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Myint O, Sakunrangsit N, Pholtaisong J, Toejing P, Pho-on P, Leelahavanichkul A, Sridurongrit S, Aporntewan C, Greenblatt MB, Lotinun S. Differential Gene Expression Involved in Bone Turnover of Mice Expressing Constitutively Active TGFβ Receptor Type I. Int J Mol Sci 2024; 25:5829. [PMID: 38892016 PMCID: PMC11173332 DOI: 10.3390/ijms25115829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Transforming growth factor beta (TGF-β) is ubiquitously found in bone and plays a key role in bone turnover. Mice expressing constitutively active TGF-β receptor type I (Mx1;TβRICA mice) are osteopenic. Here, we identified the candidate genes involved in bone turnover in Mx1;TβRICA mice using RNA sequencing analysis. A total of 285 genes, including 87 upregulated and 198 downregulated genes, were differentially expressed. According to the KEGG analysis, some genes were involved in osteoclast differentiation (Fcgr4, Lilrb4a), B cell receptor signaling (Cd72, Lilrb4a), and neutrophil extracellular trap formation (Hdac7, Padi4). Lilrb4 is related to osteoclast inhibition protein, whereas Hdac7 is a Runx2 corepressor that regulates osteoblast differentiation. Silencing Lilrb4 increased the number of osteoclasts and osteoclast marker genes. The knocking down of Hdac7 increased alkaline phosphatase activity, mineralization, and osteoblast marker genes. Therefore, our present study may provide an innovative idea for potential therapeutic targets and pathways in TβRI-associated bone loss.
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Affiliation(s)
- Ohnmar Myint
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
| | - Nithidol Sakunrangsit
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
| | - Jatuphol Pholtaisong
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
| | - Parichart Toejing
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
| | - Pinyada Pho-on
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
| | - Asada Leelahavanichkul
- Division of Immunology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Somyoth Sridurongrit
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Chatchawit Aporntewan
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Matthew B. Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
- Research Division, Hospital for Special Surgery, New York, NY 10065, USA
| | - Sutada Lotinun
- Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (O.M.); (N.S.); (J.P.); (P.T.); (P.P.-o.)
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Smit V, de Mol J, Kleijn MNAB, Depuydt MAC, de Winther MPJ, Bot I, Kuiper J, Foks AC. Sexual dimorphism in atherosclerotic plaques of aged Ldlr -/- mice. Immun Ageing 2024; 21:27. [PMID: 38698438 PMCID: PMC11064395 DOI: 10.1186/s12979-024-00434-3] [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: 02/08/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND Atherosclerosis, the main underlying pathology of cardiovascular disease, is a chronic inflammatory disease characterized by lipid accumulation and immune cell responses in the vascular wall, resulting in plaque formation. It is well-known that atherosclerosis prevalence and manifestation vary by sex. However, sexual dimorphism in the immune landscape of atherosclerotic plaques has up to date not been studied at high-resolution. In this study, we investigated sex-specific differences in atherosclerosis development and the immunological landscape of aortas at single-cell level in aged Ldlr-/- mice. METHODS We compared plaque morphology between aged male and female chow diet-fed Ldlr-/- mice (22 months old) with histological analysis. Using single-cell RNA-sequencing and flow cytometry on CD45+ immune cells from aortas of aged Ldlr-/- mice, we explored the immune landscape in the atherosclerotic environment in males and females. RESULTS We show that plaque volume is comparable in aged male and female mice, and that plaques in aged female mice contain more collagen and cholesterol crystals, but less necrotic core and macrophage content compared to males. We reveal increased immune cell infiltration in female aortas and found that expression of pro-atherogenic markers and inflammatory signaling pathways was enriched in plaque immune cells of female mice. Particularly, female aortas show enhanced activation of B cells (Egr1, Cd83, Cd180), including age-associated B cells, in addition to an increased M1/M2 macrophage ratio, where Il1b+ M1-like macrophages display a more pro-inflammatory phenotype (Nlrp3, Cxcl2, Mmp9) compared to males. In contrast, increased numbers of age-associated Gzmk+CD8+ T cells, dendritic cells, and Trem2+ macrophages were observed in male aortas. CONCLUSIONS Altogether, our findings highlight that sex is a variable that contributes to immunological differences in the atherosclerotic plaque environment in mice and provide valuable insights for further preclinical studies into the impact of sex on the pathophysiology of atherosclerosis.
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Affiliation(s)
- Virginia Smit
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Jill de Mol
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Mireia N A Bernabé Kleijn
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Marie A C Depuydt
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Menno P J de Winther
- Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Ilze Bot
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Johan Kuiper
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Amanda C Foks
- LACDR, Leiden Academic Centre for Drug Research, Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.
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Zhu ZX, Liu Y, Wang J, Xie Y, Li RY, Ma Q, Tu Q, Melhem NA, Couldwell S, El-Araby RE, Tai A, Van Dyke TE, Karimbux N, Jeong YN, Chen JJ. A novel lncRNA-mediated epigenetic regulatory mechanism in periodontitis. Int J Biol Sci 2023; 19:5187-5203. [PMID: 37928259 PMCID: PMC10620817 DOI: 10.7150/ijbs.87977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/01/2023] [Indexed: 11/07/2023] Open
Abstract
Periodontitis is a highly prevalent chronic inflammatory disease with an exaggerated host immune response, resulting in periodontal tissue destruction and potential tooth loss. The long non-coding RNA, LncR-ANRIL, located on human chromosome 9p21, is recognized as a genetic risk factor for various conditions, including atherosclerosis, periodontitis, diabetes, and cancer. LncR-APDC is an ortholog of ANRIL located on mouse genome chr4. This study aims to comprehend the regulatory role of lncR-APDC in periodontitis progression. Our experimental findings, obtained from lncR-APDC gene knockout (KO) mice with induced experimental periodontitis (EP), revealed exacerbated bone loss and disrupted pro-inflammatory cytokine regulation. Downregulation of osteogenic differentiation occurred in bone marrow stem cells harvested from lncR-APDC-KO mice. Furthermore, single-cell RNA sequencing of periodontitis gingival tissue revealed alterations in the proportion and function of immune cells, including T and B cells, macrophages, and neutrophils, due to lncR-APDC silencing. Our findings also unveiled a previously unidentified epithelial cell subset that is distinctively presenting in the lncR-APDC-KO group. This epithelial subset, characterized by the positive expression of Krt8 and Krt18, engages in interactions with immune cells through a variety of ligand-receptor pairs. The expression of Tff2, now recognized for its role in chronic inflammatory conditions, exhibited a notable increase across various tissue and cell types in lncR-APDC deficient mice. Additionally, our investigation revealed the potential for a direct binding interaction between lncR-APDC and Tff2. Intra-gingival administration of AAV9-lncR-APDC was shown to have therapeutic effects in the EP model. In conclusion, our results suggest that lncR-APDC plays a critical role in the progression of periodontal disease and holds therapeutic potential for periodontitis. Furthermore, the presence of the distinctive epithelial subpopulation and significantly elevated Tff2 levels in the lncR-APDC-silenced EP model offer new perspectives on the epigenetic regulation of periodontitis pathogenesis.
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Affiliation(s)
- Zoe Xiaofang Zhu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Yao Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jinghao Wang
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Ying Xie
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Rachel Yuantong Li
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qian Ma
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Qisheng Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Neiman A Melhem
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Sandrine Couldwell
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Rady E. El-Araby
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
- Data Intensive Studies Center, Tufts University, Medford, MA, United States
| | - Thomas E. Van Dyke
- Clinical and Translational Research, Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Forsyth Institute, Boston, MA, United States
| | - Nadeem Karimbux
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Y. Natalie Jeong
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
| | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, 136 Harrison Ave, M&V Building Room 830, Boston, MA 02111, United States
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02211, United States
- Department of Genetics, Molecular and Cell Biology, Tufts University School of Medicine, Tufts School of Graduate Biomedical Sciences, 136 Harrison Ave, M&V Room 811, Boston, MA 02111, United States
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Li W, Xiang B, Yang F, Rong Y, Yin Y, Yao J, Zhang H. scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data. Brief Bioinform 2023; 24:bbad391. [PMID: 37930028 DOI: 10.1093/bib/bbad391] [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: 07/24/2023] [Revised: 09/09/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Technological advances have now made it possible to simultaneously profile the changes of epigenomic, transcriptomic and proteomic at the single cell level, allowing a more unified view of cellular phenotypes and heterogeneities. However, current computational tools for single-cell multi-omics data integration are mainly tailored for bi-modality data, so new tools are urgently needed to integrate tri-modality data with complex associations. To this end, we develop scMHNN to integrate single-cell multi-omics data based on hypergraph neural network. After modeling the complex data associations among various modalities, scMHNN performs message passing process on the multi-omics hypergraph, which can capture the high-order data relationships and integrate the multiple heterogeneous features. Followingly, scMHNN learns discriminative cell representation via a dual-contrastive loss in self-supervised manner. Based on the pretrained hypergraph encoder, we further introduce the pre-training and fine-tuning paradigm, which allows more accurate cell-type annotation with only a small number of labeled cells as reference. Benchmarking results on real and simulated single-cell tri-modality datasets indicate that scMHNN outperforms other competing methods on both cell clustering and cell-type annotation tasks. In addition, we also demonstrate scMHNN facilitates various downstream tasks, such as cell marker detection and enrichment analysis.
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Affiliation(s)
- Wei Li
- College of Artificial Intelligence, Nankai University, Tongyan Road, 300350 Tianjin, China
- AI Lab, Tencent, Gaoxin 9th South Road, 518000 Shenzhen, China
| | - Bin Xiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Yueyang Road, 200031 Shanghai, China
| | - Fan Yang
- AI Lab, Tencent, Gaoxin 9th South Road, 518000 Shenzhen, China
| | - Yu Rong
- AI Lab, Tencent, Gaoxin 9th South Road, 518000 Shenzhen, China
| | - Yanbin Yin
- Department of Food Science and Technology, University of Nebraska - Lincoln, 1400 R Street, 68588 Nebraska, USA
| | - Jianhua Yao
- AI Lab, Tencent, Gaoxin 9th South Road, 518000 Shenzhen, China
| | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tongyan Road, 300350 Tianjin, China
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Xu J, Du J, Zhong Y, Zhang H, Zhou L, Yao Q. Blockage of CD72 reduces B cell proliferation in immune thrombocytopenic purpura, involving interleukin 1 and macrophage migration inhibitory factor secretion. Hematology 2022; 27:1196-1203. [DOI: 10.1080/16078454.2022.2140992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jianhui Xu
- Hematology Department, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Jingwen Du
- Hematology Department, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yuxia Zhong
- Hematology Department, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Honghao Zhang
- Hematology Department, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Lijuan Zhou
- Hematology Department, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Qianqian Yao
- Hematology Department, Shunde Hospital of Sourthern Medical University, Foshan, People’s Republic of China
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Lu X, Chen X, Wang X, Qing J, Li J, Pan Y. Construction of lncRNA and mRNA co-expression network associated with nasopharyngeal carcinoma progression. Front Oncol 2022; 12:965088. [PMID: 35957889 PMCID: PMC9360529 DOI: 10.3389/fonc.2022.965088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Nasopharyngeal carcinoma is a type of head and neck cancer with a high incidence in men. In the past decades, the survival rate of NPC has remained around 70%, but it often leads to treatment failure due to its distant metastasis or recurrence. The lncRNA-mRNA regulatory network has not been fully elucidated. We downloaded the NPC-related gene expression datasets GSE53819 and GSE12452 from the Gene Expression Omnibus database; GSE53819 included 18 NPC tissues and 18 normal tissues, and GSE12452 included 31 NPC tissues and 10 normal tissues. Weighted gene co-expression network analysis was performed on mRNA and lncRNA to screen out modules that were highly correlated with tumor progression. The two datasets were subjected to differential analysis after removing batch effects, and then Venn diagrams were used to screen for overlapping genes in the module genes and differential genes. The lncRNA-mRNA co-expression network was then constructed, and key mRNAs were identified by MCODE analysis and expression analysis. GSEA analysis and qRT-PCR were performed on key mRNAs. Through a series of analyses, we speculated that BTK, CD72, PTPN6, and VAV1 may be independent predictors of the prognosis of NPC patients.Taken together, our study provides potential candidate biomarkers for NPC diagnosis, prognosis, or precise treatment.
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Affiliation(s)
- Xu Lu
- Ningbo First Hospital, Ningbo, China
- *Correspondence: Xu Lu,
| | - Xing Chen
- Ningbo First Hospital, Ningbo, China
| | - Xinke Wang
- Ninghai County Third Hospital, Ningbo, China
| | - Jing Qing
- Ningbo First Hospital, Ningbo, China
| | - Ji Li
- Ningbo First Hospital, Ningbo, China
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