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Boddy AM, Harrison PW, Montgomery SH, Caravas JA, Raghanti MA, Phillips KA, Mundy NI, Wildman DE. Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates. Genome Biol Evol 2017; 9:700-713. [PMID: 28391320 PMCID: PMC5381557 DOI: 10.1093/gbe/evx028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution.
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Affiliation(s)
- Amy M Boddy
- The Biodesign Institute, Arizona State University, Tempe, AZ.,Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Peter W Harrison
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen H Montgomery
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,Department of Zoology, University of Cambridge, United Kingdom
| | - Jason A Caravas
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH
| | | | | | - Derek E Wildman
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI.,Department of Molecular & Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL
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Leisner TM, Freeman TC, Black JL, Parise LV. CIB1: a small protein with big ambitions. FASEB J 2016; 30:2640-50. [PMID: 27118676 DOI: 10.1096/fj.201500073r] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
Calcium- and integrin-binding protein 1 (CIB1) is a small, ubiquitously expressed protein that was first identified as an intracellular binding partner of a platelet-specific α-integrin cytoplasmic tail. Although early studies revealed a role for CIB1 in regulating platelet integrin activity, recent studies have indicated a more diverse role for CIB1 in many different cell types and processes, including calcium signaling, migration, adhesion, proliferation, and survival. Increasing evidence also points to a novel role for CIB1 in cancer and cardiovascular disease. In addition, an array of CIB1 binding partners has been identified that provide important insight into how CIB1 may regulate these processes. Some of these binding partners include the serine/threonine kinases, p21-activated kinase 1 (PAK1), apoptosis signal-regulating kinase 1 (ASK1), and polo-like kinase 3 (PLK3). Structural and mutational studies indicate that CIB1 binds most or all of its partners via a well-defined hydrophobic cleft. Although CIB1 itself lacks known enzymatic activity, it supports the PI3K/AKT and MEK/ERK oncogenic signaling pathways, in part, by directly modulating enzymes in these pathways. In this review, we discuss our current understanding of CIB1 and key questions regarding structure and function and how this seemingly diminutive protein impacts important signaling pathways and cellular processes in human health and disease.-Leisner, T. M., Freeman, T. C., Black, J. L., Parise, L. V. CIB1: a small protein with big ambitions.
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Affiliation(s)
- Tina M Leisner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thomas C Freeman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Justin L Black
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Leslie V Parise
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, USA; and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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Poitou C, Perret C, Mathieu F, Truong V, Blum Y, Durand H, Alili R, Chelghoum N, Pelloux V, Aron-Wisnewsky J, Torcivia A, Bouillot JL, Parks BW, Ninio E, Clément K, Tiret L. Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study. PLoS One 2015; 10:e0125718. [PMID: 25938420 PMCID: PMC4418598 DOI: 10.1371/journal.pone.0125718] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/17/2015] [Indexed: 11/30/2022] Open
Abstract
Background Bariatric surgery is associated to improvements in obesity-associated comorbidities thought to be mediated by a decrease of adipose inflammation. However, the molecular mechanisms behind these beneficial effects are poorly understood. Methodology/Principal Findings We analyzed RNA-seq expression profiles in adipose tissue from 22 obese women before and 3 months after surgery. Of 15,972 detected genes, 1214 were differentially expressed after surgery at a 5% false discovery rate. Upregulated genes were mostly involved in the basal cellular machinery. Downregulated genes were enriched in metabolic functions of adipose tissue. At baseline, 26 modules of coexpressed genes were identified. The four most stable modules reflected the innate and adaptive immune responses of adipose tissue. A first module reflecting a non-specific signature of innate immune cells, mainly macrophages, was highly conserved after surgery with the exception of DUSP2 and CD300C. A second module reflected the adaptive immune response elicited by T lymphocytes; after surgery, a disconnection was observed between genes involved in T-cell signaling and mediators of the signal transduction such as CXCR1, CXCR2, GPR97, CCR7 and IL7R. A third module reflected neutrophil-mediated inflammation; after surgery, several genes were dissociated from the module, including S100A8, S100A12, CD300E, VNN2, TUBB1 and FAM65B. We also identified a dense network of 19 genes involved in the interferon-signaling pathway which was strongly preserved after surgery, with the exception of DDX60, an antiviral factor involved in RIG-I-mediated interferon signaling. A similar loss of connection was observed in lean mice compared to their obese counterparts. Conclusions/Significance These results suggest that improvements of the inflammatory state following surgery might be explained by a disruption of immuno-inflammatory cascades involving a few crucial molecules which could serve as potential therapeutic targets.
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Affiliation(s)
- Christine Poitou
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Claire Perret
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - François Mathieu
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Vinh Truong
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Yuna Blum
- Department of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Hervé Durand
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Rohia Alili
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Nadjim Chelghoum
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Post-Genomic Platform of Pitié-Salpêtrière (P3S), F-75013, Paris, France
| | - Véronique Pelloux
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Judith Aron-Wisnewsky
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Adriana Torcivia
- Assistance Publique-Hôpitaux de Paris, Department of Visceral Surgery, Pitié-Salpêtrière Hospital, F-75013, Paris, France
| | - Jean-Luc Bouillot
- Assistance Publique-Hôpitaux de Paris, Department of General, Digestive and Metabolic Surgery, Ambroise-Paré Hospital, F- 92100, Boulogne-Billancourt, France
| | - Brian W. Parks
- Department of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Ewa Ninio
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Karine Clément
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Laurence Tiret
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
- * E-mail:
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Ka M, Jung EM, Mueller U, Kim WY. MACF1 regulates the migration of pyramidal neurons via microtubule dynamics and GSK-3 signaling. Dev Biol 2014; 395:4-18. [PMID: 25224226 DOI: 10.1016/j.ydbio.2014.09.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/13/2014] [Accepted: 09/05/2014] [Indexed: 10/24/2022]
Abstract
Neuronal migration and subsequent differentiation play critical roles for establishing functional neural circuitry in the developing brain. However, the molecular mechanisms that regulate these processes are poorly understood. Here, we show that microtubule actin crosslinking factor 1 (MACF1) determines neuronal positioning by regulating microtubule dynamics and mediating GSK-3 signaling during brain development. First, using MACF1 floxed allele mice and in utero gene manipulation, we find that MACF1 deletion suppresses migration of cortical pyramidal neurons and results in aberrant neuronal positioning in the developing brain. The cell autonomous deficit in migration is associated with abnormal dynamics of leading processes and centrosomes. Furthermore, microtubule stability is severely damaged in neurons lacking MACF1, resulting in abnormal microtubule dynamics. Finally, MACF1 interacts with and mediates GSK-3 signaling in developing neurons. Our findings establish a cellular mechanism underlying neuronal migration and provide insights into the regulation of cytoskeleton dynamics in developing neurons.
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Affiliation(s)
- Minhan Ka
- Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Eui-Man Jung
- Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Ulrich Mueller
- Dorris Neuroscience Center and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Woo-Yang Kim
- Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, United States.
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