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Yen EC, Gilbert JD, Balard A, Afonso IO, Fairweather K, Newlands D, Lopes A, Correia SM, Taxonera A, Rossiter SJ, Martín-Durán JM, Eizaguirre C. DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles. Evol Appl 2024; 17:e70013. [PMID: 39286762 PMCID: PMC11403127 DOI: 10.1111/eva.70013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/23/2024] [Accepted: 08/24/2024] [Indexed: 09/19/2024] Open
Abstract
To date, studies of the impacts of climate warming on individuals and populations have mostly focused on mortality and thermal tolerance. In contrast, much less is known about the consequences of sublethal effects, which are more challenging to detect, particularly in wild species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch field experiment, we relocated clutches of wild, nesting loggerhead sea turtles (Caretta caretta) to an in situ hatchery. Eggs were then split into two sub-clutches and incubated under shallow or deep conditions, with those in the shallow treatment experiencing significantly higher temperatures in otherwise natural conditions. Although no difference in hatching success was observed between treatments, hatchlings from the shallow, warmer treatment had different length-mass relationships and were weaker at locomotion tests than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. We identified 287 differentially methylated sites between hatchlings from different treatments, including on genes with neurodevelopmental, cytoskeletal, and lipid metabolism functions. Taken together, our results show that higher incubation temperatures induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. These sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming reduces hatchling fitness, which has implications for dispersal capacity and ultimately a population's adaptive potential. Conservation efforts for these endangered species and similar climate-threatened taxa will therefore benefit from strategies for monitoring and mitigating exposure to temperatures that induce sublethal effects.
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Affiliation(s)
- Eugenie C Yen
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - James D Gilbert
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Inês O Afonso
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Débora Newlands
- Project Biodiversity, Mercado Municipal Santa Maria Ilha do Sal Cabo Verde
| | - Artur Lopes
- Project Biodiversity, Mercado Municipal Santa Maria Ilha do Sal Cabo Verde
| | - Sandra M Correia
- Instituto do Mar (IMar), Cova d'Ínglesa Mindelo Ilha do São Vicente Cabo Verde
| | - Albert Taxonera
- Project Biodiversity, Mercado Municipal Santa Maria Ilha do Sal Cabo Verde
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
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Chou CH, Yen CH, Liu CJ, Tu HF, Lin SC, Chang KW. The upregulation of VGF enhances the progression of oral squamous carcinoma. Cancer Cell Int 2024; 24:115. [PMID: 38528565 DOI: 10.1186/s12935-024-03301-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is a prevalent neoplasm worldwide, necessitating a deeper understanding of its pathogenesis. VGF nerve growth factor inducible (VGF), a neuropeptide, plays critical roles in nerve and endocrine cell regulation. METHODS In this study, the TCGA datasets were initially screened, identifying the upregulation of VGF in various malignancies. We focused on OSCC cell lines, identifying the suppressor mRNA miR-432-5p as a negative regulator of VGF. Additionally, we examined the prognostic value of VGF expression in OSCC tumors and its impact on cellular functions. RESULTS VGF expression was found to be an independent prognostic predictor in OSCC tumors. Cells expressing VGF exhibited increased oncogenicity, influencing the proliferation and migration of oral mucosal fibroblast. Transcriptome analysis revealed associations between VGF and various pathological processes, including malignancies, exosome release, fibrosis, cell cycle disruption, and tumor immune suppression. Moreover, IL23R expression, a favorable OSCC prognostic factor, was inversely correlated with VGF expression. Exogenous IL23R expression was found to suppress VGF-associated mobility phenotypes. CONCLUSIONS This study highlights the multifaceted role of VGF in OSCC pathogenesis and introduces the miR-432-5p-VGF-IL23R regulatory axis as a critical mediator. The combined expression of VGF and IL23R emerges as a potent predictor of survival in oral carcinoma cases, suggesting potential implications for future therapeutic strategies.
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Affiliation(s)
- Chung-Hsien Chou
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Han Yen
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Taipei Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsi-Feng Tu
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Chun Lin
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
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Oatman SR, Reddy JS, Quicksall Z, Carrasquillo MM, Wang X, Liu CC, Yamazaki Y, Nguyen TT, Malphrus K, Heckman M, Biswas K, Nho K, Baker M, Martens YA, Zhao N, Kim JP, Risacher SL, Rademakers R, Saykin AJ, DeTure M, Murray ME, Kanekiyo T, Dickson DW, Bu G, Allen M, Ertekin-Taner N. Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins. Mol Neurodegener 2023; 18:2. [PMID: 36609403 PMCID: PMC9825010 DOI: 10.1186/s13024-022-00592-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is neuropathologically characterized by amyloid-beta (Aβ) plaques and neurofibrillary tangles. The main protein components of these hallmarks include Aβ40, Aβ42, tau, phosphor-tau, and APOE. We hypothesize that genetic variants influence the levels and solubility of these AD-related proteins in the brain; identifying these may provide key insights into disease pathogenesis. METHODS Genome-wide genotypes were collected from 441 AD cases, imputed to the haplotype reference consortium (HRC) panel, and filtered for quality and frequency. Temporal cortex levels of five AD-related proteins from three fractions, buffer-soluble (TBS), detergent-soluble (Triton-X = TX), and insoluble (Formic acid = FA), were available for these same individuals. Variants were tested for association with each quantitative biochemical measure using linear regression, and GSA-SNP2 was used to identify enriched Gene Ontology (GO) terms. Implicated variants and genes were further assessed for association with other relevant variables. RESULTS We identified genome-wide significant associations at seven novel loci and the APOE locus. Genes and variants at these loci also associate with multiple AD-related measures, regulate gene expression, have cell-type specific enrichment, and roles in brain health and other neuropsychiatric diseases. Pathway analysis identified significant enrichment of shared and distinct biological pathways. CONCLUSIONS Although all biochemical measures tested reflect proteins core to AD pathology, our results strongly suggest that each have unique genetic architecture and biological pathways that influence their specific biochemical states in the brain. Our novel approach of deep brain biochemical endophenotype GWAS has implications for pathophysiology of proteostasis in AD that can guide therapeutic discovery efforts focused on these proteins.
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Affiliation(s)
- Stephanie R. Oatman
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | | | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Thuy T. Nguyen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kimberly Malphrus
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Michael Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Kristi Biswas
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kwangsik Nho
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
| | - Matthew Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yuka A. Martens
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Jun Pyo Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Shannon L. Risacher
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Saykin
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
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Krick MV, Desmarais E, Samaras A, Guéret E, Dimitroglou A, Pavlidis M, Tsigenopoulos C, Guinand B. Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.). BMC Genomics 2021; 22:111. [PMID: 33563212 PMCID: PMC7871408 DOI: 10.1186/s12864-021-07420-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/31/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass (Dicentrarchus labrax), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples. This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07420-9.
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Affiliation(s)
- Madoka Vera Krick
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | - Erick Desmarais
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | | | - Elise Guéret
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.,Univ. Montpellier, CNRS, INSERM, Montpellier, France.,Montpellier GenomiX, France Génomique, Montpellier, France
| | | | - Michalis Pavlidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Costas Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 715 00, Heraklion, Greece
| | - Bruno Guinand
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.
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Di Cintio F, Dal Bo M, Baboci L, De Mattia E, Polano M, Toffoli G. The Molecular and Microenvironmental Landscape of Glioblastomas: Implications for the Novel Treatment Choices. Front Neurosci 2020; 14:603647. [PMID: 33324155 PMCID: PMC7724040 DOI: 10.3389/fnins.2020.603647] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma (GBM) is the most frequent and aggressive primary central nervous system tumor. Surgery followed by radiotherapy and chemotherapy with alkylating agents constitutes standard first-line treatment of GBM. Complete resection of the GBM tumors is generally not possible given its high invasive features. Although this combination therapy can prolong survival, the prognosis is still poor due to several factors including chemoresistance. In recent years, a comprehensive characterization of the GBM-associated molecular signature has been performed. This has allowed the possibility to introduce a more personalized therapeutic approach for GBM, in which novel targeted therapies, including those employing tyrosine kinase inhibitors (TKIs), could be employed. The GBM tumor microenvironment (TME) exerts a key role in GBM tumor progression, in particular by providing an immunosuppressive state with low numbers of tumor-infiltrating lymphocytes (TILs) and other immune effector cell types that contributes to tumor proliferation and growth. The use of immune checkpoint inhibitors (ICIs) has been successfully introduced in numerous advanced cancers as well as promising results have been shown for the use of these antibodies in untreated brain metastases from melanoma and from non-small cell lung carcinoma (NSCLC). Consequently, the use of PD-1/PD-L1 inhibitors has also been proposed in several clinical trials for the treatment of GBM. In the present review, we will outline the main GBM molecular and TME aspects providing also the grounds for novel targeted therapies and immunotherapies using ICIs for GBM.
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Affiliation(s)
- Federica Di Cintio
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Lorena Baboci
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
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H3.3 Barcoding of Nucleus Accumbens Transcriptional Activity Identifies Novel Molecular Cascades Associated with Cocaine Self-administration in Mice. J Neurosci 2019; 39:5247-5254. [PMID: 31043484 DOI: 10.1523/jneurosci.0015-19.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/17/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023] Open
Abstract
Although numerous epigenetic modifications have been associated with addiction, little work has explored the turnover of histone variants. Uniquely, the H3.3 variant incorporates stably and preferentially into chromatin independently of DNA replication at active sites of transcription and transcription factor binding. Thus, genomic regions associated with H3.3-containing nucleosomes are particularly likely to be involved in plasticity, such as following repeated cocaine exposure. A recently developed mouse line expressing a neuron-specific hemagglutinin (HA)-tagged H3.3 protein was used to track transcriptionally active sites cumulatively across 19 d of cocaine self-administration. RNA-seq and H3.3-HA ChIP-seq analyses were performed on NAcc tissue collected following cocaine or food self-administration in male mice. RNA sequencing revealed five genes upregulated in cocaine relative to food self-administering mice: Fosb, Npas4, Vgf, Nptx2, and Pmepa1, which reflect known and novel cocaine plasticity-associated genes. Subsequent ChIP-seq analysis confirmed increased H3.3 aggregation at four of these five loci, thus validating H3.3 insertion as a marker of enhanced cocaine-induced transcription. Further motif recognition analysis of the ChIP-seq data showed that cocaine-associated differential H3.3 accumulation correlated with the presence of several transcription factor binding motifs, including RBPJ1, EGR1, and SOX4, suggesting that these are potentially important regulators of molecular cascades associated with cocaine-induced neuronal plasticity. Additional ontological analysis revealed differential H3.3 accumulation mainly near genes involved in neuronal differentiation and dendrite formation. These results establish the H3.3-HA transgenic mouse line as a compelling molecular barcoding tool to identify the cumulative effects of long-term environmental perturbations, such as exposure to drugs of abuse.SIGNIFICANCE STATEMENT Histone H3.3 is a core histone variant that is stably incorporated at active sites of transcription. We used a tagged version of H3.3 expressed exclusively in neurons to delineate active transcription sites following extended cocaine self-administration in mice. This approach revealed the cumulative list of genes expressed in response to cocaine taking over the course of several weeks. We combined this technique with RNA sequencing of tissue collected from the same animals 24 h after the last cocaine exposure. Comparing these datasets provided a full picture of genes that respond to chronic cocaine exposure in NAcc neurons. These studies revealed novel transcription factors that are likely involved in cocaine-induced plasticity and addiction-like behaviors.
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Luoma LM, Berry FB. Molecular analysis of NPAS3 functional domains and variants. BMC Mol Biol 2018; 19:14. [PMID: 30509165 PMCID: PMC6276216 DOI: 10.1186/s12867-018-0117-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
Background NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in Npas3 knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH–PAS transcription factors. Here we set out to characterize NPAS3 as a transcription factor, and to confirm whether NPAS3 acts as predicted for a Class 1 bHLH–PAS family member. Results Through these studies we have experimentally demonstrated that NPAS3 behaves as a true transcription factor, capable of gene regulation through direct association with DNA. NPAS3 and ARNT are confirmed to directly interact in human cells through both bHLH and PAS dimerization domains. The C-terminus of NPAS3 was found to contain a functional transactivation domain. Further, the NPAS3::ARNT heterodimer was shown to directly regulate the expression of VGF and TXNIP through binding of their proximal promoters. Finally, we assessed the effects of three human variants of NPAS3 on gene regulatory function and do not observe significant deficits. Conclusions NPAS3 is a true transcription factor capable of regulating expression of target genes through their promoters by directly cooperating with ARNT. The tested human variants of NPAS3 require further characterization to identify their effects on NPAS3 expression and function in the individuals that carry them. These data enhance our understanding of the molecular function of NPAS3 and the mechanism by which it contributes to normal and abnormal neurodevelopment and neural function. Electronic supplementary material The online version of this article (10.1186/s12867-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leiah M Luoma
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Fred B Berry
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada. .,Department of Surgery, 3002D Li Ka Shing Centre, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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Li C, Li M, Yu H, Shen X, Wang J, Sun X, Wang Q, Wang C. Neuropeptide VGF C-Terminal Peptide TLQP-62 Alleviates Lipopolysaccharide-Induced Memory Deficits and Anxiety-like and Depression-like Behaviors in Mice: The Role of BDNF/TrkB Signaling. ACS Chem Neurosci 2017; 8:2005-2018. [PMID: 28594546 DOI: 10.1021/acschemneuro.7b00154] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peripheral inflammatory responses affect central nervous system (CNS) function, manifesting in symptoms of memory deficits, depression, and anxiety. Previous studies have revealed that neuropeptide VGF (nonacronymic) C-terminal peptide TLQP-62 rapidly reinforces brain-derived neurotrophic factor (BDNF)/tropomyosin receptor kinase B (TrkB) signaling, regulating memory consolidation and antidepressant-like action. However, whether it is beneficial for lipopolysaccharide (LPS)-induced neuropsychiatric dysfunction in mice is unknown. Herein, we explored the involvement of BDNF/TrkB signaling and biochemical alterations in inflammatory or oxidative stress markers in the alleviating effects of TLQP-62 on LPS-induced neuropsychiatric dysfunction. The mice were treated with TLQP-62 (2 μg/side) via intracerebroventricular (i.c.v.) injection 1 h before LPS (0.5 mg/kg, i.p.) administration. Our results showed that a single treatment with LPS (0.5 mg/kg, i.p) is sufficient to produce recognition memory deficits (in the novel object recognition test), depression-like behavior (in the forced swim test and sucrose preference test), and anxiety-like behavior (in the elevated zero maze). However, pretreatment with TLQP-62 prevented LPS-induced behavioral dysfunction, neuroinflammatory, and oxidative responses. In addition, our results further demonstrated that a reduction in BDNF expression mediated by BDNF-shRNA lentivirus significantly blocked the effects of TLQP-62, suggesting the critical role of BDNF/TrkB signaling in the neuroprotective effects of TLQP-62 in the mice. In conclusion, TLQP-62 could be a therapeutic approach for neuropsychiatric disorders, which are closely associated with neuroinflammation and oxidative stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Chuang Wang
- Li
Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research
Center, Ningbo University, Ningbo 315211, China
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9
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Michaelson JJ, Shin MK, Koh JY, Brueggeman L, Zhang A, Katzman A, McDaniel L, Fang M, Pufall M, Pieper AA. Neuronal PAS Domain Proteins 1 and 3 Are Master Regulators of Neuropsychiatric Risk Genes. Biol Psychiatry 2017; 82:213-223. [PMID: 28499489 PMCID: PMC6901278 DOI: 10.1016/j.biopsych.2017.03.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND NPAS3 has been established as a robust genetic risk factor in major mental illness. In mice, loss of neuronal PAS domain protein 3 (NPAS3) impairs postnatal hippocampal neurogenesis, while loss of the related protein NPAS1 promotes it. These and other findings suggest a critical role for NPAS proteins in neuropsychiatric functioning, prompting interest in the molecular pathways under their control. METHODS We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to identify genes directly regulated by NPAS1 and NPAS3 in the hippocampus of wild-type, Npas1-/-, and Npas3-/- mice. Computational integration with human genetic and expression data revealed the disease relevance of NPAS-regulated genes and pathways. Specific findings were confirmed at the protein level by Western blot. RESULTS This is the first in vivo, transcriptome-scale investigation of genes regulated by NPAS1 and NPAS3. These transcription factors control an ensemble of genes that are themselves also major regulators of neuropsychiatric function. Specifically, Fmr1 (fragile X syndrome) and Ube3a (Angelman syndrome) are transcriptionally regulated by NPAS3, as is the neurogenesis regulator Notch. Dysregulation of these pathways was confirmed at the protein level. Furthermore, NPAS1/3 targets show increased human genetic burden for schizophrenia and intellectual disability. CONCLUSIONS Together, these data provide a clear, unbiased view of the full spectrum of genes regulated by NPAS1 and NPAS3 and show that these transcription factors are master regulators of neuropsychiatric function. These findings expose the molecular pathophysiology of NPAS1/3 mutations and provide a striking example of the shared, combinatorial nature of molecular pathways that underlie diagnostically distinct neuropsychiatric conditions.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Biomedical Engineering, University of Iowa College of Engineering, University of Iowa, Iowa City, Iowa; Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa; Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa; Genetics Cluster Initiative, University of Iowa, Iowa City, Iowa; The DeLTA Center, University of Iowa, Iowa City, Iowa; University of Iowa Informatics Initiative, University of Iowa, Iowa City, Iowa.
| | - Min-Kyoo Shin
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jin-Young Koh
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Angela Zhang
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Aaron Katzman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Latisha McDaniel
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Mimi Fang
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Miles Pufall
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew A Pieper
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Neurology, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Free Radical and Radiation Biology Program, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Veterans Affairs, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa; Weill Cornell Autism Research Program, Weill Cornell Medicine, Cornell University, New York, New York
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Neuropeptide VGF Promotes Maturation of Hippocampal Dendrites That Is Reduced by Single Nucleotide Polymorphisms. Int J Mol Sci 2017; 18:ijms18030612. [PMID: 28287464 PMCID: PMC5372628 DOI: 10.3390/ijms18030612] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/03/2017] [Accepted: 03/08/2017] [Indexed: 12/13/2022] Open
Abstract
The neuropeptide VGF (non-acronymic) is induced by brain-derived neurotrophic factor and promotes hippocampal neurogenesis, as well as synaptic activity. However, morphological changes induced by VGF have not been elucidated. Developing hippocampal neurons were exposed to VGF through bath application or virus-mediated expression in vitro. VGF-derived peptide, TLQP-62, enhanced dendritic branching, and outgrowth. Furthermore, VGF increased dendritic spine density and the proportion of immature spines. Spine formation was associated with increased synaptic protein expression and co-localization of pre- and postsynaptic markers. Three non-synonymous single nucleotide polymorphisms (SNPs) were selected in human VGF gene. Transfection of N2a cells with plasmids containing these SNPs revealed no relative change in protein expression levels and normal protein size, except for a truncated protein from the premature stop codon, E525X. All three SNPs resulted in a lower proportion of N2a cells bearing neurites relative to wild-type VGF. Furthermore, all three mutations reduced the total length of dendrites in developing hippocampal neurons. Taken together, our results suggest VGF enhances dendritic maturation and that these effects can be altered by common mutations in the VGF gene. The findings may have implications for people suffering from psychiatric disease or other conditions who may have altered VGF levels.
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