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Gowda S, Rana K, Kumar A, Prajapati PK, Patel N, Pandya S, Srivastava R. Extracellular mitochondrial components as new biomarkers for lupus nephritis. Lupus 2024; 33:779-786. [PMID: 38621786 DOI: 10.1177/09612033241247622] [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] [Indexed: 04/17/2024]
Abstract
Major reason for mortality among systemic lupus erythematosus patients is renal failure due to the deposition of immune complexes in the glomeruli. Being a chronic disease with multiple relapses and remissions across the lifespan, it's important to know the degree of nephritis for diagnosis as well as the long-term clinical management of the patients. Currently, renal biopsy is being used as the gold standard to diagnose and define the stages of the disease. However, renal biopsy being invasive only provides a localized picture of nephritis, and has the risk of bleeding. Additionally, it is also cost-intensive. Hence, a reliable, non-invasive biomarker is required for lupus nephritis. This study has evaluated extracellular mitochondrial components, including cell-free mitochondria, and cell-free mitochondrial DNA as probable biomarkers of the degree of nephritis. Both showed a significant correlation with proteinuria and protein-creatinine ratio. Our study substantiates their usage as clinical biomarkers of nephritis upon their validation in a larger cohort of lupus nephritis patients and other forms of nephritis. Although the current data suggest using cell-free mitochondria as a biomarker of lupus nephritis is better than the cell-free mitochondrial DNA.
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Affiliation(s)
- Sharath Gowda
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Khushboo Rana
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Ankit Kumar
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | | | | | - Sapan Pandya
- V. S. Hospital Medical College, Ahmedabad, India
| | - Ratika Srivastava
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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2
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Steinacher C, Rieder D, Turner JE, Solanky N, Nishio SY, Usami SI, Hausott B, Schrott-Fischer A, Dudas J. Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue. Int J Mol Sci 2024; 25:2907. [PMID: 38474154 DOI: 10.3390/ijms25052907] [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: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at -80 °C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19). The RNA from fresh tissue in RNAlater resulted in higher amounts and a better quality of RNA than that from the paraffin-embedded tissue. The reference gene evaluation exhibited four stably expressed reference genes (B2M, HPRT1, GAPDH and GUSB). The selected reference genes were then used to examine the effect on the expression outcome of target genes (OTOF and TECTA), which are known to be regulated during inner ear development. The selected reference genes displayed no differences in the expression profile of OTOF and TECTA, which was confirmed by immunostaining. The results underline the importance of the choice of the RNA extraction method and reference genes used in gene expression studies.
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Affiliation(s)
- Claudia Steinacher
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Jasmin E Turner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 4EP, UK
| | - Nita Solanky
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Barbara Hausott
- Institute of Neuroanatomy, Medical University Innsbruck, 6020 Innsbruck, Austria
| | | | - Jozsef Dudas
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
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3
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Mulholland PJ, Padula AE, Wilhelm LJ, Park B, Grant KA, Ferguson BM, Cervera-Juanes R. Cross-species epigenetic regulation of nucleus accumbens KCNN3 transcripts by excessive ethanol drinking. Transl Psychiatry 2023; 13:364. [PMID: 38012158 PMCID: PMC10682415 DOI: 10.1038/s41398-023-02676-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
The underlying genetic and epigenetic mechanisms driving functional adaptations in neuronal excitability and excessive alcohol intake are poorly understood. Small-conductance Ca2+-activated K+ (KCa2 or SK) channels encoded by the KCNN family of genes have emerged from preclinical studies as a key contributor to alcohol-induced functional neuroadaptations in alcohol-drinking monkeys and alcohol-dependent mice. Here, this cross-species analysis focused on KCNN3 DNA methylation, gene expression, and single nucleotide polymorphisms, including alternative promoters in KCNN3, that could influence surface trafficking and function of KCa2 channels. Bisulfite sequencing analysis of the nucleus accumbens tissue from alcohol-drinking monkeys and alcohol-dependent mice revealed a differentially methylated region in exon 1A of KCNN3 that overlaps with a predicted promoter sequence. The hypermethylation of KCNN3 in the accumbens paralleled an increase in the expression of alternative transcripts that encode apamin-insensitive and dominant-negative KCa2 channel isoforms. A polymorphic repeat in macaque KCNN3 encoded by exon 1 did not correlate with alcohol drinking. At the protein level, KCa2.3 channel expression in the accumbens was significantly reduced in very heavy-drinking monkeys. Together, our cross-species findings on epigenetic dysregulation of KCNN3 represent a complex mechanism that utilizes alternative promoters to potentially impact the firing of accumbens neurons. Thus, these results provide support for hypermethylation of KCNN3 as a possible key molecular mechanism underlying harmful alcohol intake and alcohol use disorder.
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Affiliation(s)
- Patrick J Mulholland
- Department of Neuroscience, Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Audrey E Padula
- Department of Neuroscience, Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Larry J Wilhelm
- Department of Translational Neuroscience, Atrium Health Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Byung Park
- Department of Public Health and Preventive Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kathleen A Grant
- Department of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Betsy M Ferguson
- Department of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Rita Cervera-Juanes
- Department of Translational Neuroscience, Atrium Health Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
- Center for Precision Medicine, Atrium Health Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
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4
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Juanes RC, Mulholland P, Padula A, Wilhelm L, Park B, Grant K, Ferguson B. Cross-species epigenetic regulation of nucleus accumbens KCNN3 transcripts by excessive ethanol drinking. RESEARCH SQUARE 2023:rs.3.rs-3315122. [PMID: 37790552 PMCID: PMC10543433 DOI: 10.21203/rs.3.rs-3315122/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The underlying genetic and epigenetic mechanisms driving functional adaptations in neuronal excitability and excessive alcohol intake are poorly understood. Small-conductance Ca2+-activated K+ (KCa2 or SK) channels encoded by the KCNN family of genes have emerged from preclinical studies as a key contributor to alcohol-induced functional neuroadaptations in alcohol-drinking monkeys and alcohol dependent mice. Here, this cross-species analysis focused on KCNN3 DNA methylation, gene expression, and single nucleotide polymorphisms including alternative promoters in KCNN3 that could influence surface trafficking and function of KCa2 channels. Bisulfite sequencing analysis of the nucleus accumbens tissue from alcohol-drinking monkeys and alcohol dependent mice revealed a differentially methylated region in exon 1A of KCNN3 that overlaps with a predicted promoter sequence. The hypermethylation of KCNN3 in the accumbens paralleled an increase in expression of alternative transcripts that encode apamin-insensitive and dominant-negative KCa2 channel isoforms. A polymorphic repeat in macaque KCNN3 encoded by exon 1 did not correlate with alcohol drinking. At the protein level, KCa2.3 channel expression in the accumbens was significantly reduced in very heavy drinking monkeys. Together, our cross-species findings on epigenetic dysregulation of KCNN3 represent a complex mechanism that utilizes alternative promoters to impact firing of accumbens neurons. Thus, these results provide support for hypermethylation of KCNN3 as a possible key molecular mechanism underlying harmful alcohol intake and alcohol use disorder.
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Affiliation(s)
| | | | | | | | | | | | - Betsy Ferguson
- Oregon Health & Sciences University/Oregon National Primate Research Center
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5
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Niedowicz DM, Wang WX, Price DA, Xie K, Patel E, Nelson PT. Impact of thyroid hormone perturbations in adult mice: brain weight and blood vessel changes, gene expression variation, and neurobehavioral outcomes. Neurobiol Aging 2023; 128:74-84. [PMID: 37229849 DOI: 10.1016/j.neurobiolaging.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
Mouse models of hyper- and hypothyroidism were used to examine the effects of thyroid hormone (TH) dyshomeostasis on the aging mammalian brain. 13-14 month-old mice were treated for 4months with either levothyroxine (hyperthyroid) or a propylthiouracil and methimazole combination (PTU/Met; hypothyroid). Hyperthyroid mice performed better on Morris Water Maze than control mice, while hypothyroid mice performed worse. Brain weight was increased in thyroxine-treated, and decreased in PTU/Met-treated animals. The brain weight change was strongly correlated with circulating and tissue T4. Quantitative measurements of microvessels were compared using digital neuropathologic methods. There was an increase in microvessel area in hyperthyroid mice. Hypothyroid mice showed a trend for elevated glial fibrillary acidic protein-immunoreactive astrocytes, indicating an increase in neuroinflammation. Gene expression alterations were associated with TH perturbation and astrocyte-expressed transcripts were particularly affected. For example, expression of Gli2 and Gli3, mediators in the Sonic Hedgehog signaling pathway, were strongly impacted by both treatments. We conclude that TH perturbations produce robust neurobehavioral, pathological, and brain gene expression changes in aging mouse models.
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Affiliation(s)
- Dana M Niedowicz
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
| | - Wang-Xia Wang
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Pathology, Division of Neuropathology, University of Kentucky, Lexington, KY, USA
| | - Douglas A Price
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Kevin Xie
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Ela Patel
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Peter T Nelson
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Pathology, Division of Neuropathology, University of Kentucky, Lexington, KY, USA
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6
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Baumann V, Athanasiou AT, Faridani OR, Schwerdtfeger AR, Wallner B, Steinborn R. Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma. Front Genet 2023; 13:1058668. [PMID: 36685854 PMCID: PMC9846067 DOI: 10.3389/fgene.2022.1058668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/02/2022] [Indexed: 01/05/2023] Open
Abstract
We aimed at extending the repertoire of high-quality miRNA normalizers for reverse transcription-quantitative PCR (RT-qPCR) of human plasma with special emphasis on the extremely guanine-cytosine-rich portion of the miRNome. For high-throughput selection of stable candidates, microarray technology was preferred over small-RNA sequencing (sRNA-seq) since the latter underrepresented miRNAs with a guanine-cytosine (GC) content of at least 75% (p = 0.0002, n = 2). miRNA abundances measured on the microarray were ranked for consistency and uniformity using nine normalization approaches. The eleven most stable sequences included miRNAs of moderate, but also extreme GC content (45%-65%: miR-320d, miR-425-5p, miR-185-5p, miR-486-5p; 80%-95%: miR-1915-3p, miR-3656-5p, miR-3665-5p, miR-3960-5p, miR-4488-5p, miR-4497 and miR-4787-5p). In contrast, the seven extremely GC-rich miRNAs were not found in the two plasma miRNomes screened by sRNA-seq. Stem-loop RT-qPCR was employed for stability verification in 32 plasma samples of healthy male Caucasians (age range: 18-55 years). In general, inter-individual variance of miRNA abundance was low or very low as indicated by coefficient of variation (CV) values of 0.6%-8.2%. miR-3665 and miR-1915-3p outperformed in this analysis (CVs: 0.6 and 2.4%, respectively). The eight most stable sequences included four extremely GC-rich miRNAs (miR-1915-3p, miR-3665, miR-4787-5p and miR-4497). The best-performing duo normalization factor (NF) for the condition of human plasma, miR-320d and miR-4787-5p, also included a GC-extreme miRNA. In summary, the identification of extremely guanine-cytosine-rich plasma normalizers will help to increase accuracy of PCR-based miRNA quantification, thus raise the potential that miRNAs become markers for psychological stress reactions or early and precise diagnosis of clinical phenotypes. The novel miRNAs might also be useful for orthologous contexts considering their conservation in related animal genomes.
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Affiliation(s)
- Volker Baumann
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | | | - Omid R. Faridani
- Garvan Institute of Medical Research, Sydney, NSW, Australia,Lowy Cancer Research Centre, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Bernard Wallner
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria,Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria,*Correspondence: Ralf Steinborn,
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7
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Precise measurement of gene expression changes in mouse brain areas denervated by injury. Sci Rep 2022; 12:22530. [PMID: 36581670 PMCID: PMC9800364 DOI: 10.1038/s41598-022-26228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
Quantitative PCR (qPCR) is a widely used method to study gene expression changes following brain injury. The accuracy of this method depends on the tissue harvested, the time course analyzed and, in particular on the choice of appropriate internal controls, i.e., reference genes (RGs). In the present study we have developed and validated an algorithm for the accurate normalization of qPCR data using laser microdissected tissue from the mouse dentate gyrus after entorhinal denervation at 0, 1, 3, 7, 14 and 28 days postlesion. The expression stabilities of ten candidate RGs were evaluated in the denervated granule cell layer (gcl) and outer molecular layer (oml) of the dentate gyrus. Advanced software algorithms demonstrated differences in stability for single RGs in the two layers at several time points postlesion. In comparison, a normalization index of several stable RGs covered the entire post-lesional time course and showed high stability. Using these RGs, we validated our findings and quantified glial fibrillary acidic protein (Gfap) mRNA and allograft inflammatory factor 1 (Aif1/Iba1) mRNA in the denervated oml. We compared the use of single RGs for normalization with the normalization index and found that single RGs yield variable results. In contrast, the normalization index gave stable results. In sum, our study shows that qPCR can yield precise, reliable, and reproducible datasets even under such complex conditions as brain injury or denervation, provided appropriate RGs for the model are used. The algorithm reported here can easily be adapted and transferred to any other brain injury model.
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8
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Yuan ZW, Zhang XH, Pang YZ, Qi YX, Wang QK, Ren SW, Hu YQ, Zhao YW, Wang T, Huo LK. Screening of Stably Expressed Internal Reference Genes for Quantitative Real-Time PCR Analysis in Quail. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022050223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Kipryushina YO, Maiorova MA, Yakovlev KV. An approach to quantitate maternal transcripts localized in sea urchin egg cortex using RT-qPCR with accurate normalization. PLoS One 2022; 17:e0260831. [PMID: 35709154 PMCID: PMC9202947 DOI: 10.1371/journal.pone.0260831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/13/2022] [Indexed: 11/19/2022] Open
Abstract
The sea urchin egg cortex is a peripheral region of eggs comprising a cell membrane and adjacent cytoplasm, which contains actin and tubulin cytoskeleton, cortical granules and some proteins required for early development. Method for isolation of cortices from sea urchin eggs and early embryos was developed in 1970s. Since then, this method has been reliable tool to study protein localization and cytoskeletal organization in cortex of unfertilized eggs and embryos during first cleavages. This study was aimed to estimate the reliability of RT-qPCR to analyze levels of maternal transcripts that are localized in egg cortex. Firstly, we selected seven potential reference genes, 28S, Cycb, Ebr1, GAPDH, Hmg1, Smtnl1 and Ubb, the transcripts of which are maternally deposited in sea urchin eggs. The candidate reference genes were ranked by five different algorithms (BestKeeper, CV, ΔCt, geNorm and NormFinder) based on calculated level of stability in both eggs as well as isolated cortices. Our results showed that gene ranking differs in total RNA and mRNA samples, though Ubb is most suitable reference gene in both cases. To validate feasibility of comparative analysis of eggs and isolated egg cortices, we selected Daglb-2 as a gene of interest, which transcripts are potentially localized in cortex according to transcriptome analysis, and observed increased level of Daglb-2 in egg cortices by RT-qPCR. This suggests that proposed RNA isolation method with subsequent quantitative RT-qPCR analysis can be used to determine cortical association of transcripts in sea urchin eggs.
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Affiliation(s)
- Yulia O. Kipryushina
- Laboratory of Cytotechnology, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Mariia A. Maiorova
- Laboratory of Cytotechnology, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Konstantin V. Yakovlev
- Laboratory of Cytotechnology, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- * E-mail:
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Giasafaki C, Grant E, Hoerder‐Suabedissen A, Hayashi S, Lee S, Molnár Z. Cross-hierarchical plasticity of corticofugal projections to dLGN after neonatal monocular enucleation. J Comp Neurol 2022; 530:978-997. [PMID: 35078267 PMCID: PMC9305932 DOI: 10.1002/cne.25304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 11/10/2022]
Abstract
Perception is the result of interactions between the sensory periphery, thalamus, and cerebral cortex. Inputs from the retina project to the first-order dorsal lateral geniculate nucleus (dLGN), which projects to the primary visual cortex (V1). In return, the cortex innervates the thalamus. While layer 6 projections innervate all thalamic nuclei, cortical layer 5 neurons selectively project to the higher order lateral posterior nucleus (LP) and not to dLGN. It has been demonstrated that a subpopulation of layer 5 (Rbp4-Cre+) projections rewires to dLGN after monocular or binocular enucleation in young postnatal mice. However, the exact cortical regional origin of these projections was not fully determined, and it remained unclear whether these changes persisted into adulthood. In this study, we report gene expression changes observed in the dLGN after monocular enucleation at birth using microarray, qPCR at P6, and in situ hybridization at P8. We report that genes that are normally enriched in dLGN, but not LP during development are preferentially downregulated in dLGN following monocular enucleation. Comparisons with developmental gene expression patters in dLGN suggest more immature and delayed gene expression in enucleated dLGN. Combined tracing and immuno-histochemical analysis revealed that the induced layer 5 fibers that innervate enucleated dLGN originate from putative primary visual cortex and they retain increased VGluT1+ synapse formation into adulthood. Our results indicate a new form of plasticity when layer 5 driver input takes over the innervation of an originally first-order thalamic nucleus after early sensory deficit.
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Affiliation(s)
- Chrysoula Giasafaki
- Department of PhysiologyAnatomy and GeneticsOxfordUK,Instituto de Neurociencias de AlicanteCSIC‐UMH, Av. Ramon y Cajals/n 03550 San Juan de AlicanteAlicanteSpain
| | - Eleanor Grant
- Department of PhysiologyAnatomy and GeneticsOxfordUK
| | | | - Shuichi Hayashi
- Department of PhysiologyAnatomy and GeneticsOxfordUK,Department of AnatomyKawasaki Medical SchoolKurashikiOkayama701‐0192Japan
| | - Sheena Lee
- Department of PhysiologyAnatomy and GeneticsOxfordUK
| | - Zoltán Molnár
- Department of PhysiologyAnatomy and GeneticsOxfordUK
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Characterization of Cysteine Cathepsin Expression in the Central Nervous System of Aged Wild-Type and Cathepsin-Deficient Mice. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The association of cathepsin proteases in neurobiology is increasingly recognized. Our previous studies indicated that cathepsin-K-deficient (Ctsk−/−) mice have learning and memory impairments. Alterations in cathepsin expression are known to result in compensatory changes in levels of related cathepsins. To gain insight into the therapeutic usefulness of cathepsin inhibitors in aging individuals with osteoporosis or neurodegenerative diseases, we studied for variations in cathepsin expression and activity in aged (18–20 months) versus young (5–7 months) wild-type (WT) and cathepsin-deficient mice brains. There were age-dependent increases in cathepsin B, D, and L and cystatin C protein levels in various brain regions, mainly of WT and Ctsk−/− mice. This corresponded with changes in activity levels of cathepsins B and L, but not cathepsin D. In contrast, very little age-dependent variation was observed in cathepsin-B- and cathepsin-L-deficient mouse brain, especially at the protein level. The observed alterations in cathepsin protein amounts and activity are likely contributing to changes in important aging-related processes such as autophagy. In addition, the results provide insight into the potential impact of cathepsin inhibitor therapy in aged individuals, as well as in long-term use of cathepsin inhibitor therapy.
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12
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Sampathkumar NK, Sundaram VK, Danthi PS, Barakat R, Solomon S, Mondal M, Carre I, El Jalkh T, Padilla-Ferrer A, Grenier J, Massaad C, Mitchell JC. RNA-Seq is not required to determine stable reference genes for qPCR normalization. PLoS Comput Biol 2022; 18:e1009868. [PMID: 35226660 PMCID: PMC8912902 DOI: 10.1371/journal.pcbi.1009868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/10/2022] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
Assessment of differential gene expression by qPCR is heavily influenced by the choice of reference genes. Although numerous statistical approaches have been proposed to determine the best reference genes, they can give rise to conflicting results depending on experimental conditions. Hence, recent studies propose the use of RNA-Seq to identify stable genes followed by the application of different statistical approaches to determine the best set of reference genes for qPCR data normalization. In this study, however, we demonstrate that the statistical approach to determine the best reference genes from commonly used conventional candidates is more important than the preselection of ‘stable’ candidates from RNA-Seq data. Using a qPCR data normalization workflow that we have previously established; we show that qPCR data normalization using conventional reference genes render the same results as stable reference genes selected from RNA-Seq data. We validated these observations in two distinct cross-sectional experimental conditions involving human iPSC derived microglial cells and mouse sciatic nerves. These results taken together show that given a robust statistical approach for reference gene selection, stable genes selected from RNA-Seq data do not offer any significant advantage over commonly used reference genes for normalizing qPCR assays. RTqPCR is a powerful technique that is widely used to quantify gene expression in research and diagnostics of different diseases. The technique involves making multiple copies (amplification) of a specific target DNA. The amplified target DNA binds to a molecule that emits fluorescence upon binding. The extent of fluorescence correlates to the amount of DNA present. To precisely quantify this fluorescence (and thus the quantities of target DNA), internal control genes also called as reference genes need to be determined. Such genes, in principle, do not have varied expression across samples and would exhibit the same fluorescence in all samples. They can thus be used to normalize the expression of the Target DNA. Unfortunately, choosing the right reference gene is very tricky and poor choice of reference genes results in unreliable data both in research and in diagnostics. In this study, we validate a statistical approach to find stably expressed reference genes for any experimental setting using a given set of candidates. We compare our approach to RNA sequencing which quantifies the expression of thousands of genes at the same time. We highlight the advantages of our approach which is cost effective and saves a lot of time when compared to sequencing.
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Affiliation(s)
- Nirmal Kumar Sampathkumar
- UK-Dementia Research Institute, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- * E-mail: (NKS); (VKS)
| | - Venkat Krishnan Sundaram
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
- * E-mail: (NKS); (VKS)
| | - Prakroothi S. Danthi
- McGill Group for Suicide Studies, The Douglas Research Center, McGill University, Montréal, Canada
| | - Rasha Barakat
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
- INSERM U1016, Institut Cochin, Paris, France
| | - Shiden Solomon
- UK-Dementia Research Institute, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Mrityunjoy Mondal
- UK-Dementia Research Institute, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Ivo Carre
- UK-Dementia Research Institute, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Tatiana El Jalkh
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
| | - Aïda Padilla-Ferrer
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
| | - Julien Grenier
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
| | - Charbel Massaad
- INSERM U1124, Université de Paris, Faculty of Basic and Biomedical Sciences, Paris, France
| | - Jacqueline C. Mitchell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, King’s College London, London, United Kingdom
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13
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El Hajj A, Herzine A, Calcagno G, Désor F, Djelti F, Bombail V, Denis I, Oster T, Malaplate C, Vigier M, Kaminski S, Pauron L, Corbier C, Yen FT, Lanhers MC, Claudepierre T. Targeted Suppression of Lipoprotein Receptor LSR in Astrocytes Leads to Olfactory and Memory Deficits in Mice. Int J Mol Sci 2022; 23:ijms23042049. [PMID: 35216163 PMCID: PMC8878779 DOI: 10.3390/ijms23042049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 12/25/2022] Open
Abstract
Perturbations of cholesterol metabolism have been linked to neurodegenerative diseases. Glia–neuron crosstalk is essential to achieve a tight regulation of brain cholesterol trafficking. Adequate cholesterol supply from glia via apolipoprotein E-containing lipoproteins ensures neuronal development and function. The lipolysis-stimulated lipoprotein receptor (LSR), plays an important role in brain cholesterol homeostasis. Aged heterozygote Lsr+/− mice show altered brain cholesterol distribution and increased susceptibility to amyloid stress. Since LSR expression is higher in astroglia as compared to neurons, we sought to determine if astroglial LSR deficiency could lead to cognitive defects similar to those of Alzheimer’s disease (AD). Cre recombinase was activated in adult Glast-CreERT/lsrfl/fl mice by tamoxifen to induce astroglial Lsr deletion. Behavioral phenotyping of young and old astroglial Lsr KO animals revealed hyperactivity during the nocturnal period, deficits in olfactory function affecting social memory and causing possible apathy, as well as visual memory and short-term working memory problems, and deficits similar to those reported in neurodegenerative diseases, such as AD. Furthermore, GFAP staining revealed astroglial activation in the olfactory bulb. Therefore, astroglial LSR is important for working, spatial, and social memory related to sensory input, and represents a novel pathway for the study of brain aging and neurodegeneration.
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Affiliation(s)
- Aseel El Hajj
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
- Correspondence: (A.E.H.); (T.C.); Tel.: +33-(0)4-8110-6500 (A.E.H.); +33-(0)3-7274-4152 (T.C.)
| | - Ameziane Herzine
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Gaetano Calcagno
- UR 7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, University of Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.C.); (S.K.)
| | - Frédéric Désor
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Fathia Djelti
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Vincent Bombail
- UMR 914, Physiology of Nutrition and Feeding Behaviour, INRAE-Agroparistech-Université Paris-Saclay, 78352 Jouy-en-Josas, France; (V.B.); (I.D.)
| | - Isabelle Denis
- UMR 914, Physiology of Nutrition and Feeding Behaviour, INRAE-Agroparistech-Université Paris-Saclay, 78352 Jouy-en-Josas, France; (V.B.); (I.D.)
| | - Thierry Oster
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Catherine Malaplate
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Maxime Vigier
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Sandra Kaminski
- UR 7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, University of Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.C.); (S.K.)
| | - Lynn Pauron
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Catherine Corbier
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Frances T. Yen
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Marie-Claire Lanhers
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
| | - Thomas Claudepierre
- UR AFPA Laboratory, Qualivie Team, University of Lorraine, 54505 Vandoeuvre-lès-Nancy, France; (A.H.); (F.D.); (F.D.); (T.O.); (C.M.); (M.V.); (L.P.); (C.C.); (F.T.Y.); (M.-C.L.)
- Correspondence: (A.E.H.); (T.C.); Tel.: +33-(0)4-8110-6500 (A.E.H.); +33-(0)3-7274-4152 (T.C.)
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14
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Fischer F, Best R, LaRocca-Stravalle Z, Kauffman J, Gillen K. Validation of three reference genes for quantitative RT-PCR analyses in regenerating Lumbriculus variegatus. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Booze ML, Eyster KM. Extraction of RNA and Analysis of Estrogen-Responsive Genes by RT-qPCR. Methods Mol Biol 2022; 2418:113-127. [PMID: 35119663 DOI: 10.1007/978-1-0716-1920-9_8] [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] [Indexed: 06/14/2023]
Abstract
Reverse transcription-quantitative RT-PCR (RT-qPCR) is a powerful tool for assessing gene transcription levels. The technique is especially useful for measuring estrogen receptor transcript levels as well as gene expression changes in response to estrogen stimulation as it is quick, accurate, and robust and allows the measurement of gene expression in a variety of tissues and cells. This chapter describes the protocols used for RNA extraction and analysis as well as for RT-qPCR assay using hydrolysis (TaqMan-type) probes.
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Affiliation(s)
- Michelle L Booze
- Sanford Fertility and Reproductive Medicine, Sioux Falls, SD, USA.
| | - Kathleen M Eyster
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA.
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16
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Cuzon Carlson VC, Aylwin CF, Carlson TL, Ford M, Mesnaoui H, Lomniczi A, Ferguson B, Cervera‐Juanes RP. Neurobeachin, a promising target for use in the treatment of alcohol use disorder. Addict Biol 2022; 27:e13107. [PMID: 34699111 DOI: 10.1111/adb.13107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/23/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022]
Abstract
Hazardous, heavy drinking increases risk for developing alcohol use disorder (AUD), which affects ~7% of adult Americans. Thus, understanding the molecular mechanisms promoting risk for heavy drinking is essential to developing more effective AUD pharmacotherapies than those currently approved by the FDA. Using genome-wide bisulfate sequencing, we identified DNA methylation (DNAm) signals within the nucleus accumbens core (NAcC) that differentiate nonheavy and heavy ethanol-drinking rhesus macaques. One differentially DNAm region (D-DMR) located within the gene neurobeachin (NBEA), which promotes synaptic membrane protein trafficking, was hypermethylated in heavy drinking macaques. A parallel study identified a similar NBEA D-DMR in human NAcC that distinguished alcoholic and nonalcoholic individuals. To investigate the role of NBEA in heavy ethanol drinking, we engineered a viral vector carrying a short hairpin RNA (shRNA) to reduce the expression of NBEA. Using two murine models of ethanol consumption: 4 days of drinking-in-the-dark and 4 weeks of chronic intermittent access, the knockdown of NBEA expression did not alter average ethanol consumption in either model. However, it did lead to a significant increase in the ethanol preference ratio. Following withdrawal, whole-cell patch clamp electrophysiological experiments revealed that Nbea knockdown led to an increase in spontaneous excitatory postsynaptic current amplitude with no alteration in spontaneous inhibitory postsynaptic currents, suggesting a specific role of NBEA in trafficking of glutamatergic receptors. Together, our findings suggest that NBEA could be targeted to modulate the preference for alcohol use.
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Affiliation(s)
- Verginia C. Cuzon Carlson
- Division of Neuroscience, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Carlos F. Aylwin
- Division of Genetics, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Timothy L. Carlson
- Division of Neuroscience, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Matthew Ford
- Division of Neuroscience, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Houda Mesnaoui
- Division of Genetics, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
| | - Rita P. Cervera‐Juanes
- Division of Genetics, Oregon National Primate Research Center Oregon Health & Science University Beaverton Oregon USA
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17
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Berruien NNA, Murray JF, Smith CL. Pregnancy influences the selection of appropriate reference genes in mouse tissue: Determination of appropriate reference genes for quantitative reverse transcription PCR studies in tissues from the female mouse reproductive axis. Gene 2021; 801:145855. [PMID: 34293448 DOI: 10.1016/j.gene.2021.145855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
Selecting stably expressed reference genes which are not affected by physiological or pathophysiological conditions is crucial for reliable quantification in gene expression studies. This study examined the expression stability of a panel of twelve reference genes in tissues from the female mouse reproductive axis and the uterus. Gene expression studies were carried out using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). cDNA was synthesised from RNA extracted from hypothalami, pituitaries, ovaries and uteri of female mice at ages representing weaning, puberty and adulthood as well as pregnancy (13 ± 1 days post-coitus) (n = a minimum of 3 at each age and at pregnancy). The reference genes examined included 18 s, Actb, Atp5b, B2m, Canx, Cyc1, Eif4a2, Gapdh, Rpl13a, Sdha, Ubc and Ywhaz. The RT-qPCR raw data were imported into the qBASE+ software to analyse the expression stability using GeNorm. These data were also subsequently analysed using other software packages (Delta CT, Normfinder, BestKeeper). A comprehensive ranking was conducted considering all stability rankings generated from the different software analyses. B2m and Eif4a2 deviated from the acceptable range for amplification efficiency and therefore were excluded from the further analyses. The stability of the reference genes is influenced by the software used for the analysis with BestKeeper providing markedly different results than the other analyses. GeNorm analysis of tissues taken at different ages but not including pregnant animals, indicated that the expression of the reference genes is tissue specific with the most stable genes being: in the hypothalamus, Canx and Actb; in the pituitary, Sdha and Cyc1; in the ovary, 18s, Sdha and Ubc; and in the uterus, Ywhaz, Cyc1, Atp5b, 18s and Rpl13a. The optimal number of reference genes to be used was determined to be 2 in the first three tissues while in the uterus, the V-score generated by the GeNorm analysis was higher than 0.15 suggesting that 3 or more genes should be used for normalisation. Inclusion of tissues from pregnant mice changed the reference genes identified as being the most stable: Ubc and Sdha were the most stable genes in the hypothalamus, pituitary and the ovary. The addition of pregnant tissue had no effect on the stability of the genes in uterus (Ywhaz, Cyc1, Atp5b, 18s and Rpl13a). Identification of these stable reference genes will be of use to those interested in studying female fertility and researchers should be alert to the effects of pregnancy on reference gene stability. This study also signifies the importance of re-examining reference gene stability if the experimental conditions are changed, as shown with the introduction of pregnancy as a new factor in this research.
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Affiliation(s)
- Nasrin N A Berruien
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom
| | - Joanne F Murray
- University of Edinburgh, Centre for Discovery Brain Science, Hugh Robson Building, 15 George Square, Edinburgh EH8 9XD, United Kingdom
| | - Caroline L Smith
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
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18
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Smyth LML, Crosbie JC, Sloggett C, Rogers PAW, Donoghue JF. Spatially Fractionated X-Ray Microbeams Elicit a More Sustained Immune and Inflammatory Response in the Brainstem than Homogenous Irradiation. Radiat Res 2021; 196:355-365. [PMID: 34270776 DOI: 10.1667/rade-20-00082.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2021] [Indexed: 11/03/2022]
Abstract
Synchrotron microbeam radiation therapy (MRT) is a preclinical irradiation technique which could be used to treat intracranial malignancies. The goal of this work was to discern differences in gene expression and the predicted regulation of molecular pathways in the brainstem after MRT versus synchrotron broad-beam radiation therapy (SBBR). Healthy C57BL/6 mice received whole-head irradiation with median acute toxic doses of MRT (241 Gy peak dose) or SBBR (13 Gy). Brains were harvested 4 and 48 h postirradiation and RNA was extracted from the brainstem. RNA-sequencing was performed to identify differentially expressed genes (false discovery rate < 0.01) relative to nonirradiated controls and significantly regulated molecular pathways and biological functions were identified (Benjamini-Hochberg corrected P < 0.05). Differentially expressed genes and regulated pathways largely reflected a pro-inflammatory response 4 h after both MRT and SBBR which was sustained at 48 h postirradiation for MRT. Pathways relating to radiation-induced viral mimicry, including HMGB1, NF-κB and interferon signaling cascades, were predicted to be uniquely activated by MRT. Local microglia, as well as circulating leukocytes, including T cells, were predicted to be activated by MRT. Our findings affirm that the transcriptomic signature of MRT is distinct from broad-beam radiotherapy, with a sustained inflammatory and immune response up to 48 h postirradiation.
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Affiliation(s)
- Lloyd M L Smyth
- Department of Obstetrics & Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Australia
| | | | - Clare Sloggett
- Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - Peter A W Rogers
- Department of Obstetrics & Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Australia
| | - Jacqueline F Donoghue
- Department of Obstetrics & Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Australia
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19
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Modulating Thyroid Hormone Levels in Adult Mice: Impact on Behavior and Compensatory Brain Changes. J Thyroid Res 2021; 2021:9960188. [PMID: 34257897 PMCID: PMC8253651 DOI: 10.1155/2021/9960188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Thyroid hormone (TH) perturbation is a common medical problem. Because of substantial public health impact, prior researchers have studied hyper- and hypothyroidism in animal models. Although most prior research focused on in utero and/or developmental effects, changes in circulating TH levels are commonly seen in elderly individuals: approximately 20% of persons older than 80 years have clinically impactful hypothyroidism and up to 5% have clinical hyperthyroidism, with women being more often affected than men. TH disease model methodology in mice have varied but usually focus on a single sex, and the impact(s) of TH perturbation on the adult brain are not well understood. We administered thyroxine to middle-aged (13 to 14 months) male and female mice to model hyperthyroidism and TH-lowering drugs propylthiouracil (PTU) and methimazole, to induce hypothyroidism. These pharmacological agents are used commonly in adult humans. Circulating TH-level changes were observed when thyroxine was dosed at 20 µg/mL in drinking water for two weeks. By contrast, PTU and methimazole did not elicit a consistent reproducible effect until two months of treatment. No substantial changes in TH levels were detected in brain tissues of treated animals; however, pronounced changes in gene expression, specifically for TH-processing transcripts, were observed following the treatment with thyroxine. Our study indicated a robust compensatory mechanism by which the brain tissue/cells minimize the TH fluctuation in CNS by altering gene expression. Neurobehavioral changes were related to the TH perturbation and suggested potential associations between cognitive status and hyper- and hypothyroidism.
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20
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Jureckova K, Raschmanova H, Kolek J, Vasylkivska M, Branska B, Patakova P, Provaznik I, Sedlar K. Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data. Front Microbiol 2021; 12:640054. [PMID: 33815328 PMCID: PMC8012504 DOI: 10.3389/fmicb.2021.640054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Hana Raschmanova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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21
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Danoff JS, Wroblewski KL, Graves AJ, Quinn GC, Perkeybile AM, Kenkel WM, Lillard TS, Parikh HI, Golino HF, Gregory SG, Carter CS, Bales KL, Connelly JJ. Genetic, epigenetic, and environmental factors controlling oxytocin receptor gene expression. Clin Epigenetics 2021; 13:23. [PMID: 33516250 PMCID: PMC7847178 DOI: 10.1186/s13148-021-01017-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The neuropeptide oxytocin regulates mammalian social behavior. Disruptions in oxytocin signaling are a feature of many psychopathologies. One commonly studied biomarker for oxytocin involvement in psychiatric diseases is DNA methylation at the oxytocin receptor gene (OXTR). Such studies focus on DNA methylation in two regions of OXTR, exon 3 and a region termed MT2 which overlaps exon 1 and intron 1. However, the relative contribution of exon 3 and MT2 in regulating OXTR gene expression in the brain is currently unknown. RESULTS Here, we use the prairie vole as a translational animal model to investigate genetic, epigenetic, and environmental factors affecting Oxtr gene expression in a region of the brain that has been shown to drive Oxtr related behavior in the vole, the nucleus accumbens. We show that the genetic structure of Oxtr in prairie voles resembles human OXTR. We then studied the effects of early life experience on DNA methylation in two regions of a CpG island surrounding the Oxtr promoter: MT2 and exon 3. We show that early nurture in the form of parental care results in DNA hypomethylation of Oxtr in both MT2 and exon 3, but only DNA methylation in MT2 is associated with Oxtr gene expression. Network analyses indicate that CpG sites in the 3' portion of MT2 are most highly associated with Oxtr gene expression. We also identify two novel SNPs in exon 3 of Oxtr in prairie voles and a novel alternative transcript originating from the third intron of the gene. Expression of the novel alternative transcript is associated with genotype at SNP KLW2. CONCLUSIONS These results identify putative regulatory features of Oxtr in prairie voles which inform future studies examining OXTR in human social behaviors and disorders. These studies indicate that in prairie voles, DNA methylation in MT2, particularly in the 3' portion, is more predictive of Oxtr gene expression than DNA methylation in exon 3. Similarly, in human temporal cortex, we find that DNA methylation in the 3' portion of MT2 is associated with OXTR expression. Together, these results suggest that among the CpG sites studied, DNA methylation of MT2 may be the most reliable indicator of OXTR gene expression. We also identify novel features of prairie vole Oxtr, including SNPs and an alternative transcript, which further develop the prairie vole as a translational model for studies of OXTR.
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Affiliation(s)
- Joshua S Danoff
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Kelly L Wroblewski
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Andrew J Graves
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Graham C Quinn
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Allison M Perkeybile
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - William M Kenkel
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
- Department of Psychological and Brain Sciences, University of Delaware, 105 The Green, Newark, DE, 19716, USA
| | - Travis S Lillard
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Hardik I Parikh
- Division of Infectious Diseases and International Health, University of Virginia, 345 Crispell Drive, Charlottesville, VA, 22908, USA
- Research Computing, University of Virginia, 560 Ray C. Hunt Drive, Charlottesville, VA, 22903, USA
| | - Hudson F Golino
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, 300 N Duke St, Durham, NC, 27701, USA
| | - C Sue Carter
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Karen L Bales
- Department of Psychology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jessica J Connelly
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA.
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22
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Edler MK, Johnson CT, Ahmed HS, Richardson JR. Age, sex, and regional differences in scavenger receptor CD36 in the mouse brain: Potential relevance to cerebral amyloid angiopathy and Alzheimer's disease. J Comp Neurol 2020; 529:2209-2226. [PMID: 33319367 DOI: 10.1002/cne.25089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/29/2022]
Abstract
Scavenger receptor CD36 contributes significantly to lipid homeostasis, inflammation, and amyloid deposition, while CD36 deficiency is associated with restored cerebrovascular function in an Alzheimer's disease (AD) mouse model. Yet the distribution of CD36 has not been examined in the brain. Here, we characterized CD36 gene and protein expression in the brains of young, middle aged, aged, and elderly male and female C57BL/6J mice. Age-related increases in CD36 mRNA expression were observed in the male hippocampus and female midbrain. Additionally, male mice had greater CD36 mRNA expression than females in the striatum, hippocampus, and midbrain. CD36 protein was primarily expressed intravascularly, and this expression differed by region, age, and sex in the mouse brain. Although male mice brains demonstrated an increase in CD36 protein with age in several cortices, basal ganglia, hippocampus, and midbrain, a decrease with age was observed in female mice in the same regions. These data suggest that distinctive age, region, and sex expression of CD36 in the brain may contribute to Aβ deposition and neuroinflammation in AD.
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Affiliation(s)
- Melissa K Edler
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA.,Brain Health Research Institute, Kent State University, Kent, Ohio, USA.,Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Cooper T Johnson
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Hashim S Ahmed
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Jason R Richardson
- Robert Stempel School of Public Health and Social Work, Florida International University, Miami, Florida, USA
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Post-inflammatory behavioural despair in male mice is associated with reduced cortical glutamate-glutamine ratios, and circulating lipid and energy metabolites. Sci Rep 2020; 10:16857. [PMID: 33033375 PMCID: PMC7545201 DOI: 10.1038/s41598-020-74008-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
Post-inflammatory behaviours in rodents are widely used to model human depression and to test the efficacy of novel anti-depressants. Mice injected with lipopolysaccharide (LPS) display a depressive-like phenotype twenty-four hours after endotoxin administration. Despite the widespread use of this model, the mechanisms that underlie the persistent behavioural changes after the transient peripheral inflammatory response remain elusive. The study of the metabolome, the collection of all the small molecule metabolites in a sample, combined with multivariate statistical techniques provides a way of studying biochemical pathways influenced by an LPS challenge. Adult male CD-1 mice received an intraperitoneal injection of either LPS (0.83 mg/kg) or saline, and were assessed for depressive-like behaviour 24 h later. In a separate mouse cohort, pro-inflammatory cytokine gene expression and 1H nuclear magnetic resonance (NMR) metabolomics measurements were made in brain tissue and blood. Statistical analyses included Independent Sample t-tests for gene expression data, and supervised multi-variate analysis using orthogonal partial least squares discriminant analysis for metabolomics. Both plasma and brain metabolites in male mice were altered following a single peripheral LPS challenge that led to depressive-like behaviour in the forced swim test. The plasma metabolites altered by LPS are involved in energy metabolism, including lipoproteins, glucose, creatine, and isoleucine. In the brain, glutamate, serine, and N-acetylaspartate (NAA) were reduced after LPS, whereas glutamine was increased. Serine-modulated glutamatergic signalling and changes in bioenergetics may mediate the behavioural phenotype induced by LPS. In light of other data supporting a central imbalance of glutamate-glutamine cycling in depression, our results suggest that aberrant central glutaminergic signalling may underpin the depressive-like behaviours that result from both inflammation and non-immune pathophysiology. Normalising glutaminergic signalling, rather than seeking to increase serotonergic signalling, might prove to be a more coherent approach to the development of new treatments for mood disorder.
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Bustelo M, Bruno MA, Loidl CF, Rey-Funes M, Steinbusch HWM, Gavilanes AWD, van den Hove DLA. Statistical differences resulting from selection of stable reference genes after hypoxia and hypothermia in the neonatal rat brain. PLoS One 2020; 15:e0233387. [PMID: 32437382 PMCID: PMC7241816 DOI: 10.1371/journal.pone.0233387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Real-time reverse transcription PCR (qPCR) normalized to an internal reference gene (RG), is a frequently used method for quantifying gene expression changes in neuroscience. Although RG expression is assumed to be constant independent of physiological or experimental conditions, several studies have shown that commonly used RGs are not expressed stably. The use of unstable RGs has a profound effect on the conclusions drawn from studies on gene expression, and almost universally results in spurious estimation of target gene expression. Approaches aimed at selecting and validating RGs often make use of different statistical methods, which may lead to conflicting results. Based on published RG validation studies involving hypoxia the present study evaluates the expression of 5 candidate RGs (Actb, Pgk1, Sdha, Gapdh, Rnu6b) as a function of hypoxia exposure and hypothermic treatment in the neonatal rat cerebral cortex–in order to identify RGs that are stably expressed under these experimental conditions–using several statistical approaches that have been proposed to validate RGs. In doing so, we first analyzed RG ranking stability proposed by several widely used statistical methods and related tools, i.e. the Coefficient of Variation (CV) analysis, GeNorm, NormFinder, BestKeeper, and the ΔCt method. Using the Geometric mean rank, Pgk1 was identified as the most stable gene. Subsequently, we compared RG expression patterns between the various experimental groups. We found that these statistical methods, next to producing different rankings per se, all ranked RGs displaying significant differences in expression levels between groups as the most stable RG. As a consequence, when assessing the impact of RG selection on target gene expression quantification, substantial differences in target gene expression profiles were observed. Altogether, by assessing mRNA expression profiles within the neonatal rat brain cortex in hypoxia and hypothermia as a showcase, this study underlines the importance of further validating RGs for each individual experimental paradigm, considering the limitations of the statistical methods used for this aim.
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Affiliation(s)
- Martín Bustelo
- Department of Pediatrics, Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
- Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- * E-mail:
| | - Martín A. Bruno
- Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina
| | - César F. Loidl
- Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Manuel Rey-Funes
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Harry W. M. Steinbusch
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Antonio W. D. Gavilanes
- Department of Pediatrics, Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
- Instituto de Investigación e Innovación de Salud Integral, Facultad de Ciencias Médicas, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - D. L. A. van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
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25
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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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Blossom SJ, Melnyk SB, Simmen FA. Complex epigenetic patterns in cerebellum generated after developmental exposure to trichloroethylene and/or high fat diet in autoimmune-prone mice. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:583-594. [PMID: 31894794 PMCID: PMC7350281 DOI: 10.1039/c9em00514e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE) is an environmental contaminant associated with immune-mediated inflammatory disorders and neurotoxicity. Based on known negative effects of developmental overnutrition on neurodevelopment, we hypothesized that developmental exposure to high fat diet (HFD) consisting of 40% kcal fat would enhance neurotoxicity of low-level (6 μg per kg per day) TCE exposure in offspring over either stressor alone. Male offspring were evaluated at ∼6 weeks of age after exposure beginning 4 weeks preconception in the dams until weaning. TCE, whether used as a single exposure or together with HFD, appeared to be more robust than HFD alone in altering one-carbon metabolites involved in glutathione redox homeostasis and methylation capacity. In contrast, opposing effects of expression of key enzymes related to DNA methylation related to HFD and TCE exposure were observed. The mice generated unique patterns of anti-brain antibodies detected by western blotting attributable to both TCE and HFD. Taken together, developmental exposure to TCE and/or HFD appear to act in complex ways to alter brain biomarkers in offspring.
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Affiliation(s)
- Sarah J Blossom
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, AR 72202, USA.
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Selection of Reliable Reference Genes for Analysis of Gene Expression in Spinal Cord during Rat Postnatal Development and after Injury. Brain Sci 2019; 10:brainsci10010006. [PMID: 31861889 PMCID: PMC7017034 DOI: 10.3390/brainsci10010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 11/17/2022] Open
Abstract
In order to obtain unbiased results of target gene expression, selection of the most appropriate reference gene (RG) remains a key precondition. However, an experimental study focused on the validation of stably expressed RGs in the rat spinal cord (SC) during development or after spinal cord injury (SCI) is missing. In our study, we tested the stability of the expression of nine selected RGs in rat SC tissue during normal development (postnatal days 1-43, adulthood) and after minimal (mSCI) and contusion (cSCI) spinal cord injury. The following RGs were tested: common housekeeping genes of basal cell metabolism (Gapdh, Hprt1, Mapk6) and protein translation (Rpl29, Eef1a1, Eif2b2), as well as newly designed RGs (Gpatch1, Gorasp1, Cds2) selected according to the RefGenes tool of GeneVestigator. The stability of RGs was assessed by geNorm, NormFinder, and BestKeeper. All three applets favored Gapdh and Eef1a1 as the most stable genes in SC during development. In both models of SCI, Eif2b2 displayed the highest stability of expression, followed by Gapdh and Gorasp1/Hprt1 in cSCI, and Gapdh and Eef1a1 in the mSCI experiments. To verify our results, selected RGs were employed for normalization of the expression of genes with a clear biological context in the SC-Gfap and Slc1a3/Glast during postnatal development and Aif1/Iba1 and Cd68/Ed1 after SCI.
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IL-6 deficiency attenuates p53 protein accumulation in aged male mouse hippocampus. Biogerontology 2019; 21:29-43. [PMID: 31598806 PMCID: PMC6942598 DOI: 10.1007/s10522-019-09841-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
Our earlier studies demonstrated slower age-related memory decline in IL-6-deficient than in control mice. Therefore, in the present study we evaluated the effect of IL-6 deficiency and aging on expression of p53, connected with accumulation of age-related cellular damages, in hippocampus of 4- and 24-month-old IL-6-deficient C57BL/6J (IL-6KO) and wild type control (WT) mice. The accumulation of p53 protein in hippocampus of aged IL-6KO mice was significantly lower than in aged WT ones, while p53 mRNA level was significantly higher in IL-6-deficient mice, what indicates that the effect was independent on p53 transcription. Presence of few apoptotic cells in hippocampal dentate gyrus and lack of changes in levels of pro-apoptotic Bax, antiapoptotic Bcl-2, as well as in p21 protein in aged animals of both genotypes, points to low transcriptional activity of p53, especially in aged WT mice. Because the amount of p53 protein did not correlate with the level of Mdm2 protein, its main negative regulator, other than Mdm2-dependent mechanism was involved in p53 build-up. Significantly higher mRNA levels of autophagy-associated genes: Pten, Tsc2, and Dram1 in IL-6KO mice, in conjunction with significantly lower amount of Bcl-2 protein in 4-month-old IL-6KO mice, suggests that lack of IL-6/STAT3/Bcl-2 signaling could account for better autophagy performance in these mice, preventing excessive accumulation of proteins. Taken together, attenuated p53 protein build-up, absence of enhanced apoptosis, and transcriptional up-regulation of autophagy-associated genes imply that IL-6 deficiency may protect hippocampus from age-related accumulation of cellular damages.
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Yamakage Y, Kato M, Hongo A, Ogino H, Ishii K, Ishizuka T, Kamei T, Tsuiji H, Miyamoto T, Oishi H, Kohno T, Hattori M. A disintegrin and metalloproteinase with thrombospondin motifs 2 cleaves and inactivates Reelin in the postnatal cerebral cortex and hippocampus, but not in the cerebellum. Mol Cell Neurosci 2019; 100:103401. [PMID: 31491533 DOI: 10.1016/j.mcn.2019.103401] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/30/2019] [Accepted: 09/02/2019] [Indexed: 02/02/2023] Open
Abstract
Reelin plays important roles in regulating neuronal development, modulating synaptic function, and counteracting amyloid β toxicity. A specific proteolytic cleavage (N-t cleavage) of Reelin abolishes its biological activity. We recently identified ADAMTS-3 (a disintegrin and metalloproteinase with thrombospondin motifs 3) as the major N-t cleavage enzyme in the embryonic and early postnatal brain. The contribution of other proteases, particularly in the postnatal brain, has not been demonstrated in vivo. ADAMTS-2, -3 and -14 share similar domain structures and substrate specificity, raising the possibility that ADAMTS-2 and -14 may cleave Reelin. We found that recombinant ADAMTS-2 protein expressed in cultured cell lines cleaves Reelin at the N-t site as efficiently as ADAMTS-3 while recombinant ADAMTS-14 hardly cleaves Reelin. The disintegrin domain is necessary for the Reelin-cleaving activity of ADAMTS-2 and -3. ADAMTS-2 is expressed in the adult brain at approximately the same level as ADAMTS-3. We generated ADAMTS-2 knockout (KO) mice and found that ADAMTS-2 significantly contributes to the N-t cleavage and inactivation of Reelin in the postnatal cerebral cortex and hippocampus, but much less in the cerebellum. Therefore, it was suggested that ADAMTS-2 can be a therapeutic target for adult brain disorders such as schizophrenia and Alzheimer's disease.
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Affiliation(s)
- Yuko Yamakage
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Michinao Kato
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Aya Hongo
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Himari Ogino
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Keisuke Ishii
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Takumi Ishizuka
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Takana Kamei
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Hitomi Tsuiji
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Tomomi Miyamoto
- Department of Comparative and Experimental Medicine, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi Mizuho-cho, Mizuho-ku, Nagoya, Aichi, Japan
| | - Hisashi Oishi
- Department of Comparative and Experimental Medicine, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi Mizuho-cho, Mizuho-ku, Nagoya, Aichi, Japan
| | - Takao Kohno
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Mitsuharu Hattori
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan.
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Bag AK, Mandloi S, Jarmalavicius S, Mondal S, Kumar K, Mandal C, Walden P, Chakrabarti S, Mandal C. Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PLoS Comput Biol 2019; 15:e1007090. [PMID: 31386654 PMCID: PMC6684045 DOI: 10.1371/journal.pcbi.1007090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
As malignant transformation requires synchronization of growth-driving signaling (S) and metabolic (M) pathways, defining cancer-specific S-M interconnected networks (SMINs) could lead to better understanding of oncogenic processes. In a systems-biology approach, we developed a mathematical model for SMINs in mutated EGF receptor (EGFRvIII) compared to wild-type EGF receptor (EGFRwt) expressing glioblastoma multiforme (GBM). Starting with experimentally validated human protein-protein interactome data for S-M pathways, and incorporating proteomic data for EGFRvIII and EGFRwt GBM cells and patient transcriptomic data, we designed a dynamic model for EGFR-driven GBM-specific information flow. Key nodes and paths identified by in silico perturbation were validated experimentally when inhibition of signaling pathway proteins altered expression of metabolic proteins as predicted by the model. This demonstrated capacity of the model to identify unknown connections between signaling and metabolic pathways, explain the robustness of oncogenic SMINs, predict drug escape, and assist identification of drug targets and the development of combination therapies. Complex and highly dynamic interconnected networks allow cancer to take different routes and circumvent chemotherapy. Therefore, understanding these context-specific networks and their dynamics of molecular interactions driven by different oncogenic signaling and metabolic pathways is very much needed to predict drug targets and the effect of therapeutics. We incorporated high-throughput transcriptome and proteome data into mathematical models to deduce properties of cancer cells through systems biology approach. Here we report the development, testing and validation of an integrated systems biology model of information flow between signaling and metabolic pathways to understand the regulation of the interconnection between them in cancer. Our model efficiently identified unique connections and key nodes important in signaling-metabolic information flow. We predicted some potential novel targets before performing actual drug tests. We have successfully applied this model to identify the interconnections altered in the constitutive signaling of the mutated EGFR by comparing EGF-dependent and wild-type EGFR signaling in glioblastoma multiforme.
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Affiliation(s)
- Arup K. Bag
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Sapan Mandloi
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Saulius Jarmalavicius
- Department of Dermatology, Venerology and Allergology, Charité– Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susmita Mondal
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Krishna Kumar
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Chhabinath Mandal
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Peter Walden
- Department of Dermatology, Venerology and Allergology, Charité– Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- * E-mail: (PW); , (SC); , (CM)
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
- * E-mail: (PW); , (SC); , (CM)
| | - Chitra Mandal
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
- * E-mail: (PW); , (SC); , (CM)
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Moysés-Oliveira M, Cabral V, Gigek CO, Corrêa DCDC, Di-Battista A, Stumpp T, Melaragno MI. Search for appropriate reference genes for quantitative reverse transcription PCR studies in somite, prosencephalon and heart of early mouse embryo. Gene 2019; 710:148-155. [DOI: 10.1016/j.gene.2019.05.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 11/30/2022]
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Sundaram VK, Sampathkumar NK, Massaad C, Grenier J. Optimal use of statistical methods to validate reference gene stability in longitudinal studies. PLoS One 2019; 14:e0219440. [PMID: 31335863 PMCID: PMC6650036 DOI: 10.1371/journal.pone.0219440] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/24/2019] [Indexed: 01/25/2023] Open
Abstract
Multiple statistical approaches have been proposed to validate reference genes in qPCR assays. However, conflicting results from these statistical methods pose a major hurdle in the choice of the best reference genes. Recent studies have proposed the use of at least three different methods but there is no consensus on how to interpret conflicting results. Researchers resort to averaging the stability ranks assessed by different approaches or attributing a weighted rank to candidate genes. However, we report here that the suitability of these validation methods can be influenced by the experimental setting. Therefore, averaging the ranks can lead to suboptimal assessment of stable reference genes if the method used is not suitable for analysis. As the respective approaches of these statistical methods are different, a clear understanding of the fundamental assumptions and the parameters that influence the calculation of reference gene stability is necessary. In this study, the stability of 10 candidate reference genes (Actb, Gapdh, Tbp, Sdha, Pgk1, Ppia, Rpl13a, Hsp60, Mrpl10, Rps26) was assessed using four common statistical approaches (GeNorm, NormFinder, Coefficient of Variation or CV analysis and Pairwise ΔCt method) in a longitudinal experimental setting. We used the development of the cerebellum and the spinal cord of mice as a model to assess the suitability of these statistical methods for reference gene validation. GeNorm and the Pairwise ΔCt were found to be ill suited due to a fundamental assumption in their stability calculations. Highly correlated genes were given better stability ranks despite significant overall variation. NormFinder fares better but the presence of highly variable genes influences the ranking of all genes because of the algorithm’s construct. CV analysis estimates overall variation, but it fails to consider variation across groups. We thus highlight the assumptions and potential pitfalls of each method using our longitudinal data. Based on our results, we have devised a workflow combining NormFinder, CV analysis along with visual representation of mRNA fold changes and one-way ANOVA for validating reference genes in longitudinal studies. This workflow proves to be more robust than any of these methods used individually.
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Affiliation(s)
- Venkat Krishnan Sundaram
- Faculty of Basic and Biomedical Sciences, Paris Descartes University, INSERM UMRS 1124, Paris, France
- * E-mail:
| | - Nirmal Kumar Sampathkumar
- Faculty of Basic and Biomedical Sciences, Paris Descartes University, INSERM UMRS 1124, Paris, France
| | - Charbel Massaad
- Faculty of Basic and Biomedical Sciences, Paris Descartes University, INSERM UMRS 1124, Paris, France
| | - Julien Grenier
- Faculty of Basic and Biomedical Sciences, Paris Descartes University, INSERM UMRS 1124, Paris, France
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El Hajj A, Yen FT, Oster T, Malaplate C, Pauron L, Corbier C, Lanhers MC, Claudepierre T. Age-related changes in regiospecific expression of Lipolysis Stimulated Receptor (LSR) in mice brain. PLoS One 2019; 14:e0218812. [PMID: 31233547 PMCID: PMC6590887 DOI: 10.1371/journal.pone.0218812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
The regulation of cholesterol, an essential brain lipid, ensures proper neuronal development and function, as demonstrated by links between perturbations of cholesterol metabolism and neurodegenerative diseases, including Alzheimer’s disease. The central nervous system (CNS) acquires cholesterol via de novo synthesis, where glial cells provide cholesterol to neurons. Both lipoproteins and lipoprotein receptors are key elements in this intercellular transport, where the latter recognize, bind and endocytose cholesterol containing glia-produced lipoproteins. CNS lipoprotein receptors are like those in the periphery, among which include the ApoB, E binding lipolysis stimulated lipoprotein receptor (LSR). LSR is a multimeric protein complex that has multiple isoforms including α and α’, which are seen as a doublet at 68 kDa, and β at 56 kDa. While complete inactivation of murine lsr gene is embryonic lethal, studies on lsr +/- mice revealed altered brain cholesterol distribution and cognitive functions. In the present study, LSR profiling in different CNS regions revealed regiospecific expression of LSR at both RNA and protein levels. At the RNA level, the hippocampus, hypothalamus, cerebellum, and olfactory bulb, all showed high levels of total lsr compared to whole brain tissues, whereas at the protein level, only the hypothalamus, olfactory bulb, and retina showed the highest levels of total LSR. Interestingly, major regional changes in LSR expression were observed in aged mice which suggests changes in cholesterol homeostasis in specific structures in the aging brain. Immunocytostaining of primary cultures of mature murine neurons and glial cells isolated from different CNS regions showed that LSR is expressed in both neurons and glial cells. However, lsr RNA expression in the cerebellum was predominantly higher in glial cells, which was confirmed by the immunocytostaining profile of cerebellar neurons and glia. Based on this observation, we would propose that LSR in glial cells may play a key role in glia-neuron cross talk, particularly in the feedback control of cholesterol synthesis to avoid cholesterol overload in neurons and to maintain proper functioning of the brain throughout life.
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Affiliation(s)
- Aseel El Hajj
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Frances T. Yen
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
- * E-mail: (TC); (FTY)
| | - Thierry Oster
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Catherine Malaplate
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Lynn Pauron
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Catherine Corbier
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Marie-Claire Lanhers
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
| | - Thomas Claudepierre
- Qualivie, UR AFPA laboratory, ENSAIA, University of Lorraine, Vandoeuvre-les-Nancy, Lorraine, France
- * E-mail: (TC); (FTY)
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Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer’s disease. J Neurosci Methods 2019; 320:128-137. [DOI: 10.1016/j.jneumeth.2019.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 01/04/2023]
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Omura S, Sato F, Martinez NE, Park AM, Fujita M, Kennett NJ, Cvek U, Minagar A, Alexander JS, Tsunoda I. Bioinformatics Analyses Determined the Distinct CNS and Peripheral Surrogate Biomarker Candidates Between Two Mouse Models for Progressive Multiple Sclerosis. Front Immunol 2019; 10:516. [PMID: 30941144 PMCID: PMC6434997 DOI: 10.3389/fimmu.2019.00516] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/26/2019] [Indexed: 02/05/2023] Open
Abstract
Previously, we have established two distinct progressive multiple sclerosis (MS) models by induction of experimental autoimmune encephalomyelitis (EAE) with myelin oligodendrocyte glycoprotein (MOG) in two mouse strains. A.SW mice develop ataxia with antibody deposition, but no T cell infiltration, in the central nervous system (CNS), while SJL/J mice develop paralysis with CNS T cell infiltration. In this study, we determined biomarkers contributing to the homogeneity and heterogeneity of two models. Using the CNS and spleen microarray transcriptome and cytokine data, we conducted computational analyses. We identified up-regulation of immune-related genes, including immunoglobulins, in the CNS of both models. Pro-inflammatory cytokines, interferon (IFN)-γ and interleukin (IL)-17, were associated with the disease progression in SJL/J mice, while the expression of both cytokines was detected only at the EAE onset in A.SW mice. Principal component analysis (PCA) of CNS transcriptome data demonstrated that down-regulation of prolactin may reflect disease progression. Pattern matching analysis of spleen transcriptome with CNS PCA identified 333 splenic surrogate markers, including Stfa2l1, which reflected the changes in the CNS. Among them, we found that two genes (PER1/MIR6883 and FKBP5) and one gene (SLC16A1/MCT1) were also significantly up-regulated and down-regulated, respectively, in human MS peripheral blood, using data mining.
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Affiliation(s)
- Seiichi Omura
- Department of Microbiology, Kindai University Faculty of Medicine, Osakasayama, Japan.,Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
| | - Fumitaka Sato
- Department of Microbiology, Kindai University Faculty of Medicine, Osakasayama, Japan.,Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
| | - Nicholas E Martinez
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
| | - Ah-Mee Park
- Department of Microbiology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Mitsugu Fujita
- Department of Microbiology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Nikki J Kennett
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Urška Cvek
- Department of Computer Science, Louisiana State University Shreveport, Shreveport, LA, United States
| | - Alireza Minagar
- Department of Neurology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
| | - J Steven Alexander
- Department of Neurology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States.,Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
| | - Ikuo Tsunoda
- Department of Microbiology, Kindai University Faculty of Medicine, Osakasayama, Japan.,Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States.,Department of Neurology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, United States
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Leary S, Das P, Ponnalagu D, Singh H, Bhandari V. Genetic Strain and Sex Differences in a Hyperoxia-Induced Mouse Model of Varying Severity of Bronchopulmonary Dysplasia. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:999-1014. [PMID: 30794808 DOI: 10.1016/j.ajpath.2019.01.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/21/2018] [Accepted: 01/24/2019] [Indexed: 01/11/2023]
Abstract
Bronchopulmonary dysplasia (BPD) is a disease prevalent in preterm babies with a need for supplemental oxygen, resulting in impaired lung development and dysregulated vascularization. Epidemiologic studies have shown that males are more prone to BPD and have a delayed recovery compared with females, for reasons unknown. Herein, we tried to recapitulate mild, moderate, and severe BPD, using two different strains of mice, in males and females: CD1 (outbred) and C57BL/6 (inbred). Aside from higher body weight in the CD1 strain, there were no other gross morphologic differences with respect to alveolar development between the two strains. With respect to lung morphology after oxygen exposure, females had less injury with better preservation of alveolar chord length and decreased alveolar protein leak and inflammatory cells in the bronchoalveolar lavage fluid. In addition, housekeeping genes, which are routinely used as loading controls, were expressed differently in males and females. In the BPD mouse model, gonadotropin-releasing hormone was increased in females compared with males. Specific miRNAs (miR-146 and miR-34a) were expressed differently in the sexes. In the severe BPD mouse model, administering miR-146 mimic to males attenuated lung damage, whereas administering miR-146 inhibitor to females increased pulmonary injury.
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Affiliation(s)
- Sean Leary
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Pragnya Das
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Devasena Ponnalagu
- Department of Pharmacology, Physiology and Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Harpreet Singh
- Department of Pharmacology, Physiology and Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Vineet Bhandari
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, Pennsylvania; Division of Neonatology, St. Christopher's Hospital for Children, Philadelphia, Pennsylvania.
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37
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O'Connor E, Phan V, Cordts I, Cairns G, Hettwer S, Cox D, Lochmüller H, Roos A. MYO9A deficiency in motor neurons is associated with reduced neuromuscular agrin secretion. Hum Mol Genet 2019; 27:1434-1446. [PMID: 29462312 PMCID: PMC5991207 DOI: 10.1093/hmg/ddy054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/08/2018] [Indexed: 12/12/2022] Open
Abstract
Congenital myasthenic syndromes (CMS) are a group of rare, inherited disorders characterized by compromised function of the neuromuscular junction, manifesting with fatigable muscle weakness. Mutations in MYO9A were previously identified as causative for CMS but the precise pathomechanism remained to be characterized. On the basis of the role of MYO9A as an actin-based molecular motor and as a negative regulator of RhoA, we hypothesized that loss of MYO9A may affect the neuronal cytoskeleton, leading to impaired intracellular transport. To investigate this, we used MYO9A-depleted NSC-34 cells (mouse motor neuron-derived cells), revealing altered expression of a number of cytoskeletal proteins important for neuron structure and intracellular transport. On the basis of these findings, the effect on protein transport was determined using a vesicular recycling assay which revealed impaired recycling of a neuronal growth factor receptor. In addition, an unbiased approach utilizing proteomic profiling of the secretome revealed a key role for defective intracellular transport affecting proper protein secretion in the pathophysiology of MYO9A-related CMS. This also led to the identification of agrin as being affected by the defective transport. Zebrafish with reduced MYO9A orthologue expression were treated with an artificial agrin compound, ameliorating defects in neurite extension and improving motility. In summary, loss of MYO9A affects the neuronal cytoskeleton and leads to impaired transport of proteins, including agrin, which may provide a new and unexpected treatment option.
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Affiliation(s)
- Emily O'Connor
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Vietxuan Phan
- Leibniz-Institut für Analytische Wissenschaften-ISAS e.V, Dortmund 44227, Germany
| | - Isabell Cordts
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - George Cairns
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | | | - Daniel Cox
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Andreas Roos
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK.,Leibniz-Institut für Analytische Wissenschaften-ISAS e.V, Dortmund 44227, Germany
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38
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Peeters SB, Korecki AJ, Simpson EM, Brown CJ. Human cis-acting elements regulating escape from X-chromosome inactivation function in mouse. Hum Mol Genet 2019; 27:1252-1262. [PMID: 29401310 PMCID: PMC6159535 DOI: 10.1093/hmg/ddy039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 12/18/2022] Open
Abstract
A long-standing question concerning X-chromosome inactivation (XCI) has been how some genes avoid the otherwise stable chromosome-wide heterochromatinization of the inactive X chromosome. As 20% or more of human X-linked genes escape from inactivation, such genes are an important contributor to sex differences in gene expression. Although both human and mouse have genes that escape from XCI, more genes escape in humans than mice, with human escape genes often clustering in larger domains than the single escape genes of mouse. Mouse models offer a well-characterized and readily manipulated system in which to study XCI, but given the differences in genes that escape it is unclear whether the mechanism of escape gene regulation is conserved. To address conservation of the process and the potential to identify elements by modelling human escape gene regulation using mouse, we integrated a human and a mouse BAC each containing an escape gene and flanking subject genes at the mouse X-linked Hprt gene. Escape-level expression and corresponding low promoter DNA methylation of human genes RPS4X and CITED1 demonstrated that the mouse system is capable of recognizing human elements and therefore can be used as a model for further refinement of critical elements necessary for escape from XCI in humans.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Marinello M, Werner A, Giannone M, Tahiri K, Alves S, Tesson C, den Dunnen W, Seeler JS, Brice A, Sittler A. SUMOylation by SUMO2 is implicated in the degradation of misfolded ataxin-7 via RNF4 in SCA7 models. Dis Model Mech 2019; 12:dmm.036145. [PMID: 30559154 PMCID: PMC6361149 DOI: 10.1242/dmm.036145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/04/2018] [Indexed: 01/10/2023] Open
Abstract
Perturbation of protein homeostasis and aggregation of misfolded proteins is a major cause of many human diseases. A hallmark of the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7) is the intranuclear accumulation of mutant, misfolded ataxin-7 (polyQ-ATXN7). Here, we show that endogenous ATXN7 is modified by SUMO proteins, thus also suggesting a physiological role for this modification under conditions of proteotoxic stress caused by the accumulation of polyQ-ATXN7. Co-immunoprecipitation experiments, immunofluorescence microscopy and proximity ligation assays confirmed the colocalization and interaction of polyQ-ATXN7 with SUMO2 in cells. Moreover, upon inhibition of the proteasome, both endogenous SUMO2/3 and the RNF4 ubiquitin ligase surround large polyQ-ATXN7 intranuclear inclusions. Overexpression of RNF4 and/or SUMO2 significantly decreased levels of polyQ-ATXN7 and, upon proteasomal inhibition, led to a marked increase in the polyubiquitination of polyQ-ATXN7. This provides a mechanism for the clearance of polyQ-ATXN7 from affected cells that involves the recruitment of RNF4 by SUMO2/3-modified polyQ-ATXN7, thus leading to its ubiquitination and proteasomal degradation. In a SCA7 knock-in mouse model, we similarly observed colocalization of SUMO2/3 with polyQ-ATXN7 inclusions in the cerebellum and retina. Furthermore, we detected accumulation of SUMO2/3 high-molecular-mass species in the cerebellum of SCA7 knock-in mice, compared with their wild-type littermates, and changes in SUMO-related transcripts. Immunohistochemical analysis showed the accumulation of SUMO proteins and RNF4 in the cerebellum of SCA7 patients. Taken together, our results show that the SUMO pathway contributes to the clearance of aggregated ATXN7 and suggest that its deregulation might be associated with SCA7 disease progression.
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Affiliation(s)
- Martina Marinello
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Andreas Werner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Mariagiovanna Giannone
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Khadija Tahiri
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Sandro Alves
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Christelle Tesson
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Wilfred den Dunnen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Jacob-S Seeler
- Nuclear Organization and Oncogenesis Unit, INSERM U.993, Department of Cell Biology and Infection, Institut Pasteur, F-75015 Paris, France
| | - Alexis Brice
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,AP-HP, Genetic Department, Pitié-Salpêtrière University Hospital, F-75013 Paris, France
| | - Annie Sittler
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
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40
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Perkeybile AM, Carter CS, Wroblewski KL, Puglia MH, Kenkel WM, Lillard TS, Karaoli T, Gregory SG, Mohammadi N, Epstein L, Bales KL, Connelly JJ. Early nurture epigenetically tunes the oxytocin receptor. Psychoneuroendocrinology 2019; 99:128-136. [PMID: 30227351 PMCID: PMC6231974 DOI: 10.1016/j.psyneuen.2018.08.037] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022]
Abstract
Mammalian sociality is regulated in part by the neuropeptide oxytocin. In prairie voles, subtle variation in early life experience changes oxytocin receptor-mediated social behaviors. We report that low levels of early care in voles leads to de novo DNA methylation at specific regulatory sites in the oxytocin receptor gene (Oxtr), impacting gene expression and protein distribution in the nucleus accumbens. DNA methylation state of the blood predicts expression in the brain indicating the utility of the blood as a biomarker for the transcription state of the brain. These experience-sensitive CpG sites are conserved in humans, are related to gene expression in the brain, and have been associated with psychiatric disorders and individual differences in neural response to social stimuli. These results identify a mechanism by which early care regulates later displays of typical prairie vole social behavior and suggest the potential for nurture driven epigenetic tuning of OXTR in humans.
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Affiliation(s)
- Allison M. Perkeybile
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - C. Sue Carter
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - Kelly L. Wroblewski
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Meghan H. Puglia
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - William M. Kenkel
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - Travis S. Lillard
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Themistoclis Karaoli
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Simon G. Gregory
- Duke University, Duke Molecular Physiology Institute, 300 N Duke St, Durham, NC, 27701
| | - Niaz Mohammadi
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Larissa Epstein
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Karen L. Bales
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Jessica J. Connelly
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
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Viudez-Martínez A, García-Gutiérrez MS, Manzanares J. Cannabidiol regulates the expression of hypothalamus-pituitary-adrenal axis-related genes in response to acute restraint stress. J Psychopharmacol 2018; 32:1379-1384. [PMID: 30324842 DOI: 10.1177/0269881118805495] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Research interest has grown around the potential therapeutic use of cannabidiol in mood-related disorders, due to its anxiolytic and antidepressant-like effects. These have been partially attributed to its action as an allosteric modulator of 5-HTR1A. However, the exact mechanism supporting cannabidiol properties remains unclear. AIMS To assess the effects of cannabidiol on different targets of the hypothalamus-pituitary-adrenal axis under baseline and stress conditions. METHODS We administered cannabidiol (5 mg/kg, 15 mg/kg or 30 mg/kg, intraperitoneally) or vehicle to male C57BL/6J mice 90 min before single restraint stress exposure (20 min). Using real-time polymerase chain reaction analysis, we measured alterations in the relative gene expression of corticotropin-releasing factor in the paraventricular nucleus, pro-opiomelanocortin in the arcuate nucleus of the hypothalamus, glucocorticoid receptor in the hippocampus, and serotonin 5-HTR1A receptor in the hippocampus and amygdala. RESULTS Under baseline conditions, cannabidiol did not modify any element of the hypothalamus-pituitary-adrenal axis. In contrast, all doses induced alterations in 5-HTR1A in the amygdala and hippocampus. Interestingly, cannabidiol at low (5 mg/kg) and intermediate doses (15 mg/kg) successfully blocked the effects induced by acute stress on corticotropin-releasing factor, pro-opiomelanocortin and glucocorticoid receptor gene expression. Also, restraint stress induced the opposite effects in 5-HTR1A gene expression in the hippocampus and amygdala, an effect not seen in mice treated with cannabidiol at low doses. CONCLUSIONS Taken together, these data suggest the ability of cannabidiol to regulate acute stress hypothalamus-pituitary-adrenal axis activation might be explained, at least in part, by its action on 5-HTR1A receptors.
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Affiliation(s)
| | - María S García-Gutiérrez
- 1 Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,2 Red Temática de Investigación Cooperativa en Salud, Red de Trastornos Adictivos, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Manzanares
- 1 Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,2 Red Temática de Investigación Cooperativa en Salud, Red de Trastornos Adictivos, Instituto de Salud Carlos III, Madrid, Spain
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42
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Watkins AJ, Pearce G, Unak P, Guldu OK, Yasakci V, Akin O, Aras O, Wong J, Ma X. Tissue Morphology and Gene Expression Characterisation of Transplantable Adenocarcinoma Bearing Mice Exposed to Fluorodeoxyglucose-Conjugated Magnetic Nanoparticles. J Biomed Nanotechnol 2018; 14:1979-1991. [PMID: 30165933 DOI: 10.1166/jbn.2018.2631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorodeoxyglucose-conjugated magnetic nanoparticles, designed to target cancer cells with high specificity when heated by an alternating magnetic field, could provide a low-cost, non-toxic treatment for cancer. However, it is essential that the in vivo impacts of such technologies on both tumour and healthy tissues are characterised fully. Profiling tissue gene expression by semi-quantitative reverse transcriptase real-time PCR can provide a sensitive measurement of tissue response to treatment. However, the accuracy of such analyses is dependent on the selection of stable reference genes. In this study, we determined the impact of fluorodeoxyglucose-conjugated magnetic nanoparticles on tumour and non-tumour tissue gene expression and morphology in MAC16 adenocarcinoma established male NMRI mice. Mice received an injection of 8 mg/kg body weight fluorodeoxyglucose-conjugated magnetic nanoparticles either intravenously in to the tail vein, directly into the tumour or subcutaneously directly overlying the tumour. Tissues from mice were sampled between 70 minutes and 12 hours post injection. Using the bioinformatic geNorm tool, we established the stability of six candidate reference genes (Hprt, Pgk1, Ppib, Sdha, Tbp and Tuba); we observed Pgk1 and Ppib to be the most stable. We then characterised the expression profiles of several apoptosis genes of interest in our adenocarcinoma samples, observing differential expression in response to mode of administration and exposure duration. Using histological assessment and fluorescent TUNNEL staining, we observed no detrimental impact on either tumour or non-tumour tissue morphology or levels of apoptosis. These observations define the underlying efficacy of fluorodeoxyglucose-conjugated magnetic nanoparticles on tumour and non-tumour tissue morphology and gene expression, setting the basis for future studies.
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43
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Bräunig J, Mergler S, Jyrch S, Hoefig CS, Rosowski M, Mittag J, Biebermann H, Khajavi N. 3-Iodothyronamine Activates a Set of Membrane Proteins in Murine Hypothalamic Cell Lines. Front Endocrinol (Lausanne) 2018; 9:523. [PMID: 30298050 PMCID: PMC6161562 DOI: 10.3389/fendo.2018.00523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/21/2018] [Indexed: 01/26/2023] Open
Abstract
3-Iodothyronamine (3-T1AM) is an endogenous thyroid hormone metabolite. The profound pharmacological effects of 3-T1AM on energy metabolism and thermal homeostasis have raised interest to elucidate its signaling properties in tissues that pertain to metabolic regulation and thermogenesis. Previous studies identified G protein-coupled receptors (GPCRs) and transient receptor potential channels (TRPs) as targets of 3-T1AM in different cell types. These two superfamilies of membrane proteins are largely expressed in tissue which influences energy balance and metabolism. As the first indication that 3-T1AM virtually modulates the function of the neurons in hypothalamus, we observed that intraperitoneal administration of 50 mg/kg bodyweight of 3-T1AM significantly increased the c-FOS activation in the paraventricular nucleus (PVN) of C57BL/6 mice. To elucidate the underlying mechanism behind this 3-T1AM-induced signalosome, we used three different murine hypothalamic cell lines, which are all known to express PVN markers, GT1-7, mHypoE-N39 (N39) and mHypoE-N41 (N41). Various aminergic GPCRs, which are the known targets of 3-T1AM, as well as numerous members of TRP channel superfamily, are expressed in these cell lines. Effects of 3-T1AM on activation of GPCRs were tested for the two major signaling pathways, the action of Gαs/adenylyl cyclase and Gi/o. Here, we demonstrated that this thyroid hormone metabolite has no significant effect on Gi/o signaling and only a minor effect on the Gαs/adenylyl cyclase pathway, despite the expression of known GPCR targets of 3-T1AM. Next, to test for other potential mechanisms involved in 3-T1AM-induced c-FOS activation in PVN, we evaluated the effect of 3-T1AM on the intracellular Ca2+ concentration and whole-cell currents. The fluorescence-optic measurements showed a significant increase of intracellular Ca2+ concentration in the three cell lines in the presence of 10 μM 3-T1AM. Furthermore, this thyroid hormone metabolite led to an increase of whole-cell currents in N41 cells. Interestingly, the TRPM8 selective inhibitor (10 μM AMTB) reduced the 3-T1AM stimulatory effects on cytosolic Ca2+ and whole-cell currents. Our results suggest that the profound pharmacological effects of 3-T1AM on selected brain nuclei of murine hypothalamus, which are known to be involved in energy metabolism and thermoregulation, might be partially attributable to TRP channel activation in hypothalamic cells.
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Affiliation(s)
- Julia Bräunig
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Pediatric Endocrinology, Berlin, Germany
| | - Stefan Mergler
- Klinik für Augenheilkunde, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sabine Jyrch
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Pediatric Endocrinology, Berlin, Germany
| | - Carolin S. Hoefig
- Institute of Experimental Endocrinology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Cell & Molecular Biology, Karolinska Instituet, Stockholm, Sweden
| | - Mark Rosowski
- Department Medical Biotechnology, Institute of Biotechnology, Technical University of Berlin, Berlin, Germany
| | - Jens Mittag
- Department of Cell & Molecular Biology, Karolinska Instituet, Stockholm, Sweden
- University of Lübeck – Center of Brain Behavior and Metabolism, Lübeck, Germany
| | - Heike Biebermann
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Pediatric Endocrinology, Berlin, Germany
| | - Noushafarin Khajavi
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Pediatric Endocrinology, Berlin, Germany
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Drulis‐Fajdasz D, Gizak A, Wójtowicz T, Wiśniewski JR, Rakus D. Aging-associated changes in hippocampal glycogen metabolism in mice. Evidence for and against astrocyte-to-neuron lactate shuttle. Glia 2018; 66:1481-1495. [PMID: 29493012 PMCID: PMC6001795 DOI: 10.1002/glia.23319] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/01/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Lactate derived from astrocytic glycogen has been shown to support memory formation in hippocampi of young animals, inhibiting it in old animals. Here we show, using quantitative mass spectrometry-based proteomics, immunofluorescence, and qPCR that aging is associated with an increase of glycogen metabolism enzymes concentration and shift in their localization from astrocytes to neurons. These changes are accompanied with reorganization of hippocampal energy metabolism which is manifested by elevated capacity of aging neurons to oxidize glucose in glycolysis and mitochondria, and decreased ability for fatty acids utilization. Our observations suggest that astrocyte-to-neuron lactate shuttle may operate in young hippocampi, however, during aging neurons become independent on astrocytic lactate and the metabolic crosstalk between the brain's cells is disrupted.
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Affiliation(s)
- Dominika Drulis‐Fajdasz
- Department of Molecular Physiology and NeurobiologyUniversity of Wroclaw, Sienkiewicza 21Wroclaw50‐335Poland
| | - Agnieszka Gizak
- Department of Molecular Physiology and NeurobiologyUniversity of Wroclaw, Sienkiewicza 21Wroclaw50‐335Poland
| | - Tomasz Wójtowicz
- Department of Molecular Physiology and NeurobiologyUniversity of Wroclaw, Sienkiewicza 21Wroclaw50‐335Poland
| | - Jacek R. Wiśniewski
- Department of Proteomics and Signal TransductionMax‐Planck‐Institute of Biochemistry, Am Klopferspitz 18Martinsried82152Germany
| | - Dariusz Rakus
- Department of Molecular Physiology and NeurobiologyUniversity of Wroclaw, Sienkiewicza 21Wroclaw50‐335Poland
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45
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Pohland M, Pellowska M, Asseburg H, Hagl S, Reutzel M, Joppe A, Berressem D, Eckert SH, Wurglics M, Schubert‐Zsilavecz M, Eckert GP. MH84 improves mitochondrial dysfunction in a mouse model of early Alzheimer's disease. Alzheimers Res Ther 2018; 10:18. [PMID: 29433569 PMCID: PMC5809956 DOI: 10.1186/s13195-018-0342-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/12/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Current approved drugs for Alzheimer's disease (AD) only attenuate symptoms, but do not cure the disease. The pirinixic acid derivate MH84 has been characterized as a dual gamma-secretase/proliferator activated receptor gamma (PPARγ) modulator in vitro. Pharmacokinetic studies in mice showed that MH84 is bioavailable after oral administration and reaches the brain. We recently demonstrated that MH84 improved mitochondrial dysfunction in a cellular model of AD. In the present study, we extended the pharmacological characterization of MH84 to 3-month-old Thy-1 AβPPSL mice (harboring the Swedish and London mutation in human amyloid precursor protein (APP)) which are characterized by enhanced AβPP processing and cerebral mitochondrial dysfunction, representing a mouse model of early AD. METHODS Three-month-old Thy-1 AβPPSL mice received 12 mg/kg b.w. MH84 by oral gavage once a day for 21 days. Mitochondrial respiration was analyzed in isolated brain mitochondria, and mitochondrial membrane potential and ATP levels were determined in dissociated brain cells. Citrate synthase (CS) activity was determined in brain tissues and MitoTracker Green fluorescence was measured in HEK293-AβPPwt and HEK293-AβPPsw cells. Soluble Aβ1-40 and Aβ1-42 levels were determined using ELISA. Western blot analysis and qRT-PCR were used to measure protein and mRNA levels, respectively. RESULTS MH84 reduced cerebral levels of the β-secretase-related C99 peptide and of Aβ40 levels. Mitochondrial dysfunction was ameliorated by restoring complex IV (cytochrome-c oxidase) respiration, mitochondrial membrane potential, and levels of ATP. Induction of PPARγ coactivator-1α (PGC-1α) mRNA and protein expression was identified as a possible mode of action that leads to increased mitochondrial mass as indicated by enhanced CS activity, OXPHOS levels, and MitoTracker Green fluorescence. CONCLUSIONS MH84 modulates β-secretase processing of APP and improves mitochondrial dysfunction by a PGC-1α-dependent mechanism. Thus, MH84 seems to be a new promising therapeutic agent with approved in-vivo activity for the treatment of AD.
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Affiliation(s)
| | - Maren Pellowska
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Heike Asseburg
- Institute of Pharmacology, Goethe University, Frankfurt, Germany
- Institute of Nutritional Sciences, Justus-Liebig-University, Giessen, Germany
| | - Stephanie Hagl
- Institute of Pharmacology, Goethe University, Frankfurt, Germany
| | - Martina Reutzel
- Institute of Nutritional Sciences, Justus-Liebig-University, Giessen, Germany
| | - Aljoscha Joppe
- Institute of Pharmacology, Goethe University, Frankfurt, Germany
| | - Dirk Berressem
- Institute of Pharmacology, Goethe University, Frankfurt, Germany
| | | | - Mario Wurglics
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | | | - Gunter P. Eckert
- Institute of Nutritional Sciences, Justus-Liebig-University, Giessen, Germany
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46
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Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, Keane TM, Zuber J, Adams DJ, Flint J, Honzik T, Gut M, Beltran S, Mechtler K, Sherr E, Kmoch S, Gut I, Keays DA. Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nat Neurosci 2018; 21:207-217. [PMID: 29311744 PMCID: PMC5897053 DOI: 10.1038/s41593-017-0053-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/22/2017] [Indexed: 01/31/2023]
Abstract
The formation of the vertebrate brain requires the generation, migration, differentiation and survival of neurons. Genetic mutations that perturb these critical cellular events can result in malformations of the telencephalon, providing a molecular window into brain development. Here we report the identification of an N-ethyl-N-nitrosourea-induced mouse mutant characterized by a fractured hippocampal pyramidal cell layer, attributable to defects in neuronal migration. We show that this is caused by a hypomorphic mutation in Vps15 that perturbs endosomal-lysosomal trafficking and autophagy, resulting in an upregulation of Nischarin, which inhibits Pak1 signaling. The complete ablation of Vps15 results in the accumulation of autophagic substrates, the induction of apoptosis and severe cortical atrophy. Finally, we report that mutations in VPS15 are associated with cortical atrophy and epilepsy in humans. These data highlight the importance of the Vps15-Vps34 complex and the Nischarin-Pak1 signaling hub in the development of the telencephalon.
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Affiliation(s)
- Thomas Gstrein
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Andrew Edwards
- Wellcome Trust Center for Human Genetics (WTCHG), Oxford, UK
| | - Anna Přistoupilová
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ines Leca
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Martin Breuss
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | | | - Andi H Hansen
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Ratna Tripathy
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Anna K Traunbauer
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Tobias Hochstoeger
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Gavril Rosoklija
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Marco Repic
- Institute for Molecular Biotechnology (IMBA), Vienna, Austria
| | - Lukas Landler
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Viktor Stránecký
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
| | - Gerhard Dürnberger
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Thomas M Keane
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Johannes Zuber
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jonathan Flint
- Wellcome Trust Center for Human Genetics (WTCHG), Oxford, UK
| | - Tomas Honzik
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria
| | - Elliott Sherr
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stanislav Kmoch
- Institute of Inherited Metabolic Disorders, Charles University, Prague, Czech Republic
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - David A Keays
- Institute of Molecular Pathology (IMP), Vienna Biocentre (VBC), Vienna, Austria.
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47
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Davey RA, Clarke MV, Russell PK, Rana K, Seto J, Roeszler KN, How JMY, Chia LY, North K, Zajac JD. Androgen Action via the Androgen Receptor in Neurons Within the Brain Positively Regulates Muscle Mass in Male Mice. Endocrinology 2017; 158:3684-3695. [PMID: 28977603 DOI: 10.1210/en.2017-00470] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022]
Abstract
Although it is well established that exogenous androgens have anabolic effects on skeletal muscle mass in humans and mice, data from muscle-specific androgen receptor (AR) knockout (ARKO) mice indicate that myocytic expression of the AR is dispensable for hind-limb muscle mass accrual in males. To identify possible indirect actions of androgens via the AR in neurons to regulate muscle, we generated neuron-ARKO mice in which the dominant DNA binding-dependent actions of the AR are deleted in neurons of the cortex, forebrain, hypothalamus, and olfactory bulb. Serum testosterone and luteinizing hormone levels were elevated twofold in neuron-ARKO males compared with wild-type littermates due to disruption of negative feedback to the hypothalamic-pituitary-gonadal axis. Despite this increase in serum testosterone levels, which was expected to increase muscle mass, the mass of the mixed-fiber gastrocnemius (Gast) and the fast-twitch fiber extensor digitorum longus hind-limb muscles was decreased by 10% in neuron-ARKOs at 12 weeks of age, whereas muscle strength and fatigue of the Gast were unaffected. The mass of the soleus muscle, however, which consists of a high proportion of slow-twitch fibers, was unaffected in neuron-ARKOs, demonstrating a stimulatory action of androgens via the AR in neurons to increase the mass of fast-twitch hind-limb muscles. Furthermore, neuron-ARKOs displayed reductions in voluntary and involuntary physical activity by up to 60%. These data provide evidence for a role of androgens via the AR in neurons to positively regulate fast-twitch hind-limb muscle mass and physical activity in male mice.
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Affiliation(s)
- Rachel A Davey
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Michele V Clarke
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Patricia K Russell
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Kesha Rana
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Jane Seto
- Murdoch Children's Research Institute, Parkville 3052, Victoria, Australia
| | - Kelly N Roeszler
- Murdoch Children's Research Institute, Parkville 3052, Victoria, Australia
| | - Jackie M Y How
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Ling Yeong Chia
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Kathryn North
- Murdoch Children's Research Institute, Parkville 3052, Victoria, Australia
| | - Jeffrey D Zajac
- Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
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Postpartum estrogen withdrawal impairs GABAergic inhibition and LTD induction in basolateral amygdala complex via down-regulation of GPR30. Eur Neuropsychopharmacol 2017; 27:759-772. [PMID: 28619359 DOI: 10.1016/j.euroneuro.2017.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/22/2017] [Accepted: 05/29/2017] [Indexed: 01/22/2023]
Abstract
Postpartum estrogen (E2) withdrawal is known to be a particularly vulnerable time for depressive symptoms. In this study, ovariectomized (OVX) mice were treated with co-administration of estradiol benzoate and progesterone (E2/P4) followed by administration of E2 alone (E2) and a subsequent E2 withdrawal (EW) to mimic the hormonal changes during pregnancy and postpartum. The objective of this study was to investigate the influence of E2 withdrawal after hormone-simulated pregnancy on synaptic function and plasticity in basolateral amygdala complex (BLA). In comparison to control mice, EW mice spent less time in the central portion of open-field test and open arms of elevated plus-maze. Excitatory postsynaptic potentials (EPSPs) slopes at external capsule BLA synapse were reduced in E2/P4-mice, recovered in E2-mice, and increased in EW-mice. EW-mice showed a significant increase in duration of EPSPs and paired-pulse inhibition (PPI) with multi-spike responses of EPSPs and impairment of long-term depression (LTD) induction, which were corrected by GABAAR agonist muscimol. Levels of estrogen receptor (ER) GPR30, ERα and ERβ expression in BLA of EW-mice were lower than those in control mice. The bath-application of GPR30 agonist G-1 in BLA of EW-mice recovered the GABAAR-mediated inhibition and LTD indication, but ERβ agonist DPN or ERα agonist PPT could not. A single BLA-injection of G-1 rather than DPN or PPT in EW-mice could partially relieve the anxiety-like behaviors. The results indicate that postpartum E2 withdrawal causes dysfunction of GABAAR-mediated inhibition in the BLA through reducing GPR30 expression, which impairs LTD induction and causes anxiety-like behaviors.
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49
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Cervera-Juanes R, Wilhelm LJ, Park B, Grant KA, Ferguson B. Genome-wide analysis of the nucleus accumbens identifies DNA methylation signals differentiating low/binge from heavy alcohol drinking. Alcohol 2017; 60:103-113. [PMID: 27866807 DOI: 10.1016/j.alcohol.2016.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023]
Abstract
Alcohol-use disorders encompass a range of drinking levels and behaviors, including low, binge, and heavy drinking. In this regard, investigating the neural state of individuals who chronically self-administer lower doses of alcohol may provide insight into mechanisms that prevent the escalation of alcohol use. DNA methylation is one of the epigenetic mechanisms that stabilizes adaptations in gene expression and has been associated with alcohol use. Thus, we investigated DNA methylation, gene expression, and the predicted neural effects in the nucleus accumbens core (NAcc) of male rhesus macaques categorized as "low" or "binge" drinkers, compared to "alcohol-naïve" and "heavy" drinkers based on drinking patterns during a 12-month alcohol self-administration protocol. Using genome-wide CpG-rich region enrichment and bisulfite sequencing, the methylation levels of 2.6 million CpGs were compared between alcohol-naïve (AN), low/binge (L/BD), and heavy/very heavy (H/VHD) drinking subjects (n = 24). Through regional clustering analysis, we identified nine significant differential methylation regions (DMRs) that specifically distinguished ANs and L/BDs, and then compared those DMRs among H/VHDs. The DMRs mapped to genes encoding ion channels, receptors, cell adhesion molecules, and cAMP, NF-κβ and Wnt signaling pathway proteins. Two of the DMRs, linked to PDE10A and PKD2L2, were also differentially methylated in H/VHDs, suggesting an alcohol-dose independent effect. However, two other DMRs, linked to the CCBE1 and FZD5 genes, had L/BD methylation levels that significantly differed from both ANs and H/VHDs. The remaining five DMRs also differentiated L/BDs and ANs. However, H/VHDs methylation levels were not distinguishable from either of the two groups. Functional validation of two DMRs, linked to FZD5 and PDE10A, support their role in regulating gene expression and exon usage, respectively. In summary, the findings demonstrate that L/BD is associated with unique DNA methylation signatures in the primate NAcc, and that the methylation signatures identify synaptic genes that may play a role in preventing the escalation of alcohol use.
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50
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Röhr D, Halfter H, Schulz JB, Young P, Gess B. Sodium-dependent Vitamin C transporter 2 deficiency impairs myelination and remyelination after injury: Roles of collagen and demethylation. Glia 2017; 65:1186-1200. [PMID: 28456003 DOI: 10.1002/glia.23152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 12/29/2022]
Abstract
Peripheral nerve myelination involves rapid production of tightly bound lipid layers requiring cholesterol biosynthesis and myelin protein expression, but also a collagen-containing extracellular matrix providing mechanical stability. In previous studies, we showed a function of ascorbic acid in peripheral nerve myelination and extracellular matrix formation in adult mice. Here, we sought the mechanism of action of ascorbic acid in peripheral nerve myelination using different paradigms of myelination in vivo and in vitro. We found impaired myelination and reduced collagen expression in Sodium-dependent Vitamin C Transporter 2 heterozygous mice (SVCT2+/- ) during peripheral nerve development and after peripheral nerve injury. In dorsal root ganglion (DRG) explant cultures, hypo-myelination could be rescued by precoating with different collagen types. The activity of the ascorbic acid-dependent demethylating Ten-eleven-translocation (Tet) enzymes was reduced in ascorbic acid deprived and SVCT2+/- DRG cultures. Further, in ascorbic acid-deprived DRG cultures, methylation of a CpG island in the collagen alpha1 (IV) and alpha2 (IV) bidirectional promoter region was increased compared to wild-type and ascorbic acid treated controls. Taken together, these results provide further evidence for the function of ascorbic acid in myelination and extracellular matrix formation in peripheral nerves and suggest a putative molecular mechanism of ascorbic acid function in Tet-dependent demethylation of collagen promoters.
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Affiliation(s)
- Dominik Röhr
- Department of Sleep Medicine and Neuromuscular Disorders, University Hospital Muenster, Muenster, Germany.,Department of Biology, University of Muenster, Muenster, Germany
| | - Hartmut Halfter
- Department of Sleep Medicine and Neuromuscular Disorders, University Hospital Muenster, Muenster, Germany
| | - Jörg B Schulz
- Department of Neurology, RWTH University Hospital Aachen, Aachen, Germany.,JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Peter Young
- Department of Sleep Medicine and Neuromuscular Disorders, University Hospital Muenster, Muenster, Germany
| | - Burkhard Gess
- Department of Neurology, RWTH University Hospital Aachen, Aachen, Germany
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