding proteins, the membrane-associated guanylate kinases (MAGUKs), that are highly enriched in the postsynaptic density of synapses and play an important role in organizing protein complexes necessary for synaptic development and plasticity. The Dlg-MAGUK family of proteins are structurally very similar, and an effort has been made to parse apart the unique function of each Dlg-MAGUK protein by characterization of knockout mice. Knockout mice have been generated and characterized for PSD-95, PSD-93, and SAP102, however SAP97 knockout mice have been impossible to study because the SAP97 null mice die soon after birth due to a craniofacial defect. We studied the transcriptomic and behavioral consequences of a brain-specific conditional knockout of SAP97 (SAP97-cKO). RNA sequencing from hippocampi from control and SAP97-cKO male animals identified 67 SAP97 regulated transcripts. As large-scale genetic studies have implicated MAGUKs in neuropsychiatric disorders such as intellectual disability, autism spectrum disorders, and schizophrenia (SCZ), we analyzed our differentially expressed gene (DEG) set for enrichment of disease risk-associated genes, and found our DEG set to be specifically enriched for SCZ-related genes. Subjecting SAP97-cKO mice to a battery of behavioral tests revealed a subtle male-specific cognitive deficit and female-specific motor deficit, while other behaviors were largely unaffected. These data suggest that loss of SAP97 may have a modest contribution to organismal behavior. The SAP97-cKO mouse serves as a stepping stone for understanding the unique role of SAP97 in biology.
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Affiliation(s)
- Preetika Gupta
- Neuroscience Graduate Group, Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ogul E. Uner
- School of Arts and Sciences, Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert G. Kalb
- Feinberg School of Medicine, Department of Neurology, Northwestern University, Chicago, Illinois, United States of America
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30
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Manners MT, Yohn NL, Lahens NF, Grant GR, Bartolomei MS, Blendy JA. Transgenerational inheritance of chronic adolescent stress: Effects of stress response and the amygdala transcriptome. Genes Brain Behav 2018; 18:e12493. [PMID: 29896789 DOI: 10.1111/gbb.12493] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Adolescent stress can impact health and well-being not only during adulthood of the exposed individual but even in future generations. To investigate the molecular mechanisms underlying these long-term effects, we exposed adolescent males to stress and measured anxiety behaviors and gene expression in the amygdala-a critical region in the control of emotional states-in their progeny for two generations, offspring and grandoffspring. Male C57BL/6 mice underwent chronic unpredictable stress (CUS) for 2 weeks during adolescence and were used to produce two generations of offspring. Male and female offspring and grandoffspring were tested in behavioral assays to measure affective behavior and stress reactivity. Remarkably, transgenerational inheritance of paternal stress exposure produced a protective phenotype in the male, but not the female lineage. RNA-seq analysis of the amygdala from male offspring and grandoffspring identified differentially expressed genes (DEGs) in mice derived from fathers exposed to CUS. The DEGSs clustered into numerous pathways, and the "notch signaling" pathway was the most significantly altered in male grandoffspring. Therefore, we show that paternal stress exposure impacts future generations which manifest in behavioral changes and molecular adaptations.
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Affiliation(s)
- M T Manners
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - N L Yohn
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - N F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - G R Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - M S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - J A Blendy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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31
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Guo X, Riobo-Del Galdo NA, Kim EJ, Grant GR, Manning DR. Overlap in signaling between Smoothened and the α subunit of the heterotrimeric G protein G13. PLoS One 2018; 13:e0197442. [PMID: 29763457 PMCID: PMC5953476 DOI: 10.1371/journal.pone.0197442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/02/2018] [Indexed: 01/20/2023] Open
Abstract
The Hedgehog family of morphogens has long been known to utilize, through the 7-transmembrane protein Smoothened (Smo), the heterotrimeric G protein Gi in both canonical and noncanonical forms of signaling. Other G proteins, while not specifically utilized by Smo, may nonetheless provide access to some of the events controlled by it. We reported several years ago that the G protein G13 activates one or more forms of the Gli family of transcription factors. While the Gli transcription factors are well known targets for Smo, the uncertain mechanism of activation by G13 and the identity of the targeted Gli(s) limited predictions as to the extent to which G13 might mimic Smo's actions. We evaluate here the potential for overlap in G13 and Smo signaling using C3H10T1/2 and 3T3-L1 cells as models of osteogenesis and adipogenesis, respectively. We find in C3H10T1/2 cells that a constitutively active form of Gα13 (Gα13QL) increases Gli1 mRNA, as does a constitutively active form of Smo (SmoA1). We find as well that Gα13QL induces alkaline phosphatase activity, a marker of osteogenesis, albeit the induction is far less substantial than that achieved by SmoA1. In 3T3-L1 cells both Gα13QL and SmoA1 markedly suppress adipogenic differentiation as determined by triglyceride accumulation. RNA sequencing reveals that Gα13QL and SmoA1 regulate many of the same genes but that quantitative and qualitative differences exist. Differences also exist, we find, between SmoA1 and purmorphamine, an agonist for Smo. Therefore, while comparisons of constitutively active proteins are informative, extrapolations to the setting of agonists require care.
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Affiliation(s)
- Xueshui Guo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Natalia A. Riobo-Del Galdo
- Leeds Institute of Cancer and Pathology and School of Molecular and Cellular Biology, University of Leeds, United Kingdom
| | - Eun Ji Kim
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David R. Manning
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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32
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Norton SS, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y. Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Bioinformatics 2018; 34:1488-1497. [PMID: 29236961 PMCID: PMC6454425 DOI: 10.1093/bioinformatics/btx790] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/17/2017] [Accepted: 12/07/2017] [Indexed: 01/20/2023] Open
Abstract
Motivation A key component in many RNA-Seq-based studies is contrasting multiple replicates from different experimental conditions. In this setup, replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as experimental variability. However, what constitutes a 'bad' replicate is not necessarily well defined. Consequently, researchers might discard valuable data or downstream analysis may be hampered by failed experiments. Results Here we develop a probability model to weigh a given RNA-Seq sample as a representative of an experimental condition when performing alternative splicing analysis. We demonstrate that this model detects outlier samples which are consistently and significantly different compared with other samples from the same condition. Moreover, we show that instead of discarding such samples the proposed weighting scheme can be used to downweight samples and specific splicing variations suspected as outliers, gaining statistical power. These weights can then be used for differential splicing (DS) analysis, where the resulting algorithm offers a generalization of the MAJIQ algorithm. Using both synthetic and real-life data, we perform an extensive evaluation of the improved MAJIQ algorithm in different scenarios involving perturbed samples, mislabeled samples, same condition groups, and different levels of coverage, showing it compares favorably to other tools. Overall, this work offers an outlier detection algorithm that can be combined with any splicing pipeline, a generalized and improved version of MAJIQ for DS detection, and evaluation metrics with matching code and data for DS algorithms. Availability and implementation Software and data are accessible via majiq.biociphers.org/norton_et_al_2017/. Contact yosephb@upenn.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Scott S Norton
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorge Vaquero-Garcia
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA
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33
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Kim EJ, Grant GR, Bowman AS, Haider N, Gudiseva HV, Chavali VRM. Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription. Sci Rep 2018; 8:3040. [PMID: 29445097 PMCID: PMC5813239 DOI: 10.1038/s41598-018-21104-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/30/2018] [Indexed: 11/21/2022] Open
Abstract
Age-related macular degeneration (AMD) predominantly affects the retina and retinal pigment epithelium in the posterior eye. While there are numerous studies investigating the non-coding transcriptome of retina and RPE, few significant differences between AMD and normal tissues have been reported. Strand specific RNA sequencing of both peripheral retina (PR) and RPE-Choroid-Sclera (PRCS), in both AMD and matched normal controls were generated. The transcriptome analysis reveals a highly significant and consistent impact on anti-sense transcription as well as moderate changes in the regulation of non-coding (sense) RNA. Hundreds of genes that do not express anti-sense transcripts in normal PR and PRCS demonstrate significant anti-sense expression in AMD in all patient samples. Several pathways are highly enriched in the upregulated anti-sense transcripts—in particular the EIF2 signaling pathway. These results call for a deeper exploration into anti-sense and noncoding RNA regulation in AMD and their potential as therapeutic targets.
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Affiliation(s)
- Eun Ji Kim
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anita S Bowman
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.,Functional Genomics Lab, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Naqi Haider
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.,Functional Genomics Lab, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harini V Gudiseva
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Venkata Ramana Murthy Chavali
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA. .,Functional Genomics Lab, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Palozola KC, Donahue G, Liu H, Grant GR, Becker JS, Cote A, Yu H, Raj A, Zaret KS. Mitotic transcription and waves of gene reactivation during mitotic exit. Science 2017; 358:119-122. [PMID: 28912132 DOI: 10.1126/science.aal4671] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 05/30/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022]
Abstract
Although the genome is generally thought to be transcriptionally silent during mitosis, technical limitations have prevented sensitive mapping of transcription during mitosis and mitotic exit. Thus, the means by which the interphase expression pattern is transduced to daughter cells have been unclear. We used 5-ethynyluridine to pulse-label transcripts during mitosis and mitotic exit and found that many genes exhibit transcription during mitosis, as confirmed with fluorescein isothiocyanate-uridine 5'-triphosphate labeling, RNA fluorescence in situ hybridization, and quantitative reverse transcription polymerase chain reaction. The first round of transcription immediately after mitosis primarily activates genes involved in the growth and rebuilding of daughter cells, rather than cell type-specific functions. We propose that the cell's transcription pattern is largely retained at a low level through mitosis, whereas the amplitude of transcription observed in interphase is reestablished during mitotic exit.
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Affiliation(s)
- Katherine C Palozola
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA
| | - Hong Liu
- Department of Biochemistry and Molecular Biology and Tulane Center for Aging, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin S Becker
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA
| | - Allison Cote
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA. .,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5157, USA
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35
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Lahens NF, Ricciotti E, Smirnova O, Toorens E, Kim EJ, Baruzzo G, Hayer KE, Ganguly T, Schug J, Grant GR. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. BMC Genomics 2017; 18:602. [PMID: 28797240 PMCID: PMC5553782 DOI: 10.1186/s12864-017-4011-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. Results Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs. Conclusions Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4011-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Olga Smirnova
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik Toorens
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eun Ji Kim
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tapan Ganguly
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jonathan Schug
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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36
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Hu Q, Kim EJ, Feng J, Grant GR, Heller EA. Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. PLoS Comput Biol 2017; 13:e1005602. [PMID: 28609483 PMCID: PMC5487056 DOI: 10.1371/journal.pcbi.1005602] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/27/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022] Open
Abstract
A compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is implicated in cocaine exposure in mice. Recent literature has described chromatin-regulated alternative splicing, suggesting a novel function for drug-induced neuroepigenetic remodeling. However, the extent of the genome-wide association between particular histone modifications and alternative splicing remains unexplored. To address this, we have developed novel computational approaches to model the association between alternative splicing and histone posttranslational modifications in the nucleus accumbens (NAc), a brain reward region. Using classical statistical methods and machine learning to combine ChIP-Seq and RNA-Seq data, we found that specific histone modifications are strongly associated with various aspects of differential splicing. H3K36me3 and H3K4me1 have the strongest association with splicing indicating they play a significant role in alternative splicing in brain reward tissue.
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Affiliation(s)
- Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Eun Ji Kim
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Jian Feng
- Department of Biological Science, Florida State University, Tallahassee, FL, United States of America
| | - Gregory R. Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Elizabeth A. Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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Danford ID, Verkuil LD, Choi DJ, Collins DW, Gudiseva HV, Uyhazi KE, Lau MK, Kanu LN, Grant GR, Chavali VRM, O'Brien JM. Characterizing the "POAGome": A bioinformatics-driven approach to primary open-angle glaucoma. Prog Retin Eye Res 2017; 58:89-114. [PMID: 28223208 DOI: 10.1016/j.preteyeres.2017.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 01/10/2023]
Abstract
Primary open-angle glaucoma (POAG) is a genetically, physiologically, and phenotypically complex neurodegenerative disorder. This study addressed the expanding collection of genes associated with POAG, referred to as the "POAGome." We used bioinformatics tools to perform an extensive, systematic literature search and compiled 542 genes with confirmed associations with POAG and its related phenotypes (normal tension glaucoma, ocular hypertension, juvenile open-angle glaucoma, and primary congenital glaucoma). The genes were classified according to their associated ocular tissues and phenotypes, and functional annotation and pathway analyses were subsequently performed. Our study reveals that no single molecular pathway can encompass the pathophysiology of POAG. The analyses suggested that inflammation and senescence may play pivotal roles in both the development and perpetuation of the retinal ganglion cell degeneration seen in POAG. The TGF-β signaling pathway was repeatedly implicated in our analyses, suggesting that it may be an important contributor to the manifestation of POAG in the anterior and posterior segments of the globe. We propose a molecular model of POAG revolving around TGF-β signaling, which incorporates the roles of inflammation and senescence in this disease. Finally, we highlight emerging molecular therapies that show promise for treating POAG.
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Affiliation(s)
- Ian D Danford
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lana D Verkuil
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel J Choi
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David W Collins
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Harini V Gudiseva
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katherine E Uyhazi
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marisa K Lau
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Levi N Kanu
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Venkata R M Chavali
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Joan M O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Tang SY, Monslow J, R Grant G, Todd L, Pawelzik SC, Chen L, Lawson J, Puré E, FitzGerald GA. Cardiovascular Consequences of Prostanoid I Receptor Deletion in Microsomal Prostaglandin E Synthase-1-Deficient Hyperlipidemic Mice. Circulation 2016; 134:328-38. [PMID: 27440004 DOI: 10.1161/circulationaha.116.022308] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/02/2016] [Indexed: 02/02/2023]
Abstract
BACKGROUND Inhibitors of cyclooxygenase-2 alleviate pain and reduce fever and inflammation by suppressing the biosynthesis of prostacyclin (PGI2) and prostaglandin E2. However, suppression of these prostaglandins, particularly PGI2, by cyclooxygenase-2 inhibition or deletion of its I prostanoid receptor also predisposes to accelerated atherogenesis and thrombosis in mice. By contrast, deletion of microsomal prostaglandin E synthase 1 (mPGES-1) confers analgesia, attenuates atherogenesis, and fails to accelerate thrombogenesis, while suppressing prostaglandin E2, but increasing biosynthesis of PGI2. METHODS To address the cardioprotective contribution of PGI2, we generated mice lacking the I prostanoid receptor together with mPges-1 on a hyperlipidemic background (low-density lipoprotein receptor knockouts). RESULTS mPges-1 depletion modestly increased thrombogenesis, but this response was markedly further augmented by coincident deletion of the I prostanoid receptor (n=10-18). By contrast, deletion of the I prostanoid receptor had no effect on the attenuation of atherogenesis by mPGES-1 deletion in the low-density lipoprotein receptor knockout mice (n=17-21). CONCLUSIONS Although suppression of prostaglandin E2 accounts for the protective effect of mPGES-1 deletion in atherosclerosis, augmentation of PGI2 is the dominant contributor to its favorable thrombogenic profile. The divergent effects on these prostaglandins suggest that inhibitors of mPGES-1 may be less likely to cause cardiovascular adverse effects than nonsteroidal anti-inflammatory drugs specific for inhibition of cyclooxygenase-2.
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Affiliation(s)
- Soon Yew Tang
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - James Monslow
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Gregory R Grant
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Leslie Todd
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Sven-Christian Pawelzik
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Lihong Chen
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - John Lawson
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Ellen Puré
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.)
| | - Garret A FitzGerald
- From Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics (S.Y.T., J.M., L.T., S.-C.P., L.C., E.P., G.A.F.); Department of Animal Biology, School of Veterinary Medicine (S.Y.T., G.R.G., J.L.); and Department of Genetics, University of Pennsylvania, Philadelphia (J.M.).
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Yang G, Chen L, Grant GR, Paschos G, Song WL, Musiek ES, Lee V, McLoughlin SC, Grosser T, Cotsarelis G, FitzGerald GA. Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Sci Transl Med 2016; 8:324ra16. [PMID: 26843191 PMCID: PMC4870001 DOI: 10.1126/scitranslmed.aad3305] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022]
Abstract
The absence of Bmal1, a core clock gene, results in a loss of circadian rhythms, an acceleration of aging, and a shortened life span in mice. To address the importance of circadian rhythms in the aging process, we generated conditional Bmal1 knockout mice that lacked the BMAL1 protein during adult life and found that wild-type circadian variations in wheel-running activity, heart rate, and blood pressure were abolished. Ocular abnormalities and brain astrogliosis were conserved irrespective of the timing of Bmal1 deletion. However, life span, fertility, body weight, blood glucose levels, and age-dependent arthropathy, which are altered in standard Bmal1 knockout mice, remained unaltered, whereas atherosclerosis and hair growth improved, in the conditional adult-life Bmal1 knockout mice, despite abolition of clock function. Hepatic RNA-Seq revealed that expression of oscillatory genes was dampened in the adult-life Bmal1 knockout mice, whereas overall gene expression was largely unchanged. Thus, many phenotypes in conventional Bmal1 knockout mice, hitherto attributed to disruption of circadian rhythms, reflect the loss of properties of BMAL1 that are independent of its role in the clock. These findings prompt reevaluation of the systemic consequences of disruption of the molecular clock.
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Affiliation(s)
- Guangrui Yang
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lihong Chen
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Georgios Paschos
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wen-Liang Song
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik S Musiek
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vivian Lee
- Department of Ophthalmology, University of Pennsylvania Scheie Eye Institute, Philadelphia, PA 19104, USA
| | - Sarah C McLoughlin
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tilo Grosser
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George Cotsarelis
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Garret A FitzGerald
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics 2015; 31:3938-45. [PMID: 26338770 PMCID: PMC4673975 DOI: 10.1093/bioinformatics/btv488] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
MOTIVATION Because of the advantages of RNA sequencing (RNA-Seq) over microarrays, it is gaining widespread popularity for highly parallel gene expression analysis. For example, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length splice forms. A number of informatics packages have been developed for this purpose, but short reads make it a difficult problem in principle. Sequencing error and polymorphisms add further complications. It has become necessary to perform studies to determine which algorithms perform best and which if any algorithms perform adequately. However, there is a dearth of independent and unbiased benchmarking studies. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy. RESULTS We conclude that most methods are inaccurate even using idealized data, and that no method is highly accurate once multiple splice forms, polymorphisms, intron signal, sequencing errors, alignment errors, annotation errors and other complicating factors are present. These results point to the pressing need for further algorithm development. AVAILABILITY AND IMPLEMENTATION Simulated datasets and other supporting information can be found at http://bioinf.itmat.upenn.edu/BEERS/bp2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katharina E Hayer
- University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104
| | - Angel Pizarro
- Scientific Computing at Amazon Web Services, Seattle, WA 98108
| | | | | | - Gregory R Grant
- University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Ricciotti E, Grosser T, Grant GR, Liu SL, Lawson JA, Assoian R, FitzGerald GA. Abstract 238: Distinct Vascular Effects of Celecoxib and Rofecoxib in vivo. Arterioscler Thromb Vasc Biol 2015. [DOI: 10.1161/atvb.35.suppl_1.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Randomized controlled trials of cyclooxygenase (COX)-2 selective NSAIDs revealed that these drugs confer a cardiovascular hazard, resulting mainly from suppression of COX-2 derived prostacyclin (PGI2).
Disruption of rodent COX-2-derived PGI2 in vascular cells and cardiomyocytes has recapitulated all elements of the cardiovascular hazard attributable to NSAIDs in humans.
To investigate further the impact of COX-2 inhibition in the vasculature, we examined the effects of therapeutic concentrations of two selective COX-2 inhibitors, celecoxib and rofecoxib, on thrombosis and vascular injury. Furthermore, we used RNA sequencing (RNA-Seq) to assess whether celecoxib and rofecoxib might elicit distinct genomic effects in mouse aorta.
Celecoxib (100 mg/Kg) and rofecoxib (50 mg/Kg) caused a selective and equipotent COX-2 inhibition as indicated by measuring thromboxane (TXB-M, an in vivo index of COX-1 activity) and prostacyclin (PGI-M, an in vivo index of COX-2 activity) urinary metabolites by mass spectrometry.
Both celecoxib and rofecoxib augmented platelet deposition and prolonged platelet disaggregation after laser-induced injury in the cremaster arterioles.
A similar effect was observed in mice lacking PGI2 receptor IP. There was no additional pro-thrombotic effect of the drugs on an IPKO background, consistent with suppression of COX-2 dependent PGI2 mediating the predisposition to thrombosis induced by celecoxib and rofecoxib.
Celecoxib, but not rofecoxib, caused a reduction of neointimal hyperplasia and the intima/media ratio of injured femoral artery at 3 weeks after wire injury.
RNA-seq analysis revealed 903 transcripts differentially expressed between celecoxib and control group and 3,127 transcripts between rofecoxib and control group (at a false discovery rate of 10%) in mouse aorta.
Thus, both celecoxib and rofecoxib cause a similar predisposition to thrombosis in mice.
Celecoxib, but not rofecoxib, reduces neointimal hyperplasia after vascular injury and COX-2 independent genetic actions might modulate this effect.
The predisposition to thrombosis and attenuation of the response to vascular injury by celecoxib recapitulates what has been found in humans.
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Affiliation(s)
- Emanuela Ricciotti
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - Tilo Grosser
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - Gregory R Grant
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - Shu-Lin Liu
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - John A Lawson
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - Richard Assoian
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
| | - Garret A FitzGerald
- Systems Pharmacology and Translational Therapeutics, Univ of Pennsylvania, Philadelphia, PA
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Abstract
Circadian rhythms are daily endogenous oscillations of behavior, metabolism, and physiology. At a molecular level, these oscillations are generated by transcriptional-translational feedback loops composed of core clock genes. In turn, core clock genes drive the rhythmic accumulation of downstream outputs-termed clock-controlled genes (CCGs)-whose rhythmic translation and function ultimately underlie daily oscillations at a cellular and organismal level. Given the circadian clock's profound influence on human health and behavior, considerable efforts have been made to systematically identify CCGs. The recent development of next-generation sequencing has dramatically expanded our ability to study the expression, processing, and stability of rhythmically expressed mRNAs. Nevertheless, like any new technology, there are many technical issues to be addressed. Here, we discuss considerations for studying circadian rhythms using genome scale transcriptional profiling, with a particular emphasis on RNA sequencing. We make a number of practical recommendations-including the choice of sampling density, read depth, alignment algorithms, read-depth normalization, and cycling detection algorithms-based on computational simulations and our experience from previous studies. We believe that these results will be of interest to the circadian field and help investigators design experiments to derive most values from these large and complex data sets.
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Affiliation(s)
- Jiajia Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John B Hogenesch
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael E Hughes
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA.
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Karamanian VA, Harhay M, Grant GR, Palevsky HI, Grizzle WE, Zamanian RT, Ihida-Stansbury K, Taichman DB, Kawut SM, Jones PL. Erythropoietin upregulation in pulmonary arterial hypertension. Pulm Circ 2014; 4:269-79. [PMID: 25006446 DOI: 10.1086/675990] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/07/2014] [Indexed: 01/05/2023] Open
Abstract
The pathophysiologic alterations of patients with pulmonary arterial hypertension (PAH) are diverse. We aimed to determine novel pathogenic pathways from circulating proteins in patients with PAH. Multianalyte profiling (MAP) was used to measure 90 specifically selected antigens in the plasma of 113 PAH patients and 51 control patients. Erythropoietin (EPO) functional activity was assessed via in vitro pulmonary artery endothelial cell networking and smooth muscle cell proliferation assays. Fifty-eight patients had idiopathic PAH, whereas 55 had other forms of PAH; 5 had heritable PAH, 18 had connective tissue disease (15 with scleroderma and 3 with lupus erythematosis), 13 had portopulmonary hypertension, 6 had PAH associated with drugs or toxins, and 5 had congenital heart disease. The plasma-antigen profile of PAH revealed increased levels of several novel biomarkers, including EPO. Immune quantitative and histochemical studies revealed that EPO not only was significantly elevated in the plasma of PAH patients but also promoted pulmonary artery endothelial cell network formation and smooth muscle cell proliferation. MAP is a hypothesis-generating approach to identifying novel pathophysiologic pathways in PAH. EPO is upregulated in the circulation and lungs of patients with PAH and may affect endothelial and smooth muscle cell proliferation.
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Affiliation(s)
- Vanesa A Karamanian
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael Harhay
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harold I Palevsky
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - William E Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Roham T Zamanian
- Department of Pulmonary and Critical Care Medicine, Stanford University, Stanford, California, USA; and Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, California, USA
| | - Kaori Ihida-Stansbury
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Darren B Taichman
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steven M Kawut
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; These authors contributed equally
| | - Peter L Jones
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA ; These authors contributed equally
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Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol 2014; 15:R86. [PMID: 24981968 PMCID: PMC4197826 DOI: 10.1186/gb-2014-15-6-r86] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 06/30/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. RESULTS We present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of over 1,000 in vitro transcribed RNAs from a full-length human cDNA library and sequenced them with polyA and total RNA-seq, the most common protocols. Because each cDNA is full length, and we show in vitro transcription is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find 50% of transcripts have more than two-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. We also find greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. We use a combination of experimental and computational approaches to show rRNA depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation. CONCLUSIONS These results show the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq. We find rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. These biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting RNA-seq results.
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Chen EP, Markosyan N, Connolly E, Lawson JA, Li X, Grant GR, Grosser T, FitzGerald GA, Smyth EM. Myeloid Cell COX-2 deletion reduces mammary tumor growth through enhanced cytotoxic T-lymphocyte function. Carcinogenesis 2014; 35:1788-97. [PMID: 24590894 DOI: 10.1093/carcin/bgu053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cyclooxygenase-2 (COX-2) expression is associated with poor prognosis across a range of human cancers, including breast cancer. The contribution of tumor cell-derived COX-2 to tumorigenesis has been examined in numerous studies; however, the role of stromal-derived COX-2 is ill-defined. Here, we examined how COX-2 in myeloid cells, an immune cell subset that includes macrophages, influences mammary tumor progression. In mice engineered to selectively lack myeloid cell COX-2 [myeloid-COX-2 knockout (KO) mice], spontaneous neu oncogene-induced tumor onset was delayed, tumor burden reduced, and tumor growth slowed compared with wild-type (WT). Similarly, growth of neu-transformed mammary tumor cells as orthotopic tumors in immune competent syngeneic myeloid-COX-2 KO host mice was reduced compared with WT. By flow cytometric analysis, orthotopic myeloid-COX-2 KO tumors had lower tumor-associated macrophage (TAM) infiltration consistent with impaired colony stimulating factor-1-dependent chemotaxis by COX-2 deficient macrophages in vitro. Further, in both spontaneous and orthotopic tumors, COX-2-deficient TAM displayed lower immunosuppressive M2 markers and this was coincident with less suppression of CD8(+) cytotoxic T lymphocytes (CTLs) in myeloid-COX-2 KO tumors. These studies suggest that reduced tumor growth in myeloid-COX-2 KO mice resulted from disruption of M2-like TAM function, thereby enhancing T-cell survival and immune surveillance. Antibody-mediated depletion of CD8(+), but not CD4(+) cells, restored tumor growth in myeloid-COX-2 KO to WT levels, indicating that CD8(+) CTLs are dominant antitumor effectors in myeloid-COX-2 KO mice. Our studies suggest that inhibition of myeloid cell COX-2 can potentiate CTL-mediated tumor cytotoxicity and may provide a novel therapeutic approach in breast cancer therapy.
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Affiliation(s)
- Edward P Chen
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nune Markosyan
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emma Connolly
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John A Lawson
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xuanwen Li
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emer M Smyth
- Institute for Translational Medicine and Therapeutics and Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics 2013; 14:486. [PMID: 23865674 PMCID: PMC3924432 DOI: 10.1186/1471-2164-14-486] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease. RESULTS We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3' and 5' alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further, 15-36% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products. CONCLUSIONS To our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.
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Affiliation(s)
- Michael H Farkas
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Gregory R Grant
- Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A White
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Maria E Sousa
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Mark B Consugar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
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Abstract
BACKGROUND Low dose aspirin reduces the secondary incidence of myocardial infarction and stroke. Drug resistance to aspirin might result in treatment failure. Despite this concern, no clear definition of aspirin resistance has emerged, and estimates of its incidence have varied remarkably. We aimed to determine the commonality of a mechanistically consistent, stable, and specific phenotype of true pharmacological resistance to aspirin-such as might be explained by genetic causes. METHODS AND RESULTS Healthy volunteers (n=400) were screened for their response to a single oral dose of 325-mg immediate release or enteric coated aspirin. Response parameters reflected the activity of the molecular target of aspirin, cyclooxygenase-1. Individuals who appeared aspirin resistant on 1 occasion underwent repeat testing, and if still resistant were exposed to low-dose enteric coated aspirin (81 mg) and clopidogrel (75 mg) for 1 week each. Variable absorption caused a high frequency of apparent resistance to a single dose of 325-mg enteric coated aspirin (up to 49%) but not to immediate release aspirin (0%). All individuals responded to aspirin on repeated exposure, extension of the postdosing interval, or addition of aspirin to their platelets ex vivo. CONCLUSIONS Pharmacological resistance to aspirin is rare; this study failed to identify a single case of true drug resistance. Pseudoresistance, reflecting delayed and reduced drug absorption, complicates enteric coated but not immediate release aspirin administration. CLINICAL TRIAL REGISTRATION URL: http://www.clinicaltrials.gov. Unique identifier: NCT00948987.
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Affiliation(s)
- Tilo Grosser
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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48
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Abstract
Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-h rhythms of transcription. These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over the last decade have used microarrays to profile circadian transcriptional rhythms in various organisms and tissues. Here we use RNA sequencing (RNA-seq) to profile the circadian transcriptome of Drosophila melanogaster brain from wild-type and period-null clock-defective animals. We identify several hundred transcripts whose abundance oscillates with 24-h periods in either constant darkness or 12 h light/dark diurnal cycles, including several noncoding RNAs (ncRNAs) that were not identified in previous microarray studies. Of particular interest are U snoRNA host genes (Uhgs), a family of diurnal cycling noncoding RNAs that encode the precursors of more than 50 box-C/D small nucleolar RNAs, key regulators of ribosomal biogenesis. Transcriptional profiling at the level of individual exons reveals alternative splice isoforms for many genes whose relative abundances are regulated by either period or circadian time, although the effect of circadian time is muted in comparison to that of period. Interestingly, period loss of function significantly alters the frequency of RNA editing at several editing sites, suggesting an unexpected link between a key circadian gene and RNA editing. We also identify tens of thousands of novel splicing events beyond those previously annotated by the modENCODE Consortium, including several that affect key circadian genes. These studies demonstrate extensive circadian control of ncRNA expression, reveal the extent of clock control of alternative splicing and RNA editing, and provide a novel, genome-wide map of splicing in Drosophila brain.
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Affiliation(s)
- Michael E Hughes
- Department of Cellular and Molecular Physiology, and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, Connecticut 06520, USA
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Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). ACTA ACUST UNITED AC 2011; 27:2518-28. [PMID: 21775302 DOI: 10.1093/bioinformatics/btr427] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously. RESULTS We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability. AVAILABILITY The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM). CONTACT ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu SUPPLEMENTARY INFORMATION The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.
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Affiliation(s)
- Gregory R Grant
- Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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50
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Guerraty MA, Grant GR, Karanian JW, Chiesa OA, Pritchard WF, Davies PF. Side-specific expression of activated leukocyte adhesion molecule (ALCAM; CD166) in pathosusceptible regions of swine aortic valve endothelium. J Heart Valve Dis 2011; 20:165-167. [PMID: 21560815 PMCID: PMC3817713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Aortic valve sclerosis (AVS), an early form of aortic valve disease, develops preferentially on the aortic side of valve leaflets, a predilection that is reflected in an heterogeneous side-specific gene expression profile. It has been ascertained that hypercholesterolemia is sufficient to initiate the endothelial expression of activated leukocyte adhesion molecule (ALCAM; CD166), restricted to the aortic side of the leaflet. Intercellular adhesion molecule-1 (ICAM-1) or vascular cell adhesion molecule-1 (VCAM-1)--both of which are more typically associated with early arterial inflammation--are not differentially expressed. ALCAM up-regulation by hypercholesterolemia suggests a side-specific spatial role in the recruitment of leukocytes to AVS sites.
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Affiliation(s)
- Marie A. Guerraty
- Institute for Medicine and Engineering, US Food and Drug Administration, Laurel, MD
| | - Gregory R. Grant
- Center for Bioinformatics, US Food and Drug Administration, Laurel, MD
| | - John W. Karanian
- Laboratory of Cardiovascular and Interventional Therapeutics, US Food and Drug Administration, Laurel, MD
| | - Oscar A. Chiesa
- Laboratory of Cardiovascular and Interventional Therapeutics, US Food and Drug Administration, Laurel, MD
| | - William F. Pritchard
- Laboratory of Cardiovascular and Interventional Therapeutics, US Food and Drug Administration, Laurel, MD
| | - Peter F. Davies
- Institute for Medicine and Engineering, US Food and Drug Administration, Laurel, MD
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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