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Carvalho Silva R, Martini P, Hohoff C, Mattevi S, Bortolomasi M, Abate M, Menesello V, Gennarelli M, Baune BT, Minelli A. Unraveling epigenomic signatures and effectiveness of electroconvulsive therapy in treatment-resistant depression patients: a prospective longitudinal study. Clin Epigenetics 2024; 16:93. [PMID: 39020437 PMCID: PMC11256624 DOI: 10.1186/s13148-024-01704-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Electroconvulsive therapy (ECT) benefits patients with treatment-resistant depression (TRD), but the underlying biological processes are unclear. We conducted an epigenome-wide association study in 32 TRD patients undergoing ECT to depict ECT-associated methylation changes. Illness severity and ECT outcomes were assessed with the Montgomery-Åsberg Depression Rating Scale at baseline (T0) and 1 month after its end (T1). Methylation was profiled at T0 and T1 with the Illumina Infinium Methylation EPIC BeadChip array. RESULTS Longitudinal T0-T1 analyses showed 3 differentially methylated probes (DMPs) with nominal p values ≤ 10-5, with 2 annotated in the genes CYB5B and PVRL4. Including covariates, we found 4 DMPs for symptoms variation, annotated in FAM20C, EPB41, OTUB1 and ADARB1, and 3 DMPs for response status, with 2 annotated in IQCE and FAM20C. Regional analysis revealed 54 differentially methylated regions (DMRs) with nominal p value area ≤ 0.05, with 9 presenting adjusted p-value area ≤ 0.10, annotated in MCF2L, SLC25A24, RUNX3, MIR637, FOXK2, FAM180B, POU6F1, ALS2CL and CCRL2. Considering covariates, we found 21 DMRs for symptoms variation and 26 DMRs for response (nominal p value area ≤ 0.05), with 4 presenting adjusted p-value area ≤ 0.10 for response, annotated in SNORD34, NLRP6, GALNT2 and SFT2D3. None remained significant after false discovery rate correction. Notably, ADARB1 variants are associated with suicide attempt in patients with psychiatric disorders, and SLC25A24 relates to conduct disorder. Several DMPs and DMRs are annotated in genes associated with inflammatory/immune processes. Longitudinal analyses on females (n = 22) revealed statistically significant DMRs (adjusted p value area ≤ 0.05) and trend-significant DMRs (adjusted p value area ≤ 0.07) for symptoms variation and response status, annotated in genes related to psychiatric disorders (ZFP57, POLD4, TRIM10, GAS7, ADORA2A, TOLLIP), trauma exposure (RIPOR2) and inflammatory/immune responses (LAT, DLX4, POLD4, FAM30A, H19). Pathway analysis on females revealed enrichment for transcriptional activity, growth factors, DNA maintenance, and immune pathways including IRF7 and IRF2. CONCLUSION Although no significant results were found for the whole cohort, the study provides insights into ECT-associated methylation changes, highlighting DMPs and DMRs related to ECT outcomes. Analyses on females revealed significant DMRs and pathways related to psychiatric disorders and inflammatory/immune processes.
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Affiliation(s)
- Rosana Carvalho Silva
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Christa Hohoff
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Stefania Mattevi
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | | | - Maria Abate
- Psychiatric Hospital "Villa Santa Chiara", Verona, Italy
| | - Valentina Menesello
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy.
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.
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Bao S, Romero JM, Belfort BD, Arenkiel BR. Signaling mechanisms underlying activity-dependent integration of adult-born neurons in the mouse olfactory bulb. Genesis 2024; 62:e23595. [PMID: 38553878 PMCID: PMC10987073 DOI: 10.1002/dvg.23595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Adult neurogenesis has fascinated the field of neuroscience for decades given the prospects of harnessing mechanisms that facilitate the rewiring and/or replacement of adult brain tissue. The subgranular zone of the hippocampus and the subventricular zone of the lateral ventricle are the two main areas in the brain that exhibit ongoing neurogenesis. Of these, adult-born neurons within the olfactory bulb have proven to be a powerful model for studying circuit plasticity, providing a broad and accessible avenue into neuron development, migration, and continued circuit integration within adult brain tissue. This review focuses on some of the recognized molecular and signaling mechanisms underlying activity-dependent adult-born neuron development. Notably, olfactory activity and behavioral states contribute to adult-born neuron plasticity through sensory and centrifugal inputs, in which calcium-dependent transcriptional programs, local translation, and neuropeptide signaling play important roles. This review also highlights areas of needed continued investigation to better understand the remarkable phenomenon of adult-born neuron integration.
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Affiliation(s)
- Suyang Bao
- Development, Disease Models, and Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin D.W. Belfort
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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Mihalj D, Borbelyova V, Pirnik Z, Bacova Z, Ostatnikova D, Bakos J. Shank3 Deficiency Results in a Reduction in GABAergic Postsynaptic Puncta in the Olfactory Brain Areas. Neurochem Res 2024; 49:1008-1016. [PMID: 38183586 PMCID: PMC10902016 DOI: 10.1007/s11064-023-04097-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024]
Abstract
Dysfunctional sensory systems, including altered olfactory function, have recently been reported in patients with autism spectrum disorder (ASD). Disturbances in olfactory processing can potentially result from gamma-aminobutyric acid (GABA)ergic synaptic abnormalities. The specific molecular mechanism by which GABAergic transmission affects the olfactory system in ASD remains unclear. Therefore, the present study aimed to evaluate selected components of the GABAergic system in olfactory brain regions and primary olfactory neurons isolated from Shank3-deficient (-/-) mice, which are known for their autism-like behavioral phenotype. Shank3 deficiency led to a significant reduction in GEPHYRIN/GABAAR colocalization in the piriform cortex and in primary neurons isolated from the olfactory bulb, while no change of cell morphology was observed. Gene expression analysis revealed a significant reduction in the mRNA levels of GABA transporter 1 in the olfactory bulb and Collybistin in the frontal cortex of the Shank3-/- mice compared to WT mice. A similar trend of reduction was observed in the expression of Somatostatin in the frontal cortex of Shank3-/- mice. The analysis of the expression of other GABAergic neurotransmission markers did not yield statistically significant results. Overall, it appears that Shank3 deficiency leads to changes in GABAergic synapses in the brain regions that are important for olfactory information processing, which may represent basis for understanding functional impairments in autism.
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Affiliation(s)
- Denisa Mihalj
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 05, Slovakia
| | - Veronika Borbelyova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Zdeno Pirnik
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 05, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Bacova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 05, Slovakia
| | - Daniela Ostatnikova
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Jan Bakos
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 05, Slovakia.
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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Wang J, Jia Q, Jiang S, Lu W, Ning H. POU6F1 promotes ferroptosis by increasing lncRNA-CASC2 transcription to regulate SOCS2/SLC7A11 signaling in gastric cancer. Cell Biol Toxicol 2024; 40:3. [PMID: 38267746 PMCID: PMC10808632 DOI: 10.1007/s10565-024-09843-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/22/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE This study investigated the effect and mechanism of POU6F1 and lncRNA-CASC2 on ferroptosis of gastric cancer (GC) cells. METHODS GC cells treated with erastin and RSL3 were detected for ferroptosis, reactive oxygen species (ROS) level, and cell viability. The expression levels of POU6F1, lncRNA-CASC2, SOCS2, and ferroptosis-related molecules (GPX4 and SLC7A11) were also measured. The regulations among POU6F1, lncRNA-CASC2, FMR1, SOCS2, and SLC7A11 were determined. Subcutaneous tumor models were established, in which the expressions of Ki-67, SOCS2, and GPX4 were detected by immunohistochemistry. RESULTS GC patients with decreased expressions of POU6F1 and lncRNA-CASC2 had lower survival rate. Overexpression of POU6F1 or lncRNA-CASC2 decreased cell proliferation and GSH levels in GC cells, in addition to increasing total iron, Fe2+, MDA, and ROS levels. POU6F1 directly binds to the lncRNA-CASC2 promoter to promote its transcription. LncRNA-CASC2 can target FMR1 and increase SOCS2 mRNA stability to promote SLC7A11 ubiquitination degradation and activate ferroptosis signaling. Knockdown of SOCS2 inhibited the ferroptosis sensitivity of GC cells and reversed the effects of POU6F1 and lncRNA-CASC2 overexpression on ferroptosis in GC cells. CONCLUSION Transcription factor POU6F1 binds directly to the lncRNA-CASC2 promoter to promote its expression, while upregulated lncRNA-CASC2 increases SOCS2 stability and expression by targeting FMR1, thereby inhibiting SLC7A11 signaling to promote ferroptosis in GC cells and inhibit GC progression.
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Affiliation(s)
- Jingyun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China
| | - Qiaoyu Jia
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China
| | - Shuqin Jiang
- Department of Child Development and Behavior, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, People's Republic of China
| | - Wenquan Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, No.2 JingBa Road, Jinshui District, Zhengzhou, Henan, 450014, People's Republic of China
| | - Hanbing Ning
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan, 450000, People's Republic of China.
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Zupančič M, Tretiakov E, Máté Z, Erdélyi F, Szabó G, Clotman F, Hökfelt T, Harkany T, Keimpema E. Brain-wide mapping of efferent projections of glutamatergic (Onecut3 + ) neurons in the lateral mouse hypothalamus. Acta Physiol (Oxf) 2023; 238:e13973. [PMID: 37029761 PMCID: PMC10909463 DOI: 10.1111/apha.13973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
AIM This study mapped the spatiotemporal positions and connectivity of Onecut3+ neuronal populations in the developing and adult mouse brain. METHODS We generated fluorescent reporter mice to chart Onecut3+ neurons for brain-wide analysis. Moreover, we crossed Onecut3-iCre and Mapt-mGFP (Tau-mGFP) mice to visualize axonal projections. A dual Cre/Flp-dependent AAV construct in Onecut3-iCre cross-bred with Slc17a6-FLPo mice was used in an intersectional strategy to map the connectivity of glutamatergic lateral hypothalamic neurons in the adult mouse. RESULTS We first found that Onecut3 marks a hitherto undescribed Slc17a6+ /Vglut2+ neuronal cohort in the lateral hypothalamus, with the majority expressing thyrotropin-releasing hormone. In the adult, Onecut3+ /Vglut2+ neurons of the lateral hypothalamus had both intra- and extrahypothalamic efferents, particularly to the septal complex and habenula, where they targeted other cohorts of Onecut3+ neurons and additionally to the neocortex and hippocampus. This arrangement suggests that intrinsic reinforcement loops could exist for Onecut3+ neurons to coordinate their activity along the brain's midline axis. CONCLUSION We present both a toolbox to manipulate novel subtypes of hypothalamic neurons and an anatomical arrangement by which extrahypothalamic targets can be simultaneously entrained.
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Affiliation(s)
- Maja Zupančič
- Department of Molecular Neurosciences, Center for Brain ResearchMedical University of ViennaViennaAustria
| | - Evgenii Tretiakov
- Department of Molecular Neurosciences, Center for Brain ResearchMedical University of ViennaViennaAustria
| | - Zoltán Máté
- Institute of Experimental Medicine, Hungarian Academy of SciencesBudapestHungary
| | - Ferenc Erdélyi
- Institute of Experimental Medicine, Hungarian Academy of SciencesBudapestHungary
| | - Gábor Szabó
- Institute of Experimental Medicine, Hungarian Academy of SciencesBudapestHungary
| | - Frédéric Clotman
- Animal Molecular and Cellular Biology Group, Louvain Institute of Biomolecular Science and TechnologyUniversité Catholique de LouvainLouvain‐la‐NeuveBelgium
| | - Tomas Hökfelt
- Department of Neuroscience, Biomedicum 7DKarolinska InstitutetSolnaSweden
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain ResearchMedical University of ViennaViennaAustria
- Department of Neuroscience, Biomedicum 7DKarolinska InstitutetSolnaSweden
| | - Erik Keimpema
- Department of Molecular Neurosciences, Center for Brain ResearchMedical University of ViennaViennaAustria
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Wu D, Dean J. RNA exosome ribonuclease DIS3 degrades Pou6f1 to promote mouse pre-implantation cell differentiation. Cell Rep 2023; 42:112047. [PMID: 36724075 PMCID: PMC10387129 DOI: 10.1016/j.celrep.2023.112047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/24/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Mammalian development is precisely controlled by cell differentiation. Identifying new regulators and investigating their interactions provide insight into genetic networks defining pre-implantation development. We established a knockout mouse model of Dis3, an exosome associated ribonuclease. Homozygous Dis3 null embryos arrest at the morula stage of development. Using single-embryo RNA sequencing (RNA-seq), we observed persistence of Pou6f1 mRNA in homozygous null Dis3 embryos and that the cognate protein represses transcription of Nanog and Cdx2. The resultant defects in cell differentiation disrupt the morula-to-blastocyst transition and are embryonic lethal. Microinjection of Dis3 mRNA into zygotes rescues the phenotype. Point mutations of Dis3 ribonuclease in individual blastomeres prevents their incorporation into embryos. To overcome the paucity of embryos, we derived homozygous Dis3 null mouse embryonic stem cells to identify additional gene targets of POU6F1. Our findings delineate a regulatory pathway of DIS3-POU6F1 in pre-implantation mammalian embryogenesis.
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Affiliation(s)
- Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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Pham TH, Xue Y, Brewer SM, Bernstein KE, Quake SR, Monack DM. Single-cell profiling identifies ACE + granuloma macrophages as a nonpermissive niche for intracellular bacteria during persistent Salmonella infection. SCIENCE ADVANCES 2023; 9:eadd4333. [PMID: 36608122 PMCID: PMC9821941 DOI: 10.1126/sciadv.add4333] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as Salmonella enterica. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures composed of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent S. enterica serovar Typhimurium (STm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using an STm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin-converting enzyme (ACE) defines a granuloma macrophage population that is nonpermissive for intracellular bacteria, and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE+ macrophages in infected tissues. Thus, ACE+ macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.
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Affiliation(s)
- Trung H. M. Pham
- Department of Microbiology and Immunology, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Susan M. Brewer
- Department of Microbiology and Immunology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kenneth E. Bernstein
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University, School of Medicine, Stanford, CA, USA
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Identification of Differentially Expressed Genes Particularly Associated with Immunity in Uremia Patients by Bioinformatic Analysis. Anal Cell Pathol (Amst) 2022; 2022:5437560. [PMID: 36618529 PMCID: PMC9815924 DOI: 10.1155/2022/5437560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/31/2022] Open
Abstract
Uremia is a common syndrome that happens to nearly all end-stage kidney diseases, which profound have changes in human gene expressions, but the related pathways are poorly understood. Gene Ontology categories and Kyoto Encyclopedia of Genes and Genomes pathways enriched in the differentially expressed genes (DEGs) were analyzed by using clusterProfiler, org.Hs.eg.db, and Pathview, and protein-protein interaction (PPI) network was built by Cytoscape. We identified 3432 DEGs (including 3368 down- and 64 up-regulated genes), of which there were 52 different molecular functions, and 178 genes were identified as immune genes controlled by the four transcription factors (POU domain class 6 transcription factor 1 (POU6F1), interferon regulator factor 7 [IRF7], forkhead box D3 (FOXD3), and interferon-stimulated response element [ISRE]). In the gender research, no significant difference was observed. The top 15 proteins of 178 immune-related genes were identified with the highest degree in PPI network. The DEG analysis of uremia patients was expected to provide fundamental information to relieve pain and add years to their life.
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Li WY, Li ZG, Fu XM, Wang XY, Lv ZX, Sun P, Zhu XF, Wang Y. Transgenic Schwann cells overexpressing POU6F1 promote sciatic nerve regeneration within acellular nerve allografts. J Neural Eng 2022; 19. [PMID: 36317259 DOI: 10.1088/1741-2552/ac9e1e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Objective.Acellular nerve allograft (ANA) is an effective surgical approach used to bridge the sciatic nerve gap. The molecular regulators of post-surgical recovery are not well-known. Here, we explored the effect of transgenic Schwann cells (SCs) overexpressing POU domain class 6, transcription factor 1 (POU6F1) on sciatic nerve regeneration within ANAs. We explored the functions of POU6F1 in nerve regeneration by using a cell model of H2O2-induced SCs injury and transplanting SCs overexpressing POU6F1 into ANA to repair sciatic nerve gaps.Approach.Using RNA-seq, Protein-Protein Interaction network analysis, gene ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we identified a highly and differentially expressed transcription factor, POU6F1, following ANA treatment of sciatic nerve gap. Expressing a high degree of connectivity, POU6F1 was predicted to play a role in peripheral nervous system myelination.Main results.To test the role of POU6F1 in nerve regeneration after ANA, we infected SCs with adeno-associated virus-POU6F1, demonstrating that POU6F1 overexpression promotes proliferation, anti-apoptosis, and migration of SCsin vitro. We also found that POU6F1 significantly upregulated JNK1/2 and c-Jun phosphorylation and that selective JNK1/2 inhibition attenuated the effects of POU6F1 on proliferation, survival, migration, and JNK1/2 and c-Jun phosphorylation. The direct interaction of POU6F1 and activated JNK1/2 was subsequently confirmed by co-immunoprecipitation. In rat sciatic nerve injury model with a 10 mm gap, we confirmed the pattern of POU6F1 upregulation and co-localization with transplanted SCs. ANAs loaded with POU6F1-overexpressing SCs demonstrated the enhanced survival of transplanted SCs, axonal regeneration, myelination, and functional motor recovery compared to the ANA group loaded by SCs-only in line within vitrofindings.Significance.This study identifies POU6F1 as a novel regulator of post-injury sciatic nerve repair, acting through JNK/c-Jun signaling in SCs to optimize therapeutic outcomes in the ANA surgical approach.
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Affiliation(s)
- Wen-Yuan Li
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Zhi-Gang Li
- The Second Department of General Surgery, Hongqi Hospital, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Xiu-Mei Fu
- Department of Anatomy, College of Basic Medical Sciences, Chengde Medical College, Chengde 067000, People's Republic of China.,Hebei Key Laboratory of Nerve Injury and Repair, Chengde 067000, People's Republic of China
| | - Xiao-Yu Wang
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Zhong-Xiao Lv
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Ping Sun
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Xiao-Feng Zhu
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
| | - Ying Wang
- Institute of Neural Tissue Engineering, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province, People's Republic of China
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Pouille CL, Ouaza S, Roels E, Behra J, Tourret M, Molinié R, Fontaine JX, Mathiron D, Gagneul D, Taminiau B, Daube G, Ravallec R, Rambaud C, Hilbert JL, Cudennec B, Lucau-Danila A. Chicory: Understanding the Effects and Effectors of This Functional Food. Nutrients 2022; 14:957. [PMID: 35267932 PMCID: PMC8912540 DOI: 10.3390/nu14050957] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Industrial chicory has been the subject of numerous studies, most of which provide clinical observations on its health effects. Whether it is the roasted root, the flour obtained from the roots or the different classes of molecules that enter into the composition of this plant, understanding the molecular mechanisms of action on the human organism remains incomplete. In this study, we were interested in three molecules or classes of molecules present in chicory root: fructose, chlorogenic acids, and sesquiterpene lactones. We conducted experiments on the murine model and performed a nutrigenomic analysis, a metabolic hormone assay and a gut microbiota analysis, associated with in vitro observations for different responses. We have highlighted a large number of effects of all these classes of molecules that suggest a pro-apoptotic activity, an anti-inflammatory, antimicrobial, antioxidant, hypolipidemic and hypoglycemic effect and also an important role in appetite regulation. A significant prebiotic activity was also identified. Fructose seems to be the most involved in these activities, contributing to approximately 83% of recorded responses, but the other classes of tested molecules have shown a specific role for these different effects, with an estimated contribution of 23-24%.
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Affiliation(s)
- Céline L. Pouille
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Souad Ouaza
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Elise Roels
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Josette Behra
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Melissa Tourret
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Roland Molinié
- UMR Transfontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—BIOlogie des Plantes et Innovation (BIOPI), 80025 Amiens, France; (R.M.); (J.-X.F.)
| | - Jean-Xavier Fontaine
- UMR Transfontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—BIOlogie des Plantes et Innovation (BIOPI), 80025 Amiens, France; (R.M.); (J.-X.F.)
| | - David Mathiron
- Plateforme Analytique UFR des Sciences, UPJV, Bâtiment Serres-Transfert Rue Dallery-Passage du Sourire d’Avril, 80039 Amiens, France;
| | - David Gagneul
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Bernard Taminiau
- Department of Food Sciences–Microbiology, FARAH, University of Liege, 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Georges Daube
- Department of Food Sciences–Microbiology, FARAH, University of Liege, 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Rozenn Ravallec
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Caroline Rambaud
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Jean-Louis Hilbert
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
| | - Benoit Cudennec
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
| | - Anca Lucau-Danila
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV, SFR Condorcet FR CNRS 3417—Institut Charles Viollette, 59655 Villeneuve d’Ascq, France; (C.L.P.); (S.O.); (E.R.); (J.B.); (M.T.); (D.G.); (R.R.); (C.R.); (J.-L.H.); (B.C.)
- Joint Laboratory CHIC41H University of Lille-Florimond-Desprez, Cité scientifique, 59655 Villeneuve d’Ascq, France
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11
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Navarro JF, Croteau DL, Jurek A, Andrusivova Z, Yang B, Wang Y, Ogedegbe B, Riaz T, Støen M, Desler C, Rasmussen LJ, Tønjum T, Galas MC, Lundeberg J, Bohr VA. Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease. iScience 2020; 23:101556. [PMID: 33083725 PMCID: PMC7522123 DOI: 10.1016/j.isci.2020.101556] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/24/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer disease (AD) is a devastating neurological disease associated with progressive loss of mental skills and cognitive and physical functions whose etiology is not completely understood. Here, our goal was to simultaneously uncover novel and known molecular targets in the structured layers of the hippocampus and olfactory bulbs that may contribute to early hippocampal synaptic deficits and olfactory dysfunction in AD mice. Spatially resolved transcriptomics was used to identify high-confidence genes that were differentially regulated in AD mice relative to controls. A diverse set of genes that modulate stress responses and transcription were predominant in both hippocampi and olfactory bulbs. Notably, we identify Bok, implicated in mitochondrial physiology and cell death, as a spatially downregulated gene in the hippocampus of mouse and human AD brains. In summary, we provide a rich resource of spatially differentially expressed genes, which may contribute to understanding AD pathology. Spatial transcriptomics identifies differentially expressed genes with spatial patterns Early application of spatial transcriptomics to olfactory bulbs from AD models Bok gene is spatially differentially expressed in AD mouse and patient brains Paip1 and Homer1 genes are regulated in a PolB-dependent manner
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Affiliation(s)
- José Fernández Navarro
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Aleksandra Jurek
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Beimeng Yang
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Yue Wang
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Benjamin Ogedegbe
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Tahira Riaz
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Mari Støen
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Claus Desler
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Marie-Christine Galas
- University of Lille, Inserm, CHU Lille, UMR-S 1172 - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, 59000 Lille, France
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA.,Unit for Genome Dynamics, Department of Microbiology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
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12
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Identification of Novel Targets of RBM5 in the Healthy and Injured Brain. Neuroscience 2020; 440:299-315. [PMID: 32335213 DOI: 10.1016/j.neuroscience.2020.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/20/2022]
Abstract
The tumor suppressor RNA-binding motif 5 (RBM5) regulates the expression levels and cassette exon-definition (i.e. splicing) of a select set of mRNAs in a tissue-specific manner. Most RBM5-regulated targets were identified in oncological investigations and frequently involve genes which mediate apoptotic cell death. Little is known about the role of RBM5 in the brain. Also, it is unclear if a brain injury may be required to detect RBM5 mediated effects on pro-apoptotic genes due to their low expression levels in the healthy adult CNS at baseline. Conditional/floxed (brain-specific) gene deleter mice were generated to elucidate CNS-specific RBM5 mRNA targets. Male/female mice were subjected to a severe controlled cortical impact (CCI) traumatic brain injury (TBI) in order to increase the background expression of pro-death mRNAs and facilitate testing of the hypothesis that RBM5 inhibition decreases post-injury upregulation of caspases/FAS in the CNS. As expected, a CCI increased caspases/FAS mRNA in the injured cortex. RBM5 KO did not affect their levels or splicing. Surprisingly, KO increased the mRNA levels of novel targets including casein kinase 2 alpha prime interacting protein (Csnka2ip/CKT2) - a gene not thought to be expressed in the brain, contrary to findings here. Twenty-two unique splicing events were also detected in KOs including increased block-inclusion of cassette exons 20-22 in regulating synaptic membrane exocytosis 2 (Rims2). In conclusion, here we used genome-wide transcriptomic analysis on healthy and injured RBM5 KO mouse brain tissue to elucidate the first known gene targets of this enigmatic RBP in this CNS.
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13
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Nygaard M, Larsen MJ, Thomassen M, McGue M, Christensen K, Tan Q, Christiansen L. Global expression profiling of cognitive level and decline in middle-aged monozygotic twins. Neurobiol Aging 2019; 84:141-147. [PMID: 31585296 DOI: 10.1016/j.neurobiolaging.2019.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/18/2019] [Accepted: 08/18/2019] [Indexed: 11/18/2022]
Abstract
Only few studies have investigated the genomewide transcriptome of normative cognitive aging. We therefore aimed at investigating blood gene expression patterns associated with cognitive aging using a population-based sample of 235 middle-aged monozygotic twin pairs with longitudinal data on cognitive function. This unique setup enabled examination of gene expression differences associated with individual and intrapair differences in cognitive level and change while controlling for underlying genetic variation and shared early environment. Overall, increased expression of several gene sets was found to strongly correlate with a lower cognitive level and cognitive decline. The most significantly correlated gene sets were related to protein metabolism, translation, RNA metabolism, infectious disease, and the immune system, which are all processes previously linked to transcription signatures of pathological and normal brain aging, and aging in blood. The results of our study thus suggest that gene expression patterns of cognitive level and decline in our sample mirror those seen in cognitively impaired individuals, which could point toward a more generic response to cognitive aging and aging in general.
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Affiliation(s)
- Marianne Nygaard
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark.
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Research, Human Genetics, University of Southern Denmark, Odense C, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Research, Human Genetics, University of Southern Denmark, Odense C, Denmark
| | - Matt McGue
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Kaare Christensen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Qihua Tan
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Lene Christiansen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen OE, Denmark
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14
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Polonikov A, Rymarova L, Klyosova E, Volkova A, Azarova I, Bushueva O, Bykanova M, Bocharova I, Zhabin S, Churnosov M, Laskov V, Solodilova M. Matrix metalloproteinases as target genes for gene regulatory networks driving molecular and cellular pathways related to a multistep pathogenesis of cerebrovascular disease. J Cell Biochem 2019; 120:16467-16482. [PMID: 31056794 DOI: 10.1002/jcb.28815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/30/2019] [Accepted: 04/08/2019] [Indexed: 02/04/2023]
Abstract
The present study investigated a joint contribution of matrix metalloproteinases (MMPs) genes to ischemic stroke (IS) development and analyzed interactions between MMP genes and genome-wide associated loci for IS. A total of 1288 unrelated Russians (600 IS patients and 688 healthy individuals) from Central Russia were recruited for the study. Genotyping of seven single nucleotide polymorphisms (SNPs) of MMP genes (rs1799750, rs243865, rs3025058, rs11225395, rs17576, rs486055, and rs2276109) and eight genome-wide associated loci for IS were done using Taq-Man-based assays and MALDI-TOF mass spectrometry iPLEX platform, respectively. Allele - 799T at rs11225395 of the MMP8 gene was significantly associated with a decreased risk of IS after adjustment for sex and age (OR = 0.82; 95%CI, 0.70-0.96; P = 0.016). The model-based multifactor dimensionality reduction method has revealed 21 two-order, 124 three-order, and 474 four-order gene-gene (G×G) interactions models meaningfully (Pperm < 0.05) associated with the IS risk. The bioinformatic analysis enabled establishing the studied MMP gene polymorphisms possess a clear regulatory potential and may be targeted by gene regulatory networks driving molecular and cellular pathways related to the pathogenesis of IS. In conclusion, the present study was the first to identify an association between polymorphism rs11225395 of the MMP8 gene and IS risk. The study findings also indicate that MMPs deserve special attention as a potential class of genes influencing the multistep mechanisms of cerebrovascular disease including atherosclerosis in cerebral arteries, acute cerebral artery occlusion as well as the ischemic injury of the brain and its recovery.
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Affiliation(s)
- Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation.,Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Larisa Rymarova
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Elena Klyosova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Anastasia Volkova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
| | - Iuliia Azarova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation.,Department of Biological Chemistry, Kursk State Medical University, Kursk, Russian Federation
| | - Olga Bushueva
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation.,Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Marina Bykanova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation.,Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Iuliia Bocharova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
| | - Sergey Zhabin
- Department of Surgical Diseases, Kursk State Medical University, Kursk, Russian Federation
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russian Federation
| | - Vitaliy Laskov
- Department of Neurology and Neurosurgery, Kursk State Medical University, Kursk, Russian Federation
| | - Maria Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
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15
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Bryois J, Garrett ME, Song L, Safi A, Giusti-Rodriguez P, Johnson GD, Shieh AW, Buil A, Fullard JF, Roussos P, Sklar P, Akbarian S, Haroutunian V, Stockmeier CA, Wray GA, White KP, Liu C, Reddy TE, Ashley-Koch A, Sullivan PF, Crawford GE. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nat Commun 2018; 9:3121. [PMID: 30087329 PMCID: PMC6081462 DOI: 10.1038/s41467-018-05379-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/28/2018] [Indexed: 01/19/2023] Open
Abstract
Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants.
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Affiliation(s)
- Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | | | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | | | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Annie W Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Alfonso Buil
- Research Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, 4000, Denmark
| | - John F Fullard
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Pamela Sklar
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- MIRECC, JJ Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Craig A Stockmeier
- Department of Psychiatry and Human Behavior, Center for Psychiatric Neuroscience, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Kevin P White
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Timothy E Reddy
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Durham, NC, 27701, USA
- Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-7264, USA.
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, 27599-7264, USA.
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, 27708, USA.
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16
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McClard CK, Arenkiel BR. Neuropeptide Signaling Networks and Brain Circuit Plasticity. J Exp Neurosci 2018; 12:1179069518779207. [PMID: 29899664 PMCID: PMC5985544 DOI: 10.1177/1179069518779207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 05/02/2018] [Indexed: 01/16/2023] Open
Abstract
The brain is a remarkable network of circuits dedicated to sensory integration, perception, and response. The computational power of the brain is estimated to dwarf that of most modern supercomputers, but perhaps its most fascinating capability is to structurally refine itself in response to experience. In the language of computers, the brain is loaded with programs that encode when and how to alter its own hardware. This programmed "plasticity" is a critical mechanism by which the brain shapes behavior to adapt to changing environments. The expansive array of molecular commands that help execute this programming is beginning to emerge. Notably, several neuropeptide transmitters, previously best characterized for their roles in hypothalamic endocrine regulation, have increasingly been recognized for mediating activity-dependent refinement of local brain circuits. Here, we discuss recent discoveries that reveal how local signaling by corticotropin-releasing hormone reshapes mouse olfactory bulb circuits in response to activity and further explore how other local neuropeptide networks may function toward similar ends.
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Affiliation(s)
- Cynthia K McClard
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin R Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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