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Haga M, Iida K, Okada M. Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging. iScience 2024; 27:109708. [PMID: 38706856 PMCID: PMC11066433 DOI: 10.1016/j.isci.2024.109708] [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: 07/06/2023] [Revised: 02/05/2024] [Accepted: 04/06/2024] [Indexed: 05/07/2024] Open
Abstract
During aging, skin homeostasis is essential for maintaining appearance, as well as biological defense of the human body. In this study, we identified thrombospondin-1 (THBS1) and fibromodulin (FMOD) as positive and negative regulators, respectively, of the TGF-β1-SMAD4 axis in human skin aging, based on in vitro and in vivo omics analyses and mathematical modeling. Using transcriptomic and epigenetic analyses of senescent dermal fibroblasts, TGF-β1 was identified as the key upstream regulator. Bifurcation analysis revealed a binary high-/low-TGF-β1 switch, with THBS1 as the main controller. Computational simulation of the TGF-β1 signaling pathway indicated that THBS1 expression was sensitively regulated, whereas FMOD was regulated robustly. Results of sensitivity analysis and validation showed that inhibition of SMAD4 complex formation was a promising method to control THBS1 production and senescence. Therefore, this study demonstrated the potential of combining data-driven target discovery with mathematical approaches to determine the mechanisms underlying skin aging.
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Affiliation(s)
- Masatoshi Haga
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Basic Research Development Division, ROHTO Pharmaceutical Co., Ltd, Osaka 544-8666, Japan
| | - Keita Iida
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka 565-0871, Japan
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Ji Y, Chen Y, Tan X, Huang X, Gao Q, Ma Y, Yang S, Yin M, Yu M, Fang C, Wang Y, Shi Z, Chang J. Integrated transcriptomic and proteomic profiling reveals the key molecular signatures of brain endothelial reperfusion injury. CNS Neurosci Ther 2024; 30:e14483. [PMID: 37789643 PMCID: PMC11017417 DOI: 10.1111/cns.14483] [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: 12/20/2022] [Revised: 08/25/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Reperfusion therapy after ischemic stroke often causes brain microvascular injury. However, the underlying mechanisms are unclear. METHODS Transcriptomic and proteomic analyses were performed on human cerebral microvascular endothelial cells following oxygen-glucose deprivation (OGD) or OGD plus recovery (OGD/R) to identify molecules and signaling pathways dysregulated by reperfusion. Major findings were further validated in a mouse model of cerebral ischemia and reperfusion. RESULTS Transcriptomic analysis identified 390 differentially expressed genes (DEGs) between the OGD/R and OGD group. Pathway analysis indicated that these genes were mostly associated with inflammation, including the TNF signaling pathway, TGF-β signaling pathway, cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and NF-κB signaling pathway. Proteomic analysis identified 201 differentially expressed proteins (DEPs), which were primarily associated with extracellular matrix destruction and remodeling, impairment of endothelial transport function, and inflammatory responses. Six genes (DUSP1, JUNB, NFKBIA, NR4A1, SERPINE1, and THBS1) were upregulated by OGD/R at both the mRNA and protein levels. In mice with cerebral ischemia and reperfusion, brain TNF signaling pathway was activated by reperfusion, and inhibiting TNF-α with adalimumab significantly attenuated reperfusion-induced brain endothelial inflammation. In addition, the protein level of THBS1 was substantially upregulated upon reperfusion in brain endothelial cells and the peri-endothelial area in mice receiving cerebral ischemia. CONCLUSION Our study reveals the key molecular signatures of brain endothelial reperfusion injury and provides potential therapeutic targets for the treatment of brain microvascular injury after reperfusion therapy in ischemic stroke.
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Affiliation(s)
- Yabin Ji
- Department of NeurologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Yiman Chen
- Department of NeurologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Xixi Tan
- Department of NeurologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
- Department of NeurologyYangjiang People's HospitalYangjiangChina
| | - Xiaowen Huang
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Qiang Gao
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Yinzhong Ma
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Shilun Yang
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Meifang Yin
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Min Yu
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Cheng Fang
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Yu Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Zhu Shi
- Department of Neurology10th Affiliated Hospital, Southern Medical University (Dongguan People's Hospital)DongguanChina
| | - Junlei Chang
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhenChina
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Zondervan RL, Capobianco CA, Jenkins DC, Reicha JD, Fredrick LM, Lam C, Isenberg JS, Ahn J, Marcucio RS, Hankenson KD. CD47 is Required for Mesenchymal Progenitor Proliferation and Fracture Repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583756. [PMID: 38496546 PMCID: PMC10942414 DOI: 10.1101/2024.03.06.583756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
CD47 is a ubiquitous and pleiotropic cell-surface receptor. Disrupting CD47 enhances injury repair in various tissues but the role of CD47 has not been studied in bone injuries. In a murine closed-fracture model, CD47-null mice showed decreased callus bone volume, bone mineral content, and tissue mineral content as assessed by microcomputed tomography 10 days post-fracture, and increased fibrous volume as determined by histology. To understand the cellular basis for this phenotype, mesenchymal progenitors (MSC) were harvested from bone marrow. CD47-null MSC showed decreased large fibroblast colony formation (CFU-F), significantly less proliferation, and fewer cells in S-phase, although osteoblast differentiation was unaffected. However, consistent with prior research, CD47-null endothelial cells showed increased proliferation relative to WT cells. Similarly, in a murine ischemic fracture model, CD47-null mice showed reduced fracture callus bone volume and bone mineral content relative to WT. Consistent with our in vitro results, in vivo EdU labeling showed decreased cell proliferation in the callus of CD47-null mice, while staining for CD31 and endomucin demonstrated increased endothelial cell mass. Finally, WT mice administered a CD47 morpholino, which blocks CD47 protein production, showed a callus phenotype similar to that of non-ischemic and ischemic fractures in CD47-null mice, suggesting the phenotype was not due to developmental changes in the knockout mice. Thus, inhibition of CD47 during bone healing reduces both non-ischemic and ischemic fracture healing, in part, by decreasing MSC proliferation. Furthermore, the increase in endothelial cell proliferation and early blood vessel density caused by CD47 disruption is not sufficient to overcome MSC dysfunction.
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Affiliation(s)
- Robert L. Zondervan
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
- College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States, 48824
| | - Christina A. Capobianco
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor Michigan, United States, 48109
| | - Daniel C. Jenkins
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
| | - John D. Reicha
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
| | - Livia M. Fredrick
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
| | - Charles Lam
- Department of Orthopaedic Surgery, University of California at San Francisco, San Francisco, California, United States, 94142
| | - Jeffery S. Isenberg
- Department of Diabetes Complications and Metabolism and Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope National Medical Center, Duarte, California, United States, 91010
| | - Jaimo Ahn
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
| | - Ralph S. Marcucio
- Department of Orthopaedic Surgery, University of California at San Francisco, San Francisco, California, United States, 94142
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan, United States, 48109
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Lin Z, Zhang J, Chen Q, Zhang X, Zhang D, Lin J, Lin D. Transcriptome analysis of the adenoma-carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer. Front Vet Sci 2023; 10:1192525. [PMID: 38098990 PMCID: PMC10720982 DOI: 10.3389/fvets.2023.1192525] [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: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 12/17/2023] Open
Abstract
The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in canines is not clear. We collected transcriptome data from 8 normal colon tissues, 4 adenoma tissues, and 15 cancer tissues. Differential analysis was unable to determine the dynamic changes of genes but revealed that PFKFB3 may play a key role in this process. Enrichment analysis explained metabolic dysregulation, immunosuppression, and typical cancer pathways in canine colorectal tumors. MFuzz generated specific dynamic expression patterns of five differentially expressed genes (DEGs). Weighted correlation network analysis showed that DEGs in cluster 3 were associated with malignant tissues, revealing the key role of inflammatory and immune pathways in canine CRC, and the S100A protein family was also found to be involved in the malignant transformation of canine colorectal tumors. By comparing strategies between humans and dogs, we found five novel markers that may be drivers of CRC. Among them, GTBP4 showed excellent diagnostic and prognostic ability. This study was the first systematic exploration of transformation in canine CRC, complemented the molecular characteristics of the development and progression of canine CRC, and provided new potential biomarkers and comparative oncologic evidence for biomarker studies in human colorectal cancer.
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Affiliation(s)
- Zixiang Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiatong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohu Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiahao Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Degui Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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