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Xie B, Wu T, Hong D, Lu Z. Comprehensive landscape of junctional genes and their association with overall survival of patients with lung adenocarcinoma. Front Mol Biosci 2024; 11:1380384. [PMID: 38841188 PMCID: PMC11150628 DOI: 10.3389/fmolb.2024.1380384] [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: 02/01/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Objectives Junctional proteins are involved in tumorigenesis. Therefore, this study aimed to investigate the association between junctional genes and the prognosis of patients with lung adenocarcinoma (LUAD). Methods Transcriptome, mutation, and clinical data were retrieved from The Cancer Genome Atlas (TCGA). "Limma" was used to screen differentially expressed genes. Moreover, Kaplan-Meier survival analysis was used to identify junctional genes associated with LUAD prognosis. The junctional gene-related risk score (JGRS) was generated based on multivariate Cox regression analysis. An overall survival (OS) prediction model combining the JGRS and clinicopathological properties was proposed using a nomogram and further validated in the Gene Expression Omnibus (GEO) LUAD cohort. Results To our knowledge, this study is the first to demonstrate the correlation between the mRNA levels of 14 junctional genes (CDH15, CDH17, CDH24, CLDN6, CLDN12, CLDN18, CTNND2, DSG2, ITGA2, ITGA8, ITGA11, ITGAL, ITGB4, and PKP3) and clinical outcomes of patients with LUAD. The JGRS was generated based on these 14 genes, and a higher JGRS was associated with older age, higher stage levels, and lower immune scores. Thus, a prognostic prediction nomogram was proposed based on the JGRS. Internal and external validation showed the good performance of the prediction model. Mechanistically, JGRS was associated with cell proliferation and immune regulatory pathways. Mutational analysis revealed that more somatic mutations occurred in the high-JGRS group than in the low-JGRS group. Conclusion The association between junctional genes and OS in patients with LUAD demonstrated by our "TCGA filtrating and GEO validating" model revealed a new function of junctional genes.
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Affiliation(s)
- Bin Xie
- School of Information Science and Technology, Hangzhou Normal University, Hangzhou, China
| | - Ting Wu
- School of Information Science and Technology, Hangzhou Normal University, Hangzhou, China
| | - Duiguo Hong
- Jincheng Community Health Service Center, Hangzhou, China
| | - Zhe Lu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
- School of Basic Medicine, Hangzhou Normal University, Hangzhou, China
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Ng YK, Blazev R, McNamara JW, Dutt M, Molendijk J, Porrello ER, Elliott DA, Parker BL. Affinity Purification-Mass Spectrometry and Single Fiber Physiology/Proteomics Reveals Mechanistic Insights of C18ORF25. J Proteome Res 2024; 23:1285-1297. [PMID: 38480473 DOI: 10.1021/acs.jproteome.3c00716] [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: 04/06/2024]
Abstract
C18ORF25 was recently shown to be phosphorylated at S67 by AMP-activated protein kinase (AMPK) in the skeletal muscle, following acute exercise in humans. Phosphorylation was shown to improve the ex vivo skeletal muscle contractile function in mice, but our understanding of the molecular mechanisms is incomplete. Here, we profiled the interactome of C18ORF25 in mouse myotubes using affinity purification coupled to mass spectrometry. This analysis included an investigation of AMPK-dependent and S67-dependent protein/protein interactions. Several nucleocytoplasmic and contractile-associated proteins were identified, which revealed a subset of GTPases that associate with C18ORF25 in an AMPK- and S67 phosphorylation-dependent manner. We confirmed that C18ORF25 is localized to the nucleus and the contractile apparatus in the skeletal muscle. Mice lacking C18Orf25 display defects in calcium handling specifically in fast-twitch muscle fibers. To investigate these mechanisms, we developed an integrated single fiber physiology and single fiber proteomic platform. The approach enabled a detailed assessment of various steps in the excitation-contraction pathway including SR calcium handling and force generation, followed by paired single fiber proteomic analysis. This enabled us to identify >700 protein/phenotype associations and 36 fiber-type specific differences, following loss of C18Orf25. Taken together, our data provide unique insights into the function of C18ORF25 and its role in skeletal muscle physiology.
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Affiliation(s)
- Yaan-Kit Ng
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ronnie Blazev
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - James W McNamara
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
| | - Mriga Dutt
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Jeffrey Molendijk
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Enzo R Porrello
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - David A Elliott
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
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Stengl M, Schneider AC. Contribution of membrane-associated oscillators to biological timing at different timescales. Front Physiol 2024; 14:1243455. [PMID: 38264332 PMCID: PMC10803594 DOI: 10.3389/fphys.2023.1243455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Environmental rhythms such as the daily light-dark cycle selected for endogenous clocks. These clocks predict regular environmental changes and provide the basis for well-timed adaptive homeostasis in physiology and behavior of organisms. Endogenous clocks are oscillators that are based on positive feedforward and negative feedback loops. They generate stable rhythms even under constant conditions. Since even weak interactions between oscillators allow for autonomous synchronization, coupling/synchronization of oscillators provides the basis of self-organized physiological timing. Amongst the most thoroughly researched clocks are the endogenous circadian clock neurons in mammals and insects. They comprise nuclear clockworks of transcriptional/translational feedback loops (TTFL) that generate ∼24 h rhythms in clock gene expression entrained to the environmental day-night cycle. It is generally assumed that this TTFL clockwork drives all circadian oscillations within and between clock cells, being the basis of any circadian rhythm in physiology and behavior of organisms. Instead of the current gene-based hierarchical clock model we provide here a systems view of timing. We suggest that a coupled system of autonomous TTFL and posttranslational feedback loop (PTFL) oscillators/clocks that run at multiple timescales governs adaptive, dynamic homeostasis of physiology and behavior. We focus on mammalian and insect neurons as endogenous oscillators at multiple timescales. We suggest that neuronal plasma membrane-associated signalosomes constitute specific autonomous PTFL clocks that generate localized but interlinked oscillations of membrane potential and intracellular messengers with specific endogenous frequencies. In each clock neuron multiscale interactions of TTFL and PTFL oscillators/clocks form a temporally structured oscillatory network with a common complex frequency-band comprising superimposed multiscale oscillations. Coupling between oscillator/clock neurons provides the next level of complexity of an oscillatory network. This systemic dynamic network of molecular and cellular oscillators/clocks is suggested to form the basis of any physiological homeostasis that cycles through dynamic homeostatic setpoints with a characteristic frequency-band as hallmark. We propose that mechanisms of homeostatic plasticity maintain the stability of these dynamic setpoints, whereas Hebbian plasticity enables switching between setpoints via coupling factors, like biogenic amines and/or neuropeptides. They reprogram the network to a new common frequency, a new dynamic setpoint. Our novel hypothesis is up for experimental challenge.
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Affiliation(s)
- Monika Stengl
- Department of Biology, Animal Physiology/Neuroethology, University of Kassel, Kassel, Germany
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Zhang S, Cai Z, Li H. AHNAKs roles in physiology and malignant tumors. Front Oncol 2023; 13:1258951. [PMID: 38033502 PMCID: PMC10682155 DOI: 10.3389/fonc.2023.1258951] [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: 07/14/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The AHNAK family currently consists of two members, namely AHNAK and AHNAK2, both of which have a molecular weight exceeding 600 kDa. Homologous sequences account for approximately 90% of their composition, indicating a certain degree of similarity in terms of molecular structure and biological functions. AHNAK family members are involved in the regulation of various biological functions, such as calcium channel modulation and membrane repair. Furthermore, with advancements in biological and bioinformatics technologies, research on the relationship between the AHNAK family and tumors has rapidly increased in recent years, and its regulatory role in tumor progression has gradually been discovered. This article briefly describes the physiological functions of the AHNAK family, and reviews and analyzes the expression and molecular regulatory mechanisms of the AHNAK family in malignant tumors using Pubmed and TCGA databases. In summary, AHNAK participates in various physiological and pathological processes in the human body. In multiple types of cancers, abnormal expression of AHNAK and AHNAK2 is associated with prognosis, and they play a key regulatory role in tumor progression by activating signaling pathways such as ERK, MAPK, Wnt, and MEK, as well as promoting epithelial-mesenchymal transition.
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Affiliation(s)
- Shusen Zhang
- Hebei Province Xingtai People’s Hospital Postdoctoral Workstation, Xingtai, China
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhigang Cai
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Li
- Department of surgery, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
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Lyu F, Wang L, Jia Y, Wang Y, Qi H, Dai Z, Zhou X, Zhu H, Li B, Xu Y, Liu J. Analysis of Zinc and Stromal Immunity in Disuse Osteoporosis: Mendelian Randomization and Transcriptomic Analysis. Orthop Surg 2023; 15:2947-2959. [PMID: 37752822 PMCID: PMC10622276 DOI: 10.1111/os.13840] [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: 03/27/2023] [Revised: 06/22/2023] [Accepted: 06/30/2023] [Indexed: 09/28/2023] Open
Abstract
OBJECTIVE Disuse osteoporosis is known to be primarily caused by a lack of exercise. However, the causal relationships between zinc and immunity and disuse osteoporosis remain unknown. This study investigated these relationships and their potential mechanisms. METHODS This study was an integrative study combining genome-wide association studies and transcriptomics. Two-sample Mendelian randomization analysis (MR) was used to analyze the causal relationships between exposures (zinc, immunity, physical activity) and the outcome (osteoporosis) with the aid of single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs). Four models, MR-Egger, inverse variance weighted, weighted median and MR-Pleiotrophy RESidual Sum and Outlier (MRPRESSO), were used to calculate odds ratio values. Sensitivity and heterogeneity analyses were also performed using MRPRESSO and MR-Egger methods. The mRNA transcriptomic analysis was subsequently conducted. Zinc metabolism scores were acquired through single-sample Gene Set Enrichment Analysis algorithms. Stromal scores were obtained using the R Package "estimate" algorithms. Important Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathways were also derived through gene set variation analysis. Cytoscape software helped construct the transcription factor (TF)-mRNA-microRNA (miRNA) network. Virtual screening and molecular docking were performed. Polymerase chain reaction validation was also carried out in vivo. RESULTS Causal relationships were demonstrated between zinc and exercise (95% confidence interval [CI] = 1.30-2.95, p = 0.001), exercise and immunity (95% CI = 0.36-0.80, p = 0.002), exercise and osteoporosis (95% CI = 0.97-0.99, p = 0.0007), and immunity disorder and osteoporosis (95% CI = 1.30-2.03, p = 0.00002). One hundred and seventy-nine mRNAs in important modules were screened. Combining the differential expressional genes (DEGs) and the Boruta selection, six DEGs were screened (AHNAK, CSF2, ADAMTS12, SRA1, RUNX2, and SLC39A14). TF HOXC10 and miRNA hsa-miR-204 were predicted. Then, the TF-mRNA-miRNA network was successfully constructed. RUNX2 and SLC39A14 were identified as hub mRNAs in the TF-mRNA-miRNA network. Eventually, the novel small drug C6O4NH5 was designed according to the pharmacophore structure of SLC39A14. The docking energy for the novel drug was -5.83 kcal/mol. SLC39A14 and RUNX2 were downregulated (of statistical significance p-value < 0.05) in our animal experiment. CONCLUSION This study revealed that zinc had a protective causal relationship with disuse osteoporosis by promoting exercise and immunity. SLC39A14 and RUNX2 mRNA participated in this zinc-related mechanism.
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Affiliation(s)
- Fei Lyu
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Orthopedic Center (Sports Medicine Center)Inner Mongolia People's HospitalHohhotChina
| | - Li Wang
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Yiming Jia
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Department of OrthopedicsChifeng Municipal HospitalChifengChina
| | - Yuanlin Wang
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Tianjin Institute of AnesthesiologyTianjin Medical UniversityTianjinChina
| | - Haolan Qi
- School of MedicineNankai UniversityTianjinChina
| | - Zhengxu Dai
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Xuyang Zhou
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Haoran Zhu
- School of MedicineXi'an Jiaotong UniversityXianChina
| | - Bing Li
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Yujing Xu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of PharmacyTianjin Medical UniversityTianjinChina
| | - Jun Liu
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
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6
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Liu Y, Fan J, Zhang M, Liu Z, Wang J, Liu J, Li Z, Yang F, Zhang G. A human identification system for hair shaft using RNA polymorphism. Forensic Sci Int Genet 2023; 67:102929. [PMID: 37611365 DOI: 10.1016/j.fsigen.2023.102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Hair is one of the common pieces of evidence at crime scenes, with abundant mitochondrial DNA but limited nuclear DNA in its shaft. It also helps to narrow the investigation scope to maternal lineage but fails to provide unique individual information. We assumed that RNA in hair shafts would be an alternative resource used to perform human identification based on the facts that (1) RNA retains the polymorphic information; (2) the multi-copy of RNA in a cell resists degradation as compared to the one-copy of nuclear DNA. In this study, we explored the potential of RNA polymorphism in hair shafts for forensic individual identification. A SNaPshot typing system was constructed using 18 SNPs located on 11 genes (ABCA13, AHNAK, EXPH5, KMT2D, KRT35, PPP1R15A, RBM33, S100A5, TBC1D4, TMC5, TRPV2). The RNA typing system was evaluated for sensitivity, species specificity, and feasibility for aged hair samples. Hair samples from a Shanxi population in China were used for the population study of the system. The detection limit of the assay was 2 ng RNA. The CDP of these 11 genes was 0.999969 in the Shanxi population. We also identified the concordance of the RNA and DNA typing results. In summary, we developed an RNA typing method to perform human identification from hair shafts, which performed as accurately as nuclear DNA typing. Our method provides a potential basis for solving the human identification problem from hair shafts, as well as other biological materials that lack nuclear DNA.
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Affiliation(s)
- Yao Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiajia Fan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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7
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Kim HW, Ko MK, Park SH, Hwang SY, Kim DH, Park SY, Ko YJ, Kim SM, Park JH, Lee MJ. Dectin-1 signaling coordinates innate and adaptive immunity for potent host defense against viral infection. Front Immunol 2023; 14:1194502. [PMID: 37334361 PMCID: PMC10272586 DOI: 10.3389/fimmu.2023.1194502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Background Most commercial foot-and-mouth disease (FMD) vaccines have various disadvantages, such as low antibody titers, short-lived effects, compromised host defense, and questionable safety. Objectives To address these shortcomings, we present a novel FMD vaccine containing Dectin-1 agonist, β-D-glucan, as an immunomodulatory adjuvant. The proposed vaccine was developed to effectively coordinate innate and adaptive immunity for potent host defense against viral infection. Methods We demonstrated β-D-glucan mediated innate and adaptive immune responses in mice and pigs in vitro and in vivo. The expressions of pattern recognition receptors, cytokines, transcription factors, and co-stimulatory molecules were promoted via FMD vaccine containing β-D-glucan. Results β-D-glucan elicited a robust cellular immune response and early, mid-, and long-term immunity. Moreover, it exhibited potent host defense by modulating host's innate and adaptive immunity. Conclusion Our study provides a promising approach to overcoming the limitations of conventional FMD vaccines. Based on the proposed vaccine's safety and efficacy, it represents a breakthrough among next-generation FMD vaccines.
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8
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Schiapparelli LM, Xie Y, Sharma P, McClatchy DB, Ma Y, Yates JR, Maximov A, Cline HT. Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins. J Neurosci 2022; 42:7900-7920. [PMID: 36261270 PMCID: PMC9617616 DOI: 10.1523/jneurosci.0707-22.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Neuronal activity initiates signaling cascades that culminate in diverse outcomes including structural and functional neuronal plasticity, and metabolic changes. While studies have revealed activity-dependent neuronal cell type-specific transcriptional changes, unbiased quantitative analysis of cell-specific activity-induced dynamics in newly synthesized proteins (NSPs) synthesis in vivo has been complicated by cellular heterogeneity and a relatively low abundance of NSPs within the proteome in the brain. Here we combined targeted expression of mutant MetRS (methionine tRNA synthetase) in genetically defined cortical glutamatergic neurons with tight temporal control of treatment with the noncanonical amino acid, azidonorleucine, to biotinylate NSPs within a short period after pharmacologically induced seizure in male and female mice. By purifying peptides tagged with heavy or light biotin-alkynes and using direct tandem mass spectrometry detection of biotinylated peptides, we quantified activity-induced changes in cortical glutamatergic neuron NSPs. Seizure triggered significant changes in ∼300 NSPs, 33% of which were decreased by seizure. Proteins mediating excitatory and inhibitory synaptic plasticity, including SynGAP1, Pak3, GEPH1, Copine-6, and collybistin, and DNA and chromatin remodeling proteins, including Rad21, Smarca2, and Ddb1, are differentially synthesized in response to activity. Proteins likely to play homeostatic roles in response to activity, such as regulators of proteastasis, intracellular ion control, and cytoskeleton remodeling proteins, are activity induced. Conversely, seizure decreased newly synthetized NCAM, among others, suggesting that seizure induced degradation. Overall, we identified quantitative changes in the activity-induced nascent proteome from genetically defined cortical glutamatergic neurons as a strategy to discover downstream mediators of neuronal plasticity and generate hypotheses regarding their function.SIGNIFICANCE STATEMENT Activity-induced neuronal and synaptic plasticity are mediated by changes in the protein landscape, including changes in the activity-induced newly synthesized proteins; however, identifying neuronal cell type-specific nascent proteome dynamics in the intact brain has been technically challenging. We conducted an unbiased proteomic screen from which we identified significant activity-induced changes in ∼300 newly synthesized proteins in genetically defined cortical glutamatergic neurons within 20 h after pharmacologically induced seizure. Bioinformatic analysis of the dynamic nascent proteome indicates that the newly synthesized proteins play diverse roles in excitatory and inhibitory synaptic plasticity, chromatin remodeling, homeostatic mechanisms, and proteasomal and metabolic functions, extending our understanding of the diversity of plasticity mechanisms.
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Affiliation(s)
- Lucio M Schiapparelli
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
| | - Yi Xie
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
- Skaggs Graduate School, Scripps Research Institute, La Jolla, California 92037
| | - Pranav Sharma
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
- Xosomix, San Diego, California 92121
| | - Daniel B McClatchy
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - Anton Maximov
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
| | - Hollis T Cline
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
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9
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Li H, Wei M, Ye T, Liu Y, Qi D, Cheng X. Identification of the molecular subgroups in Alzheimer's disease by transcriptomic data. Front Neurol 2022; 13:901179. [PMID: 36204002 PMCID: PMC9530954 DOI: 10.3389/fneur.2022.901179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAlzheimer's disease (AD) is a heterogeneous pathological disease with genetic background accompanied by aging. This inconsistency is present among molecular subtypes, which has led to diagnostic ambiguity and failure in drug development. We precisely distinguished patients of AD at the transcriptome level.MethodsWe collected 1,240 AD brain tissue samples collected from the GEO dataset. Consensus clustering was used to identify molecular subtypes, and the clinical characteristics were focused on. To reveal transcriptome differences among subgroups, we certificated specific upregulated genes and annotated the biological function. According to RANK METRIC SCORE in GSEA, TOP10 was defined as the hub gene. In addition, the systematic correlation between the hub gene and “A/T/N” was analyzed. Finally, we used external data sets to verify the diagnostic value of hub genes.ResultsWe identified three molecular subtypes of AD from 743 AD samples, among which subtypes I and III had high-risk factors, and subtype II had protective factors. All three subgroups had higher neuritis plaque density, and subgroups I and III had higher clinical dementia scores and neurofibrillary tangles than subgroup II. Our results confirmed a positive association between neurofibrillary tangles and dementia, but not neuritis plaques. Subgroup I genes clustered in viral infection, hypoxia injury, and angiogenesis. Subgroup II showed heterogeneity in synaptic pathology, and we found several essential beneficial synaptic proteins. Due to presenilin one amplification, Subgroup III was a risk subgroup suspected of familial AD, involving abnormal neurogenic signals, glial cell differentiation, and proliferation. Among the three subgroups, the highest combined diagnostic value of the hub genes were 0.95, 0.92, and 0.83, respectively, indicating that the hub genes had sound typing and diagnostic ability.ConclusionThe transcriptome classification of AD cases played out the pathological heterogeneity of different subgroups. It throws daylight on the personalized diagnosis and treatment of AD.
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Affiliation(s)
- He Li
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Meiqi Wei
- Institute of Chinese Medical Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tianyuan Ye
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yiduan Liu
- School of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Dongmei Qi
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaorui Cheng
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
- *Correspondence: Xiaorui Cheng
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10
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Ivanova A, Smirnikhina S, Lavrov A. Dysferlinopathies: clinical and genetic variability. Clin Genet 2022; 102:465-473. [PMID: 36029111 DOI: 10.1111/cge.14216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022]
Abstract
Dysferlinopathies are a clinically heterogeneous group of diseases caused by mutations in the DYSF gene encoding the dysferlin protein. Dysferlin is mostly expressed in muscle tissues and is localized in the sarcolemma, where it performs its main function of resealing and maintaining of the integrity of the cell membrane. At least four forms of dysferlinopathies have been described: Miyoshi myopathy, limb-girdle muscular dystrophy type 2B, distal myopathy with anterior tibial onset, and isolated hyperCKemia. Here we review the clinical features of different forms of dysferlinopathies and attempt to identify genotype-phenotype correlations. Because of the great clinical variability and rarety of the disease and mutations little is known, how different phenotypes develop as a result of different mutations. However missense mutations seem to induce more severe disease than LoF, which is typical for many muscle dystrophies. The role of several specific mutations and possible gene modifiers is also discussed in the paper.
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Affiliation(s)
- Alisa Ivanova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, Russia
| | | | - Alexander Lavrov
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, Russia
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11
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Vinci M, Kursula P, Greco D, Elia M, Vetri L, Schepis C, Chiavetta V, Donadio S, Roccella M, Carotenuto M, Romano V, Calì F. Exome sequencing in a child with neurodevelopmental disorder and epilepsy: Variant analysis of the AHNAK2 gene. Mol Genet Genomic Med 2022; 10:e2012. [PMID: 35789128 PMCID: PMC9482394 DOI: 10.1002/mgg3.2012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022] Open
Abstract
Background The AHNAK2 gene encodes a large nucleoprotein expressed in several tissues, including brain, squamous epithelia, smooth muscle, and neuropil. Its role in calcium signaling has been suggested and to date, clear evidence about its involvement in the pathogenesis of clinical disorders is still lacking. Methods Here, we report a female 24‐year‐old patient diagnosed with a cardio‐facio‐cutaneous‐like phenotype (CFC‐like), characterized by epilepsy, psychomotor development delay, atopic dermatitis, congenital heart disease, hypotonia, and facial dysmorphism, who is compound heterozygote for two missense mutations in the AHNAK2 gene detected by exome sequencing. Results This patient had no detectable variant in any of the genes known to be associated with the cardio‐facio‐cutaneous syndrome. Moreover, the mode of inheritance does not appear to be autosomal dominant, as it is in typical CFC syndrome. We have performed in silico assessment of mutation severity separately for each missense mutation, but this analysis excludes a severe effect on protein function. Protein structure predictions indicate the mutations are located in flexible regions possibly involved in molecular interactions. Conclusion We discuss an alternative interpretation on the potential involvement of the two missense mutations in the AHNAK2 gene on the expression of CFC‐like phenotype in this patient based on inter‐allelic complementation.
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Affiliation(s)
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | | | - Luigi Vetri
- Oasi Research Institute-IRCCS, Troina, Italy
| | | | | | - Serena Donadio
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Michele Roccella
- Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Marco Carotenuto
- Clinic of Child and Adolescent Neuropsychiatry, Department of Mental Health, Physical and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Valentino Romano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
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12
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Li L, Liu Y, Feng T, Zhou W, Wang Y, Li H. The AHNAK induces increased IL-6 production in CD4+ T cells and serves as a potential diagnostic biomarker for recurrent pregnancy loss. Clin Exp Immunol 2022; 209:291-304. [PMID: 35766885 PMCID: PMC9521664 DOI: 10.1093/cei/uxac067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/09/2022] [Accepted: 06/28/2022] [Indexed: 01/23/2023] Open
Abstract
Disorganized maternal-fetal immune tolerance contributes to the occurrence of unexplained recurrent pregnancy loss (RPL). AHNAK is a scaffolding protein participating in the regulation of Ca2+ entry into T cells and the pathophysiology of diverse diseases. We performed differential gene expression analysis in decidual immune cells (DICs) isolated from three patients with RPL and from three healthy controls via RNA-sequencing (RNA-seq), which revealed 407 differentially expressed genes (DEGs). Among these DEGs, we underscored the clinical significance of elevated AHNAK mRNA and protein levels in DICs, peripheral blood mononuclear cells (PBMCs), and decidua of the patients with RPL, suggesting its potential use as a biomarker for the diagnosis of RPL. Especially, the ratios of decidual and blood AHNAK+CD4+ T cells in the CD4+ T cell population were significantly increased in patients with RPL, and the loss of AHNAK was further shown to inhibit interleukin (IL)-6 secretion in the CD4+ Jurkat cell line. Similar patterns were also observed in the clinical decidual and blood specimens. We uncovered that the AHNAK+CD4+ T cells could secrete more IL-6 than that the corresponding AHNAK-CD4+ T cells. Moreover, the frequencies of decidual and blood IL-6+CD4+ T cells in the CD4+ T-cell population were also increased in patients with RPL and showed significant positive correlations with the frequencies of AHNAK+CD4+ T cells. Our findings suggest that the elevated AHNAK expressed by CD4+ T cells may be involved in the immune dysregulation of RPL by increasing IL-6 production, illustrating its potential as a novel intervention target for RPL.
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Affiliation(s)
- Liman Li
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yuan Liu
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ting Feng
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wenjie Zhou
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanyun Wang
- Correspondence: Yanyun Wang, Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China. ; or Hong Li, Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Hong Li
- Correspondence: Yanyun Wang, Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China. ; or Hong Li, Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
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Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution. Genes (Basel) 2022; 13:genes13071109. [DOI: 10.3390/genes13071109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell transcriptome studies have revealed immune dysfunction in COVID-19 patients, including lymphopenia, T cell exhaustion, and increased levels of pro-inflammatory cytokines, while DNA methylation plays an important role in the regulation of immune response and inflammatory response. The specific cell types of immune responses regulated by DNA methylation in COVID-19 patients will be better understood by exploring the COVID-19 DNA methylation variation at the cell-type level. Here, we developed an analytical pipeline to explore single-cell DNA methylation variations in COVID-19 patients by transferring bulk-tissue-level knowledge to the single-cell level. We discovered that the methylation variations in the whole blood of COVID-19 patients showed significant cell-type specificity with remarkable enrichment in gamma-delta T cells and presented a phenomenon of hypermethylation and low expression. Furthermore, we identified five genes whose methylation variations were associated with several cell types. Among them, S100A9, AHNAK, and CX3CR1 have been reported as potential COVID-19 biomarkers previously, and the others (TRAF3IP3 and LFNG) are closely associated with the immune and virus-related signaling pathways. We propose that they might serve as potential epigenetic biomarkers for COVID-19 and could play roles in important biological processes such as the immune response and antiviral activity.
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Bharadwaj A, Kempster E, Waisman DM. The Annexin A2/S100A10 Complex: The Mutualistic Symbiosis of Two Distinct Proteins. Biomolecules 2021; 11:biom11121849. [PMID: 34944495 PMCID: PMC8699243 DOI: 10.3390/biom11121849] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022] Open
Abstract
Mutualistic symbiosis refers to the symbiotic relationship between individuals of different species in which both individuals benefit from the association. S100A10, a member of the S100 family of Ca2+-binding proteins, exists as a tight dimer and binds two annexin A2 molecules. This association forms the annexin A2/S100A10 complex known as AIIt, and modifies the distinct functions of both proteins. Annexin A2 is a Ca2+-binding protein that binds F-actin, phospholipid, RNA, and specific polysaccharides such as heparin. S100A10 does not bind Ca2+, but binds tPA, plasminogen, certain plasma membrane ion channels, neurotransmitter receptors, and the structural scaffold protein, AHNAK. S100A10 relies on annexin A2 for its intracellular survival: in the absence of annexin A2, it is rapidly destroyed by ubiquitin-dependent and independent proteasomal degradation. Annexin A2 requires S100A10 to increase its affinity for Ca2+, facilitating its participation in Ca2+-dependent processes such as membrane binding. S100A10 binds tissue plasminogen activator and plasminogen, and promotes plasminogen activation to plasmin, which is a process stimulated by annexin A2. In contrast, annexin A2 acts as a plasmin reductase and facilitates the autoproteolytic destruction of plasmin. This review examines the relationship between annexin A2 and S100A10, and how their mutualistic symbiosis affects the function of both proteins.
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Affiliation(s)
- Alamelu Bharadwaj
- Department of Pathology, Faculty of Medicine, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, NS B3H 1X5, Canada; (A.B.); (E.K.)
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 1X5, Canada
| | - Emma Kempster
- Department of Pathology, Faculty of Medicine, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, NS B3H 1X5, Canada; (A.B.); (E.K.)
| | - David Morton Waisman
- Department of Pathology, Faculty of Medicine, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, NS B3H 1X5, Canada; (A.B.); (E.K.)
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 1X5, Canada
- Correspondence: ; Tel.: +1-(902)-494-1803; Fax: +1-(902)-494-1355
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