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Zhu G, Wang Y, Wang Y, Huang H, Li B, Chen P, Chen C, Zhang H, Li Y, Liu H, Chen J. Myofibroblasts derived type V collagen promoting tissue mechanical stress and facilitating metastasis and therapy resistance of lung adenocarcinoma cells. Cell Death Dis 2024; 15:493. [PMID: 38987529 PMCID: PMC11237033 DOI: 10.1038/s41419-024-06873-6] [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: 03/04/2024] [Revised: 06/22/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
Lung cancer is a leading cause of cancer-related mortality globally, with a dismal 5-year survival rate, particularly for Lung Adenocarcinoma (LUAD). Mechanical changes within the tumor microenvironment, such as extracellular matrix (ECM) remodeling and fibroblast activity, play pivotal roles in cancer progression and metastasis. However, the specific impact of the basement membrane (BM) on the mechanical characteristics of LUAD remains unclear. This study aims to identify BM genes influencing internal mechanical stress in tumors, elucidating their effects on LUAD metastasis and therapy resistance, and exploring strategies to counteract these effects. Using Matrigel overlay and Transwell assays, we found that mechanical stress, mimicked by matrix application, augmented LUAD cell migration and invasion, correlating with ECM alterations and activation of the epithelial-mesenchymal transition (EMT) pathway. Employing machine learning, we developed the SVM_Score model based on relevant BM genes, which accurately predicted LUAD patient prognosis and EMT propensity across multiple datasets. Lower SVM_Scores were associated with worse survival outcomes, elevated cancer-related pathways, increased Tumor Mutation Burden, and higher internal mechanical stress in LUAD tissues. Notably, the SVM_Score was closely linked to COL5A1 expression in myofibroblasts, a key marker of mechanical stress. High COL5A1 expression from myofibroblasts promoted tumor invasiveness and EMT pathway activation in LUAD cells. Additionally, treatment with Sorafenib, which targets COL5A1 secretion, attenuated the tumor-promoting effects of myofibroblast-derived COL5A1, inhibiting LUAD cell proliferation, migration, and enhancing chemosensitivity. In conclusion, this study elucidates the complex interplay between mechanical stress, ECM alterations, and LUAD progression. The SVM_Score emerges as a robust prognostic tool reflecting tumor mechanical characteristics, while Sorafenib intervention targeting COL5A1 secretion presents a promising therapeutic strategy to mitigate LUAD aggressiveness. These findings deepen our understanding of the biomechanical aspects of LUAD and offer insights for future research and clinical applications.
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Affiliation(s)
- Guangsheng Zhu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yanan Wang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yingjie Wang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Hua Huang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Boshi Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Peijie Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Chen Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Hongbing Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.
| | - Hongyu Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.
| | - Jun Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.
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Shengxiao X, Xinxin S, Yunxiang Z, Zhijie T, Xiaofei T. Identification of a basement membrane-related gene signature for predicting prognosis, immune infiltration, and drug sensitivity in colorectal cancer. Front Oncol 2024; 14:1428176. [PMID: 39011483 PMCID: PMC11246870 DOI: 10.3389/fonc.2024.1428176] [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: 05/05/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024] Open
Abstract
Background Colorectal cancer (CRC) is the most common malignancy affecting the gastrointestinal tract. Extensive research indicates that basement membranes (BMs) may play a crucial role in the initiation and progression of the disease. Methods Data on the RNA expression patterns and clinicopathological information of patients with CRC were sourced from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. A BM-linked risk signature for the prediction of overall survival (OS) was formulated using univariate Cox regression and combined machine learning techniques. Survival outcomes, functional pathways, the tumor microenvironment (TME), and responses to both immunotherapy and chemotherapy within varying risk classifications were also investigated. The expression trends of the model genes were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and the Human Protein Atlas (HPA) database. Results A nine-gene risk signature containing UNC5C, TINAG, TIMP1, SPOCK3, MMP1, AGRN, UNC5A, ADAMTS4, and ITGA7 was constructed for the prediction of outcomes in patients with CRC. The expression profiles of these candidate genes were verified using RT-PCR and the HPA database and were found to be consistent with the findings on differential gene expression in the TCGA dataset. The validity of the signature was confirmed using the GEO cohort. The patients were stratified into different risk groups according to differences in clinicopathological characteristics, TME features, enrichment functions, and drug sensitivities. Lastly, the prognostic nomogram model based on the risk score was found to be effective in identifying high-risk patients and predicting OS. Conclusion A basement membrane-related risk signature was constructed and found to be effective for predicting the prognosis of patients with CRC.
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Affiliation(s)
- Xiang Shengxiao
- Department of Science and Education, Suqian First Hospital, Suqian, Jiangsu, China
| | - Sun Xinxin
- Department of Science and Education, Yangzhou Maternal and Child Health Hospital, Yangzhou, Jiangsu, China
| | - Zhu Yunxiang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Tang Zhijie
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Tang Xiaofei
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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Wang X, Liu C, Wu H, Gu Y, Zhang L, Xu R, Lin Q. Basement membrane-associated gene expression as a predictor of survival in oral cancer. BMC Cancer 2024; 24:731. [PMID: 38877482 PMCID: PMC11177517 DOI: 10.1186/s12885-024-12485-2] [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: 10/17/2023] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND This study sought to investigate the prognostic value of basement membrane (BM)-associated gene expressions in oral cancer. METHODS We harvested and integrated data on BM-associated genes (BMGs), the oral cancer transcriptome, and clinical information from public repositories. After identifying differentially expressed BMGs, we used Cox and Lasso regression analyses to create a BMG-based risk score for overall survival at various intervals. We then validated this score using the GSE42743 cohort as a validation set. The prognostic potential of the risk scores and their relations to clinical features were assessed. Further, we conducted functional pathway enrichment, immune cell infiltration, and immune checkpoint analyses to elucidate the immunological implications and therapeutic potential of the BMG-based risk score and constituent genes. To confirm the expression levels of the BMG LAMA3 in clinical samples of oral cancer tissue, we performed quantitative real-time PCR (qRT-PCR) and immunohistochemical staining. RESULTS The BMGs LAMA3, MMP14, and GPC2 demonstrated notable prognostic significance, facilitating the construction of a BMG-based risk score. A higher risk score derived from BMGs correlated with a poorer survival prognosis for oral cancer patients. Moreover, the risk-associated BMGs exhibited a significant relationship with immune function variability (P < 0.05), discrepancies in infiltrating immune cell fractions, and immune checkpoint expressions (P < 0.05). The upregulated expression levels of LAMA3 in oral cancer tissues were substantiated through qRT-PCR and immunohistochemical staining. CONCLUSION The BMG-based risk score emerged as a reliable prognostic tool for oral cancer, meriting further research for validation and potential clinical application.
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Affiliation(s)
- Xu Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Chaoge Liu
- Department of Oramaxillofacial - Head and Neck Surgery, School of Medicine, Tianjin Stomatological Hospital, Nankai University, Tianjin, 300041, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, 300041, China
| | - HuiFang Wu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Yulu Gu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Le Zhang
- Department of Oral Pathology, School of Medicine, Tianjin Stomatological Hospital, Nankai University, Tianjin, 300041, China
| | - Rongqing Xu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Qing Lin
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China.
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Wu G, Li F, Guo D, Xi K, Zheng D, Huang R, Wu X, Li A, Liu X. Comprehensive evaluation of genes related to basement membrane in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:10108-10131. [PMID: 38870261 PMCID: PMC11210257 DOI: 10.18632/aging.205923] [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: 10/25/2023] [Accepted: 05/03/2024] [Indexed: 06/15/2024]
Abstract
In all mammals, the basement membrane serves as a pivotal extracellular matrix. Hepatocellular carcinoma (HCC) is a challenge among numerous cancer types shaped by basement membrane-related genes (BMGs). Our research established an innovative prognostic model that is highly accurate in its prediction of HCC prognoses and immunotherapy efficacy to summarize the crucial role of BMGs in HCC. We obtained HCC transcriptome analysis data and corresponding clinical data from The Cancer Genome Atlas (TCGA). To augment our dataset, we incorporated 222 differentially expressed BMGs identified from relevant literature. A weighted gene coexpression network analysis (WGCNA) of 10158 genes demonstrated four modules that were connected to HCC. Additionally, 66 genes that are found at the intersection of BMGs and HCC-related genes were designated as hub HCC-related BMGs. MMP1, ITGA2, P3H1, and CTSA comprise the novel model that was engineered using univariate and multivariate Cox regression analysis. Furthermore, the International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) datasets encouraged the BMs model's validity. The overall survival (OS) of individuals with HCC may be precisely predicted in the TCGA and ICGC databases utilizing the BMs model. A nomogram based on the model was created in the TCGA database at similar time, and displayed a favorable discriminating ability for HCC. Particularly, when compared to the patients at an elevated risk, the patients with a low-risk profile presented different tumor microenvironment (TME) and hallmark pathways. Moreover, we discovered that a lower risk score of HCC patients would display a greater response to immunotherapy. Finally, quantitative real-time PCR (qRT-PCR) experiments were used to verify the expression patterns of BMs model. In summary, BMs model demonstrated efficacy in prognosticating the survival probability of HCC patients and their immunotherapeutic responsiveness.
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Affiliation(s)
- Guojing Wu
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Fei Li
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Danyan Guo
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Kaiwen Xi
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Dayong Zheng
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Ruichao Huang
- Heshan Hospital of Traditional Chinese Medicine, Jiangmen 529000, China
| | - Xiuqiong Wu
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Aimin Li
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Xinhui Liu
- Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
- Heshan Hospital of Traditional Chinese Medicine, Jiangmen 529000, China
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Rosner M, Hengstschläger M. Oct4 controls basement membrane development during human embryogenesis. Dev Cell 2024; 59:1439-1456.e7. [PMID: 38579716 DOI: 10.1016/j.devcel.2024.03.007] [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: 01/10/2022] [Revised: 01/02/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
Basement membranes (BMs) are sheet-like structures of extracellular matrix (ECM) that provide structural support for many tissues and play a central role in signaling. They are key regulators of cell behavior and tissue functions, and defects in their assembly or composition are involved in numerous human diseases. Due to the differences between human and animal embryogenesis, ethical concerns, legal constraints, the scarcity of human tissue material, and the inaccessibility of the in vivo condition, BM regulation during human embryo development has remained elusive. Using the post-implantation amniotic sac embryoid (PASE), we delineate BM assembly upon post-implantation development and BM disassembly during primitive streak (PS) cell dissemination. Further, we show that the transcription factor Oct4 regulates the expression of BM structural components and receptors and controls BM development by regulating Akt signaling and the small GTPase Rac1. These results represent a relevant step toward a more comprehensive understanding of early human development.
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Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna 1090, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna 1090, Austria.
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Han J, Wang Q, Li S, Yang J, Qiu Z, Fu W. Comprehensive analysis of basement membrane-related gene based on single-cell and bulk RNA sequencing data to predict prognosis and evaluate immune characteristics in colorectal cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:3367-3380. [PMID: 38445432 DOI: 10.1002/tox.24211] [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: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
AIMS Basement membrane-related genes (BMs) participate in regulating cell polarity, invasion, metastasis, and survival across different tumor types. Nevertheless, the specific functions of BMs in colorectal cancer (CRC) remain uncertain. METHODS To investigate the clinical relevance of BMs in CRC, we retrieved both gene expression and clinical data from The Cancer Genome Atlas (TCGA) datasets for subsequent analysis. The Kaplan-Meier (K-M) survival curve was employed to evaluate prognosis in high- and low-risk groups. Furthermore, additional analyses, including nomogram construction, functional enrichment, examination of the tumor immune microenvironment, prediction of small-molecule drugs, and more, were conducted to delve into the significance of BM-related signatures in CRC. Single-cell data from seven CRC patients were obtained from the TISCH2 database, and expression validation and cell source exploration of BM-related signatures were performed. Lastly, the expression and function of TIMP1, a key gene in BMs that may play a role in the progression of CRC, was validated in vitro through a series of basic experiments. RESULTS We constructed a seven BMs-based model to categorize CRC patients into high-risk and low-risk groups. K-M survival analysis indicated a poorer prognosis for high-risk CRC patients. Cox regression analysis further identified the risk score as an independent prognostic factor for CRC patients. The nomogram model exhibited superior discrimination and calibration abilities of CRC patients. Based on the results from GO/KEGG and GSEA, genes in the high-risk subgroup were implicated in immune-related pathways and exhibited a positive correlation with immune checkpoints. In single-cell data, we found that TIMP1 is highly expressed in many cells, especially in malignant tumor cells. We also observed up-regulation of TIMP1 in CRC cell lines, promoting cancer invasion and migration in vitro. CONCLUSIONS Our study has discovered a novel prognostic index derived from BM-related genes in CRC patients. Specifically, the new model enables patient stratification, improving the selection of individuals likely to benefit from immunotherapy.
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Affiliation(s)
- Jing Han
- Xuzhou Medical University, Xuzhou, Jiangsu Province, China
- Department of General Surgery, Shuyang Hospital of TCM, Shuyang, Jiangsu Province, China
| | - Qipeng Wang
- Department of General Surgery, Shuyang Hospital of TCM, Shuyang, Jiangsu Province, China
| | - Shangshang Li
- Department of General Surgery, Shuyang Hospital of TCM, Shuyang, Jiangsu Province, China
| | - Jie Yang
- Department of General Surgery, Shuyang Hospital of TCM, Shuyang, Jiangsu Province, China
| | - Zhengcai Qiu
- Department of General Surgery, Shuyang Hospital of TCM, Shuyang, Jiangsu Province, China
| | - Wei Fu
- Xuzhou Medical University, Xuzhou, Jiangsu Province, China
- Department of General Surgery, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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Xun S, Li X, Zhuang Q, Zhu Y, Qu L. Basement membrane-related lncRNA signature for the prognosis of hepatocellular carcinoma. Heliyon 2024; 10:e30439. [PMID: 38765049 PMCID: PMC11096898 DOI: 10.1016/j.heliyon.2024.e30439] [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: 01/15/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the main type of primary liver cancer. This study aimed to develop a basement membrane (BM) related lncRNAs risk signature to evaluate the prognosis of HCC patients. We screened differentially expressed BM-related lncRNAs (DE-BMRlncRNAs) for risk evaluation, and identified six DE-BMRlncRNAs (AC072054.1, NUP50-DT, AC026412.3, AC109322.2, POLH-AS1 and LINC00595) for prognostic risk signature. HCC patients were divided to high or low risk according to median risk score. Our prognostic model predicted that patients with higher risk score had worse prognosis. We also created a nomogram to assist clinical decision-making according to risk score and clinicopathological features. Meanwhile, we confirmed the expression of six lncRNAs in HCC tissue and cells. POLH-AS1 knockdown inhibited the migration and invasion of HCC cells. In conclusion, we established a predictive model based on BMRlncRNAs to predict the prognosis of HCC. Our findings offer a rationale to further explore BM-related biomarkers for HCC.
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Affiliation(s)
- Shenmei Xun
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaocui Li
- Department of Gastroenterology, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University,1158 Park Road(E) , Qingpu, Shanghai 201700, China
| | | | - Yefei Zhu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lili Qu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Koehler S, Hengel FE, Dumoulin B, Damashek L, Holzman LB, Susztak K, Huber TB. The 14th International Podocyte Conference 2023: from podocyte biology to glomerular medicine. Kidney Int 2024; 105:935-952. [PMID: 38447880 DOI: 10.1016/j.kint.2024.01.042] [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: 10/30/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 03/08/2024]
Abstract
The 14th International Podocyte Conference took place in Philadelphia, Pennsylvania, USA from May 23 to 26, 2023. It commenced with an early-career researchers' meeting on May 23, providing young scientists with a platform to present and discuss their research findings. Throughout the main conference, 29 speakers across 9 sessions shared their insights on podocyte biology, glomerular medicine, novel technologic advancements, and translational approaches. Additionally, the event featured 3 keynote lectures addressing engineered chimeric antigen receptor T cell- and mRNA-based therapies and the use of biobanks for enhanced disease comprehension. Furthermore, 4 brief oral abstract sessions allowed scientists to present their findings to a broad audience. The program also included a panel discussion addressing the challenges of conducting human research within the American Black community. Remarkably, after a 5-year hiatus from in-person conferences, the 14th International Podocyte Conference successfully convened scientists from around the globe, fostering the presentation and discussion of crucial research findings, as summarized in this review. Furthermore, to ensure continuous and sustainable education, research, translation, and trial medicine related to podocyte and glomerular diseases for the benefit of patients, the International Society of Glomerular Disease was officially launched during the conference.
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Affiliation(s)
- Sybille Koehler
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Felicitas E Hengel
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Bernhard Dumoulin
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Laurel Damashek
- International Society of Glomerular Disease, Florence, Massachusetts, USA
| | - Lawrence B Holzman
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tobias B Huber
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; International Society of Glomerular Disease, Florence, Massachusetts, USA.
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Zhu Y, Tesone Z, Tan M, Hardin J. TIAM-1 regulates polarized protrusions during dorsal intercalation in the Caenorhabditis elegans embryo through both its GEF and N-terminal domains. J Cell Sci 2024; 137:jcs261509. [PMID: 38345070 PMCID: PMC10949065 DOI: 10.1242/jcs.261509] [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: 07/24/2023] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
Mediolateral cell intercalation is a morphogenetic strategy used throughout animal development to reshape tissues. Dorsal intercalation in the Caenorhabditis elegans embryo involves the mediolateral intercalation of two rows of dorsal epidermal cells to create a single row that straddles the dorsal midline, and thus is a simple model to study cell intercalation. Polarized protrusive activity during dorsal intercalation requires the C. elegans Rac and RhoG orthologs CED-10 and MIG-2, but how these GTPases are regulated during intercalation has not been thoroughly investigated. In this study, we characterized the role of the Rac-specific guanine nucleotide exchange factor (GEF) TIAM-1 in regulating actin-based protrusive dynamics during dorsal intercalation. We found that TIAM-1 can promote formation of the main medial lamellipodial protrusion extended by intercalating cells through its canonical GEF function, whereas its N-terminal domains function to negatively regulate the generation of ectopic filiform protrusions around the periphery of intercalating cells. We also show that the guidance receptor UNC-5 inhibits these ectopic filiform protrusions in dorsal epidermal cells and that this effect is in part mediated via TIAM-1. These results expand the network of proteins that regulate basolateral protrusive activity during directed rearrangement of epithelial cells in animal embryos.
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Affiliation(s)
- Yuyun Zhu
- Genetics PhD Program, University of Wisconsin, Madison, WI 53706, USA
| | - Zoe Tesone
- Cellular and Molecular Biology PhD Program, University of Wisconsin, Madison, WI 53706, USA
| | - Minyi Tan
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Jeff Hardin
- Genetics PhD Program, University of Wisconsin, Madison, WI 53706, USA
- Cellular and Molecular Biology PhD Program, University of Wisconsin, Madison, WI 53706, USA
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
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Lou Y, Li PH, Liu XQ, Wang TX, Liu YL, Chen CC, Ma KL. ITGAM-mediated macrophages contribute to basement membrane damage in diabetic nephropathy and atherosclerosis. BMC Nephrol 2024; 25:72. [PMID: 38413872 PMCID: PMC10900706 DOI: 10.1186/s12882-024-03505-1] [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: 10/29/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) and atherosclerosis (AS) are prevalent and severe complications associated with diabetes, exhibiting lesions in the basement membrane, an essential component found within the glomerulus, tubules, and arteries. These lesions contribute significantly to the progression of both diseases, however, the precise underlying mechanisms, as well as any potential shared pathogenic processes between them, remain elusive. METHODS Our study analyzed transcriptomic profiles from DN and AS patients, sourced from the Gene Expression Omnibus database. A combination of integrated bioinformatics approaches and machine learning models were deployed to identify crucial genes connected to basement membrane lesions in both conditions. The role of integrin subunit alpha M (ITGAM) was further explored using immune infiltration analysis and genetic correlation studies. Single-cell sequencing analysis was employed to delineate the expression of ITGAM across different cell types within DN and AS tissues. RESULTS Our analyses identified ITGAM as a key gene involved in basement membrane alterations and revealed its primary expression within macrophages in both DN and AS. ITGAM was significantly correlated with tissue immune infiltration within these diseases. Furthermore, the expression of genes encoding core components of the basement membrane was influenced by the expression level of ITGAM. CONCLUSION Our findings suggest that macrophages may contribute to basement membrane lesions in DN and AS through the action of ITGAM. Moreover, therapeutic strategies that target ITGAM may offer potential avenues to mitigate basement membrane lesions in these two diabetes-related complications.
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Affiliation(s)
- Yude Lou
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Peng Hui Li
- Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiao Qi Liu
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Tian Xiang Wang
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Yi Lan Liu
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Chen Chen Chen
- Department of Basic Medicine Sciences, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Kun Ling Ma
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
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Lin Y, Yang Q, Lin X, Liu X, Qian Y, Xu D, Cao N, Han X, Zhu Y, Hu W, He X, Yu Z, Kong X, Zhu L, Zhong Z, Liu K, Zhou B, Wang Y, Peng J, Zhu W, Wang J. Extracellular Matrix Disorganization Caused by ADAMTS16 Deficiency Leads to Bicuspid Aortic Valve With Raphe Formation. Circulation 2024; 149:605-626. [PMID: 38018454 DOI: 10.1161/circulationaha.123.065458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND A better understanding of the molecular mechanism of aortic valve development and bicuspid aortic valve (BAV) formation would significantly improve and optimize the therapeutic strategy for BAV treatment. Over the past decade, the genes involved in aortic valve development and BAV formation have been increasingly recognized. On the other hand, ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) gene family members have been reported to be able to modulate cardiovascular development and diseases. The present study aimed to further investigate the roles of ADAMTS family members in aortic valve development and BAV formation. METHODS Morpholino-based ADAMTS family gene-targeted screening for zebrafish heart outflow tract phenotypes combined with DNA sequencing in a 304 cohort BAV patient registry study was initially carried out to identify potentially related genes. Both ADAMTS gene-specific fluorescence in situ hybridization assay and genetic tracing experiments were performed to evaluate the expression pattern in the aortic valve. Accordingly, related genetic mouse models (both knockout and knockin) were generated using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9) method to further study the roles of ADAMTS family genes. The lineage-tracing technique was used again to evaluate how the cellular activity of specific progenitor cells was regulated by ADAMTS genes. Bulk RNA sequencing was used to investigate the signaling pathways involved. Inducible pluripotent stem cells derived from both BAV patients and genetic mouse tissue were used to study the molecular mechanism of ADAMTS. Immunohistochemistry was performed to examine the phenotype of cardiac valve anomalies, especially in the extracellular matrix components. RESULTS ADAMTS genes targeting and phenotype screening in zebrafish and targeted DNA sequencing on a cohort of patients with BAV identified ADAMTS16 (a disintegrin and metalloproteinase with thrombospondin motifs 16) as a BAV-causing gene and found the ADAMTS16 p. H357Q variant in an inherited BAV family. Both in situ hybridization and genetic tracing studies described a unique spatiotemporal pattern of ADAMTS16 expression during aortic valve development. Adamts16+/- and Adamts16+/H355Q mouse models both exhibited a right coronary cusp-noncoronary cusp fusion-type BAV phenotype, with progressive aortic valve thickening associated with raphe formation (fusion of the commissure). Further, ADAMTS16 deficiency in Tie2 lineage cells recapitulated the BAV phenotype. This was confirmed in lineage-tracing mouse models in which Adamts16 deficiency affected endothelial and second heart field cells, not the neural crest cells. Accordingly, the changes were mainly detected in the noncoronary and right coronary leaflets. Bulk RNA sequencing using inducible pluripotent stem cells-derived endothelial cells and genetic mouse embryonic heart tissue unveiled enhanced FAK (focal adhesion kinase) signaling, which was accompanied by elevated fibronectin levels. Both in vitro inducible pluripotent stem cells-derived endothelial cells culture and ex vivo embryonic outflow tract explant studies validated the altered FAK signaling. CONCLUSIONS Our present study identified a novel BAV-causing ADAMTS16 p. H357Q variant. ADAMTS16 deficiency led to BAV formation.
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Affiliation(s)
- Ying Lin
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Qifan Yang
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Xiaoping Lin
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Xianbao Liu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Yi Qian
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Dilin Xu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Naifang Cao
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Ximeng Han
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (X.H.)
| | - Yanqing Zhu
- Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network (Y.Z., K.L., J.P.), Hangzhou, China
| | - Wangxing Hu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Xiaopeng He
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Zhengyang Yu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Xiangmin Kong
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Lianlian Zhu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Zhiwei Zhong
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Kai Liu
- Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network (Y.Z., K.L., J.P.), Hangzhou, China
| | - Bin Zhou
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences (B.Z.)
| | - Yidong Wang
- Cardiovascular Research Center, School of Basic Medical Sciences, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Xi'an Jiaotong University Health Science Center, China (Y.W.)
| | - Jinrong Peng
- Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network (Y.Z., K.L., J.P.), Hangzhou, China
| | - Wei Zhu
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
| | - Jian'an Wang
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.), Hangzhou, China
- Research Center for Life Science and Human Health, Binjiang Institute (J.W.), Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Y.L., Q.Y., X. Lin, X. Liu, Y.Q., D.X., N.C., W.H., X.H., Z.Y., X.K., L.Z., Z.Z., W.Z., J.W.)
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Xia B, Wang J, Zhang D, Hu X. Integration of basement membrane-related genes in a risk signature for prognosis in clear cell renal cell carcinoma. Sci Rep 2024; 14:3893. [PMID: 38365923 PMCID: PMC10873511 DOI: 10.1038/s41598-024-54073-1] [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: 09/12/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is characterized by high heterogeneity and recurrence rates, posing significant challenges for stratification and treatment. Basement membrane-related genes (BMGs) play a crucial role in tumor initiation and progression. Clinical and transcriptomic data of ccRCC patients were extracted from TCGA and GEO databases. We employed univariate regression and LASSO-Cox stepwise regression analysis to construct a BMscore model based on BMGs expression level. A nomogram combining clinical features and BMscore was constructed to predict individual survival probabilities. Further enrichment analysis and immune-related analysis were conducted to explore the enriched pathways and immune features associated with BMGs. High-risk individuals predicted by BMscore exhibited poorer overall survival, which was consistent with the validation dataset. BMscore was identified as an independent risk factor for ccRCC. Functional analysis revealed that BMGs were related to cell-matrix and tumor-associated signaling pathways. Immune profiling suggests that BMGs play a key role in immune interactions and the tumor microenvironment. BMGs serve as a novel prognostic predictor for ccRCC and play a role in the immune microenvironment and treatment response. Targeting the BM may represent an alternative therapeutic approach for ccRCC.
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Affiliation(s)
- Bowen Xia
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jingwei Wang
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Dongxu Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Worker's Stadium, Chaoyang District, Beijing, 100020, China.
- Institute of Urology, Capital Medical University, Beijing, China.
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Kenny-Ganzert IW, Sherwood DR. The C. elegans anchor cell: A model to elucidate mechanisms underlying invasion through basement membrane. Semin Cell Dev Biol 2024; 154:23-34. [PMID: 37422376 PMCID: PMC10592375 DOI: 10.1016/j.semcdb.2023.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
Cell invasion through basement membrane barriers is crucial during many developmental processes and in immune surveillance. Dysregulation of invasion also drives the pathology of numerous human diseases, such as metastasis and inflammatory disorders. Cell invasion involves dynamic interactions between the invading cell, basement membrane, and neighboring tissues. Owing to this complexity, cell invasion is challenging to study in vivo, which has hampered the understanding of mechanisms controlling invasion. Caenorhabditis elegans anchor cell invasion is a powerful in vivo model where subcellular imaging of cell-basement membrane interactions can be combined with genetic, genomic, and single-cell molecular perturbation studies. In this review, we outline insights gained by studying anchor cell invasion, which span transcriptional networks, translational regulation, secretory apparatus expansion, dynamic and adaptable protrusions that breach and clear basement membrane, and a complex, localized metabolic network that fuels invasion. Together, investigation of anchor cell invasion is building a comprehensive understanding of the mechanisms that underlie invasion, which we expect will ultimately facilitate better therapeutic strategies to control cell invasive activity in human disease.
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Affiliation(s)
| | - David R Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.
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Wu X, Zhang F, Mao X, Xu F, Ding X, Sun X, Wang J. The mechanism of adipose mesenchymal stem cells to stabilize the immune microenvironment of pelvic floor injury by regulating pyroptosis and promoting tissue repair. Mater Today Bio 2024; 24:100910. [PMID: 38204481 PMCID: PMC10776425 DOI: 10.1016/j.mtbio.2023.100910] [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: 07/26/2023] [Revised: 11/19/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Pelvic organ prolapse (POP) has a high incidence rate among Chinese women. Repeated mechanical stimulation is an important factor causing POP, but the injury mechanism has not yet been elucidated. The purpose of this study is to explore the related mechanisms of pelvic floor supporting tissue damage caused by mechanical force and the application of stem cell therapy. First, we obtained vaginal wall and sacral ligament tissue samples from clinical patients for examination. Pelvic floor support tissues of POP patients displayed high expression of inflammation and immune disorders. Then, we constructed a rat model of childbirth injury. In vivo and in vitro experiments investigated the key mechanism of pelvic floor support tissue injury caused by mechanical force. We discovered that after mechanical force, a large number of reactive oxygen species (ROS) and macrophages rapidly accumulated in pelvic floor tissues. ROS stimulated macrophages to produce NLRP3 inflammatory complex, induced the release of interleukin (IL-1β) and pyroptosis and exacerbated the inflammatory state of damaged tissues, persisting chronic inflammation of fibroblasts in supporting tissues, thus causing the pelvic floor's extracellular matrix (ECM) collagen metabolic disorder. Resultingly impeding the repair process, thereby causing the onset and progression of the disease. Through their paracrine ability, we discovered that adipose mesenchymal stem cells (ADSCs) could inhibit this series of pathological processes and promote tissue repair, asserting a good therapeutic effect. Simultaneously, to overcome the low cell survival rate and poor therapeutic effect of directly injecting cells, we developed a ROS-responsive PVA@COLI hydrogel with ADSCs. The ROS-scavenging properties of the gel could reshape the site of inflammation injury, enhance cell survival, and play a role in subsequent treatment. The findings of this study could serve as a basis for early, targeted intervention therapy for POP and representing a promising approach.
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Affiliation(s)
- Xiaotong Wu
- Department of Obstetrics and Gynecology, Peking University People's Hospital, 100044, Beijing, China
- Beijing Key Laboratory of Female Pelvic Floor Disorders, 100044, Beijing, China
| | - Fengshi Zhang
- Department of Orthopedics and Trauma, Peking University People's Hospital, 100044, Beijing, China
| | - Xiaolin Mao
- College of Materials Science and Engineering, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Fujian Xu
- College of Materials Science and Engineering, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Xiaokang Ding
- College of Materials Science and Engineering, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Xiuli Sun
- Department of Obstetrics and Gynecology, Peking University People's Hospital, 100044, Beijing, China
- Beijing Key Laboratory of Female Pelvic Floor Disorders, 100044, Beijing, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, 100044, Beijing, China
- Beijing Key Laboratory of Female Pelvic Floor Disorders, 100044, Beijing, China
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Jones MJ, Jones MC. Cell cycle control by cell-matrix interactions. Curr Opin Cell Biol 2024; 86:102288. [PMID: 38056140 DOI: 10.1016/j.ceb.2023.102288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Cell adhesion to the extracellular matrix (ECM) is required for normal cell cycle progression and accurate cell division. However, how cell adhesion to the wide range of ECM proteins found in human tissues influences the cell cycle is not fully understood. The composition and physical properties of the ECM can have profound effects on cell proliferation but can also promote cell cycle exit and quiescence. Furthermore, during tumor development and progression, changes in the ECM can drive both cancer cell proliferation and dormancy. Cell-matrix adhesion is primarily sensed via integrin-associated adhesion complexes, which in turn are regulated by the cell cycle machinery. In particular, cyclin-dependent kinase 1 (CDK1) has been shown to play a crucial role in regulating adhesion complexes during interphase and entry into mitosis. These reciprocal links between cell cycle progression and cell-matrix interactions are now being identified.
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Affiliation(s)
- Michael J Jones
- Peninsula Medical School, Faculty of Health, Medicine, Dentistry and Human Sciences, University of Plymouth, PL6 8BU, United Kingdom
| | - Matthew C Jones
- Peninsula Medical School, Faculty of Health, Medicine, Dentistry and Human Sciences, University of Plymouth, PL6 8BU, United Kingdom.
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Johnson BB, Cosson MV, Tsansizi LI, Holmes TL, Gilmore T, Hampton K, Song OR, Vo NTN, Nasir A, Chabronova A, Denning C, Peffers MJ, Merry CLR, Whitelock J, Troeberg L, Rushworth SA, Bernardo AS, Smith JGW. Perlecan (HSPG2) promotes structural, contractile, and metabolic development of human cardiomyocytes. Cell Rep 2024; 43:113668. [PMID: 38198277 DOI: 10.1016/j.celrep.2023.113668] [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: 05/22/2023] [Revised: 11/01/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Perlecan (HSPG2), a heparan sulfate proteoglycan similar to agrin, is key for extracellular matrix (ECM) maturation and stabilization. Although crucial for cardiac development, its role remains elusive. We show that perlecan expression increases as cardiomyocytes mature in vivo and during human pluripotent stem cell differentiation to cardiomyocytes (hPSC-CMs). Perlecan-haploinsuffient hPSCs (HSPG2+/-) differentiate efficiently, but late-stage CMs have structural, contractile, metabolic, and ECM gene dysregulation. In keeping with this, late-stage HSPG2+/- hPSC-CMs have immature features, including reduced ⍺-actinin expression and increased glycolytic metabolism and proliferation. Moreover, perlecan-haploinsuffient engineered heart tissues have reduced tissue thickness and force generation. Conversely, hPSC-CMs grown on a perlecan-peptide substrate are enlarged and display increased nucleation, typical of hypertrophic growth. Together, perlecan appears to play the opposite role of agrin, promoting cellular maturation rather than hyperplasia and proliferation. Perlecan signaling is likely mediated via its binding to the dystroglycan complex. Targeting perlecan-dependent signaling may help reverse the phenotypic switch common to heart failure.
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Affiliation(s)
- Benjamin B Johnson
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Marie-Victoire Cosson
- The Francis Crick Institute, London NW1 1AT, UK; NHLI, Imperial College London, London, UK
| | - Lorenza I Tsansizi
- The Francis Crick Institute, London NW1 1AT, UK; NHLI, Imperial College London, London, UK
| | - Terri L Holmes
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | | | - Katherine Hampton
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Ok-Ryul Song
- The Francis Crick Institute, London NW1 1AT, UK; High-Throughput Screening Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Nguyen T N Vo
- School of Medicine, Regenerating and Modelling Tissues, Biodiscovery Institute, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Aishah Nasir
- School of Medicine, Regenerating and Modelling Tissues, Biodiscovery Institute, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alzbeta Chabronova
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Chris Denning
- School of Medicine, Regenerating and Modelling Tissues, Biodiscovery Institute, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Catherine L R Merry
- School of Medicine, Regenerating and Modelling Tissues, Biodiscovery Institute, University Park, University of Nottingham, Nottingham NG7 2RD, UK; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - John Whitelock
- School of Medicine, Regenerating and Modelling Tissues, Biodiscovery Institute, University Park, University of Nottingham, Nottingham NG7 2RD, UK; Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Linda Troeberg
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Stuart A Rushworth
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andreia S Bernardo
- The Francis Crick Institute, London NW1 1AT, UK; NHLI, Imperial College London, London, UK.
| | - James G W Smith
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK.
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Xie T, Fu DJ, Li KJ, Guo JD, Xiao ZM, Li Z, Zhao SC. Identification of a basement membrane gene signature for predicting prognosis and estimating the tumor immune microenvironment in prostate cancer. Aging (Albany NY) 2024; 16:1581-1604. [PMID: 38240702 PMCID: PMC10866409 DOI: 10.18632/aging.205445] [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: 08/23/2023] [Accepted: 12/01/2023] [Indexed: 02/06/2024]
Abstract
Basement membrane plays an important role in tumor invasion and metastasis, which is closely related to prognosis. However, the prognostic value and biology of basement membrane genes (BMGs) in prostate cancer (PCa) remain unknown. In the TCGA training set, we used differentially expressed gene analysis, protein-protein interaction networks, univariate and multivariate Cox regression, and least absolute shrinkage and selection operator regression to construct a basement membrane-related risk model (BMRM) and validated its effectiveness in the MSKCC validation set. Furthermore, the accurate nomogram was constructed to improve clinical applicability. Patients with PCa were divided into high-risk and low-risk groups according to the optimal cut-off value of the basement membrane-related risk score (BMRS). It was found that BMRS was significantly associated with RFS, T-stage, Gleason score, and tumor microenvironmental characteristics in PCa patients. Further analysis showed that the model grouping was closely related to tumor immune microenvironment characteristics, immune checkpoint inhibitors, and chemotherapeutic drug sensitivity. In this study, we developed a new BMGs-based prognostic model to determine the prognostic value of BMGs in PCa. Finally, we confirmed that THBS2, a key gene in BMRM, may be an important link in the occurrence and progression of PCa. This study provides a novel perspective to assess the prognosis of PCa patients and provides clues for the selection of future personalized treatment regimens.
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Affiliation(s)
- Tao Xie
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510500, China
| | - Du-Jiang Fu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kang-Jing Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jia-Ding Guo
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510500, China
| | - Zhao-Ming Xiao
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510500, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510500, China
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18
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Hu J, Liu X, Xu Q, Zhu M, Wang S, Quan K, Dai M, Mo F, Zhan H. Mechanism of lysine oxidase-like 1 promoting synovial inflammation mediating rheumatoid arthritis development. Aging (Albany NY) 2024; 16:928-947. [PMID: 38217541 PMCID: PMC10817408 DOI: 10.18632/aging.205429] [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] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory joint disease that causes great distress to patients and society. Early diagnosis is the key to the successful treatment of RA. The basement membrane, one of the oldest tissue structures, is localized under the epithelium. Its complex composition and rich biological functions have made it a focus of research in recent years, while basement membrane-associated genetic variants are involved in most human disease processes. The aim of this study is to find new diagnostic biomarkers for RA and explore their role and possible mechanism in rheumatoid arthritis. The GSE12021, GSE55235 and GSE55457 datasets were downloaded from the GEO database. Their fraction associated with basement membrane genes was analyzed and differentially expressed genes between the disease and normal groups were explored. We identified two basement membrane-associated genes, lysine oxidase-like 1 (LOXL1) and discoid peptide receptor 2 (DDR2). Focusing on the more interesting LOXL1, we found that LOXL1 expression was significantly elevated in the synovium of patients with rheumatoid arthritis, and LOXL1 mRNA and protein levels were elevated in tumor necrosis factor α-stimulated human synovial sarcoma cells (SW982). And LOXL1 knockdown inhibited tumor necrosis factor α-induced inhibition in SW982 cells expression of inducible nitric oxide synthase (INOS), cyclooxygenase-2 (COX2), and interleukin-6 (IL-6). Interestingly, knockdown of LOXL1 inhibited the phosphorylation of PI3K and AKT. In summary, LOXL1 may become a novel diagnostic gene for RA, and knockdown of LoxL1 may inhibit synovial inflammation by affecting PI3K/AKT pathway.
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Affiliation(s)
- Jiawei Hu
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Xuqiang Liu
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Qiang Xu
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Meisong Zhu
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Song Wang
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Kun Quan
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Min Dai
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Fengbo Mo
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
| | - Haibo Zhan
- Department of Orthopedics, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province 330006, China
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Zhou F, Liu Y, Liu D, Xie Y, Zhou X. Identification of basement membrane-related signatures for estimating prognosis, immune infiltration landscape and drug candidates in pancreatic adenocarcinoma. J Cancer 2024; 15:401-417. [PMID: 38169540 PMCID: PMC10758037 DOI: 10.7150/jca.89665] [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: 08/30/2023] [Accepted: 11/10/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is a frequent digestive system cancer, which has high mortality and bad outcome. However, the role of basement membrane (BM)-related gene in assessing patient's outcome, microenvironment and treatment response remain unclear. Methods: Basement membrane (BM)-associated genes were detected by univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses using data from the TCGA databases. A risk score system was constructed to distinguish patients in the high- and low-risk groups. Prognostic gene distribution in various immune cell forms was explored through scRNA-seq. Immune cell infiltration was assessed using CIBERSORT and ESTIMATE. The IC50 of common chemotherapeutic drugs and useful molecule compounds were evaluated. The mRNA and protein expression of important signatures were validated utilizing GEPIA and HPA databases. Results: Compared to low risk PAAD patients, PAAD patients with high risk showed a significant much worse overall survival (OS). Risk score of BM-associated genes could estimate patient outcome well, and areas under the curve (AUC) of receiver operating characteristic (ROC) survival curve were 0.76, 0.85, and 0.85 at 1-, 3-, and 5-year. Clinical impact curve (CIC) curve demonstrated the clinical importance of risk score. scRNA-seq revealed that BM-related genes were mainly distributed in malignant cells. Significant variations existed in the immune microenvironment, immune checkpoint expression and chemotherapy response between the studied groups. Furthermore, the mRNA expression levels of FAM83A, LY6D, MET, MUC16, MYEOV, and WNT7A were elevated in PAAD tissues, while the protein expression patterns of LY6D, MET, MUC16, and WNT7A were higher in tumor sample. RO-90-7501, Scriptaid, TG-101348, XMD-892, and XMD-1150 may be valuable small molecule drugs to treat PAAD. Conclusions: In conclusion, we develop a novel BM-related gene signature provide new insights and targets for the diagnosis, outcome estimation, candidate drugs and therapy management of PAAD patients.
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Affiliation(s)
- Feng Zhou
- Department of Gastroenterology, Digestive disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi Province, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi Province, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi Province, China
| | - Yang Liu
- Department of Gastroenterology, Digestive disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi Province, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi Province, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi Province, China
| | - Dingwei Liu
- Department of Gastroenterology, Digestive disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi Province, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi Province, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi Province, China
| | - Yong Xie
- Department of Gastroenterology, Digestive disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi Province, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi Province, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi Province, China
| | - Xiaojiang Zhou
- Department of Gastroenterology, Digestive disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi Province, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi Province, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi Province, China
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20
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Lin J, Chen J, Huang C. Systematic identification of key basement membrane related genes as potential new biomarkers in Alzheimer's disease. Clin Neurol Neurosurg 2024; 236:108094. [PMID: 38154381 DOI: 10.1016/j.clineuro.2023.108094] [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: 07/27/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
OBJECTIVE The study aimed to identify biomarkers associated with basement membranes (BMs)-related genes (BMGs) in Alzheimer's disease (AD) and investigate their potential role in the progression of AD pathology. METHODS Gene expression profiles were retrieved from Gene Expression Omnibus database. 222 human BMGs were collected from the relevant literature. Subsequently, the differentially expressed BMGs (DE-BMGs) were filtered, and the key DE-BMGs were identified using weighted gene correlation network analysis (WGCNA) and two machine learning algorithms. The expression levels, diagnostic values, clinical significances, enrichment analyses and regulatory networks of these candidate biomarkers were further examined. RESULTS A total of 44 DE-BMGs were acquired by comparing AD temporal cortex with nondemented controls. Using WGCNA and machine learning, versiscan (VCAN), tissue inhibitor of metalloproteinase 1 (TIMP1), structural maintenance of chromosome 3 (SMC3), and laminin β2 (LAMB2) were ultimately identified as candidate biomarkers, and they were verified in a murine model. These biomarkers had high diagnostic value (area under the curve (AUC)>0.8). The diagnostic value of the four gene combination was then evaluated in multiple databases, yielding AUCs ranging from 0.688 to 1. Furthermore, a meaningful correlation between these biomarkers and AD pathology progression was observed. Finally, comprehensive analyses involving Hallmark pathway enrichment, immune cell infiltration analysis, transcriptional regulatory, and competitive endogenous RNA networks indicated that key DE-BMGs closely correlated with oxidative stress and immune dysfunction. CONCLUSION Our study comprehensively identified four candidate BMGs and their combination model that play a crucial part in the diagnosis and pathogenesis of AD.
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Affiliation(s)
- Jia'xing Lin
- Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Jing Chen
- Department of Rheumatology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Cheng Huang
- Department of Neurology, Clinical Neuroscience Institute, The First Affiliated Hospital, Jinan University, Guangzhou, China
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21
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Chen Y, Du H, Wang X, Li B, Chen X, Yang X, Zhao C, Zhao J. ANGPTL4 May Regulate the Crosstalk Between Intervertebral Disc Degeneration and Type 2 Diabetes Mellitus: A Combined Analysis of Bioinformatics and Rat Models. J Inflamm Res 2023; 16:6361-6384. [PMID: 38161353 PMCID: PMC10757813 DOI: 10.2147/jir.s426439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The crosstalk between intervertebral disc degeneration (IVDD) and type 2 diabetes mellitus (T2DM) has been investigated. However, the common mechanism underlying this phenomenon has not been clearly elucidated. This study aimed to explore the shared gene signatures of IVDD and T2DM. Methods The expression profiles of IVDD (GSE27494) and T2DM (GSE20966) were acquired from the Gene Expression Omnibus database. Five hub genes including ANGPTL4, CCL2, CCN3, THBS2, and INHBA were preliminarily screened. GO (Gene Ontology) enrichment analysis, functional correlation analysis, immune filtration, Transcription factors (TFs)-mRNA-miRNA coregulatory network, and potential drugs prediction were performed following the identification of hub genes. RNA sequencing, in vivo and in vitro experiments on rats were further performed to validate the expression and function of the target gene. Results Five hub genes (ANGPTL4, CCL2, CCN3, THBS2, and INHBA) were identified. GO analysis demonstrated the regulation of the immune system, extracellular matrix (ECM), and SMAD protein signal transduction. There was a strong correlation between hub genes and different functions, including lipid metabolism, mitochondrial function, and ECM degradation. The immune filtration pattern grouped by disease and the expression of hub genes showed significant changes in the immune cell composition. TFs-mRNA-miRNA co-expression networks were constructed. In addition, pepstatin showed great drug-targeting relevance based on potential drugs prediction of hub genes. ANGPTL4, a gene that mediates the inhibition of lipoprotein lipase activity, was eventually determined after hub gene screening, validation by different datasets, RNA sequencing, and experiments. Discussion This study screened five hub genes and ANGPTL4 was eventually determined as a potential target for the regulation of the crosstalk in patients with IVDD and T2DM.
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Affiliation(s)
- Yan Chen
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Han Du
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Xin Wang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Baixing Li
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Xuzhuo Chen
- Department of Oral Surgery, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Xiao Yang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Changqing Zhao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
| | - Jie Zhao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People’s Republic of China
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Morais MRPT, Tian P, O'cualain R, Lawless C, Lennon R. Protocol to characterize basement membranes during kidney development using mass spectrometry-based label-free quantitative proteomics. STAR Protoc 2023; 4:102741. [PMID: 38039136 PMCID: PMC10722381 DOI: 10.1016/j.xpro.2023.102741] [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: 07/07/2023] [Revised: 10/06/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Basement membranes are specialized extracellular matrices formed by highly insoluble structural proteins and extracellular matrix (ECM)-bound components that provide structural and signaling support to tissues and are dynamic during development. Here, we present a mass spectrometry-based label-free quantitative proteomics protocol to investigate basement membranes and define their composition using samples from human kidney organoids and mouse fetal kidneys. This protocol facilitates the study of basement membrane and other ECM components during development to improve our understanding of matrix regulation and function. For complete details on the use and execution of this protocol, please refer to Morais et al.1.
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Affiliation(s)
- Mychel R P T Morais
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK.
| | - Ronan O'cualain
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK.
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23
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Shi R, Zhao W, Zhu L, Wang R, Wang D. Identification of basement membrane markers in diabetic kidney disease and immune infiltration by using bioinformatics analysis and experimental verification. IET Syst Biol 2023; 17:316-326. [PMID: 37776100 PMCID: PMC10725710 DOI: 10.1049/syb2.12078] [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: 05/22/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease worldwide. Basement membranes (BMs) are ubiquitous extracellular matrices which are affected in many diseases including DKD. Here, the authors aimed to identify BM-related markers in DKD and explored the immune cell infiltration in this process. The expression profiles of three datasets were downloaded from the Gene Expression Omnibus database. BM-related differentially expression genes (DEGs) were identified and Kyoto encyclopaedia of genes and genomes pathway enrichment analysis were applied to biological functions. Immune cell infiltration and immune function in the kidneys of patients with DKD and healthy controls were evaluated and compared using the ssGSEA algorithm. The association of hub genes and immune cells and immune function were explored. A total of 30 BM-related DEGs were identified. The functional analysis showed that BM-related DEGs were notably associated with basement membrane alterations. Crucially, BM-related hub genes in DKD were finally identified, which were able to distinguish patients with DKD from controls. Moreover, the authors observed that laminin subunit gamma 1(LAMC1) expression was significantly high in HK2 cells treated with high glucose. Immunohistochemistry results showed that, compared with those in db/m mouse kidneys, the levels of LAMC1 in db/db mouse kidneys were significantly increased. The biomarkers genes may prove crucial for DKD treatment as they could be targeted in future DKD treatment protocols.
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Affiliation(s)
- Rui Shi
- Department of NephrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Wen‐Man Zhao
- Department of NephrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Li Zhu
- Department of NephrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Rui‐Feng Wang
- Department of NephrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - De‐Guang Wang
- Department of NephrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
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24
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Adams JRG, Pooranachithra M, Jyo EM, Zheng SL, Goncharov A, Crew JR, Kramer JM, Jin Y, Ernst AM, Chisholm AD. Nanoscale patterning of collagens in C. elegans apical extracellular matrix. Nat Commun 2023; 14:7506. [PMID: 37980413 PMCID: PMC10657453 DOI: 10.1038/s41467-023-43058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Apical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer ('blistering', Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.
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Affiliation(s)
- Jennifer R G Adams
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erin M Jyo
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sherry Li Zheng
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexandr Goncharov
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer R Crew
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - James M Kramer
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andreas M Ernst
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew D Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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Eckersley A, Yamamura T, Lennon R. Matrikines in kidney ageing and age-related disease. Curr Opin Nephrol Hypertens 2023; 32:551-558. [PMID: 37584348 PMCID: PMC10552846 DOI: 10.1097/mnh.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
PURPOSE OF REVIEW Matrikines are cell-signalling extracellular matrix fragments and they have attracted recent attention from basic and translational scientists, due to their diverse roles in age-related disease and their potential as therapeutic agents. In kidney, the matrix undergoes remodelling by proteolytic fragmentation, so matrikines are likely to play a substantial, yet understudied, role in ageing and pathogenesis of age-related diseases. RECENT FINDINGS This review presents an up-to-date description of known matrikines with either a confirmed or highly anticipated role in kidney ageing and disease, including their point of origin, mechanism of cleavage, a summary of known biological actions and the current knowledge which links them to kidney health. We also highlight areas of interest, such as the prospect of matrikine cross-tissue communication, and gaps in knowledge, such as the unexplored signalling potential of many kidney disease-specific matrix fragments. SUMMARY We anticipate that knowledge of specific matrikines, and their roles in controlling processes of kidney pathology, could be leveraged for the development of exciting new future therapies through inhibition or even with their supplementation.
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Affiliation(s)
- Alexander Eckersley
- Division of Musculoskeletal & Dermatological Sciences, School of Biological Science
| | - Tomohiko Yamamura
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, The University of Manchester
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, The University of Manchester
- Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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Yang Y, McCullough CG, Seninge L, Guo L, Kwon WJ, Zhang Y, Li NY, Gaddam S, Pan C, Zhen H, Torkelson J, Glass IA, Charville G, Que J, Stuart J, Ding H, Oro A. A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563664. [PMID: 37961271 PMCID: PMC10634774 DOI: 10.1101/2023.10.24.563664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Human pluripotent stem cell-derived tissue engineering offers great promise in designer cell-based personalized therapeutics. To harness such potential, a broader approach requires a deeper understanding of tissue-level interactions. We previously developed a manufacturing system for the ectoderm-derived skin epithelium for cell replacement therapy. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium, despite both possessing similar stratified structure. Here we employ single cell and spatial technologies to generate a spatiotemporal multi-omics cell atlas for human esophageal development. We illuminate the cellular diversity, dynamics and signal communications for the developing esophageal epithelium and stroma. Using the machine-learning based Manatee, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of the Manatee predictions leads to a clinically-compatible system for manufacturing human esophageal mucosa. Our approach creates a versatile platform to accelerate human tissue manufacturing for future cell replacement therapies to treat human genetic defects and wounds.
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Li Y, Xu K, Zhang Y, Mao H, Qiu Q, Yan Z, Liu X, Du Y, Chen Z. Identification of a basement membrane-related genes signature with immune correlation in bladder urothelial carcinoma and verification in vitro. BMC Cancer 2023; 23:1021. [PMID: 37872487 PMCID: PMC10591420 DOI: 10.1186/s12885-023-11340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/26/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Bladder urothelial carcinoma (BLCA) is the most common genitourinary cancer and the prognosis of patients is often poor. However, studies of basement membrane-related genes (BM-related genes) in BLCA are less reported. Therefore, we established a BM-related genes signature to explore their functional and prognostic value in BLCA. METHODS In this study, a BM-related genes signature was constructed by LASSO-Cox regression analysis, and then a series of bioinformatics methods was used to assess the accuracy and validity of the signature. We constructed a nomogram for clinical application and also screened for possible therapeutic drugs. To investigate the functions and pathways affected by BM-related genes in BLCA, we performed functional enrichment analyses. In addition, we analyzed the immune cell infiltration landscape and immune checkpoint-related genes in the high and low-risk groups. Finally, we confirmed the prognostic value of BM-related genes in BLCA in vitro. RESULTS Combining multiple bioinformatics approaches, we identified a seven-gene signature. The accuracy and validity of this signature in predicting BLCA patients were confirmed by the test cohort. In addition, the risk score was strongly correlated with prognosis, immune checkpoint genes, drug sensitivity, and immune cell infiltration landscape. The risk score is an independent prognostic factor for BLCA patients. Further experiments revealed that all seven signature genes were differentially expressed between BLCA cell lines and normal bladder cells. Finally, overexpression of LAMA2 inhibited the migration and invasion ability of BLCA cell lines. CONCLUSIONS In summary, the BM-related genes signature was able to predict the prognosis of BLCA patients accurately, indicating that the BM-related genes possess great clinical value in the diagnosis and treatment of BLCA. Moreover, LAMA2 could be a potential therapeutic target, which provides new insights into the application of the BM-related genes in BLCA patients.
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Affiliation(s)
- Yanze Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Kai Xu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Ye Zhang
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Hu Mao
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Qiangmin Qiu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Zhiwei Yan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
| | - Yang Du
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China.
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Zhou Z, Qin W, Zhang P, He J, Cheng Z, Gong Y, Zhu G, Liang D, Ren H, Jiang X, Sun Y. Potential molecular targets and drugs for basement membranes-related intervertebral disk degeneration through bioinformatics analysis and molecular docking. BMC Musculoskelet Disord 2023; 24:772. [PMID: 37784117 PMCID: PMC10544312 DOI: 10.1186/s12891-023-06891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 09/16/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Through bioinformatics analysis to identify the hub genes of Intervertebral disc degeneration (IVDD) associated with basement membranes (BMs) and find out the potential molecular targets and drugs for BMs-related annulus fibrosus (AF) degeneration based on bioinformatic analysis and molecular approach. METHODS Intervertebral disc degeneration (IVDD) related targets were obtained from GeneCards, DisGenet and OMIM databases. BMs related genes were obtained from Basement membraneBASE database. The intersection targets were identified and subjected to protein-to-protein interaction (PPI) construction via STRING. Hub genes were identified and conducted Gene ontology (GO) and pathway enrichment analysis through MCODE and Clue GO in Cytospace respectively. DSigDB database was retrieved to predict therapeutic drugs and molecular docking was performed through PyMOL, AutoDock 1.5.6 to verify the binding energy between the drug and the different expressed hub genes. Finally, GSE70362 from GEO database was obtained to verify the different expression and correlation of each hub gene for AF degeneration. RESULTS We identified 41 intersection genes between 3 disease targets databases and Basement membraneBASE database. PPI network revealed 25 hub genes and they were mainly enriched in GO terms relating to glycosaminoglycan catabolic process, the TGF-β signaling pathway. 4 core targets were found to be significant via comparison of microarray samples and they showed strong correlation. The molecular docking results showed that the core targets have strong binding energy with predicting drugs including chitosamine and retinoic acid. CONCLUSIONS In this study, we identified hub genes, pathways, potential targets, and drugs for treatment in BMs-related AF degeneration and IVDD.
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Affiliation(s)
- Zelin Zhou
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Weicheng Qin
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Peng Zhang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Jiahui He
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Zhaojun Cheng
- Department of Spinal Surgery, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Yan Gong
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Guangye Zhu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - De Liang
- Department of Spinal Surgery, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Hui Ren
- Department of Spinal Surgery, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Xiaobing Jiang
- Department of Spinal Surgery, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Yuping Sun
- Pingshan General Hospital, Southern Medical University, Shenzhen, Guangdong, P.R. China.
- Pingshan District People's Hospital of Shenzhen, Shenzhen, Guangdong, P.R. China.
- Rehabilitation Department, Pingshan District People's Hospital, Shenzhen, P.R. China.
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Jin Z, Meng Y, Wang M, Chen D, Zhu M, Huang Y, Xiong L, Xia S, Xiong Z. Comprehensive analysis of basement membrane and immune checkpoint related lncRNA and its prognostic value in hepatocellular carcinoma via machine learning. Heliyon 2023; 9:e20462. [PMID: 37810862 PMCID: PMC10556786 DOI: 10.1016/j.heliyon.2023.e20462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC), which is characterized by its high malignancy, generally exhibits poor response to immunotherapy. As part of the tumor microenvironment, basement membranes (BMs) are involved in tumor development and immune activities. Presently, there is no integrated analysis linking the basement membrane with immune checkpoints, especially from the perspective of lncRNA. Methods Based on transcriptome data from The Cancer Genome Atlas, BMs-related and immune checkpoint-related lncRNAs were identified. By applying univariable Cox regression and Machine learning (LASSO and SVM-RFE algorithm), a 10-lncRNA prognosis signature was constructed. The prognostic significance of this signature was assessed by survival analysis. GSEA, ssGSEA, and drug sensitivity analysis were conducted to investigate potential functional pathways, immune status, and clinical implications of guiding individual treatments in HCC. Finally, the promoting migration effect of LINC01224 was validated via in vitro experiments. Results The multiple Cox regression, receiver operating characteristic curves, and stratified survival analysis of clinical subgroups exhibited the robust prognostic ability of the lncRNA signature. Results of the GSEA and drug sensitivity analysis revealed significant differences in potential functional pathways and response to drugs between the two risk groups. In addition, the risk level of HCC patients was distinctly correlated with immune cell infiltration status. More importantly, LINC01224 was independently associated with the OS of HCC patients (P < 0.05), suppressing the expression of LINC01224 inhibited the migration of HCC cells. Conclusion This study developed a reliable signature for the prognosis of HCC based on BM and immune checkpoint related lncRNA, revealing that LINC01224 might be a prognostic biomarker for HCC associated with the progression of HCC.
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Affiliation(s)
- Ze Jin
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajun Meng
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengmeng Wang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Chen
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengpei Zhu
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yumei Huang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lina Xiong
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shang Xia
- Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, NO.169 Donghu Road, Wuhan, 430071, Hubei, China
| | - Zhifan Xiong
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Lv R, Duan L, Gao J, Si J, Feng C, Hu J, Zheng X. Bioinformatics-based analysis of the roles of basement membrane-related gene AGRN in systemic lupus erythematosus and pan-cancer development. Front Immunol 2023; 14:1231611. [PMID: 37841281 PMCID: PMC10570813 DOI: 10.3389/fimmu.2023.1231611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is an autoimmune disease involving many systems and organs, and individuals with SLE exhibit unique cancer risk characteristics. The significance of the basement membrane (BM) in the occurrence and progression of human autoimmune diseases and tumors has been established through research. However, the roles of BM-related genes and their protein expression mechanisms in the pathogenesis of SLE and pan-cancer development has not been elucidated. Methods In this study, we applied bioinformatics methods to perform differential expression analysis of BM-related genes in datasets from SLE patients. We utilized LASSO logistic regression, SVM-RFE, and RandomForest to screen for feature genes and construct a diagnosis model for SLE. In order to attain a comprehensive comprehension of the biological functionalities of the feature genes, we conducted GSEA analysis, ROC analysis, and computed levels of immune cell infiltration. Finally, we sourced pan-cancer expression profiles from the TCGA and GTEx databases and performed pan-cancer analysis. Results We screened six feature genes (AGRN, PHF13, SPOCK2, TGFBI, COL4A3, and COLQ) to construct an SLE diagnostic model. Immune infiltration analysis showed a significant correlation between AGRN and immune cell functions such as parainflammation and type I IFN response. After further gene expression validation, we finally selected AGRN for pan-cancer analysis. The results showed that AGRN's expression level varied according to distinct tumor types and was closely correlated with some tumor patients' prognosis, immune cell infiltration, and other indicators. Discussion In conclusion, BM-related genes play a pivotal role in the pathogenesis of SLE, and AGRN shows immense promise as a target in SLE and the progression of multiple tumors.
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Affiliation(s)
- Rundong Lv
- Department of Clinical Pharmacy, Zibo Central Hospital, Zibo, Shandong, China
| | - Lei Duan
- Department of Clinical Pharmacy, Zibo Central Hospital, Zibo, Shandong, China
| | - Jie Gao
- Department of Clinical Pharmacy, Zibo Central Hospital, Zibo, Shandong, China
| | - Jigang Si
- Department of Clinical Pharmacy, Zibo Central Hospital, Zibo, Shandong, China
| | - Chen Feng
- Department of Pharmacy, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jun Hu
- Department of Children’s Health, Zibo Central Hospital, Zibo, Shandong, China
| | - Xiulan Zheng
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macao, Macao SAR, China
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
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Li X, Kuang Q, Peng M, Yang K, Luo P. Basement Membrane-Associated lncRNA Risk Model Predicts Prognosis and Guides Clinical Treatment in Clear Cell Renal Cell Carcinoma. Biomedicines 2023; 11:2635. [PMID: 37893009 PMCID: PMC10604562 DOI: 10.3390/biomedicines11102635] [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: 08/10/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The basement membrane (BM) affects the invasion and growth of malignant tumors. The role and mechanism of BM-associated lncRNAs in clear cell renal cell carcinoma (ccRCC) are unknown. In this study, we identified biomarkers of ccRCC and developed a risk model to assess patient prognosis. We downloaded transcripts and clinical data from the Cancer Genome Atlas (TCGA). Differential analysis, co-expression analysis, Cox regression analysis, and lasso regression were used to identify BM-associated prognostic lncRNAs and create a risk prediction model. We evaluated and validated the accuracy of the model using multiple methods and constructed a nomogram to predict the prognosis of ccRCC. GO, KEGG, and immunity analyses were used to explore differences in biological function. We constructed a risk model containing six BM-associated lncRNAs (LINC02154, IGFL2-AS1, NFE4, AC112715.1, AC092535.5, and AC105105.3). The risk model has higher diagnostic efficiency compared to clinical characteristics and can be used to forecast patient prognoses. We used renal cancer cells and tissue microarrays to verify the expression of lncRNAs in the risk model. We found that knocking down LINC02154 and AC112715.1 could inhibit the invasion ability of renal cancer cells. The risk model based on BM-associated lncRNAs can well predict ccRCC and guide clinical treatment.
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Affiliation(s)
- Xinxin Li
- Department of Urology, Wuhan Third Hospital (Tongren Hospital of Wuhan University), Wuhan 430060, China; (X.L.); (Q.K.)
| | - Qihui Kuang
- Department of Urology, Wuhan Third Hospital (Tongren Hospital of Wuhan University), Wuhan 430060, China; (X.L.); (Q.K.)
| | - Min Peng
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Kang Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China;
| | - Pengcheng Luo
- Department of Urology, Wuhan Third Hospital (Tongren Hospital of Wuhan University), Wuhan 430060, China; (X.L.); (Q.K.)
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Li Q, Zhang H. Bioinformatics analysis to identify potential biomarkers for the pulmonary artery hypertension associated with the basement membrane. Open Life Sci 2023; 18:20220730. [PMID: 37772261 PMCID: PMC10523280 DOI: 10.1515/biol-2022-0730] [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: 06/15/2023] [Revised: 08/07/2023] [Accepted: 08/26/2023] [Indexed: 09/30/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a rapidly progressing cardiopulmonary disease. It is characterized by increased pulmonary artery pressure and vascular resistance. The most notable histopathological characteristic is vascular remodeling. The changes in the basement membrane (BM) are believed to be related to vascular remodeling. It is crucial to identify potential biomarkers associated with the BM in PAH, to guide its treatment. The microarray datasets GSE117261 and GSE113439 were downloaded from the Gene Expression Omnibus. Two data sets were examined to identify genes associated with the BM by analyzing gene expression changes. Next, we analyzed the relevant genes in the Kyoto Encyclopedia of Genes and Genomes using Gene Ontology and Disease Ontology annotationand conducted pathway enrichment analysis. We conducted a protein-protein interaction network analysis on the genes related to BMs and used the cell cytoHubba plug-in to identify the hub genes. Furthermore, we conducted an immune infiltration analysis and implemented a histogram model. Finally, we predicted and analyzed potential therapeutic drugs for PAH and set up a miRNA network of genetic markers. Six candidate genes related to BMs, namely Integrin Subunit Alpha V, Integrin Subunit Alpha 4, ITGA2, ITGA9, Thrombospondin 1, and Collagen Type IV Alpha 3 Chain, were identified as potential modulators of the immune process in PAH. Furthermore, ginsenoside Rh1 was found to significantly impact drug targeting based on its interactions with the six BM-related genes identified earlier. A novel biomarker related to the BM, which plays a crucial role in the development of PAH, has been identified.
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Affiliation(s)
- Qian Li
- Department of Cardiac Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming650000, China
| | - Hu Zhang
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming650000, China
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Huang X, Meng H, Shou Z, Yu J, Hu K, Chen L, Zhou H, Bai Z, Chen C. Identification of basement membrane-related biomarkers associated with the diagnosis of osteoarthritis based on machine learning. BMC Med Genomics 2023; 16:198. [PMID: 37612746 PMCID: PMC10464276 DOI: 10.1186/s12920-023-01601-z] [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: 01/09/2023] [Accepted: 07/05/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Osteoarthritis is a very common clinical disease in middle-aged and elderly individuals, and with the advent of ageing, the incidence of this disease is gradually increasing. There are few studies on the role of basement membrane (BM)-related genes in OA. METHOD We used bioinformatics and machine learning methods to identify important genes related to BMs in OA patients and performed immune infiltration analysis, lncRNA‒miRNA-mRNA network prediction, ROC analysis, and qRT‒PCR. RESULT Based on the results of machine learning, we determined that LAMA2 and NID2 were the key diagnostic genes of OA, which were confirmed by ROC and qRT‒PCR analyses. Immune analysis showed that LAMA2 and NID2 were closely related to resting memory CD4 T cells, mast cells and plasma cells. Two lncRNAs, XIST and TTTY15, were simultaneously identified, and lncRNA‒miRNA‒mRNA network prediction was performed. CONCLUSION LAMA2 and NID2 are important potential targets for the diagnosis and treatment of OA.
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Affiliation(s)
- Xiaojing Huang
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Hongming Meng
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Zeyu Shou
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Jiahuan Yu
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Kai Hu
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Liangyan Chen
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Han Zhou
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Zhibiao Bai
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
| | - Chun Chen
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
- Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province, Wenzhou, 325000, Zhejiang, China.
- Zhejiang Engineering Research Center for Hospital Emergency and Process Digitization, Wenzhou, 325000, Zhejiang, China.
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Demler C, Lawlor JC, Yelin R, Llivichuzcha-Loja D, Shaulov L, Kim D, Stewart M, Lee F, Schultheiss T, Kurpios N. An atypical basement membrane forms a midline barrier in left-right asymmetric gut development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553395. [PMID: 37645918 PMCID: PMC10461973 DOI: 10.1101/2023.08.15.553395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Correct intestinal morphogenesis depends on the early embryonic process of gut rotation, an evolutionarily conserved program in which a straight gut tube elongates and forms into its first loops. However, the gut tube requires guidance to loop in a reproducible manner. The dorsal mesentery (DM) connects the gut tube to the body and directs the lengthening gut into stereotypical loops via left-right (LR) asymmetric cellular and extracellular behavior. The LR asymmetry of the DM also governs blood and lymphatic vessel formation for the digestive tract, which is essential for prenatal organ development and postnatal vital functions including nutrient absorption. Although the genetic LR asymmetry of the DM has been extensively studied, a divider between the left and right DM has yet to be identified. Setting up LR asymmetry for the entire body requires a Lefty1+ midline barrier to separate the two sides of the embryo-without it, embryos have lethal or congenital LR patterning defects. Individual organs including the brain, heart, and gut also have LR asymmetry, and while the consequences of left and right signals mixing are severe or even lethal, organ-specific mechanisms for separating these signals are not well understood. Here, we uncover a midline structure composed of a transient double basement membrane, which separates the left and right halves of the embryonic chick DM during the establishment of intestinal and vascular asymmetries. Unlike other basement membranes of the DM, the midline is resistant to disruption by intercalation of Netrin4 (Ntn4). We propose that this atypical midline forms the boundary between left and right sides and functions as a barrier necessary to establish and protect organ asymmetry.
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Affiliation(s)
- Cora Demler
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - John Coates Lawlor
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ronit Yelin
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Dhana Llivichuzcha-Loja
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lihi Shaulov
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - David Kim
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Megan Stewart
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Thomas Schultheiss
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Natasza Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Abstract
The basement membrane (BM) is a thin, planar-organized extracellular matrix that underlies epithelia and surrounds most organs. During development, the BM is highly dynamic and simultaneously provides mechanical properties that stabilize tissue structure and shape organs. Moreover, it is important for cell polarity, cell migration, and cell signaling. Thereby BM diverges regarding molecular composition, structure, and modes of assembly. Different BM organization leads to various physical features. The mechanisms that regulate BM composition and structure and how this affects mechanical properties are not fully understood. Recent studies show that precise control of BM deposition or degradation can result in BMs with locally different protein densities, compositions, thicknesses, or polarization. Such heterogeneous matrices can induce temporospatial force anisotropy and enable tissue sculpting. In this Review, I address recent findings that provide new perspectives on the role of the BM in morphogenesis.
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Affiliation(s)
- Uwe Töpfer
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada, V6T 1Z3
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Eckersley A, Morais MR, Ozols M, Lennon R. Peptide location fingerprinting identifies structural alterations within basement membrane components in ageing kidney. Matrix Biol 2023; 121:167-178. [PMID: 37437747 DOI: 10.1016/j.matbio.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/04/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
During ageing, the glomerular and tubular basement membranes (BM) of the kidney undergo a progressive decline in function that is underpinned by histological changes, including glomerulosclerosis and tubular interstitial fibrosis and atrophy. This BM-specific ageing is thought to result from damage accumulation to long-lived extracellular matrix (ECM) protein structures. Determining which BM proteins are susceptible to these structure-associated changes, and the possible mechanisms and downstream consequences, is critical to understand age-related kidney degeneration and to identify markers for therapeutic intervention. Peptide location fingerprinting (PLF) is an emerging proteomic mass spectrometry analysis technique capable of identifying ECM proteins with structure-associated differences that may occur by damage modifications in ageing. Here, we apply PLF as a bioinformatic screening tool to identify BM proteins with structure-associated differences between young and aged human glomerular and tubulointerstitial compartments. Several functional regions within key BM components displayed alterations in tryptic peptide yield, reflecting potential age-dependent shifts in molecular (e.g. laminin-binding regions in agrin) and cellular (e.g. integrin-binding regions in laminins 521 and 511) interactions, oxidation (e.g. collagen IV) and the fragmentation and release of matrikines (e.g. canstatin and endostatin from collagens IV and XVIII). Furthermore, we found that periostin and the collagen IV α2 chain exhibited structure-associated differences in ageing that were conserved between human kidney and previously analysed mouse lung, revealing BM components that harbour shared susceptibilities across species and organs.
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Affiliation(s)
- Alexander Eckersley
- Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
| | - Mychel Rpt Morais
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Wellcome Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Matiss Ozols
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Rachel Lennon
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Wellcome Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
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Wang Z, Qin H, Yang Q, Jia J, Yang L, Zhong S, Yuan G. Identification of Basement Membrane Genes and Related Molecular Subtypes in Nonalcoholic Fatty Liver Disease. Horm Metab Res 2023; 55:546-554. [PMID: 37268001 DOI: 10.1055/a-2081-1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Basement membranes (BMs) are widely distributed and highly specialized extracellular matrix (ECM). The goal of this study was to explore novel genes associated with nonalcoholic fatty liver disease (NAFLD) from the perspective of BMs. Sequencing results of 304 liver biopsy samples about NAFLD were systematically obtained from the Gene Expression Omnibus (GEO) database. Biological changes during NAFLD progression and hub BM-associated genes were investigated by differential gene analysis and weighted gene co-expression network analysis (WGCNA), respectively. The nonalcoholic steatohepatitis (NASH) subgroups were identified based on hub BM-associated genes expression, as well as the differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways and immune microenvironment between different subgroups were compared. Extracellular matrix (ECM) seems to play an important role in the development of NAFLD. Three representative BM-associated genes (ADAMTS2, COL5A1, and LAMC3) were finally identified. Subgroup analysis results suggested that there were significant changes in KEGG signaling pathways related to metabolism, extracellular matrix, cell proliferation, differentiation, and death. There were also changes in macrophage polarization, neutrophils, and dendritic cells abundance, and so on. In conclusion, the present study identified novel potential BM-associated biomarkers and further explored the heterogeneity of NASH that might provide new insights into the diagnosis, assessment, management, and personalized treatment of NAFLD.
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Affiliation(s)
- Zhaoxiang Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Huijuan Qin
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Qichao Yang
- Department of Endocrinology, Jiangsu University Affiliated Wujin Hospital, Changzhou, China
| | - Jue Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ling Yang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Shao Zhong
- Department of Endocrinology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Guoyue Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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Zhu Y, Hardin J. TIAM-1 regulates polarized protrusions during dorsal intercalation in the C. elegans embryo through both its GEF and N-terminal domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550374. [PMID: 37546890 PMCID: PMC10402040 DOI: 10.1101/2023.07.24.550374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Mediolateral cell intercalation is a morphogenetic strategy used throughout animal development to reshape tissues. Dorsal intercalation in the C. elegans embryo involves the mediolateral intercalation of two rows of dorsal epidermal cells to create a single row that straddles the dorsal midline, and so is a simple model to study cell intercalation. Polarized protrusive activity during dorsal intercalation requires the C. elegans Rac and RhoG orthologs CED-10 and MIG-2, but how these GTPases are regulated during intercalation has not been thoroughly investigated. In this study, we characterize the role of the Rac-specific guanine nucleotide exchange factor (GEF), TIAM-1, in regulating actin-based protrusive dynamics during dorsal intercalation. We find that TIAM-1 can promote protrusion formation through its canonical GEF function, while its N-terminal domains function to negatively regulate this activity, preventing the generation of ectopic protrusions in intercalating cells. We also show that the guidance receptor UNC-5 inhibits ectopic protrusive activity in dorsal epidermal cells, and that this effect is in part mediated via TIAM-1. These results expand the network of proteins that regulate basolateral protrusive activity during directed cell rearrangement. Summary statement TIAM-1 activates the Rac pathway to promote protrusion formation via its GEF domain, while its N-terminal domains suppress ectopic protrusions during dorsal intercalation in the C. elegans embryo.
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Lin P, Hua J, Teng Z, Lin C, Liu S, He R, Chen H, Yao H, Ye J, Zhu G. Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes. Eur J Med Res 2023; 28:247. [PMID: 37481583 PMCID: PMC10362583 DOI: 10.1186/s40001-023-01193-5] [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: 08/21/2022] [Accepted: 06/23/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is a chronic, inflammatory, and autoimmune disease, but its specific etiology and pathogenesis are still unclear. This study aimed to better discover the causative basement membrane (BM) genes of their subtypes and their associations. METHODS The differential expression of BM genes between CD and UC was analyzed and validated by downloading relevant datasets from the GEO database. We divided the samples into 3 groups for comparative analysis. Construction of PPI networks, enrichment of differential gene functions, screening of Lasso regression models, validation of ROC curves, nomogram for disease prediction and other analytical methods were used. The immune cell infiltration was further explored by ssGSEA analysis, the immune correlates of hub BM genes were found, and finally, the hub central genes were screened by machine learning. RESULTS We obtained 6 candidate hub BM genes related to cellular immune infiltration in the CD and UC groups, respectively, and further screened the central hub genes ADAMTS17 and ADAMTS9 through machine learning. And in the ROC curve models, AUC > 0.7, indicating that this characteristic gene has a more accurate predictive effect on IBD. We also found that the pathogenicity-related BM genes of the CD and UC groups were mainly concentrated in the ADAMTS family (ADAMTS17 and ADAMTS9). Addition there are some differences between the two subtypes, and the central different hub BM genes are SPARC, POSTN, and ADAMTS2. CONCLUSIONS In the current study, we provided a nomogram model of CD and UC composed of BM genes, identified central hub genes, and clarified the similarities and differences between CD and UC. This will have potential value for preclinical, clinical, and translational guidance and differential research in IBD.
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Affiliation(s)
- Penghang Lin
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
| | - Jin Hua
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
| | - Zuhong Teng
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
| | - Chunlin Lin
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Songyi Liu
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Ruofan He
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Hui Chen
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Hengxin Yao
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350000, China
| | - Jianxin Ye
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China.
| | - Guangwei Zhu
- Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20th, Chazhong Road, Fuzhou, 350005, Fujian, China.
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Wang J, Liu D, Wang Q, Xie Y. Identification of Basement Membrane-Related Signatures in Gastric Cancer. Diagnostics (Basel) 2023; 13:diagnostics13111844. [PMID: 37296697 DOI: 10.3390/diagnostics13111844] [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: 02/28/2023] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND The basement membrane (BM) serves as a major barrier to impede tumor cell invasion and extravasation during metastasis. However, the associations between BM-related genes and GC remain unclear. METHODS RNA expression data and corresponding clinical information of STAD samples were downloaded from the TCGA database. We identified BM-related subtypes and constructed a BM-related gene prognostic model using lasso-Cox regression analysis. We also investigated the single-cell properties of prognostic-related genes and the TME characteristic, TMB status, and chemotherapy response in high- and low-risk groups. Finally, we verified our results in the GEPIA database and human tissue specimens. RESULTS A six-gene lasso Cox regression model (APOD, CAPN6, GPC3, PDK4, SLC7A2, SVEP1) was developed. Activated CD4+ T cells and follicular T cells were shown to infiltrate more widely in the low-risk group. The low-risk group harbored significantly higher TMB and better prognosis, favoring immunotherapy. CONCLUSIONS We constructed a six-gene BM-related prognostic model for predicting GC prognosis, immune cell infiltration, TMB status, and chemotherapy response. This research provides new ideas for developing more effective individualized treatment of GC patients.
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Affiliation(s)
- Jinyun Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Dingwei Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Qixuan Wang
- Queen Mary School, Medical College of Nanchang University, Nanchang 330006, China
| | - Yong Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
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Sun W, Wang J, Wang Z, Xu M, Lin Q, Sun P, Yuan Y. Combining WGCNA and machine learning to construct basement membrane-related gene index helps to predict the prognosis and tumor microenvironment of HCC patients and verifies the carcinogenesis of key gene CTSA. Front Immunol 2023; 14:1185916. [PMID: 37287981 PMCID: PMC10242074 DOI: 10.3389/fimmu.2023.1185916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high recurrence and metastasis rates and poor prognosis. Basement membrane is a ubiquitous extracellular matrix and is a key physical factor in cancer metastasis. Therefore, basement membrane-related genes may be new targets for the diagnosis and treatment of HCC. We systematically analyzed the expression pattern and prognostic value of basement membrane-related genes in HCC using the TCGA-HCC dataset, and constructed a new BMRGI based on WGCNA and machine learning. We used the HCC single-cell RNA-sequencing data in GSE146115 to describe the single-cell map of HCC, analyzed the interaction between different cell types, and explored the expression of model genes in different cell types. BMRGI can accurately predict the prognosis of HCC patients and was validated in the ICGC cohort. In addition, we also explored the underlying molecular mechanisms and tumor immune infiltration in different BMRGI subgroups, and confirmed the differences in response to immunotherapy in different BMRGI subgroups based on the TIDE algorithm. Then, we assessed the sensitivity of HCC patients to common drugs. In conclusion, our study provides a theoretical basis for the selection of immunotherapy and sensitive drugs in HCC patients. Finally, we also considered CTSA as the most critical basement membrane-related gene affecting HCC progression. In vitro experiments showed that the proliferation, migration and invasion abilities of HCC cells were significantly impaired when CTSA was knocked down.
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Affiliation(s)
- Weijie Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jue Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiqiang Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Xu
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quanjun Lin
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihang Yuan
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang Y, Li T, Liu H, Wang L. Function and prognostic value of basement membrane -related genes in lung adenocarcinoma. Front Pharmacol 2023; 14:1185380. [PMID: 37214471 PMCID: PMC10196008 DOI: 10.3389/fphar.2023.1185380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD) has become a common cause of cancer-related death. Many studies have shown that the basement membrane (BM) is associated with the development of cancer. However, BM-related gene expression and its relationship to LUAD prognosis remains unclear. Methods: BM-related genes from previous studies were used. Clinical and mRNA expression information were obtained from TCGA database. Cox, minimum absolute contraction, and selection operator regression were applied to analyze the selected genes affecting LUAD prognosis. A prognostic-risk model was then established. Furthermore, this study applied Kaplan-Meier analysis to assess the outcomes of high- and low-risk groups, then explored their differences in drug sensitivity. The DSigDB database was used to screen for therapeutic small-molecule drugs. Results: Fourteen prognostic models based on BM-related genes were successfully constructed and validated in patients with LUAD. We also found that independence was a prognostic factor in all 14 BM-based models. Functional analysis showed that the enrichment of BM-related genes mainly originated from signaling pathways related to cancer. The BM-based model also suggested that immune cell infiltration is associated with checkpoints. The low-risk patients may benefit from cyclopamine and docetaxel treatments. Conclusion: This study identified a reliable biomarker to predict survival in patients with LUAD and offered new insights into the function of BM-related genes in LUAD.
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Affiliation(s)
- Yurong Zhang
- Department of Scientific Research, The First Affiliated Hospital, Xi’an Medical University, Xi’an, Shaanxi, China
| | - Tingting Li
- Department of Pharmacy, Xi’an Chest Hospital, Xi’an, Shaanxi, China
| | - Huanqing Liu
- Information Construction and Management Office, Northwest Polytechnical University, Xi’an, Shaanxi, China
| | - Li Wang
- Department of Scientific Research, The First Affiliated Hospital, Xi’an Medical University, Xi’an, Shaanxi, China
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Costa DS, Kenny-Ganzert IW, Chi Q, Park K, Kelley LC, Garde A, Matus DQ, Park J, Yogev S, Goldstein B, Gibney TV, Pani AM, Sherwood DR. The Caenorhabditis elegans anchor cell transcriptome: ribosome biogenesis drives cell invasion through basement membrane. Development 2023; 150:dev201570. [PMID: 37039075 PMCID: PMC10259517 DOI: 10.1242/dev.201570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/27/2023] [Indexed: 04/12/2023]
Abstract
Cell invasion through basement membrane (BM) barriers is important in development, immune function and cancer progression. As invasion through BM is often stochastic, capturing gene expression profiles of actively invading cells in vivo remains elusive. Using the stereotyped timing of Caenorhabditis elegans anchor cell (AC) invasion, we generated an AC transcriptome during BM breaching. Through a focused RNAi screen of transcriptionally enriched genes, we identified new invasion regulators, including translationally controlled tumor protein (TCTP). We also discovered gene enrichment of ribosomal proteins. AC-specific RNAi, endogenous ribosome labeling and ribosome biogenesis analysis revealed that a burst of ribosome production occurs shortly after AC specification, which drives the translation of proteins mediating BM removal. Ribosomes also enrich near the AC endoplasmic reticulum (ER) Sec61 translocon and the endomembrane system expands before invasion. We show that AC invasion is sensitive to ER stress, indicating a heightened requirement for translation of ER-trafficked proteins. These studies reveal key roles for ribosome biogenesis and endomembrane expansion in cell invasion through BM and establish the AC transcriptome as a resource to identify mechanisms underlying BM transmigration.
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Affiliation(s)
- Daniel S. Costa
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Kieop Park
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Laura C. Kelley
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Aastha Garde
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Junhyun Park
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 29904, USA
| | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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Ding R, Zhao C, Jing Y, Chen R, Meng Q. Basement membrane-related regulators for prediction of prognoses and responses to diverse therapies in hepatocellular carcinoma. BMC Med Genomics 2023; 16:81. [PMID: 37081465 PMCID: PMC10116671 DOI: 10.1186/s12920-023-01504-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/28/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) remains a global health threat. Finding a novel biomarker for assessing the prognosis and new therapeutic targets is vital to treating this patient population. Our study aimed to explore the contribution of basement membrane-related regulators (BMR) to prognostic assessment and therapeutic response prediction in HCC. MATERIAL AND METHODS The RNA sequencing and clinical information of HCC were downloaded from TCGA-LIHC, ICGC-JP, GSE14520, GSE104580, and CCLE datasets. The BMR signature was created by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm and used to separate HCC patients into low- and high-risk groups. We conducted analyses using various R 4.1.3 software packages to compare prognoses and responses to immunotherapy, transcatheter arterial chemoembolization (TACE), and chemotherapeutic drugs between the groups. Additionally, stemness indices, molecular functions, and somatic mutation analyses were further explored in these subgroups. RESULTS The BMR signature included 3 basement membrane-related genes (CTSA, P3H1, and ADAM9). We revealed that BMR signature was an independent risk contributor to poor prognosis in HCC, and high-risk group patients presented shorter overall survival. We discovered that patients in the high-risk group might be responsive to immunotherapy, while patients in the low-risk group may be susceptible to TACE therapy. Over 300 agents were screened to identify effective drugs for the two subgroups. CONCLUSION Overall, basement membrane-related regulators represent novel biomarkers in HCC for assessing prognosis, response to immunotherapy, the effectiveness of TACE therapy, and drug susceptibility.
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Affiliation(s)
- Ruili Ding
- Department of Anesthesiology, Renmin Hospital of Wuhan University, No.238, Jiefang Road, Wuhan, 430061, Hubei Province, China
| | - Chuanbing Zhao
- Department of Pancreatic Surgery, Renmin Hospital of Wuhan University, No.238, Jiefang Road, Wuhan, 430061, Hubei Province, China
| | - Yixin Jing
- Department of Anesthesiology, Renmin Hospital of Wuhan University, No.238, Jiefang Road, Wuhan, 430061, Hubei Province, China
| | - Rong Chen
- Department of Anesthesiology, Renmin Hospital of Wuhan University, No.238, Jiefang Road, Wuhan, 430061, Hubei Province, China
| | - Qingtao Meng
- Department of Anesthesiology, Renmin Hospital of Wuhan University, No.238, Jiefang Road, Wuhan, 430061, Hubei Province, China.
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Xi Y, Song L, Wang S, Zhou H, Ren J, Zhang R, Fu F, Yang Q, Duan G, Wang J. Identification of basement membrane-related prognostic signature for predicting prognosis, immune response and potential drug prediction in papillary renal cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10694-10724. [PMID: 37322956 DOI: 10.3934/mbe.2023474] [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: 06/17/2023]
Abstract
Papillary renal cell carcinoma (PRCC) is a malignant neoplasm of the kidney and is highly interesting due to its increasing incidence. Many studies have shown that the basement membrane (BM) plays an important role in the development of cancer, and structural and functional changes in the BM can be observed in most renal lesions. However, the role of BM in the malignant progression of PRCC and its impact on prognosis has not been fully studied. Therefore, this study aimed to explore the functional and prognostic value of basement membrane-associated genes (BMs) in PRCC patients. We identified differentially expressed BMs between PRCC tumor samples and normal tissue and systematically explored the relevance of BMs to immune infiltration. Moreover, we constructed a risk signature based on these differentially expressed genes (DEGs) using Lasso regression analysis and demonstrated their independence using Cox regression analysis. Finally, we predicted 9 small molecule drugs with the potential to treat PRCC and compared the differences in sensitivity to commonly used chemotherapeutic agents between high and low-risk groups to better target patients for more precise treatment planning. Taken together, our study suggested that BMs might play a crucial role in the development of PRCC, and these results might provide new insights into the treatment of PRCC.
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Affiliation(s)
- Yujia Xi
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Liying Song
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Shuang Wang
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Haonan Zhou
- First School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jieying Ren
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Ran Zhang
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Feifan Fu
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Qian Yang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Guosheng Duan
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jingqi Wang
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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Gui H, Chen X, Ye L, Ma H. Seven basement membrane-specific expressed genes are considered potential biomarkers for the diagnosis and treatment of diabetic nephropathy. Acta Diabetol 2023; 60:493-505. [PMID: 36627452 DOI: 10.1007/s00592-022-02027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/26/2022] [Indexed: 01/12/2023]
Abstract
AIMS Diabetic nephropathy (DN) is a diabetes-related chronic vasculitis. DN diminishes kidney function over time and, of course, leads to end stage renal disease in people (ESRD). In spite of the advances in diagnostic and treatment methods for DN, DN continues to impose a significant physical and psychological burden on patients, severely impacting their quality of life, making the hunt for novel therapeutic targets necessary. METHODS The Gene Expression Omnibus (GEO) microarray datasets GSE1009, GSE30122, GSE142153, and GSE96804 were downloaded to identify differentially expressed genes (DEGs) in kidney tissues from patients in the DN group and normal controls. These three datasets were examined for genes associated with basement membranes (BMs) with differential gene expression. The target genes were then subjected to gene ontology (GO) annotation and Kyoto Gene and Genome Encyclopedia (KEGG) pathway enrichment analysis. BM-related genes underwent PPI network analysis and screening of the top 10 hub genes, along with immune infiltration analysis and column line graph model development. Finally, we conducted DN therapeutic medication prediction and the creation of something like a miRNA network for genetic markers with BMs. RESULTS Seven candidate BM-related genes (COL4A1, COL4A2, COL6A2, COL6A3, FN1, ITGQ4, and LAMB1) with acceptable helps the healthcare were discovered. Enrichment analysis of diabetes-related genes event occurred the role of biological processes including extracellular matrix organization, extracellular structural organization, and collagen-containing extracellular matrix, as well as the PI3K-Akt signaling pathway and the AGE-RAGE signaling pathway, in diabetic complications. These genes may also be associated in immune cells and autoimmune activities, such as Macrophages and MHC class I, in order to impact the immune process in DN. In the meanwhile, based on these seven BM-related genes, we discovered that Ginsenoside Rh1 was very significant for drug targeting. CONCLUSIONS This research identified seven BM-related genes as possible diagnostic and therapeutic biomarkers for DN. Analysis of inflammatory infiltration indicated that these genes may be important in inflammatory processes through Macrophages and MHC class I, hence impacting the course and development of DN illness. The development of a correlated column line graph model for it also shown excellent predictive capabilities. In addition, we have found pharmaceuticals, such as Ginsenoside Rh1, that may provide fresh insights into the personalized management of patients with DN.
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Affiliation(s)
- HouShan Gui
- School of Chemistry and Biological Engineering, Yichun University, Yichun, 336000, China
| | - Xin Chen
- School of Chemistry and Biological Engineering, Yichun University, Yichun, 336000, China
| | - LuFen Ye
- School of Chemistry and Biological Engineering, Yichun University, Yichun, 336000, China
| | - Hao Ma
- Yichun University School of Aesthetic Medicine, No. 576 Yuanzhou District, Yichun, 336000, Jiangxi Province, China.
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Park K, Jayadev R, Payne SG, Kenny-Ganzert IW, Chi Q, Costa DS, Ramos-Lewis W, Thendral SB, Sherwood DR. Reciprocal discoidin domain receptor signaling strengthens integrin adhesion to connect adjacent tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532639. [PMID: 36993349 PMCID: PMC10055161 DOI: 10.1101/2023.03.14.532639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Separate tissues connect through adjoining basement membranes to carry out molecular barrier, exchange, and organ support functions. Cell adhesion at these connections must be robust and balanced to withstand independent tissue movement. Yet, how cells achieve synchronized adhesion to connect tissues is unknown. Here, we have investigated this question using the C. elegans utse-seam tissue connection that supports the uterus during egg-laying. Through genetics, quantitative fluorescence, and cell specific molecular disruption, we show that type IV collagen, which fastens the linkage, also activates the collagen receptor discoidin domain receptor 2 (DDR-2) in both the utse and seam. RNAi depletion, genome editing, and photobleaching experiments revealed that DDR-2 signals through LET-60/Ras to coordinately strengthen an integrin adhesion in the utse and seam that stabilizes their connection. These results uncover a synchronizing mechanism for robust adhesion during tissue connection, where collagen both affixes the linkage and signals to both tissues to bolster their adhesion.
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Affiliation(s)
- Kieop Park
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Ranjay Jayadev
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Sara G. Payne
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Daniel S. Costa
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | | | | | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Correspondence:
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Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Mol Cell Proteomics 2023; 22:100528. [PMID: 36918099 PMCID: PMC10152135 DOI: 10.1016/j.mcpro.2023.100528] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
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Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
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Zhang Z, Zhu H, Wang X, Lin S, Ruan C, Wang Q. A novel basement membrane-related gene signature for prognosis of lung adenocarcinomas. Comput Biol Med 2023; 154:106597. [PMID: 36708655 DOI: 10.1016/j.compbiomed.2023.106597] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/01/2022] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) remains a global health concern with its poor prognosis and high mortality. Whether tumor cells invade through the basement membrane (BM) is the key factor to determine the prognosis of LUAD. This study aimed to identify the BM-related gene signatures to improve the overall prognosis of LUAD. MATERIALS & METHODS A series of bioinformatics analyses were conducted based on TCGA and GEO datasets. Unsupervised consistent cluster analysis was performed, and 500 LUAD patients were assigned to two different groups according to expressions of 222 BM-related genes. The differentially expressed genes (DEGs) between the two clusters were identified, and Lasso regression, ROC curve, univariate and multivariate Cox regression analyses and enrichment analysis were conducted. Besides, ssGSEA, CIBERSORT and ESTIMATE algorithmwere were employed to understand the relationship between the tumor microenvironment (TME) and risk scores. Moreover, single cell clustering and trajectory analyses were performed to further understand the significance of BM-related genes. Finally, qRT-PCR was used to verify the prognosis model. RESULTS A total of 31 prognostic BM-related genes were determined for LUAD, and a novel 17-mRNA prognostic model named BMsocre was successfully established to predict the overall survival of LUAD patients. The high BMscore group indicated worse prognosis. Seventeen DEGs were enriched mainly in metabolism, ECM-receptor interaction and immune response. In addition, the high-risk group showed higher TMB and lower immune score. The low-risk group had a better immunotherapeutic response where immune escape was less likely. The BMscore model was verified in our patient cohort. Furthermore, NELL2 was mainly expressed in clusters of T cells, and was identified to play a critical role in T-cell differentiation. CONCLUSIONS A novel BMscore model was successfully established and might be effective for providing guidance to LUAD therapy.
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Affiliation(s)
- Zhenxing Zhang
- Department of Thoracic and Maxillofacial Surgery (B7X), Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Haoran Zhu
- Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Xiaojun Wang
- Department of Thoracic Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Shanan Lin
- Department of Thoracic Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Chenjin Ruan
- Department of Thoracic Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Qiang Wang
- Department of Thoracic Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China.
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Lin K, Xu D, Wang X, Shi J, Gao W. Development of a basement membrane gene signature and identification of the potential candidate therapeutic targets for pancreatic cancer. Gland Surg 2023; 12:263-281. [PMID: 36915817 PMCID: PMC10005979 DOI: 10.21037/gs-23-24] [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: 12/21/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023]
Abstract
Background Pancreatic cancer is a deadly cancer with a poor prognosis. In light of mounting evidence that basement membrane genes (BMGs) play a role in the development of cancer, we sought to examine the prognostic importance and role of BMGs in pancreatic ductal adenocarcinoma (PDAC) patients. Methods BMGs were obtained from previous top research studies. The clinical and messenger ribonucleic acid expression data were retrieved from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data sets, respectively. Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were used for the PDAC risk modeling and gene identification. The Kaplan-Meier method was used to compare outcomes between the low- and high-risk groups. Finally, we analyzed small-molecule drugs that could be used to target BMGs for treatment using the Enrichr data set and validated the function of the tubulointerstitial nephritis antigen (TINAG) in pancreatic cancer. Results We successfully constructed and validated a 7 BMG-based model to predict PDAC patient outcomes. Additionally, we discovered that 7 BMG-based model was an independent predictive factor for PDAC. According to our functional analysis, the majority of the signaling pathways enriched in BMGs were those connected to malignancy. Immune cell infiltration and immunological checkpoints were also linked to the BMG-based model. Further, we identified 5 small-molecule drugs that may be useful in treating PDAC patients. We also found that TINAG promoted cell proliferation in pancreatic cancer. Conclusions Our study extended understandings of how BMGs work in PDAC. We identified a credible predictive biomarker for PDAC patients' survival.
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Affiliation(s)
- Kai Lin
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Gastrointestinal Surgery, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dong Xu
- Department of General Surgery, Gaochun People’s Hospital, Nanjing, China
| | - Xiaoxiao Wang
- Department of GCP Research Center, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Shi
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wentao Gao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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