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Gu L, Chen J, Hu C, Wang D, Huan S, Rong G, Lv R, Xu T. Integrated transcriptomics and metabolomics study of embryonic breast muscle of Jiaji ducks. BMC Genomics 2024; 25:551. [PMID: 38824564 PMCID: PMC11144331 DOI: 10.1186/s12864-024-10452-6] [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: 10/14/2023] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
Because number of matured muscle fibers in poultry does not increase after birth, the meat yield is mainly determined during embryogenesis. We previously indicated breast muscle grew rapidly from 18th day after hatching (E18) to E27, and almost stopped from E27 to E34 of Jiaji ducks, while the mechanism is unclear. This study utilized RNA-seq to explore the related genes of muscle development and their relationship with small molecule metabolites at E18, E27 and E34 of Jiaji ducks. Several thousand differentially expressed genes (DEGs) were detected among E18, E27 and E34. DEGs expression profiles included 8 trend maps, among which trend 1 was opposite to and trend 6 was consistent with breast muscle development trend of Jiaji ducks. Through joint analysis between trend 1 of DEGs and trend 1 of differential metabolites (DEMs), protein digestion and absorption pathway stood out. The decrease of COL8A2 gene expression will lead to the decrease of arginine content, which will inhibit the development of breast muscle in embryonic Jiaji duck. Similarly, joint analysis between trend 6 of DEGs and trend 6 of DEMs indicated the increase of GAMT gene expression will cause the increase of proline content, and then promote the development of breast muscle of Jiaji duck in embryonic period. These results will be helpful for further understanding the mechanism of muscle yields of Jiaji ducks.
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Affiliation(s)
- Lihong Gu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, P.R. China
| | - Jile Chen
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
- School of Animal Science and Technology, School of Animal Medicine, Huazhong Agricultural University, Hubei Province, Hongshan District, Wuhan, 430072, China
| | - Chengjun Hu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Dingfa Wang
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Shuqian Huan
- College of Animal Science, Hainan University, Haikou, 570228, P.R. China
| | - Guang Rong
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Renlong Lv
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Tieshan Xu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China.
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Lai W, Wang Y, Huang C, Xu H, Zheng X, Li K, Wang J, Lou Z. DIREN mitigates DSS-induced colitis in mice and attenuates collagen deposition via inhibiting the Wnt/β-catenin and focal adhesion pathways. Biomed Pharmacother 2024; 175:116671. [PMID: 38678963 DOI: 10.1016/j.biopha.2024.116671] [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: 03/11/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND DIREN is a SHE ethnic medicine with stasis-resolving, hemostasis, clearing heat, and removing toxin effects. It is clinically used in the treatment of gastrointestinal bleeding, such as ulcerative colitis (UC). AIM OF THE STUDY Fibrosis is one of the pathological changes in the progression of UC, which can make it challenging to respond to a treatment. We aimed to illuminate the role of DIREN in DSS-induced UC and tried to unveil its related mechanisms from two perspectives: intestinal inflammation and collagen deposition. MATERIALS AND METHODS A 2.5 % dextran sulfate sodium (DSS) water solution was used to induce colitis in mice. The therapeutic effect of DIREN was assessed using the disease activity index, histopathological score, and colon length. Masson and Sirius Red staining was used to observe the fibrosis in the colon. Apoptosis of colonic epithelial cells was observed by TUNEL immunofluorescence staining. RNA-seq observed differential genes and enrichment pathways. Immunohistochemistry and RT-qPCR were used to detect the expression of molecules related to fibrosis and focal adhesion signaling in colon tissue. RESULTS The administration of DIREN resulted in a reduction of disease activity index (DAI) in mice with UC while simultaneously promoting an increase in colon length. DIREN mitigated the loss of goblet cells in the colon of UC mice and maintained the integrity of the intestinal mucosa barrier. Masson staining revealed a reduction in colonic fibrosis with DIREN treatment, while Sirius red staining demonstrated a decrease in collagen Ⅰ deposition. DIREN reduced apoptosis of colonic epithelial cells and the expression of genes, such as CDH2, ITGA1, and TGF-β2. Additionally, the results of GSEA analysis of colon tissue transcriptome showed that the differentially expressed genes were enriched in the focal adhesion pathway. DIREN was found to downregulate the protein expression of BAX, N-cadherin, β-catenin, Integrin A1, and Vinculin while upregulating the protein expression of BCL2. Additionally, it led to the co-expression of N-cadherin and α-SMA. CONCLUSION DIREN exerts a protective effect against DSS-induced UC by ameliorating colonic fibrosis via regulation of focal adhesion and the WNT/β-catenin signaling pathway, thereby inhibiting fibroblast migration and reducing collagen secretion.
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Affiliation(s)
- Weizhi Lai
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yingying Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Chen Huang
- The First School of Clinical Medical, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Hao Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Xunjie Zheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Ke Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Jue Wang
- Department of Oncology, the Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310005, China
| | - Zhaohuan Lou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China; Songyang Institute of Zhejiang Chinese Medical University, Lishui, Zhejiang 323400, China.
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Chen M, Pan Y, Chen Z, Qi F, Gu J, Qiu Y, He A, Liu J. miRSNP rs188493331: A key player in genetic control of microRNA-induced pathway activation in hypertrophic scars and keloids. Skin Res Technol 2024; 30:e13686. [PMID: 38682767 PMCID: PMC11057055 DOI: 10.1111/srt.13686] [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: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Our study aims to delineate the miRSNP-microRNA-gene-pathway interactions in the context of hypertrophic scars (HS) and keloids. MATERIALS AND METHODS We performed a computational biology study involving differential expression analysis to identify genes and their mRNAs in HS and keloid tissues compared to normal skin, identifying key hub genes and enriching their functional roles, comprehensively analyzing microRNA-target genes and related signaling pathways through bioinformatics, identifying MiRSNPs, and constructing a pathway-based network to illustrate miRSNP-miRNA-gene-signaling pathway interactions. RESULTS Our results revealed a total of 429 hub genes, with a strong enrichment in signaling pathways related to proteoglycans in cancer, focal adhesion, TGF-β, PI3K/Akt, and EGFR tyrosine kinase inhibitor resistance. Particularly noteworthy was the substantial crosstalk between the focal adhesion and PI3K/Akt signaling pathways, making them more susceptible to regulation by microRNAs. We also identified specific miRNAs, including miRNA-1279, miRNA-429, and miRNA-302e, which harbored multiple SNP loci, with miRSNPs rs188493331 and rs78979933 exerting control over a significant number of miRNA target genes. Furthermore, we observed that miRSNP rs188493331 shared a location with microRNA302e, microRNA202a-3p, and microRNA20b-5p, and these three microRNAs collectively targeted the gene LAMA3, which is integral to the focal adhesion signaling pathway. CONCLUSIONS The study successfully unveils the complex interactions between miRSNPs, miRNAs, genes, and signaling pathways, shedding light on the genetic factors contributing to HS and keloid formation.
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Affiliation(s)
- Meiqing Chen
- Department of DermatologyZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
- Xiamen Clinical Research Center for Cancer TherapyZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
| | - Yuyan Pan
- Department of Plastic and Reconstructive SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Zhiwei Chen
- Big Data and Artificial Intelligence CenterZhongshan HospitalFudan UniversityShanghaiChina
| | - Fazhi Qi
- Department of Plastic and Reconstructive SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Jianying Gu
- Department of Plastic and Reconstructive SurgeryZhongshan HospitalFudan UniversityShanghaiChina
- Artificial Intelligence Center for Plastic Surgery and Cutaneous Soft Tissue CancersZhongshan HospitalFudan UniversityShanghaiChina
| | - Yangyang Qiu
- Department of DermatologyZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
- Xiamen Clinical Research Center for Cancer TherapyZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
| | - Anqi He
- Xiamen Clinical Research Center for Cancer TherapyZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
- Department of Plastic and Reconstructive SurgeryZhongshan hospital (Xiamen)Fudan UniversityXiamenChina
| | - Jiaqi Liu
- Department of Plastic and Reconstructive SurgeryZhongshan HospitalFudan UniversityShanghaiChina
- Artificial Intelligence Center for Plastic Surgery and Cutaneous Soft Tissue CancersZhongshan HospitalFudan UniversityShanghaiChina
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Huang D, Zhu Y, Shen J, Song C. Identification of Potential Neddylation-related Key Genes in Ischemic Stroke based on Machine Learning Methods. Mol Neurobiol 2024; 61:2530-2541. [PMID: 37910287 DOI: 10.1007/s12035-023-03738-5] [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: 08/21/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Ischemic stroke (IS) is a complex neurological disease that can lead to severe disability or even death. Understanding the molecular mechanisms involved in the occurrence and progression of IS is of great significance for developing effective treatment strategies. In this context, the role of neddylation refers to the potential impact of neddylation on various cellular processes, which may contribute to the pathogenesis and outcome of IS. First, differential analysis was conducted on the GSE16561 dataset from the GEO database to identify 350 differentially expressed genes (DEGs) between the IS and Control groups. By intersecting the differential genes with neddylation-related genes, 11 neddylation-related DEGs were obtained. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the DEGs were mainly enriched in hematopoietic cell lineage and neutrophil degranulation, while the neddylation-related DEGs were mainly enriched in apoptosis and post-translational protein modification. Further Lasso-Cox and random forest analyses were performed on the 11 neddylation-related DEGs, identifying key genes SRPK1, BIRC2, and KLHL3. Additionally, validation of the key genes was carried out using the GSE58294 dataset and clinical patients. Finally, the correlation between the key genes and ferroptosis and cuproptosis was analyzed, and a ceRNA network was constructed. Our study helps to elucidate the complex role of neddylation in the mechanism of ischemic stroke, providing potential opportunities for the development of therapeutic interventions.
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Affiliation(s)
- Dian Huang
- Department of Radiology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Yan Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Junfei Shen
- Cardiac Color Doppler Ultrasound Room, Wuxi No.2 People's Hospital, Wuxi, 214000, China.
| | - Chenglin Song
- Nutritional Department, The Second People's Hospital of Lianyungang, Lianyungang, 222000, China.
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Junaid M, Lu H, Li Y, Liu Y, Din AU, Qi Z, Xiong Y, Yan J. Novel Synergistic Probiotic Intervention: Transcriptomic and Metabolomic Analysis Reveals Ameliorative Effects on Immunity, Gut Barrier, and Metabolism of Mice during Salmonella typhimurium Infection. Genes (Basel) 2024; 15:435. [PMID: 38674370 PMCID: PMC11050207 DOI: 10.3390/genes15040435] [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: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Salmonella typhimurium (S. typhimurium), a prevalent cause of foodborne infection, induces significant changes in the host transcriptome and metabolome. The lack of therapeutics with minimal or no side effects prompts the scientific community to explore alternative therapies. This study investigates the therapeutic potential of a probiotic mixture comprising Lactobacillus acidophilus (L. acidophilus 1.3251) and Lactobacillus plantarum (L. plantarum 9513) against S. typhimurium, utilizing transcriptome and metabolomic analyses, a novel approach that has not been previously documented. Twenty-four SPF-BALB/c mice were divided into four groups: control negative group (CNG); positive control group (CPG); probiotic-supplemented non-challenged group (LAPG); and probiotic-supplemented Salmonella-challenged group (LAPST). An RNA-sequencing analysis of small intestinal (ileum) tissue revealed 2907 upregulated and 394 downregulated DEGs in the LAPST vs. CPG group. A functional analysis of DEGs highlighted their significantly altered gene ontology (GO) terms related to metabolism, gut integrity, cellular development, and immunity (p ≤ 0.05). The KEGG analysis showed that differentially expressed genes (DEGs) in the LAPST group were primarily involved in pathways related to gut integrity, immunity, and metabolism, such as MAPK, PI3K-Akt, AMPK, the tryptophan metabolism, the glycine, serine, and threonine metabolism, ECM-receptor interaction, and others. Additionally, the fecal metabolic analysis identified 1215 upregulated and 305 downregulated metabolites in the LAPST vs. CPG group, implying their involvement in KEGG pathways including bile secretion, propanoate metabolism, arginine and proline metabolism, amino acid biosynthesis, and protein digestion and absorption, which are vital for maintaining barrier integrity, immunity, and metabolism. In conclusion, these findings suggest that the administration of a probiotic mixture improves immunity, maintains gut homeostasis and barrier integrity, and enhances metabolism in Salmonella infection.
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Affiliation(s)
- Muhammad Junaid
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
| | - Hongyu Lu
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
| | - Yixiang Li
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
| | - Yu Liu
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
| | - Ahmad Ud Din
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC 28081, USA
| | - Zhongquan Qi
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
| | - Yi Xiong
- Guangxi Center for Animals Disease Control and Prevention, Nanning 530004, China
| | - Jianhua Yan
- Medical College, Guangxi University, Nanning 530004, China; (M.J.); (H.L.); (Y.L.); (Y.L.); (Z.Q.)
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Hamadmad S, Heisler-Taylor T, Goswami S, Hawthorn E, Chaurasia S, Martini D, Summitt D, Zaatari A, Urbanski EG, Bernstein K, Racine J, Satoskar A, El-Hodiri HM, Fischer AJ, Cebulla CM. Ibudilast Protects Retinal Bipolar Cells from Excitotoxic Retinal Damage and Activates the mTOR Pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585556. [PMID: 38562805 PMCID: PMC10983953 DOI: 10.1101/2024.03.18.585556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilast's potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography, and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilast's neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Müller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilast's potential to protect inner retinal neurons during damage and show promise for future clinical translation.
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Guerrache A, Micheau O. TNF-Related Apoptosis-Inducing Ligand: Non-Apoptotic Signalling. Cells 2024; 13:521. [PMID: 38534365 DOI: 10.3390/cells13060521] [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: 02/07/2024] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
TNF-related apoptosis-inducing ligand (TRAIL or Apo2 or TNFSF10) belongs to the TNF superfamily. When bound to its agonistic receptors, TRAIL can induce apoptosis in tumour cells, while sparing healthy cells. Over the last three decades, this tumour selectivity has prompted many studies aiming at evaluating the anti-tumoral potential of TRAIL or its derivatives. Although most of these attempts have failed, so far, novel formulations are still being evaluated. However, emerging evidence indicates that TRAIL can also trigger a non-canonical signal transduction pathway that is likely to be detrimental for its use in oncology. Likewise, an increasing number of studies suggest that in some circumstances TRAIL can induce, via Death receptor 5 (DR5), tumour cell motility, potentially leading to and contributing to tumour metastasis. While the pro-apoptotic signal transduction machinery of TRAIL is well known from a mechanistic point of view, that of the non-canonical pathway is less understood. In this study, we the current state of knowledge of TRAIL non-canonical signalling.
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Affiliation(s)
- Abderrahmane Guerrache
- Université de Bourgogne, 21000 Dijon, France
- INSERM Research Center U1231, «Equipe DesCarTes», 21000 Dijon, France
| | - Olivier Micheau
- Université de Bourgogne, 21000 Dijon, France
- INSERM Research Center U1231, «Equipe DesCarTes», 21000 Dijon, France
- Laboratoire d'Excellence LipSTIC, 21000 Dijon, France
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Hernandez C, Gorska AM, Eugenin E. Mechanisms of HIV-mediated blood-brain barrier compromise and leukocyte transmigration under the current antiretroviral era. iScience 2024; 27:109236. [PMID: 38487019 PMCID: PMC10937838 DOI: 10.1016/j.isci.2024.109236] [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: 11/06/2023] [Revised: 12/18/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
HIV-associated neurological compromise is observed in more than half of all people with HIV (PWH), even under antiretroviral therapy (ART). The mechanism has been associated with the early transmigration of HIV-infected monocytes across the BBB in a CCL2 and HIV replication-dependent manner. However, the mechanisms of chronic brain damage are unknown. We demonstrate that all PWH under ART have elevated circulating ATP levels that correlate with the onset of cognitive impairment even in the absence of a circulating virus. Serum ATP levels found in PWH with the most severe neurocognitive impairment trigger the transcellular migration of HIV-infected leukocytes across the BBB in a JAM-A and LFA-1-dependent manner. We propose that targeting transcellular leukocyte transmigration could reduce or prevent the devastating consequences of HIV within the brains of PWH under ART.
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Affiliation(s)
- Cristian Hernandez
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Anna Maria Gorska
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Department of Pathology, University of Oslo, Oslo, Norway
| | - Eliseo Eugenin
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
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Li Y, Liao Z, Fan X, Wang Y, Liu F, Zhang X, He J, Buttino I, Yan X, Tang C. The molecular response of Mytilus coruscus mantle to shell damage under acute acidified sea water revealed by iTRAQ based quantitative proteomic analysis. J Proteomics 2024; 294:105062. [PMID: 38158015 DOI: 10.1016/j.jprot.2023.105062] [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: 08/01/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Mytilus coruscus is an economically important marine bivalve that lives in estuarine sea areas with seasonal coastal acidification and frequently suffers shell injury in the natural environment. However, the molecular responses and biochemical properties of Mytilus under these conditions are not fully understood. In the present study, we employed tandem mass spectrometry combined with isobaric tagging to identify differentially expressed proteins in the mantle tissue of M. coruscus under different short-term treatments, including shell-complete mussels raised in normal seawater (pH 8.1), shell-damaged mussels raised in normal seawater (pH 8.1), and acidified seawater (pH 7.4). A total of 2694 proteins were identified in the mantle, and analysis of their relative abundance from the three different treatments revealed alterations in the proteins involved in immune regulation, oxidation-reduction processes, protein folding and processing, energy provision, and cytoskeleton. The results obtained by quantitative proteomic analysis of the mantle allowed us to delineate the molecular strategies adopted by M. coruscus in the shell repair process in acidified environments, including an increase in proteins involved in oxidation-reduction processes, protein processing, and cell growth at the expense of proteins involved in immune capacity and energy metabolism. SIGNIFICANCE: The impact of global ocean acidification on calcifying organisms has become a major ecological and environmental problem in the world. Mytilus coruscus is an economically important marine bivalve living in estuary sea area with seasonal coastal acidification, and frequently suffering shell injury in natural environment. Molecular responses of M coruscus under the shell damage and acute acidification is still largely unknown. For this reason, iTRAQ based quantitative proteomic and histological analysis of the mantle from M. coruscus under shell damage and acute acidification were performed, for revealing the proteomic response and possible adaptation mechanism of Mytilus under combined shell damage and acidified sea water, and understanding how the mussel mantle implement a shell-repair process under acidified sea water. Our study provides important data for understanding the shell repair process and proteomic response of Mytilus under ocean acidification, and providing insights into potential adaptation of mussels to future global change.
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Affiliation(s)
- Yingao Li
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China.
| | - Xiaojun Fan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Ying Wang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Fei Liu
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Jianyu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research (ISPRA), Via Vitaliano Brancati 48, 00144 Rome, Italy
| | - Xiaojun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China
| | - Changsheng Tang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City 316022, Zhejiang, China.
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Yang Q, Lin Z, Xue M, Jiang Y, Chen L, Chen J, Liao Y, Lv J, Guo B, Zheng P, Huang H, Sun B. Deciphering the omicron variant: integrated omics analysis reveals critical biomarkers and pathophysiological pathways. J Transl Med 2024; 22:219. [PMID: 38424541 PMCID: PMC10905948 DOI: 10.1186/s12967-024-05022-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The rapid emergence and global dissemination of the Omicron variant of SARS-CoV-2 have posed formidable challenges in public health. This scenario underscores the urgent need for an enhanced understanding of Omicron's pathophysiological mechanisms to guide clinical management and shape public health strategies. Our study is aimed at deciphering the intricate molecular mechanisms underlying Omicron infections, particularly focusing on the identification of specific biomarkers. METHODS This investigation employed a robust and systematic approach, initially encompassing 15 Omicron-infected patients and an equal number of healthy controls, followed by a validation cohort of 20 individuals per group. The study's methodological framework included a comprehensive multi-omics analysis that integrated proteomics and metabolomics, augmented by extensive bioinformatics. Proteomic exploration was conducted via an advanced Ultra-High-Performance Liquid Chromatography (UHPLC) system linked with mass spectrometry. Concurrently, metabolomic profiling was executed using an Ultra-Performance Liquid Chromatography (UPLC) system. The bioinformatics component, fundamental to this research, entailed an exhaustive analysis of protein-protein interactions, pathway enrichment, and metabolic network dynamics, utilizing state-of-the-art tools such as the STRING database and Cytoscape software, ensuring a holistic interpretation of the data. RESULTS Our proteomic inquiry identified eight notably dysregulated proteins (THBS1, ACTN1, ACTC1, POTEF, ACTB, TPM4, VCL, ICAM1) in individuals infected with the Omicron variant. These proteins play critical roles in essential physiological processes, especially within the coagulation cascade and hemostatic mechanisms, suggesting their significant involvement in the pathogenesis of Omicron infection. Complementing these proteomic insights, metabolomic analysis discerned 146 differentially expressed metabolites, intricately associated with pivotal metabolic pathways such as tryptophan metabolism, retinol metabolism, and steroid hormone biosynthesis. This comprehensive metabolic profiling sheds light on the systemic implications of Omicron infection, underscoring profound alterations in metabolic equilibrium. CONCLUSIONS This study substantially enriches our comprehension of the physiological ramifications induced by the Omicron variant, with a particular emphasis on the pivotal roles of coagulation and platelet pathways in disease pathogenesis. The discovery of these specific biomarkers illuminates their potential as critical targets for diagnostic and therapeutic strategies, providing invaluable insights for the development of tailored treatments and enhancing patient care in the dynamic context of the ongoing pandemic.
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Affiliation(s)
- Qianyue Yang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Zhiwei Lin
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- Respiratory Mechanics Laboratory, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Mingshan Xue
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio Island, XingDaoHuanBei Road, Guangzhou, 510005, Guangdong Province, China
| | - Yueting Jiang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Libing Chen
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jiahong Chen
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yuhong Liao
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jiali Lv
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Baojun Guo
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Peiyan Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Huimin Huang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, XingDaoHuanBei Road, Guangzhou, 510005, Guangdong Province, China.
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11
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Zhang X, Wu L, Jia L, Hu X, Yao Y, Liu H, Ma J, Wang W, Li L, Chen K, Liu B. The implication of integrative multiple RNA modification-based subtypes in gastric cancer immunotherapy and prognosis. iScience 2024; 27:108897. [PMID: 38318382 PMCID: PMC10839690 DOI: 10.1016/j.isci.2024.108897] [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: 07/28/2023] [Revised: 10/28/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Previous studies have focused on the impact of individual RNA modifications on tumor development. This study comprehensively investigated the effects of multiple RNA modifications, including m6A, alternative polyadenylation, pseudouridine, adenosine-to-inosine editing, and uridylation, on gastric cancer (GC). By analyzing 1,946 GC samples from eleven independent cohorts, we identified distinct clusters of RNA modification genes with varying survival rates and immunological characteristics. We assessed the chromatin activity of these RNA modification clusters through regulon enrichment analysis. A prognostic model was developed using Stepwise Regression and Random Survival Forest algorithms and validated in ten independent datasets. Notably, the low-risk group showed a more favorable prognosis and positive response to immune checkpoint blockade therapy. Single-cell RNA sequencing confirmed the abundant expression of signature genes in B cells and plasma cells. Overall, our findings shed light on the potential significance of multiple RNA modifications in GC prognosis, stemness development, and chemotherapy resistance.
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Affiliation(s)
- Xiangnan Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Liuxing Wu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Liqing Jia
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Yanxin Yao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Huahuan Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Junfu Ma
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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12
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He Y, Gang B, Zhang M, Bai Y, Wan Z, Pan J, Liu J, Liu G, Gu W. ACE2 improves endothelial cell function and reduces acute lung injury by downregulating FAK expression. Int Immunopharmacol 2024; 128:111535. [PMID: 38246001 DOI: 10.1016/j.intimp.2024.111535] [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: 11/16/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Endothelial cell (EC) barrier dysfunction and increased adhesion of immune inflammatory cells to ECs crucially contribute to acute lung injury (ALI). Angiotensin-converting enzyme 2 (ACE2) is an essential regulator of the renin-angiotensin system (RAS) and exerts characteristic vasodilatory and anti-inflammatory effects. SARS-COV-2 infects the lungs by binding to ACE2, which can lead to dysregulation of ACE2 expression, further leading to ALI with predominantly vascular inflammation and eventually to more severe acute respiratory distress syndrome (ARDS). Therefore, restoration of ACE2 expression represents a valuable therapeutic approach for SARS-COV-2-related ALI/ARDS. In this study, we used polyinosinic-polycytidylic acid (Poly(I:C)), a double-stranded RNA analog, to construct a mouse ALI model that mimics virus infection. After Poly(I:C) exposure, ACE2 was downregulated in mouse lung tissues and in cultured ECs. Treatment with DIZE, an ACE2-activating compound, upregulated ACE2 expression and relieved ALI in mice. DIZE also improved barrier function and reduced the number of THP-1 monocytes adhering to cultured ECs. Focal adhesion kinase (FAK) and phosphorylated FAK (p-FAK) levels were increased in lung tissues of ALI mice as well as in Poly(I:C)-treated ECs in vitro. Both DIZE and the FAK inhibitor PF562271 decreased FAK/p-FAK expression in both ALI models, attenuating ALI severity in vivo and increasing barrier function and reducing monocyte adhesion in cultured ECs. Furthermore, in vivo experiments using ANG 1-7 and the MAS inhibitor A779 corroborated that DIZE-mediated ACE2 activation stimulated the activity of the ANG 1-7/MAS axis, which inhibited FAK/p-FAK expression in the mouse lung. These findings provide further evidence that activation of ACE2 in ECs may be a valuable therapeutic strategy for ALI.
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Affiliation(s)
- Yixuan He
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Baocai Gang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Yuting Bai
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Ziyu Wan
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Jiesong Pan
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Jie Liu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan Province, PR China
| | - Guoquan Liu
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China.
| | - Wei Gu
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China.
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13
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Zhang C, Wang Y, Zhen Z, Li J, Su J, Wu C. mTORC1 Mediates Biphasic Mechano-Response to Orchestrate Adhesion-Dependent Cell Growth and Anoikis Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307206. [PMID: 38041494 PMCID: PMC10853740 DOI: 10.1002/advs.202307206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Indexed: 12/03/2023]
Abstract
Cells constantly sense and respond to not only biochemical but also biomechanical changes in their microenvironment, demanding for dynamic metabolic adaptation. ECM stiffening is a hallmark of cancer aggressiveness, while survival under substrate detachment also associates with poor prognosis. Mechanisms underlying this, non-linear mechano-response of tumor cells may reveal potential double-hit targets for cancers. Here, an integrin-GSK3β-FTO-mTOR axis is reported, that can integrate stiffness sensing to ensure both the growth advantage endowed by rigid substrate and cell death resistance under matrix detachment. It is demonstrated that substrate stiffening can activate mTORC1 and elevate mTOR level through integrins and GSK3β-FTO mediated mRNA m6 A modification, promoting anabolic metabolism. Inhibition of this axis upon ECM detachment enhances autophagy, which in turn conveys resilience of tumor cells to anoikis, as it is demonstrated in human breast ductal carcinoma in situ (DCIS) and mice malignant ascites. Collectively, these results highlight the biphasic mechano-regulation of cellular metabolism, with implications in tumor growth under stiffened conditions such as fibrosis, as well as in anoikis-resistance during cancer metastasis.
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Affiliation(s)
- Chunlei Zhang
- Institute of Systems BiomedicineSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- International Cancer InstituteBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191China
| | - Yuan Wang
- Institute of Systems BiomedicineSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- International Cancer InstituteBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191China
| | - Zifeng Zhen
- Institute of Systems BiomedicineSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- International Cancer InstituteBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191China
| | - Jiayi Li
- Institute of Systems BiomedicineSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- International Cancer InstituteBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191China
| | - Jing Su
- Pathology DepartmentPeking University Third HospitalBeijing100191China
| | - Congying Wu
- Institute of Systems BiomedicineSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- International Cancer InstituteBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191China
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14
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Chen WK, Zhang HJ, Liu J, Dai Z, Zhan XL. COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes. Int Immunopharmacol 2024; 127:111416. [PMID: 38145599 DOI: 10.1016/j.intimp.2023.111416] [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: 07/20/2023] [Revised: 12/02/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Synovial chondromatosis (SC) primarily affects the major joints and is characterized by the formation of benign cartilaginous nodules. In the present study, we evaluated the differences in the histology and gene expression of SC and normal cartilages and further elucidated the function of hub genes in SC. METHODS Histological staining and biochemical analysis were performed to measure collagen and glycosaminoglycan (GAG) contents in SC and normal cartilage samples. Then, microarray analysis was performed using knee joint samples (three normal and three SC samples) to identify the differentially expressed genes (DEGs). Subsequently, bioinformatics analysis was performed to identify the hub genes and explore the mechanisms underlying SC. The intersection of the top 10 upregulated DEGs, top 10 downregulated DEGs, and hub genes was validated in SC tissues. Lastly, in vitro experiments and our clinical cohort were used to determine the potential biological functions and diagnostic value, respectively, of the most significant gene. RESULTS The GAG and collagen contents were comparable to or higher in SC tissues than in normal tissues. Microarray analysis revealed 143 upregulated and 107 downregulated DEGs in SC. Furthermore, functional enrichment analysis revealed an association between immunity and metabolism-related pathways and SC development. Among 20 hub genes, two intersection genes, namely, collagen type III alpha 1 chain (COL3A1) and HSPA8, were notably expressed in SC tissues, with COL3A1 exhibiting a more significant difference in mRNA expression. Furthermore, COL3A1 can promote chondrocyte migration and cell cycle progression. Additionally, clinical data revealed COL3A1 can be a diagnostic marker for primary SC (AUC = 0.82) and be a positive correlation with neutrophil-to-lymphocyte ratio. CONCLUSIONS These results suggest that SC tissues contained the abundant GAG and collagen. COL3A1 can affect the function of chondrocytes and be a diagnostic marker of primary SC patients. These findings provide a novel approach and a fundamental contribution for diagnosis and treatment in SC.
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Affiliation(s)
- Wen-Kang Chen
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China; The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Han-Jing Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, No. 69 ChuanShan Road, Shigu District, Hengyang, 421001, Hunan, China
| | - Jianghua Liu
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhu Dai
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Xin-Li Zhan
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China.
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15
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Zhao X, Zhang Y, Wu F, Li X, Guo S, Li X. MeCP2-Induced Alternations of Transcript Levels and m6A Methylation in Human Retinal Pigment Epithelium Cells. ACS OMEGA 2023; 8:47964-47973. [PMID: 38144074 PMCID: PMC10734004 DOI: 10.1021/acsomega.3c06610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
MeCP2 is a transcriptional regulator that is involved in epithelial-mesenchymal transition (EMT) and is highly expressed in proliferative vitreoretinopathy. m6A methylation is a critical post-transcriptional regulation in eukaryotic cells. However, the connection between MeCP2 and m6A methylation has not been revealed in retinal pigment epithelium (RPE), and the regulatory role of MeCP2 at the post-transcriptional level in an m6A-dependent manner is rarely investigated. In this study, we used sequencing to reveal differences in transcript levels and m6A abundance of individual genes in RPE cells after treatment with human recombinant protein MeCP2. The biological functions and processes of differential genes were further analyzed by bioinformatics. The results exhibited that after MeCP2 treatment, 65 genes were up-regulated and 43 genes were down-regulated at the transcription level, and 4 peaks were hypermethylated and 9,041 peaks were hypomethylated at the m6A modification level. Enrichment analysis found that differentially expressed genes were associated with organic acid metabolism, melanogenesis, and vascular smooth muscle contraction. In addition, differentially methylated genes were related to cell junction, RNA processing and metabolism, cell activity, actin cytoskeleton, and several signaling pathways associated with EMT. Further conjoint analysis indicated that the transcription and m6A levels of the EGR1, ELOVL2, and SFR1 genes were altered, and EGR1 is an essential transcription factor in the EMT process. The RNA levels and m6A levels of the three genes were verified by qPCR and m6A-IP-qPCR, respectively. Overall, this study preliminarily revealed the differential mapping of MeCP2-induced m6A modifications, which contributes to the study of the epigenetic and EMT mechanism in RPE cells.
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Affiliation(s)
- Xueru Zhao
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Zhengzhou
University People’s Hospital, 450000 Zhengzhou, China
- People’s
Hospital of Henan University, 450003 Zhengzhou, China
- Eye
Institute, Henan Academy of Innovations
in Medical Science, 450000 Zhengzhou, China
| | - Yongya Zhang
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Zhengzhou
University People’s Hospital, 450000 Zhengzhou, China
| | - Fei Wu
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Zhengzhou
University People’s Hospital, 450000 Zhengzhou, China
| | - Xue Li
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Zhengzhou
University People’s Hospital, 450000 Zhengzhou, China
- People’s
Hospital of Henan University, 450003 Zhengzhou, China
- Eye
Institute, Henan Academy of Innovations
in Medical Science, 450000 Zhengzhou, China
| | - Sibei Guo
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Xinxiang
Medical University Henan Provincial People’s Hospital, 453003 Xinxiang, China
| | - Xiaohua Li
- Henan
Eye Hospital, Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Zhengzhou
University People’s Hospital, 450000 Zhengzhou, China
- People’s
Hospital of Henan University, 450003 Zhengzhou, China
- Eye
Institute, Henan Academy of Innovations
in Medical Science, 450000 Zhengzhou, China
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16
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Negrutskii BS, Porubleva LV, Malinowska A, Novosylna OV, Dadlez M, Knudsen CR. Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:67-99. [PMID: 38220433 DOI: 10.1016/bs.apcsb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.
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Affiliation(s)
- Boris S Negrutskii
- Institute of Molecular Biology and Genetics, Kyiv, Ukraine; Aarhus Institute of Advanced Sciences, Høegh-Guldbergs, Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark.
| | | | - Agata Malinowska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | | | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | - Charlotte R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark
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17
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He S, Zhang J, Liu Z, Wang Y, Hao X, Wang X, Zhou Z, Ye X, Zhao Y, Zhao Y, Wang R. Upregulated Cytoskeletal Proteins Promote Pathological Angiogenesis in Moyamoya Disease. Stroke 2023; 54:3153-3164. [PMID: 37886851 DOI: 10.1161/strokeaha.123.044476] [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: 01/03/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Moyamoya disease (MMD) is a rare progressive vascular disease that leads to intracranial internal carotid artery stenosis and eventual occlusion. However, its pathogenesis remains unclear. The purpose of this study is to explore the role of abnormally expressed proteins in the pathogenesis of MMD. METHODS Data-independent acquisition mass spectrometry identifies the differentially expressed proteins in MMD serum by detecting the serum from 60 patients with MMD and 20 health controls. The differentially expressed proteins were validated using enzyme linked immunosorbent assays. Immunofluorescence for superficial temporal artery and middle cerebral artery specimens was used to explore the morphological changes of vascular wall in MMD. In vitro experiments were used to explore the changes and mechanisms of differentially expressed proteins on endothelial cells. RESULTS Proteomic analysis showed that a total of 14 726 peptides and 1555 proteins were quantified by mass spectrometry data. FLNA (filamin A) and ZYX (zyxin) proteins were significantly higher in MMD serum compared with those in health controls (Log2FC >2.9 and >2.8, respectively). Immunofluorescence revealed an intimal hyperplasia in superficial temporal artery and middle cerebral artery specimens of MMD. FLNA and ZYX proteins increased the proportion of endothelial cells in S phase and promoted their proliferation, angiogenesis, and cytoskeleton enlargement. Mechanistic studies revealed that AKT (serine/threonine kinase)/GSK-3β (glycogen synthase kinase 3β)/β-catenin signaling pathway plays a major role in these FLNA- and ZYX-induced changes in endothelial cells. CONCLUSIONS This study provides proteomic data on a large sample size of MMD. The differential expression of FLNA and ZYX in patient with MMD and following in vitro experiments suggest that these upregulated proteins are related to the pathology of cerebrovascular intimal hyperplasia in MMD and are involved in MMD pathogenesis, with diagnostic and therapeutic ramifications.
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Affiliation(s)
- Shihao He
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
- China National Clinical Research Center for Neurological Diseases, Beijing, China (S.H., Yuanli Zhao, R.W.)
- Center of Stroke, Beijing Institute for Brain Disorders, China (S.H., Yuanli Zhao)
| | - Junze Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Ziqi Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Yanru Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Xiaokuan Hao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Xilong Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Zhenyu Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Xun Ye
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Yahui Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
| | - Yuanli Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
- China National Clinical Research Center for Neurological Diseases, Beijing, China (S.H., Yuanli Zhao, R.W.)
- Center of Stroke, Beijing Institute for Brain Disorders, China (S.H., Yuanli Zhao)
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, China (Yuanli Zhao, R.W.)
| | - Rong Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China (S.H., J.Z., Z.L., Y.W., X.H., X.W., Z.Z., X.Y., Yahui Zhao, Yuanli Zhao, R.W.)
- China National Clinical Research Center for Neurological Diseases, Beijing, China (S.H., Yuanli Zhao, R.W.)
- Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, China (Yuanli Zhao, R.W.)
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18
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He R, Zhang X, Wu Y, Weng Z, Li L. TTC7B is a new prognostic biomarker in head and neck squamous cell carcinoma linked to immune infiltration and ferroptosis. Cancer Med 2023; 12:22354-22369. [PMID: 37990988 PMCID: PMC10757123 DOI: 10.1002/cam4.6715] [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: 08/22/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
OBJECTIVE To investigate the expression of TTC7B and its prognostic significance, biological roles, and impact on the immune system in patients with head and neck squamous cell carcinoma (HNSCC). MATERIALS AND METHODS Clinical and genomic data were obtained from TCGA (The Cancer Genome Atlas), GEO (Gene Expression Omnibus), GEPIA2 (Gene Expression Profiling Interactive Analysis 2.0), and TIMER2.0 (Tumor Immune Estimation Resource 2.0) databases. R software was utilized to process the retrieved data. qPCR and immunohistochemical assays were performed to validate the findings obtained from the databases. RESULTS High expression of TTC7B was observed in HNSCC, and this heightened expression is significantly associated with reduced overall survival (OS) in patients, making it an independent risk factor impacting OS. TTC7B is correlated with focal adhesions and cell migration pathways based on functional enrichment analysis. CIBERSORT analysis and TIMER2.0 show a positive link between TTC7B and multiple immune cells, particularly macrophages. Pearson's analysis reveals a significant correlation between TTC7B and ferroptosis-related genes. CONCLUSION In all, TTC7B could serve as a promising prognostic indicator of HNSCC, and is closely associated with focal adhesions, immune infiltration, and ferroptosis.
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Affiliation(s)
- Rong He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Xun Zhang
- Guangyuan Hospital of Traditional Chinese MedicineGuangyuanChina
| | - Yongzhi Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Zhijie Weng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Longjiang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversityChengduChina
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19
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Valdivia A, Avalos AM, Leyton L. Thy-1 (CD90)-regulated cell adhesion and migration of mesenchymal cells: insights into adhesomes, mechanical forces, and signaling pathways. Front Cell Dev Biol 2023; 11:1221306. [PMID: 38099295 PMCID: PMC10720913 DOI: 10.3389/fcell.2023.1221306] [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: 05/12/2023] [Accepted: 09/25/2023] [Indexed: 12/17/2023] Open
Abstract
Cell adhesion and migration depend on the assembly and disassembly of adhesive structures known as focal adhesions. Cells adhere to the extracellular matrix (ECM) and form these structures via receptors, such as integrins and syndecans, which initiate signal transduction pathways that bridge the ECM to the cytoskeleton, thus governing adhesion and migration processes. Integrins bind to the ECM and soluble or cell surface ligands to form integrin adhesion complexes (IAC), whose composition depends on the cellular context and cell type. Proteomic analyses of these IACs led to the curation of the term adhesome, which is a complex molecular network containing hundreds of proteins involved in signaling, adhesion, and cell movement. One of the hallmarks of these IACs is to sense mechanical cues that arise due to ECM rigidity, as well as the tension exerted by cell-cell interactions, and transduce this force by modifying the actin cytoskeleton to regulate cell migration. Among the integrin/syndecan cell surface ligands, we have described Thy-1 (CD90), a GPI-anchored protein that possesses binding domains for each of these receptors and, upon engaging them, stimulates cell adhesion and migration. In this review, we examine what is currently known about adhesomes, revise how mechanical forces have changed our view on the regulation of cell migration, and, in this context, discuss how we have contributed to the understanding of signaling mechanisms that control cell adhesion and migration.
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Affiliation(s)
- Alejandra Valdivia
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Ana María Avalos
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Lisette Leyton
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
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20
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Güler BE, Linnert J, Wolfrum U. Monitoring paxillin in astrocytes reveals the significance of the adhesion G protein coupled receptor VLGR1/ADGRV1 for focal adhesion assembly. Basic Clin Pharmacol Toxicol 2023; 133:301-312. [PMID: 36929698 DOI: 10.1111/bcpt.13860] [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: 01/03/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
VLGR1/ADGRV1 (very large G protein-coupled receptor-1) is the largest adhesion G protein-coupled receptor (aGPCR). Mutations in VLGR1/ADGRV1 are associated with human Usher syndrome, the most common form of deaf-blindness, and also with epilepsy in humans and mice. VLGR1 is expressed almost ubiquitously but is mainly found in the CNS and in the sensory cells of the eye and inner ear. Little is known about the pathogenesis of the diseases related to VLGR1. We previously identified VLGR1 as a vital component of focal adhesions (FAs) serving as a metabotropic mechanoreceptor controls cell spreading and migration. FAs are highly dynamic and turnover in response to internal and external signals. Here, we aimed to elucidate how VLGR1 participates in FA turnover. Nocodazole washouts and live cell imaging of paxillin-DsRed2 consistently showed that FA disassembly was not altered, but de novo assembly of FA was significantly delayed in Vlgr1-deficient astrocytes, indicating that VLGR1 is enrolled in FA assembly. In FRAP experiments, recovery rates were significantly reduced in Vlgr1-deficient FAs, indicating reduced turnover kinetics in VLGR1-deficient FAs. We showed that VLGR1 regulates cell migration by controlling the FA turnover during their assembly and expect novel insights into pathomechanisms related to pathogenic dysfunctions of VLGR1.
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Affiliation(s)
- Baran E Güler
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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21
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Neumann AJ, Prekeris R. A Rab-bit hole: Rab40 GTPases as new regulators of the actin cytoskeleton and cell migration. Front Cell Dev Biol 2023; 11:1268922. [PMID: 37736498 PMCID: PMC10509765 DOI: 10.3389/fcell.2023.1268922] [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: 08/01/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023] Open
Abstract
The regulation of machinery involved in cell migration is vital to the maintenance of proper organism function. When migration is dysregulated, a variety of phenotypes ranging from developmental disorders to cancer metastasis can occur. One of the primary structures involved in cell migration is the actin cytoskeleton. Actin assembly and disassembly form a variety of dynamic structures which provide the pushing and contractile forces necessary for cells to properly migrate. As such, actin dynamics are tightly regulated. Classically, the Rho family of GTPases are considered the major regulators of the actin cytoskeleton during cell migration. Together, this family establishes polarity in the migrating cell by stimulating the formation of various actin structures in specific cellular locations. However, while the Rho GTPases are acknowledged as the core machinery regulating actin dynamics and cell migration, a variety of other proteins have become established as modulators of actin structures and cell migration. One such group of proteins is the Rab40 family of GTPases, an evolutionarily and functionally unique family of Rabs. Rab40 originated as a single protein in the bilaterians and, through multiple duplication events, expanded to a four-protein family in higher primates. Furthermore, unlike other members of the Rab family, Rab40 proteins contain a C-terminally located suppressor of cytokine signaling (SOCS) box domain. Through the SOCS box, Rab40 proteins interact with Cullin5 to form an E3 ubiquitin ligase complex. As a member of this complex, Rab40 ubiquitinates its effectors, controlling their degradation, localization, and activation. Because substrates of the Rab40/Cullin5 complex can play a role in regulating actin structures and cell migration, the Rab40 family of proteins has recently emerged as unique modulators of cell migration machinery.
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Affiliation(s)
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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22
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Gil‐Redondo JC, Weber A, Vivanco MDM, Toca‐Herrera JL. Measuring (biological) materials mechanics with atomic force microscopy. 5. Traction force microscopy (cell traction forces). Microsc Res Tech 2023; 86:1069-1078. [PMID: 37345422 PMCID: PMC10952526 DOI: 10.1002/jemt.24368] [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: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Cells generate traction forces to probe the mechanical properties of the surroundings and maintain a basal equilibrium state of stress. Traction forces are also implicated in cell migration, adhesion and ECM remodeling, and alteration of these forces is often observed in pathologies such as cancer. Thus, analyzing the traction forces is important for studies of cell mechanics in cancer and metastasis. In this primer, the methodology for conducting two-dimensional traction force microscopy (2D-TFM) experiments is reported. As a practical example, we analyzed the traction forces generated by three human breast cancer cell lines of different metastatic potential: MCF10-A, MCF-7 and MDA-MB-231 cells, and studied the effects of actin cytoskeleton disruption on those traction forces. Contrary to what is often reported in literature, lower traction forces were observed in cells with higher metastatic potential (MDA-MB-231). Implications of substrate stiffness and concentration of extracellular matrix proteins in such findings are discussed in the text. RESEARCH HIGHLIGHTS: Traction force microscopy (TFM) is suitable for studying and quantifying cell-substrate and cell-cell forces. TFM is suitable for investigating the relationship between chemical to mechanical signal transduction and vice versa. TFM can be combined with classical indentation studies providing a compact picture of cell mechanics. TFM still needs new physico-chemical (sample preparation) and computational approaches for more accurate data evaluation.
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Affiliation(s)
- Juan Carlos Gil‐Redondo
- Institute of Biophysics, Department of BionanosciencesUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Andreas Weber
- Institute of Biophysics, Department of BionanosciencesUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Maria dM. Vivanco
- Cancer Heterogeneity Lab, CIC BioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology ParkDerioSpain
| | - José L. Toca‐Herrera
- Institute of Biophysics, Department of BionanosciencesUniversity of Natural Resources and Life Sciences ViennaViennaAustria
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23
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Mitsou I, Carlson CR, Multhaupt HA, Brakebusch C, Couchman JR. Two Transient Receptor Potential Channels at Focal Adhesions. J Histochem Cytochem 2023; 71:495-508. [PMID: 37596792 PMCID: PMC10501361 DOI: 10.1369/00221554231194119] [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: 03/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023] Open
Abstract
Recently there have been reports that identify two transient receptor potential channels in cell-matrix junctions known as focal adhesions. These are the calcium channel TRP canonical 7 and the calcium-activated monovalent ion channel, TRP melastatin (TRPM) 4. Here, we report on the occurrence of TRPM4 in focal adhesions of fibroblasts. Of three commercial antibodies recognizing this channel, only one yielded focal adhesion staining, while the other two did not. The epitope recognized by the focal adhesion-localizing antibody was mapped to the extreme C-terminus of the TRPM4 protein. The other two antibodies bind to N-terminal regions of the TRPM4 proteins. Deletion of the TRPM4 gene by CRISPR/cas9 techniques confirmed that this channel is a bona fide focal adhesion component, while expression of full-length TRPM4 proteins suggested that processing may occur to yield a form that localizes to focal adhesions. Given the reports that this channel may influence migratory behavior of cells and is linked to cardiovascular disease, TRPM4 functions in adhesion should be explored in greater depth. (J Histochem Cytochem 71: 495-508, 2023).
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Affiliation(s)
- Ioli Mitsou
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
- Agilent Technologies Denmark ApS, Glostrup, Denmark
| | - Cathrine Rein Carlson
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hinke A.B. Multhaupt
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Cord Brakebusch
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - John R. Couchman
- Biotech Research & Innovation Center, University of Copenhagen, Copenhagen, Denmark
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24
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Ding X, Zhang Y, Li D, Xu J, Wu C, Cui X, Sun Y. Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus. BMC Genom Data 2023; 24:45. [PMID: 37573319 PMCID: PMC10422732 DOI: 10.1186/s12863-023-01141-6] [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: 05/08/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant hybridization fertility. In this study, the gonadal tissue transcriptomes of BSB, TC, BT-F1, and TB-F1 were sequenced using Illumina high-throughput sequencing technology to analyze the reproductive characteristics of BT and TB. RESULTS Differential gene expression analysis showed that the differentially expressed genes in BT vs BSB and BT vs TC were mainly enriched in signaling pathways not directly associated with meiosis. While, the differentially expressed genes of TB vs BSB and TB vs TC were mainly enriched in pathways related to meiosis, and most of them were down-regulated, indicating that meiosis is suppressed in TB. Under-dominance (UD) genes were enriched in pathways related to meiosis and DNA repair in TB. Over-dominance (OD) genes were enriched in MAPK signaling pathway, expression level dominance-BSB (ELD-B) genes were enriched in pathways related to steroid hormone synthesis and expression level dominance-TC (ELD-T) genes were not significantly enriched in any pathway in both BT and TB. CONCLUSIONS These results suggest that meiotic progression may not be affected in BT, whereas it is clearly inhibited in TB. Offspring of M. amblycephala maternal parent may have better genomic compatibility and fertility. Our study provides important information on the molecular mechanisms of breaking reproductive isolation in distantly hybridized fertile lineages.
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Affiliation(s)
- Xue Ding
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Yifei Zhang
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Die Li
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Jia Xu
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fishes, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xiaojuan Cui
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| | - Yuandong Sun
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
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25
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Yan M, Zheng H, Yan R, Lang L, Wang Q, Xiao B, Zhang D, Lin H, Jia Y, Pan S, Chen Q. Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis. J Proteome Res 2023; 22:2714-2726. [PMID: 37437295 PMCID: PMC10408646 DOI: 10.1021/acs.jproteome.3c00277] [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: 05/09/2023] [Indexed: 07/14/2023]
Abstract
Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.
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Affiliation(s)
- Maosheng Yan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Hanjun Zheng
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rong Yan
- The
Centers for Disease Control and Prevention of Haizhu District, Guangzhou, Guangdong 510230, China
| | - Li Lang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Qia Wang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Bin Xiao
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Danying Zhang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Hansheng Lin
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Yanxia Jia
- Department
of Public Health, Shanxi Medical University, Tai Yuan, Shanxi 030000, China
| | - Siyu Pan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| | - Qingsong Chen
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
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26
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Shen X, Yin L, Xu S, Wang J, Yin D, Zhao R, Pan X, Dai Y, Hou H, Zhou X, Hu X. Altered Proteomic Profile of Exosomes Secreted from Vero Cells Infected with Porcine Epidemic Diarrhea Virus. Viruses 2023; 15:1640. [PMID: 37631983 PMCID: PMC10459195 DOI: 10.3390/v15081640] [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: 06/26/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) infection causes severe diarrhea in pigs and can be fatal in newborn piglets. Exosomes are extracellular vesicles secreted by cells that transfer biologically active proteins, lipids, and RNA to neighboring or distant cells. Herein, the morphology, particle size, and secretion of exosomes derived from a control and PEDV-infected group are examined, followed by a proteomic analysis of the exosomes. The results show that the exosomes secreted from the Vero cells had a typical cup-shaped structure. The average particle size of the exosomes from the PEDV-infected group was 112.4 nm, whereas that from the control group was 150.8 nm. The exosome density analysis and characteristic protein determination revealed that the content of exosomes in the PEDV-infected group was significantly higher than that in the control group. The quantitative proteomics assays revealed 544 differentially expressed proteins (DEPs) in the PEDV-infected group's exosomes compared with those in the controls, with 236 upregulated and 308 downregulated proteins. The DEPs were closely associated with cellular regulatory pathways, such as the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, extracellular matrix-receptor interaction, focal adhesion, and cytoskeletal regulation. These findings provide the basis for further investigation of the pathogenic mechanisms of PEDV and the discovery of novel antiviral targets.
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Affiliation(s)
- Xuehuai Shen
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Shuangshuang Xu
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Jieru Wang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Dongdong Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Ruihong Zhao
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Xiaocheng Pan
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Yin Dai
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Hongyan Hou
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Xueli Zhou
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
| | - Xiaomiao Hu
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230031, China; (X.S.); (L.Y.); (S.X.); (J.W.); (D.Y.); (R.Z.); (Y.D.); (H.H.); (X.Z.); (X.H.)
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
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Ma W, Zhu J, Bai L, Zhao P, Li F, Zhang S. The role of neutrophil extracellular traps and proinflammatory damage-associated molecular patterns in idiopathic inflammatory myopathies. Clin Exp Immunol 2023; 213:202-208. [PMID: 37289984 PMCID: PMC10361739 DOI: 10.1093/cei/uxad059] [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: 02/11/2023] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
Idiopathic inflammatory myopathies (IIMs) are a group of systemic autoimmune diseases characterized by immune-mediated muscle injury. Abnormal neutrophil extracellular traps (NETs) can be used as a biomarker of IIM disease activity, but the mechanism of NET involvement in IIMs needs to be elucidated. Important components of NETs, including high-mobility group box 1, DNA, histones, extracellular matrix, serum amyloid A, and S100A8/A9, act as damage-associated molecular patterns (DAMPs) to promote inflammation in IIMs. NETs can act on different cells to release large amounts of cytokines and activate the inflammasome, which can subsequently aggravate the inflammatory response. Based on the idea that NETs may be proinflammatory DAMPs of IIMs, we describe the role of NETs, DAMPs, and their interaction in the pathogenesis of IIMs and discuss the possible targeted treatment strategies in IIMs.
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Affiliation(s)
- Wenlan Ma
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Jiarui Zhu
- Department of Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Ling Bai
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Peipei Zhao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Feifei Li
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Sigong Zhang
- Department of Rheumatology, Lanzhou University Second Hospital, Lanzhou, China
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28
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Chen Y, Cai G, Jiang J, He C, Chen Y, Ding Y, Lu J, Zhao W, Yang Y, Zhang Y, Wu G, Wang H, Zhou Z, Teng L. Proteomic profiling of gastric cancer with peritoneal metastasis identifies a protein signature associated with immune microenvironment and patient outcome. Gastric Cancer 2023; 26:504-516. [PMID: 36930369 PMCID: PMC10284991 DOI: 10.1007/s10120-023-01379-0] [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: 01/15/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Peritoneal metastasis (PM) frequently occurs in patients with gastric cancer (GC) and is a major cause of mortality. Risk stratification for PM can optimize decision making in GC treatment. METHODS A total of 25 GC patients (13 with synchronous, 6 with metachronous PM and 6 PM-free) were included in this study. Quantitative proteomics by high-depth tandem mass tags labeling and whole-exome sequencing were conducted in primary GC and PM samples. Proteomic signature and prognostic model were established by machine learning algorithms in PM and PM-free GC, then validated in two external cohorts. Tumor-infiltrating immune cells in GC were analyzed by CIBERSORT. RESULTS Heterogeneity between paired primary and PM samples was observed at both genomic and proteomic levels. Compared to primary GC, proteome of PM samples was enriched in RNA binding and extracellular exosomes. 641 differently expressed proteins (DEPs) between primary GC of PM group and PM-free group were screened, which were enriched in extracellular exosome and cell adhesion pathways. Subsequently, a ten-protein signature was derived based on DEPs by machine learning. This signature was significantly associated with patient prognosis in internal cohort and two external proteomic datasets of diffuse and mixed type GC. Tumor-infiltrating immune cell analysis showed that the signature was associated with immune microenvironment of GC. CONCLUSIONS We characterized proteomic features that were informative for PM progression of GC. A protein signature associated with immune microenvironment and patient outcome was derived, and it could guide risk stratification and individualized treatment.
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Affiliation(s)
- Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Guoxin Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao He
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Wenyi Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yan Yang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yiqin Zhang
- Department of Informatics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guanghao Wu
- School of Clinical Medicine, Hangzhou Normal University Medical College, Hangzhou, China
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China.
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Adhicary S, Fanelli K, Nakisli S, Ward B, Pearce I, Nielsen CM. Rbpj Deficiency Disrupts Vascular Remodeling via Abnormal Apelin and Cdc42 (Cell Division Cycle 42) Activity in Brain Arteriovenous Malformation. Stroke 2023; 54:1593-1605. [PMID: 37051908 PMCID: PMC10213117 DOI: 10.1161/strokeaha.122.041853] [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: 11/01/2022] [Accepted: 03/13/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND Brain arteriovenous malformations (bAVM) are characterized by enlarged blood vessels, which direct blood through arteriovenous shunts, bypassing the artery-capillary-vein network and disrupting blood flow. Clinically, bAVM treatments are invasive and not routinely applicable. There is critical need to understand mechanisms of bAVM pathologies and develop pharmacological therapies. METHODS We used an in vivo mouse model of Rbpj-mediated bAVM, which develops pathologies in the early postnatal period and an siRNA in vitro system to knockdown RBPJ in human brain microvascular endothelial cells (ECs). To understand molecular events regulated by endothelial Rbpj, we conducted RNA-Seq and chromatin immunoprecipitation-Seq analyses from isolated brain ECs. RESULTS Rbpj-deficient (mutant) brain ECs acquired abnormally rounded shape (with no change to cell area), altered basement membrane dynamics, and increased endothelial cell density along arteriovenous shunts, compared to controls, suggesting impaired remodeling of neonatal brain vasculature. Consistent with impaired endothelial cell dynamics, we found increased Cdc42 (cell division cycle 42) activity in isolated mutant ECs, suggesting that Rbpj regulates small GTPase (guanosine triphosphate hydrolase)-mediated cellular functions in brain ECs. siRNA-treated, RBPJ-deficient human brain ECs displayed increased Cdc42 activity, disrupted cell polarity and focal adhesion properties, and impaired migration in vitro. RNA-Seq analysis from isolated brain ECs identified differentially expressed genes in mutants, including Apelin, which encodes a ligand for G protein-coupled receptor signaling known to influence small GTPase activity. Chromatin immunoprecipitation-Seq analysis revealed chromatin loci occupied by Rbpj in brain ECs that corresponded to G-protein and Apelin signaling molecules. In vivo administration of a competitive peptide antagonist against the Apelin receptor (Aplnr/Apj) attenuated Cdc42 activity and restored endothelial cell morphology and arteriovenous connection diameter in Rbpj-mutant brain vessels. CONCLUSIONS Our data suggest that endothelial Rbpj promotes rearrangement of brain ECs during cerebrovascular remodeling, through Apelin/Apj-mediated small GTPase activity, and prevents bAVM. By inhibiting Apelin/Apj signaling in vivo, we demonstrated pharmacological prevention of Rbpj-mediated bAVM.
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Affiliation(s)
- Subhodip Adhicary
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Translational Biomedical Sciences Program, Ohio University, Athens, OH
| | - Kayleigh Fanelli
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Neuroscience Program, Ohio University, Athens, OH
| | - Sera Nakisli
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Neuroscience Program, Ohio University, Athens, OH
| | - Brittney Ward
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Neuroscience Program, Ohio University, Athens, OH
- Honors Tutorial College, Ohio University, Athens, OH
| | - Isaac Pearce
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH
| | - Corinne M. Nielsen
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Neuroscience Program, Ohio University, Athens, OH
- Molecular and Cellular Biology Program, Ohio University, Athens, OH
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30
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Rashid S, Wilson SG, Zhu K, Walsh JP, Xu J, Mullin BH. Identification of Differentially Expressed Genes and Molecular Pathways Involved in Osteoclastogenesis Using RNA-seq. Genes (Basel) 2023; 14:genes14040916. [PMID: 37107674 PMCID: PMC10137460 DOI: 10.3390/genes14040916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Osteoporosis is a disease that is characterised by reduced bone mineral density (BMD) and can be exacerbated by the excessive bone resorption of osteoclasts (OCs). Bioinformatic methods, including functional enrichment and network analysis, can provide information about the underlying molecular mechanisms that participate in the progression of osteoporosis. In this study, we harvested human OC-like cells differentiated in culture and their precursor peripheral blood mononuclear cells (PBMCs) and characterised the transcriptome of the two cell types using RNA-sequencing in order to identify differentially expressed genes. Differential gene expression analysis was performed in RStudio using the edgeR package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to identify enriched GO terms and signalling pathways, with inter-connected regions characterised using protein-protein interaction analysis. In this study, we identified 3201 differentially expressed genes using a 5% false discovery rate; 1834 genes were upregulated, whereas 1367 genes were downregulated. We confirmed a significant upregulation of several well-established OC genes including CTSK, DCSTAMP, ACP5, MMP9, ITGB3, and ATP6V0D2. The GO analysis suggested that upregulated genes are involved in cell division, cell migration, and cell adhesion, while the KEGG pathway analysis highlighted oxidative phosphorylation, glycolysis and gluconeogenesis, lysosome, and focal adhesion pathways. This study provides new information about changes in gene expression and highlights key biological pathways involved in osteoclastogenesis.
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Affiliation(s)
- Sarah Rashid
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6907, Australia
| | - Scott G Wilson
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6907, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Kun Zhu
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Perth, WA 6907, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Perth, WA 6907, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6907, Australia
| | - Benjamin H Mullin
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6907, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
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Gao Q, Jia F, Li X, Kong Y, Tian Z, Bi L, Li L. Biophysical cues to improve the immunomodulatory capacity of mesenchymal stem cells: The progress and mechanisms. Biomed Pharmacother 2023; 162:114655. [PMID: 37031489 DOI: 10.1016/j.biopha.2023.114655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/11/2023] Open
Abstract
Mesenchymal stem cells (MSCs) can maintain immune homeostasis and many preclinical trials with MSCs have been carried out around the world. In vitro culture of MSCs has been found to result in the decline of immunomodulatory capacity, migration and proliferation. To address these problems, simulating the extracellular environment for preconditioning of MSCs is a promising and inexpensive method. Biophysical cues in the external environment that MSCs are exposed to have been shown to affect MSC migration, residency, differentiation, secretion, etc. We review the main ways in which MSCs exert their immunomodulatory ability, and summarize recent advances in mechanical preconditioning of MSCs to enhance immunomodulatory capacity and related mechanical signal sensing and transduction mechanisms.
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Affiliation(s)
- Qingyuan Gao
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Fangru Jia
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Xiangpan Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Yanan Kong
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Zhenya Tian
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Lintao Bi
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun 130021, China.
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China.
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Raskov H, Gaggar S, Tajik A, Orhan A, Gögenur I. The Matrix Reloaded—The Role of the Extracellular Matrix in Cancer. Cancers (Basel) 2023; 15:cancers15072057. [PMID: 37046716 PMCID: PMC10093330 DOI: 10.3390/cancers15072057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
As the core component of all organs, the extracellular matrix (ECM) is an interlocking macromolecular meshwork of proteins, glycoproteins, and proteoglycans that provides mechanical support to cells and tissues. In cancer, the ECM can be remodelled in response to environmental cues, and it controls a plethora of cellular functions, including metabolism, cell polarity, migration, and proliferation, to sustain and support oncogenesis. The biophysical and biochemical properties of the ECM, such as its structural arrangement and being a reservoir for bioactive molecules, control several intra- and intercellular signalling pathways and induce cytoskeletal changes that alter cell shapes, behaviour, and viability. Desmoplasia is a major component of solid tumours. The abnormal deposition and composition of the tumour matrix lead to biochemical and biomechanical alterations that determine disease development and resistance to treatment. This review summarises the complex roles of ECM in cancer and highlights the possible therapeutic targets and how to potentially remodel the dysregulated ECM in the future. Furthering our understanding of the ECM in cancer is important as the modification of the ECM will probably become an important tool in the characterisation of individual tumours and personalised treatment options.
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Integration of Transcriptomics and Non-Targeted Metabolomics Reveals the Underlying Mechanism of Skeletal Muscle Development in Duck during Embryonic Stage. Int J Mol Sci 2023; 24:ijms24065214. [PMID: 36982289 PMCID: PMC10049352 DOI: 10.3390/ijms24065214] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Skeletal muscle is an important economic trait in duck breeding; however, little is known about the molecular mechanisms of its embryonic development. Here, the transcriptomes and metabolomes of breast muscle of Pekin duck from 15 (E15_BM), 21 (E21_BM), and 27 (E27_BM) days of incubation were compared and analyzed. The metabolome results showed that the differentially accumulated metabolites (DAMs), including the up-regulated metabolites, l-glutamic acid, n-acetyl-1-aspartylglutamic acid, l-2-aminoadipic acid, 3-hydroxybutyric acid, bilirubin, and the significantly down-regulated metabolites, palmitic acid, 4-guanidinobutanoate, myristic acid, 3-dehydroxycarnitine, and s-adenosylmethioninamine, were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of cofactors, protein digestion and absorption, and histidine metabolism, suggesting that these pathways may play important roles in the muscle development of duck during the embryonic stage. Moreover, a total of 2142 (1552 up-regulated and 590 down-regulated), 4873 (3810 up-regulated and 1063 down-regulated), and 2401 (1606 up-regulated and 795 down-regulated) DEGs were identified from E15_BM vs. E21_BM, E15_BM vs. E27_BM and E21_BM vs. E27_BM in the transcriptome, respectively. The significantly enriched GO terms from biological processes were positive regulation of cell proliferation, regulation of cell cycle, actin filament organization, and regulation of actin cytoskeleton organization, which were associated with muscle or cell growth and development. Seven significant pathways, highly enriched by FYN, PTK2, PXN, CRK, CRKL, PAK, RHOA, ROCK, INSR, PDPK1, and ARHGEF, were focal adhesion, regulation of actin cytoskeleton, wnt signaling pathway, insulin signaling pathway, extracellular matrix (ECM)-receptor interaction, cell cycle, and adherens junction, which participated in regulating the development of skeletal muscle in Pekin duck during the embryonic stage. KEGG pathway analysis of the integrated transcriptome and metabolome indicated that the pathways, including arginine and proline metabolism, protein digestion and absorption, and histidine metabolism, were involved in regulating skeletal muscle development in embryonic Pekin duck. These findings suggested that the candidate genes and metabolites involved in crucial biological pathways may regulate muscle development in the Pekin duck at the embryonic stage, and increased our understanding of the molecular mechanisms underlying the avian muscle development.
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Chen ZH, Wu JJ, Guo DY, Li YY, Chen MN, Zhang ZY, Yuan ZD, Zhang KW, Chen WW, Tian F, Ye JX, Li X, Yuan FL. Physiological functions of podosomes: From structure and function to therapy implications in osteoclast biology of bone resorption. Ageing Res Rev 2023; 85:101842. [PMID: 36621647 DOI: 10.1016/j.arr.2023.101842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
With increasing age, bone tissue undergoes significant alterations in composition, architecture, and metabolic functions, probably causing senile osteoporosis. Osteoporosis possess the vast majority of bone disease and associates with a reduction in bone mass and increased fracture risk. Bone loss is on account of the disorder in osteoblast-induced bone formation and osteoclast-induced bone resorption. As a unique bone resorptive cell type, mature bone-resorbing osteoclasts exhibit dynamic actin-based cytoskeletal structures called podosomes that participate in cell-matrix adhesions specialized in the degradation of mineralized bone matrix. Podosomes share many of the same molecular constitutions as focal adhesions, but they have a unique structural organization, with a central core abundant in F-actin and encircled by scaffolding proteins, kinases and integrins. Here, we conclude recent advancements in our knowledge of the architecture and the functions of podosomes. We also discuss the regulatory pathways in osteoclast podosomes, providing a reference for future research on the podosomes of osteoclasts and considering podosomes as a therapeutic target for inhibiting bone resorption.
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Affiliation(s)
- Zhong-Hua Chen
- Affiliated Hospital 3 of Nantong University, Nantong University, Jiangsu, China
| | - Jun-Jie Wu
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Dan-Yang Guo
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Yue-Yue Li
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Meng-Nan Chen
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Zhen-Yu Zhang
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Zheng-Dong Yuan
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Kai-Wen Zhang
- Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Wei-Wei Chen
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Fan Tian
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Jun-Xing Ye
- Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Xia Li
- Affiliated Hospital 3 of Nantong University, Nantong University, Jiangsu, China; Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China.
| | - Feng-Lai Yuan
- Affiliated Hospital 3 of Nantong University, Nantong University, Jiangsu, China; Institute of Integrated Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Jiangsu, China.
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Deng H, Li T, Wei F, Han W, Xu X, Zhang Y. High expression of TMEM200A is associated with a poor prognosis and immune infiltration in gastric cancer. Pathol Oncol Res 2023; 29:1610893. [PMID: 36741965 PMCID: PMC9892064 DOI: 10.3389/pore.2023.1610893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Background: Gastric cancer (GC) is one of the global malignant tumors with high incidence and poor prognosis. Exploring new GC molecular markers is important to improve GC prognosis. Transmembrane protein 200A (TMEM200A) is a member of the family of transmembrane proteins (TMEM). This study is the first to investigate the potential function of TMEM200A and its relationship with immune infiltration in GC. Methods: The differential expression of TMEM200A was determined through the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The receiver operating characteristic (ROC) curve was drawn to assess the diagnostic value of TMEM200A for GC. The relationship between TMEM200A and the clinical characteristics of patients with GC was investigated using the Wilcoxon test and the Kruskal-Wallis test. The effect of TMEM200A on overall survival (OS) was identified using the Kaplan-Meier method, the Log-rank test, the univariate/multivariate Cox regression analysis, and the nomogram prediction model. The co-expressed genes and gene set enrichment analysis (GSEA) were used to explore the potential biological functions of TMEM200A. We used the Tumor Immune Estimation Resource (TIMER) database and the ssGSEA algorithm to estimate the relationship between TMEM200A and immune cell infiltration. Furthermore, we investigated the correlation of TMEM200A with immune checkpoint/immune cell surface markers using the TCGA-STAD data set. Finally, we identified prognosis-related methylation sites in TMEM200A using MethSurv. Results: TMEM200A was highly expressed in GC tissues. TMEM200A had a good diagnostic value for GC. High expression of TMEM200A may shorten the OS of GC patients and may be an independent risk factor for OS in GC patients. TMEM200A participates in the construction of a predictive model with a good predictive effect on the survival rate of GC patients at 1, 3, and 5 years. Co-expressed genes and GSEA indicated that TMEM200A may be an adhesion molecule closely associated with tumor invasion and metastasis. In addition, TMEM200A may be significantly associated with immune cell infiltration and immune checkpoint expression. We also found that TMEM200A contains three methylation sites associated with a poor prognosis. Conclusion: Upregulated TMEM200A may be a promising prognostic marker for GC and is closely associated with the tumor microenvironment (TME).
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Gu Z, Fan S, Kundu SC, Yao X, Zhang Y. Fiber diameters and parallel patterns: proliferation and osteogenesis of stem cells. Regen Biomater 2023; 10:rbad001. [PMID: 36726609 PMCID: PMC9887345 DOI: 10.1093/rb/rbad001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Due to the innate extracellular matrix mimicking features, fibrous materials exhibited great application potential in biomedicine. In developing excellent fibrous biomaterial, it is essential to reveal the corresponding inherent fiber features' effects on cell behaviors. Due to the inevitable 'interference' cell adhesions to the background or between adjacent fibers, it is difficult to precisely reveal the inherent fiber diameter effect on cell behaviors by using a traditional fiber mat. A single-layer and parallel-arranged polycaprolactone fiber pattern platform with an excellent non-fouling background is designed and constructed herein. In this unique material platform, the 'interference' cell adhesions through interspace between fibers to the environment could be effectively ruled out by the non-fouling background. The 'interference' cell adhesions between adjacent fibers could also be excluded from the sparsely arranged (SA) fiber patterns. The influence of fiber diameter on stem cell behaviors is precisely and comprehensively investigated based on eliminating the undesired 'interference' cell adhesions in a controllable way. On the SA fiber patterns, small diameter fiber (SA-D1, D1 means 1 μm in diameter) may seriously restrict cell proliferation and osteogenesis when compared to the middle (SA-D8) and large (SA-D56) ones and SA-D8 shows the optimal osteogenesis enhancement effect. At the same time, the cells present similar proliferation ability and even the highest osteogenic ability on the densely arranged (DA) fiber patterns with small diameter fiber (DA-D1) when compared to the middle (DA-D8) and large (DA-D56) ones. The 'interference' cell adhesion between adjacent fibers under dense fiber arrangement may be the main reason for inducing these different cell behavior trends along with fiber diameters. Related results and comparisons have illustrated the effects of fiber diameter on stem cell behaviors more precisely and objectively, thus providing valuable reference and guidance for developing effective fibrous biomaterials.
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Affiliation(s)
- Zhanghong Gu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Materials Science and Engineering, Donghua University, Shanghai 201620, People’s Republic of China
| | - Suna Fan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Materials Science and Engineering, Donghua University, Shanghai 201620, People’s Republic of China
| | - Subhas C Kundu
- I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, University of Minho, Barco, Guimarães 4805-017, Portugal
| | - Xiang Yao
- Correspondence address. E-mail: (X.Y.); (Y.Z.)
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Pang X, He X, Qiu Z, Zhang H, Xie R, Liu Z, Gu Y, Zhao N, Xiang Q, Cui Y. Targeting integrin pathways: mechanisms and advances in therapy. Signal Transduct Target Ther 2023; 8:1. [PMID: 36588107 PMCID: PMC9805914 DOI: 10.1038/s41392-022-01259-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 01/03/2023] Open
Abstract
Integrins are considered the main cell-adhesion transmembrane receptors that play multifaceted roles as extracellular matrix (ECM)-cytoskeletal linkers and transducers in biochemical and mechanical signals between cells and their environment in a wide range of states in health and diseases. Integrin functions are dependable on a delicate balance between active and inactive status via multiple mechanisms, including protein-protein interactions, conformational changes, and trafficking. Due to their exposure on the cell surface and sensitivity to the molecular blockade, integrins have been investigated as pharmacological targets for nearly 40 years, but given the complexity of integrins and sometimes opposite characteristics, targeting integrin therapeutics has been a challenge. To date, only seven drugs targeting integrins have been successfully marketed, including abciximab, eptifibatide, tirofiban, natalizumab, vedolizumab, lifitegrast, and carotegrast. Currently, there are approximately 90 kinds of integrin-based therapeutic drugs or imaging agents in clinical studies, including small molecules, antibodies, synthetic mimic peptides, antibody-drug conjugates (ADCs), chimeric antigen receptor (CAR) T-cell therapy, imaging agents, etc. A serious lesson from past integrin drug discovery and research efforts is that successes rely on both a deep understanding of integrin-regulatory mechanisms and unmet clinical needs. Herein, we provide a systematic and complete review of all integrin family members and integrin-mediated downstream signal transduction to highlight ongoing efforts to develop new therapies/diagnoses from bench to clinic. In addition, we further discuss the trend of drug development, how to improve the success rate of clinical trials targeting integrin therapies, and the key points for clinical research, basic research, and translational research.
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Affiliation(s)
- Xiaocong Pang
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Xu He
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Zhiwei Qiu
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Hanxu Zhang
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Ran Xie
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Zhiyan Liu
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Yanlun Gu
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Nan Zhao
- grid.411472.50000 0004 1764 1621Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China ,grid.411472.50000 0004 1764 1621Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Qian Xiang
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034, Beijing, China. .,Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191, Beijing, China.
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034, Beijing, China. .,Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191, Beijing, China.
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38
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Nano porous polycarbonate membranes stimulating cell adhesion and promoting osteogenic differentiation and differential mRNA expression. Biochem Biophys Res Commun 2023; 638:147-154. [PMID: 36459878 DOI: 10.1016/j.bbrc.2022.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Tissue engineering is thought to be the ideal therapy for bone defect reconstructive treatment. In this study, we present a method of utilizing micro/nano porous polycarbonate membranes (PCMs) as the extracellular matrix to cultivate the human periodontal ligament cells (hPDLCs) and investigate the osteogenic differentiation of those cells. We also compared the osteogenic enhancing abilities of different pore size PCMs. The pore diameters of the candidate membranes are 200 nm, 800 nm, 1200 nm, and 10 μm respectively, and their physical properties are identified. After seeding and cultivating on the PCMs, hPDLCs can be stimulated to undergo osteogenic differentiation, in which the 200 nm PCM is proved to have the most optimal osteo-induction ability. The results of in vivo experiments provide strong evidence suggesting that the hPDLCs stimulated by 200 nm PCM greatly accelerates the healing of bone reconstruction in mice skull defects, as well as promote the process of ectopic osteogenesis. RNA-sequencing was conducted to determine the differential mRNA expression profile during the osteogenesis process of hPDLCs on PCMs. GO and KEGG enrichment analysis were conducted to study the regulatory mechanisms, in which osteogenic marker expression such as Hippo, TGF-β, and PI3K-Akt signaling pathways were significantly up-regulated. The up-regulation indicates the promising potential of nano porous PCMs for promoting osteogenesis for bone regeneration applications. Ultimately, signaling pathways that promote osteogenesis warrants further exploration.
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39
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Bun T, Sato Y, Futami H, Tagawa Y, Murakami Y, Takahashi M. Cytoskeletal fractionation identifies LMO7 as a positive regulator of fibroblast polarization and directed migration. Biochem Biophys Res Commun 2023; 638:58-65. [PMID: 36442233 DOI: 10.1016/j.bbrc.2022.11.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
Cell migration is a cytoskeleton-driven cellular process involved in physiological and pathological events such as embryonic development and cancer metastasis. Fibroblasts have often been used to elucidate the mechanism of cell migration due to their high morphological polarity and migratory activity. We recently reported that human lung fibroblasts migrate straight for a long duration without external stimuli, which phenomenon we named intrinsic and directed migration (IDM) of fibroblasts. In this study, we explored proteins involved in IDM in order to elucidate the molecular mechanism. First, we focused on the differences in morphology and migratory behaviors between normal and immortalized fibroblasts-the former exhibit obvious polarity and IDM; the latter exhibit poorly polarized morphology and random migration. We compared the abundance of proteins functioning as the cytoskeletal components between them through proteomic analysis and found that LIM domain only protein 7 (LMO7) is overwhelmingly incorporated into the cytoskeletons of normal fibroblasts. Depletion of LMO7 inhibited the directed migration of normal fibroblast on the fibronectin (FN)-rich surface, suggesting that LMO7 is important for IDM. Moreover, on the FN-free surface, LMO7-depleted fibroblasts often failed to establish morphological polarity and hardly migrated. Thus, the present study identified LMO7 as a positive regulator of fibroblast polarization and IDM, especially in an environment where integrin-mediated substrate attachment is insufficient.
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Affiliation(s)
- Taichi Bun
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yuta Sato
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Hajime Futami
- Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuki Tagawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Masayuki Takahashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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40
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Pourmasoumi P, Moghaddam A, Nemati Mahand S, Heidari F, Salehi Moghaddam Z, Arjmand M, Kühnert I, Kruppke B, Wiesmann HP, Khonakdar HA. A review on the recent progress, opportunities, and challenges of 4D printing and bioprinting in regenerative medicine. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:108-146. [PMID: 35924585 DOI: 10.1080/09205063.2022.2110480] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Four-dimensional (4 D) printing is a novel emerging technology, which can be defined as the ability of 3 D printed materials to change their form and functions. The term 'time' is added to 3 D printing as the fourth dimension, in which materials can respond to a stimulus after finishing the manufacturing process. 4 D printing provides more versatility in terms of size, shape, and structure after printing the construct. Complex material programmability, multi-material printing, and precise structure design are the essential requirements of 4 D printing systems. The utilization of stimuli-responsive polymers has increasingly taken the place of cell traction force-dependent methods and manual folding, offering a more advanced technique to affect a construct's adjusted shape transformation. The present review highlights the concept of 4 D printing and the responsive bioinks used in 4 D printing, such as water-responsive, pH-responsive, thermo-responsive, and light-responsive materials used in tissue regeneration. Cell traction force methods are described as well. Finally, this paper aims to introduce the limitations and future trends of 4 D printing in biomedical applications based on selected key references from the last decade.
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Affiliation(s)
| | | | | | - Fatemeh Heidari
- Iran Polymer and Petrochemical Institute (IPPI), Tehran, Iran
| | - Zahra Salehi Moghaddam
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Arjmand
- Nanomaterials and Polymer Nanocomposites Laboratory, School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Ines Kühnert
- Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Benjamin Kruppke
- Max Bergmann Center of Biomaterials and Institute of Materials Science, Technische Universität Dresden, Dresden, Germany
| | - Hans-Peter Wiesmann
- Max Bergmann Center of Biomaterials and Institute of Materials Science, Technische Universität Dresden, Dresden, Germany
| | - Hossein Ali Khonakdar
- Iran Polymer and Petrochemical Institute (IPPI), Tehran, Iran.,Leibniz Institute of Polymer Research Dresden, Dresden, Germany
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41
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Panchenko AY, Tchaicheeyan O, Berinskii IE, Lesman A. Does the Extracellular Matrix Support Cell-Cell Communication by Elastic Wave Packets? ACS Biomater Sci Eng 2022; 8:5155-5170. [PMID: 36346743 DOI: 10.1021/acsbiomaterials.2c01049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The extracellular matrix (ECM) is a fibrous network supporting biological cells and provides them a medium for interaction. Cells modify the ECM by applying traction forces, and these forces can propagate to long ranges and establish a mechanism of mechanical communication between neighboring cells. Previous studies have mainly focused on analysis of static force transmission across the ECM. In this study, we explore the plausibility of dynamic mechanical interaction, expressed as vibrations or abrupt fluctuations, giving rise to elastic waves propagating along ECM fibers. We use a numerical mass-spring model to simulate the longitudinal and transversal waves propagating along a single ECM fiber and across a 2D random fiber network. The elastic waves are induced by an active contracting cell (signaler) and received by a passive neighboring cell (receiver). We show that dynamic wave propagation may amplify the signal at the receiver end and support up to an order of magnitude stronger mechanical cues and longer-ranged communication relative to static transmission. Also, we report an optimal impulse duration corresponding to the most effective transmission, as well as extreme fast impulses, in which the waves are encaged around the active cell and do not reach the neighboring cell, possibly due to the Anderson localization effect. Finally, we also demonstrate that extracellular fluid viscosity reduces, but still allows, dynamic propagation along embedded ECM fibers. Our results motivate future biological experiments in mechanobiology to investigate, on the one hand, the mechanosensitivity of cells to dynamic forces traveling and guided by the ECM and, on the other hand, the impact of ECM architecture and remodeling on dynamic force transmission and its spectral filtering, dispersion, and decay.
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Affiliation(s)
- Artem Y Panchenko
- School of Mechanical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv69978, Israel
| | - Oren Tchaicheeyan
- School of Mechanical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv69978, Israel
| | - Igor E Berinskii
- School of Mechanical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv69978, Israel
| | - Ayelet Lesman
- School of Mechanical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv69978, Israel.,The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
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42
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Sun X, Zhou L, Wang X, Li Y, Liu X, Chen Y, Zhong Z, Chen J. FYCO1 regulates migration, invasion, and invadopodia formation in HeLa cells through CDC42/N-WASP/Arp2/3 signaling pathway. Biochem Cell Biol 2022; 100:458-472. [PMID: 36342046 DOI: 10.1139/bcb-2021-0575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
FYCO1, an autophagy adaptor, plays an essential role in the trafficking toward the plus-end of microtubules and the fusion of autophagosomes. Autophagic dysfunction is involved in numerous disease states, including cancers. Previous studies have implicated FYCO1 as one of the critical genes involved in the adenoma to carcinoma transition, but the biological function and mechanism of FYCO1 in carcinogenesis remain unclear. This study aims to elucidate the role and mechanism of up- and downregulation of FYCO1 in mediating tumor effects in HeLa cells. Functionally, FYCO1 promotes cellular migration, invasion, epithelial-mesenchymal transition, invadopodia formation, and matrix degradation, which are detected through wound healing, transwell, immunofluorescence, and Western blot approaches. Interestingly, the data show that although FYCO1 does not affect HeLa cell proliferation, cell cycle distribution, nor vessels' formation, FYCO1 can block the apoptotic function. FYCO1 inhibits cleavage of PARP, caspase3, and caspase9 and increases Bcl-2/Bax ratio. Then, we used CK666, an Arp2/3 specific inhibitor, to confirm that FYCO1 may promote the migration and invasion of HeLa cells through the CDC42/N-WASP/Arp2/3 signaling pathway. Taken together, these results provide a new insight that FYCO1, an autophagy adaptor, may also be a new regulator of tumor metastasis.
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Affiliation(s)
- Xuejiao Sun
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Linlin Zhou
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Xinyao Wang
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Yuying Li
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Xiangyuan Liu
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Yu Chen
- Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Zilin Zhong
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Jianjun Chen
- Translational Research Institute of Brain and Brain-like Intelligence, People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.,Department of Medical Genetics, School of Medicine, Tongji University, Shanghai 200092, China.,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
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43
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Legerstee K, Sueters J, Abraham TE, Slotman JA, Kremers GJ, Hoogenboom JP, Houtsmuller AB. Correlative light and electron microscopy reveals fork-shaped structures at actin entry sites of focal adhesions. Biol Open 2022; 11:283176. [PMID: 36409550 PMCID: PMC9836080 DOI: 10.1242/bio.059417] [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: 05/05/2022] [Accepted: 10/21/2022] [Indexed: 11/23/2022] Open
Abstract
Focal adhesions (FAs) are the main cellular structures to link the intracellular cytoskeleton to the extracellular matrix. FAs mediate cell adhesion, are important for cell migration and are involved in many (patho)-physiological processes. Here we examined FAs and their associated actin fibres using correlative fluorescence and scanning electron microscopy (SEM). We used fluorescence images of cells expressing paxillin-GFP to define the boundaries of FA complexes in SEM images, without using SEM contrast enhancing stains. We observed that SEM contrast was increased around the actin fibre entry site in 98% of FAs, indicating increases in protein density and possibly also phosphorylation levels in this area. In nearly three quarters of the FAs, these nanostructures had a fork shape, with the actin forming the stem and the high-contrast FA areas the fork. In conclusion, the combination of fluorescent and electron microscopy allowed accurate localisation of a highly abundant, novel fork structure at the FA-actin interface.
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Affiliation(s)
- Karin Legerstee
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Jason Sueters
- Delft University of Technology, Department of Imaging Physics, 2628 CD, Delft, The Netherlands
| | - Tsion E. Abraham
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Johan A. Slotman
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Gert-Jan Kremers
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Jacob P. Hoogenboom
- Delft University of Technology, Department of Imaging Physics, 2628 CD, Delft, The Netherlands
| | - Adriaan B. Houtsmuller
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands,Author for correspondence ()
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Wang Y, Zhang J, Zhang X, Zhang H, Cao X, Hu T, Lin J, Tang X, Chen X, Jiang Y, Yan X, Zhuang H, Luo P, Shen L. Study on the Mechanism of Arsenic-Induced Lung Injury Based on SWATH Proteomics Technology. Biol Trace Elem Res 2022:10.1007/s12011-022-03466-2. [PMID: 36333559 DOI: 10.1007/s12011-022-03466-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/07/2022]
Abstract
Chronic arsenic poisoning is a global health problem that affects millions of people, and studies have found that long-term ingestion of arsenic-containing compounds can lead to lung damage, but the exact mechanism is unknown. In this study, Sprague-Dawley (SD) rats were used as the research object, and the proteomic analysis method based on sequential window acquisition of all theoretical fragment ions (SWATH) was used to detect the changes in the expression levels of related proteins in the lung tissue of arsenic-exposed rats, and to explore the mechanism of arsenic compound-induced lung injury. The results showed that arsenic exposure resulted in the abnormal expression of collagen type III and proteins involved in metabolic, immune, and cellular processes, leading to the dysfunction of important pathways associated with these proteins, resulting in lung injury. It suggested that the underlying mechanism of arsenic-induced lung injury may be related to oxidative stress, immune injury, cell junction, and collagen type III. This result provides a new research idea for revealing the mechanism of lung injury caused by arsenic exposure.
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Affiliation(s)
- Yi Wang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Jun Zhang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xinglai Zhang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Ting Hu
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xiaolu Chen
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Yuxuan Jiang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xi Yan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Peng Luo
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China.
| | - Liming Shen
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China.
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, People's Republic of China.
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45
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Ngalim SH, Yusoff N, Johnson RR, Abdul Razak SR, Chen X, Hobbs JK, Lee YY. A review on mechanobiology of cell adhesion networks in different stages of sporadic colorectal cancer to explain its tumorigenesis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:63-72. [PMID: 36116549 DOI: 10.1016/j.pbiomolbio.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Sporadic colorectal cancer (CRC) is strongly linked to extraneous factors, like poor diet and lifestyle, but not to inherent factors like familial genetics. The changes at the epigenomics and signalling pathways are known across the sporadic CRC stages. The catch is that temporal information of the onset, the feedback loop, and the crosstalk of signalling and noise are still unclear. This makes it challenging to diagnose and treat colon cancer effectively with no relapse. Various microbial cells and native cells of the colon, contribute to sporadic CRC development. These cells secrete autocrine and paracrine for their bioenergetics and communications with other cell types. Imbalances of the biochemicals affect the epithelial lining of colon. One side of this epithelial lining is interfacing the dense colon tissue, while the other side is exposed to microbiota and excrement from the lumen. Hence, the epithelial lining is prone to tumorigenesis due to the influence of both biochemical and mechanical cues from its complex surrounding. The role of physical transformations in tumorigenesis have been limitedly discussed. In this context, cellular and tissue structures, and force transductions are heavily regulated by cell adhesion networks. These networks include cell anchoring mechanism to the surrounding, cell structural integrity mechanism, and cell effector molecules. This review will focus on the progression of the sporadic CRC stages that are governed by the underlaying cell adhesion networks within the epithelial cells. Additionally, current and potential technologies and therapeutics that target cell adhesion networks for treatments of sporadic CRC will be incorporated.
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Affiliation(s)
- Siti Hawa Ngalim
- Advanced Medical and Dental Institute, Universiti Sains Malaysia (USM) Bertam, 13200 Kepala Batas, Penang, Malaysia.
| | - Norwahida Yusoff
- School of Mechanical Engineering, Universiti Sains Malaysia (USM) Engineering Campus, 14300 Nibong Tebal, Penang, Malaysia
| | - Rayzel Renitha Johnson
- Advanced Medical and Dental Institute, Universiti Sains Malaysia (USM) Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Siti Razila Abdul Razak
- Advanced Medical and Dental Institute, Universiti Sains Malaysia (USM) Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Xinyue Chen
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, United Kingdom
| | - Jamie K Hobbs
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, United Kingdom
| | - Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains Malaysia (USM) Kubang Kerian, 16150 Kota Bharu, Kelantan, Malaysia
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Mahmoudi A, Atkin SL, Jamialahmadi T, Banach M, Sahebkar A. Effect of Curcumin on Attenuation of Liver Cirrhosis via Genes/Proteins and Pathways: A System Pharmacology Study. Nutrients 2022; 14:nu14204344. [PMID: 36297027 PMCID: PMC9609422 DOI: 10.3390/nu14204344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 01/30/2023] Open
Abstract
Background: Liver cirrhosis is a life-threatening seqsuel of many chronic liver disorders of varying etiologies. In this study, we investigated protein targets of curcumin in liver cirrhosis based on a bioinformatics approach. Methods: Gene/protein associations with curcumin and liver cirrhosis were probed in drug−gene and gene−diseases databases including STITCH/DGIdb/DisGeNET/OMIM/DISEASES/CTD/Pharos and SwissTargetPrediction. Critical clustering groups (MCODE), hub candidates and critical hub genes in liver cirrhosis were identified, and connections between curcumin and liver cirrhosis-related genes were analyzed via Venn diagram. Interaction of hub genes with curcumin by molecular docking using PyRx-virtual screening tools was performed. Results: MCODE analysis indicated three MCODEs; the cluster (MCODE 1) comprised 79 nodes and 881 edges (score: 22.59). Curcumin database interactions recognized 318 protein targets. Liver cirrhosis genes and curcumin protein targets analysis demonstrated 96 shared proteins, suggesting that curcumin may influence 20 candidate and 13 hub genes, covering 81% of liver cirrhosis critical genes and proteins. Thirteen shared proteins affected oxidative stress regulation, RNA, telomerase activity, cell proliferation, and cell death. Molecular docking analysis showed the affinity of curcumin binding hub genes (Binding affinity: ΔG < −4.9 kcal/mol). Conclusions: Curcumin impacted on several critical liver cirrhosis genes mainly involved in extracellular matrix communication, focal adhesion, and the response to oxidative stress.
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Affiliation(s)
- Ali Mahmoudi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stephen L. Atkin
- School of Postgraduate Studies and Research, RCSI Medical University of Bahrain, Busaiteen, Bahrain
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maciej Banach
- Department of Preventive Cardiology and Lipidology, Medical University of Lodz (MUL), 93-338 Lodz, Poland
- Cardiovascular Research Center, University of Zielona Gora, 65-417 Zielona Gora, Poland
- Correspondence: (M.B.); or (A.S.); Tel.: +98-513-180-1239 (A.S.); Fax: +98-513-800-2287 (A.S.)
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Correspondence: (M.B.); or (A.S.); Tel.: +98-513-180-1239 (A.S.); Fax: +98-513-800-2287 (A.S.)
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Quantitative Proteomic Analysis of Zearalenone Exposure on Uterine Development in Weaned Gilts. Toxins (Basel) 2022; 14:toxins14100692. [PMID: 36287961 PMCID: PMC9610722 DOI: 10.3390/toxins14100692] [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: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
The aim of this study was to explore the effect of zearalenone (ZEA) exposure on uterine development in weaned gilts by quantitative proteome analysis with tandem mass spectrometry tags (TMT). A total of 16 healthy weaned gilts were randomly divided into control (basal diet) and ZEA3.0 treatments groups (basal diet supplemented with 3.0 mg/kg ZEA). Results showed that vulva size and uterine development index were increased (p < 0.05), whereas serum follicle stimulation hormone, luteinizing hormone and gonadotropin-releasing hormone were decreased in gilts fed the ZEA diet (p < 0.05). ZEA, α-zearalenol (α-ZOL) and β-zearalenol (β-ZOL) were detected in the uteri of gilts fed a 3.0 mg/kg ZEA diet (p < 0.05). The relative protein expression levels of creatine kinase M-type (CKM), atriopeptidase (MME) and myeloperoxidase (MPO) were up-regulated (p < 0.05), whereas aldehyde dehydrogenase 1 family member (ALDH1A2), secretogranin-1 (CHGB) and SURP and G-patch domain containing 1 (SUGP1) were down-regulated (p < 0.05) in the ZEA3.0 group by western blot, which indicated that the proteomics data were dependable. In addition, the functions of differentially expressed proteins (DEPs) mainly involved the cellular process, biological regulation and metabolic process in the biological process category. Some important signaling pathways were changed in the ZEA3.0 group, such as extracellular matrix (ECM)-receptor interaction, focal adhesion and the phosphoinositide 3-kinase−protein kinase B (PI3K-AKT) signaling pathway (p < 0.01). This study sheds new light on the molecular mechanism of ZEA in the uterine development of gilts.
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The explorations of dynamic interactions of paxillin at the focal adhesions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140825. [PMID: 35926716 DOI: 10.1016/j.bbapap.2022.140825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022]
Abstract
Paxillin is one of the most important adapters in integrin-mediated adhesions that performs numerous crucial functions relying on its dynamic interactions. Its structural behavior serves different purposes, providing a base for several activities. The various domains of paxillin display different functions in the whole process of cell movements and have a significant role in cell adhesion, migration, signal transmission, and protein-protein interactions. On the other hand, some paxillin-associated proteins provide a unique spatiotemporal mechanism for regulating its dynamic characteristics in the tissue homeostasis and make it a more complex and decisive protein at the focal adhesions. This review briefly describes the structural adaptations and molecular mechanisms of recruitment of paxillin into adhesions, explains paxillin's binding dynamics and impact on adhesion stability and turnover, and reveals a variety of paxillin-associated regulatory mechanisms and how paxillin is embedded into the signaling networks.
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Chen S, He T, Zhong Y, Chen M, Yao Q, Chen D, Shao Z, Xiao G. Roles of focal adhesion proteins in skeleton and diseases. Acta Pharm Sin B 2022; 13:998-1013. [PMID: 36970189 PMCID: PMC10031257 DOI: 10.1016/j.apsb.2022.09.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/04/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
The skeletal system, which contains bones, joints, tendons, ligaments and other elements, plays a wide variety of roles in body shaping, support and movement, protection of internal organs, production of blood cells and regulation of calcium and phosphate metabolism. The prevalence of skeletal diseases and disorders, such as osteoporosis and bone fracture, osteoarthritis, rheumatoid arthritis, and intervertebral disc degeneration, increases with age, causing pain and loss of mobility and creating a huge social and economic burden globally. Focal adhesions (FAs) are macromolecular assemblies that are composed of the extracellular matrix (ECM), integrins, intracellular cytoskeleton and other proteins, including kindlin, talin, vinculin, paxillin, pinch, Src, focal adhesion kinase (FAK) and integrin-linked protein kinase (ILK) and other proteins. FA acts as a mechanical linkage connecting the ECM and cytoskeleton and plays a key role in mediating cell-environment communications and modulates important processes, such as cell attachment, spreading, migration, differentiation and mechanotransduction, in different cells in skeletal system by impacting distinct outside-in and inside-out signaling pathways. This review aims to integrate the up-to-date knowledge of the roles of FA proteins in the health and disease of skeletal system and focuses on the specific molecular mechanisms and underlying therapeutic targets for skeletal diseases.
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Affiliation(s)
- Sheng Chen
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tailin He
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yiming Zhong
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Mingjue Chen
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qing Yao
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Di Chen
- Research Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zengwu Shao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Corresponding authors.
| | - Guozhi Xiao
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
- Corresponding authors.
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WDR73 Depletion Destabilizes PIP4K2C Activity and Impairs Focal Adhesion Formation in Galloway–Mowat Syndrome. BIOLOGY 2022; 11:biology11101397. [PMID: 36290302 PMCID: PMC9598763 DOI: 10.3390/biology11101397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Galloway–Mowat syndrome is a rare genetic disease, classically characterized by a combination of various neurological symptoms and nephrotic syndrome. WDR73 is the pathogenic gene responsible for Galloway–Mowat syndrome. However, the pathological and molecular mechanisms of Galloway–Mowat syndrome, especially nephrotic syndrome caused by WDR73 deficiency, remains unknown. In this study, we knocked out the WDR73 in human embryonic kidney 293 cells to observe the morphological characteristics of the cells and elucidate the functions of WDR73. Additionally, we used a combination of proteomics, transcriptomics, and biochemical assays to identify the regulated targets of WDR73. We aimed to discover directly interacting molecules and the regulatory pathway of WDR73 and to illustrate the molecular mechanism between the WDR73 pathway and nephrotic disease in Galloway–Mowat syndrome. From the molecular mechanism we found in vitro, we draw a hypothesis that the damage to focal adhesion of podocytes caused by WDR73 defect is the key issue of kidney dysfunction. Finally, we verified the hypothesis in a podocyte-specific conditional knockout Wdr73 mouse model. Abstract (1) Background: Galloway–Mowat syndrome (GAMOS) is a rare genetic disease, classically characterized by a combination of various neurological symptoms and nephrotic syndrome. WDR73 is the pathogenic gene responsible for GAMOS1. However, the pathological and molecular mechanisms of GAMOS1, especially nephrotic syndrome caused by WDR73 deficiency, remain unknown. (2) Methods and Results: In this study, we first observed remarkable cellular morphological changes including impaired cell adhesion, decreased pseudopodia, and G2/M phase arrest in WDR73 knockout (KO) HEK 293 cells. The differentially expressed genes in WDR73 KO cells were enriched in the focal adhesion (FA) pathway. Additionally, PIP4K2C, a phospholipid kinase also involved in the FA pathway, was subsequently validated to interact with WDR73 via protein microarray and GST pulldown. WDR73 regulates PIP4K2C protein stability through the autophagy–lysosomal pathway. The stability of PIP4K2C was significantly disrupted by WDR73 KO, leading to a remarkable reduction in PIP2 and thus weakening the FA formation. In addition, we found that podocyte-specific conditional knockout (Wdr73 CKO) mice showed high levels of albuminuria and podocyte foot process injury in the ADR-induced model. FA formation was impaired in primary podocytes derived from Wdr73 CKO mice. (3) Conclusions: Since FA has been well known for its critical roles in maintaining podocyte structures and function, our study indicated that nephrotic syndrome in GAMOS1 is associated with disruption of FA caused by WDR73 deficiency.
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