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Liang F, Peng C, Luo X, Wang L, Huang Y, Yin L, Yue L, Yang J, Zhao X. A single-cell atlas of immunocytes in the spleen of a mouse model of Wiskott-Aldrich syndrome. Cell Immunol 2023; 393-394:104783. [PMID: 37944382 DOI: 10.1016/j.cellimm.2023.104783] [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: 05/25/2023] [Revised: 08/28/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Wiskott-Aldrich syndrome (WAS) is a disorder characterized by rare X-linked genetic immune deficiency with mutations in the Was gene, which is specifically expressed in hematopoietic cells. The spleen plays a major role in hematopoiesis and red blood cell clearance. However, to date, comprehensive analyses of the spleen in wild-type (WT) and WASp-deficient (WAS-KO) mice, especially at the transcriptome level, have not been reported. In this study, single-cell RNA sequencing (scRNA-seq) was adopted to identify various types of immune cells and investigate the mechanisms underlying immune deficiency. We identified 30 clusters and 10 major cell subtypes among 11,269 cells; these cell types included B cells, T cells, dendritic cells (DCs), natural killer (NK) cells, monocytes, macrophages, granulocytes, stem cells and erythrocytes. Moreover, we evaluated gene expression differences among cell subtypes, identified differentially expressed genes (DEGs), and performed enrichment analyses to identify the reasons for the dysfunction in these different cell populations in WAS. Furthermore, some key genes were identified based on a comparison of the DEGs in each cell type involved in specific and nonspecific immune responses, and further analysis showed that these key genes were previously undiscovered pathology-related genes in WAS-KO mice. In summary, we present a landscape of immune cells in the spleen of WAS-KO mice based on detailed data obtained at single-cell resolution. These unprecedented data revealed the transcriptional characteristics of specific and nonspecific immune cells, and the key genes were identified, laying a foundation for future studies of WAS, especially studies into novel and underexplored mechanisms that may improve gene therapies for WAS.
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Affiliation(s)
- Fangfang Liang
- Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Rheumatism and Immunology, Shenzhen Children's Hospital, Shenzhen, China
| | - Cheng Peng
- Department of Radiology, The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Xianze Luo
- Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Linlin Wang
- Department of Rheumatism and Immunology, Shenzhen Children's Hospital, Shenzhen, China
| | - Yanyan Huang
- Department of Rheumatism and Immunology, Shenzhen Children's Hospital, Shenzhen, China
| | - Le Yin
- Department of Rheumatism and Immunology, Shenzhen Children's Hospital, Shenzhen, China
| | - Luming Yue
- Singleron Biotechnologies, Nanjing, Jiangsu, China
| | - Jun Yang
- Department of Rheumatism and Immunology, Shenzhen Children's Hospital, Shenzhen, China.
| | - Xiaodong Zhao
- Department of Rheumatism and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
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Analysis of Minor Proteins Present in Breast Milk by Using WGA Lectin. CHILDREN 2022; 9:children9071084. [PMID: 35884068 PMCID: PMC9318462 DOI: 10.3390/children9071084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
Breast milk is a complex and dynamic biological fluid and considered an essential source of nutrition in early life. In its composition, the proteins have a relevant biological activity and are related to the multiple benefits demonstrated when compared with artificial milks derived from cow’s milk. Understanding human milk composition provides an important tool for health care providers toward the management of infant feeding and the establishment of breastfeeding. In this work, a new technique was developed to increase the knowledge of human milk, because many of the components remain unknown. To isolate minor proteins present in breast milk by using WGA lectin, breast milk was centrifuged to remove cells and separate the fat phase from the serum phase. The serum obtained was separated into two groups: control (n = 3; whole serum sample from mature milk) and WGA lectin (n = 3; sample processed with WGA lectin to isolate glycosylated proteins). The samples were analyzed by high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS). A total of 84 different proteins were identified from all of the samples. In the WGA lectin group, 55 different proteins were isolated, 77% of which had biological functions related to the immune response. Of these proteins, there were eight WGA lectin group exclusives, and two had not previously been described in breast milk (polyubiquitin-B and POTE ankyrin domain family member F). Isolation by WGA lectin is a useful technique to detect minor proteins in breast milk and to identify proteins that could not be observed in whole serum.
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | | | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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Pinson MR, Chung DD, Mahnke AH, Salem NA, Osorio D, Nair V, Payne EA, Del Real JJ, Cai JJ, Miranda RC. Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. Alcohol Clin Exp Res 2022; 46:556-569. [PMID: 35187673 PMCID: PMC9018584 DOI: 10.1111/acer.14796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 01/08/2023]
Abstract
Background We previously showed that ethanol did not kill fetal neural stem cells (NSCs), but that their numbers nevertheless are decreased due to aberrant maturation and loss of self‐renewal. To identify mechanisms that mediate this loss of NSCs, we focused on a family of Gag‐like proteins (GLPs), derived from retroviral gene remnants within mammalian genomes. GLPs are important for fetal development, though their role in brain development is virtually unexplored. Moreover, GLPs may be transferred between cells in extracellular vesicles (EVs) and thereby transfer environmental adaptations between cells. We hypothesized that GLPs may mediate some effects of ethanol in NSCs. Methods Sex‐segregated male and female fetal murine cortical NSCs, cultured ex vivo as nonadherent neurospheres, were exposed to a dose range of ethanol and to mitogen‐withdrawal‐induced differentiation. We used siRNAs to assess the effects of NSC‐expressed GLP knockdown on growth, survival, and maturation and in silico GLP knockout, in an in vivo single‐cell RNA‐sequencing dataset, to identify GLP‐mediated developmental pathways that were also ethanol‐sensitive. Results PEG10 isoform‐1, isoform‐2, and PNMA2 were identified as dominant GLP species in both NSCs and their EVs. Ethanol‐exposed NSCs exhibited significantly elevated PEG10 isoform‐2 and PNMA2 protein during differentiation. Both PEG10 and PNMA2 were mediated apoptosis resistance and additionally, PEG10 promoted neuronal and astrocyte lineage maturation. Neither GLP influenced metabolism nor cell cycle in NSCs. Virtual PEG10 and PNMA2 knockout identified gene transcription regulation and ubiquitin‐ligation processes as candidate mediators of GLP‐linked prenatal alcohol effects. Conclusions Collectively, GLPs present in NSCs and their EVs may confer apoptosis resistance within the NSC niche and contribute to the abnormal maturation induced by ethanol.
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Affiliation(s)
- Marisa R Pinson
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Dae D Chung
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Amanda H Mahnke
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA.,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Nihal A Salem
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Daniel Osorio
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Vijay Nair
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Elizabeth A Payne
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - Jonathan J Del Real
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA.,Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA.,Interdisciplinary Program of Genetics, Texas A&M University, College Station, Texas, USA.,Center for Statistical Bioinformatics, Texas A&M University, College Station, Texas, USA
| | - Rajesh C Miranda
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, Texas, USA.,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, Texas, USA.,Interdisciplinary Program of Genetics, Texas A&M University, College Station, Texas, USA
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Zhang D, Ji Y, Chen X, Chen R, Wei Y, Peng Q, Lin J, Yin J, Li H, Cui L, Lin Z, Cai Y. Peripheral Blood Circular RNAs as a Biomarker for Major Depressive Disorder and Prediction of Possible Pathways. Front Neurosci 2022; 16:844422. [PMID: 35431783 PMCID: PMC9009243 DOI: 10.3389/fnins.2022.844422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/10/2022] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs) are highly expressed in the central nervous system and have been reported to be associated with neuropsychiatric diseases, but their potential role in major depressive disorder (MDD) remains unclear. Here, we demonstrated that there was a disorder of circRNAs in the blood of MDD patients. It has been preliminarily proved that hsa_circ_0002473, hsa_circ_0079651, hsa_circ_0137187, hsa_circ_0006010, and hsa_circ_0113010 were highly expressed in MDD patients and can be used as diagnostic markers for MDD. Bioinformatics analysis revealed that hsa_circ_0079651, hsa_circ_0137187, hsa_circ_0006010, and hsa_circ_0113010 may affect the neuroplasticity of MDD through the ceRNA mechanism.
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Affiliation(s)
- Dandan Zhang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yao Ji
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiongjin Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - RunSen Chen
- Department of Rehabilitation Medicine Guangzhou Red Cross Hospital Affiliated to Jinan University, Guangzhou, China
| | - Yaxue Wei
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qian Peng
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Juda Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jingwen Yin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hezhan Li
- School of Humanities and Management, Guangdong Medical University, Dongguan, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhixiong Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- *Correspondence: Zhixiong Lin,
| | - Yujie Cai
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Yujie Cai,
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Xie HM, Su X, Zhang FY, Dai CL, Wu RH, Li Y, Han XX, Feng XM, Yu B, Zhu SX, Zhou SL. Profile of the RNA in exosomes from astrocytes and microglia using deep sequencing: implications for neurodegeneration mechanisms. Neural Regen Res 2022; 17:608-617. [PMID: 34380901 PMCID: PMC8504369 DOI: 10.4103/1673-5374.320999] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Glial cells play an important role in signal transduction, energy metabolism, extracellular ion homeostasis and neuroprotection of the central nervous system. However, few studies have explained the potential effects of exosomes from glial cells on central nervous system health and disease. In this study, the genes expressed in exosomes from astrocytes and microglia were identified by deep RNA sequencing. Kyoto Encyclopedia of Genes and Genomes analysis indicated that several pathways in these exosomes are responsible for promoting neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease and Huntington’s disease. Gene ontology analysis showed that extracellular exosome, mitochondrion and growth factor activity were enriched in exosomes from the unique astrocyte group, while extracellular exosome and mitochondrion were enriched in exosomes from the unique microglia group. Next, combined with the screening of hub genes, the protein-protein interaction network analysis showed that exosomes from astrocytes influence neurodegenerative diseases through metabolic balance and ubiquitin-dependent protein balance, whereas exosomes from microglia influence neurodegenerative diseases through immune inflammation and oxidative stress. Although there were differences in RNA expression between exosomes from astrocytes and microglia, the groups were related by the hub genes, ubiquitin B and heat shock protein family A (Hsp70) member 8. Ubiquitin B appeared to be involved in pleiotropic regulatory functions, including immune regulation, inflammation inhibition, protein catabolism, intracellular protein transport, exosomes and oxidative stress. The results revealed the clinical significance of exosomes from glia in neurodegenerative diseases. This study was approved by the Animal Ethics Committee of Nantong University, China (approval No. S20180102-152) on January 2, 2018.
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Affiliation(s)
- Hui-Min Xie
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University; Department of Stomatology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xing Su
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Feng-Yuan Zhang
- Medical College of Nantong University, Nantong, Jiangsu Province, China
| | - Chao-Lun Dai
- Medical College of Nantong University, Nantong, Jiangsu Province, China
| | - Rong-Hua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Yan Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Xiao Han
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xing-Mei Feng
- Department of Stomatology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Shun-Xing Zhu
- Laboratory Animals Center, Nantong University, Nantong, Jiangsu Province, China
| | - Song-Lin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
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