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Hulahan TS, Spruill L, Wallace EN, Park Y, West RB, Marks JR, Hwang ES, Drake RR, Angel PM. Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics. Int J Mol Sci 2024; 25:6748. [PMID: 38928454 PMCID: PMC11203487 DOI: 10.3390/ijms25126748] [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: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.
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Affiliation(s)
- Taylor S. Hulahan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Elizabeth N. Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA;
| | - Robert B. West
- Department of Pathology Clinical, Stanford University, Stanford, CA 94305, USA;
| | - Jeffrey R. Marks
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - E. Shelley Hwang
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
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Tian P, Koudis NM, Morais MRPT, Pickard A, Fresquet M, Adamson A, Derby B, Lennon R. Collagen IV assembly is influenced by fluid flow in kidney cell-derived matrices. Cells Dev 2024:203923. [PMID: 38670459 DOI: 10.1016/j.cdev.2024.203923] [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: 09/30/2023] [Revised: 01/30/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Kidney podocytes and endothelial cells assemble a complex and dynamic basement membrane that is essential for kidney filtration. Whilst many components of this specialised matrix are known, the influence of fluid flow on its assembly and organisation remains poorly understood. Using the coculture of podocytes and glomerular endothelial cells in a low-shear stress, high-flow bioreactor, we investigated the effect of laminar fluid flow on the composition and assembly of cell-derived matrix. With immunofluorescence and matrix image analysis we found flow-mediated remodelling of collagen IV. Using proteomic analysis of the cell-derived matrix we identified changes in both abundance and composition of matrix proteins under flow, including the collagen-modifying enzyme, prolyl 4-hydroxylase (P4HA1). To track collagen IV assembly, we used CRISPR-Cas9 to knock in the luminescent marker HiBiT to the endogenous COL4A2 gene in podocytes. With this system, we found that collagen IV was secreted and accumulated consistently under both static and flow conditions. However knockdown of P4HA1 in podocytes led to a reduction in the secretion of collagen IV and this was more pronounced under flow. Together, this work demonstrates the effect of fluid flow on the composition, modification, and organisation of kidney cell-derived matrix and provides an in vitro system for investigating flow-induced matrix alteration in the context of kidney development and disease.
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Affiliation(s)
- Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
| | - Nikki-Maria Koudis
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Mychel R P T Morais
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
| | - Adam Pickard
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
| | - Antony Adamson
- Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, UK.
| | - Brian Derby
- School of Materials, University of Manchester, UK.
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, UK; Royal Manchester Children's Hospital, Manchester, UK.
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Greco F, Panunzio A, Tafuri A, Bernetti C, Pagliarulo V, Zobel BB, Scardapane A, Mallio CA. CT-Based Radiogenomics of P4HA3 Expression in Clear Cell Renal Cell Carcinoma. Acad Radiol 2024; 31:902-908. [PMID: 37537130 DOI: 10.1016/j.acra.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
RATIONALE AND OBJECTIVES The sequencing of the renal cell carcinoma (RCC) genome identified several mutations with prognostic significance. Genomic analysis, collected in The Cancer Genome Atlas Research Network, revealed several clear cell renal cell carcinoma (ccRCC) gene mutations and gene expressions. Radiogenomics is a new branch of diagnostic imaging based on the association between imaging phenotypes and genomics of diseases. P4HA3 expression has recently been shown to correlate with increased aggressiveness of ccRCC, with poor prognosis, proliferation, migration, invasion, and metastases, suggesting P4HA3 as a prognostic marker and therapeutic target in ccRCC. The aim of this study is to investigate the computed tomography (CT) imaging phenotype of P4HA3 expression in ccRCC patients. MATERIALS AND METHODS In this retrospective study we enrolled 196 ccRCC patients divided into two groups: ccRCC patients with P4HA3 expression (n = 13) and ccRCC patients without P4HA3 expression (n = 183). Several imaging features were evaluated on preoperative CT scan. The statistical significance threshold was set at P < .05. RESULTS A statistically significant association was found with larger primary tumor size (P = .033), tumor infiltration (P = .023), ill-defined tumor margins (P = .025), and advanced tumor stage American Joint Committee of Cancer (P = .014). CONCLUSION This study demonstrates CT imaging features associated with P4HA3 expression in ccRCC. These results could contribute to better understand P4HA3 expression with a noninvasive approach and could be applied to the development of targeted therapies.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy (F.G.).
| | - Andrea Panunzio
- Department of Urology, "Vito Fazzi" Hospital, Lecce, Italy (A.P., A.T., V.P.)
| | - Alessandro Tafuri
- Department of Urology, "Vito Fazzi" Hospital, Lecce, Italy (A.P., A.T., V.P.)
| | - Caterina Bernetti
- Unit of Diagnostic Imaging and Interventional Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Roma, Italy (C.B., B.B.Z., C.A.M.); Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy (C.B., B.B.Z., C.A.M.)
| | - Vincenzo Pagliarulo
- Department of Urology, "Vito Fazzi" Hospital, Lecce, Italy (A.P., A.T., V.P.)
| | - Bruno Beomonte Zobel
- Unit of Diagnostic Imaging and Interventional Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Roma, Italy (C.B., B.B.Z., C.A.M.); Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy (C.B., B.B.Z., C.A.M.)
| | - Arnaldo Scardapane
- Dipartimento Interdisciplinare di Medicina, Sezione di Diagnostica per immagini, Università degli Studi di Bari "Aldo Moro", Bari, Italy (A.S.)
| | - Carlo Augusto Mallio
- Unit of Diagnostic Imaging and Interventional Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Roma, Italy (C.B., B.B.Z., C.A.M.); Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy (C.B., B.B.Z., C.A.M.)
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Xie Y, Peng X, Li P. MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy. BMC Bioinformatics 2024; 25:44. [PMID: 38280998 PMCID: PMC10822190 DOI: 10.1186/s12859-024-05667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 01/29/2024] Open
Abstract
Complex biological systems often undergo sudden qualitative changes during their dynamic evolution. These critical transitions are typically characterized by a catastrophic progression of the system. Identifying the critical point is critical to uncovering the underlying mechanisms of complex biological systems. However, the system may exhibit minimal changes in its state until the critical point is reached, and in the face of high throughput and strong noise data, traditional biomarkers may not be effective in distinguishing the critical state. In this study, we propose a novel approach, mutual information weighted entropy (MIWE), which uses mutual information between genes to build networks and identifies critical states by quantifying molecular dynamic differences at each stage through weighted differential entropy. The method is applied to one numerical simulation dataset and four real datasets, including bulk and single-cell expression datasets. The critical states of the system can be recognized and the robustness of MIWE method is verified by numerical simulation under the influence of different noises. Moreover, we identify two key transcription factors (TFs), CREB1 and CREB3, that regulate downstream signaling genes to coordinate cell fate commitment. The dark genes in the single-cell expression datasets are mined to reveal the potential pathway regulation mechanism.
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Affiliation(s)
- Yuke Xie
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Xueqing Peng
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471000, China.
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5
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Zhao Z, Deng J, Fan D. Green biomanufacturing in recombinant collagen biosynthesis: trends and selection in various expression systems. Biomater Sci 2023; 11:5439-5461. [PMID: 37401335 DOI: 10.1039/d3bm00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Collagen, classically derived from animal tissue, is an all-important protein material widely used in biomedical materials, cosmetics, fodder, food, etc. The production of recombinant collagen through different biological expression systems using bioengineering techniques has attracted significant interest in consideration of increasing market demand and the process complexity of extraction. Green biomanufacturing of recombinant collagen has become one of the focus topics. While the bioproduction of recombinant collagens (type I, II, III, etc.) has been commercialized in recent years, the biosynthesis of recombinant collagen is extremely challenging due to protein immunogenicity, yield, degradation, and other issues. The rapid development of synthetic biology allows us to perform a heterologous expression of proteins in diverse expression systems, thus optimizing the production and bioactivities of recombinant collagen. This review describes the research progress in the bioproduction of recombinant collagen over the past two decades, focusing on different expression systems (prokaryotic organisms, yeasts, plants, insects, mammalian and human cells, etc.). We also discuss the challenges and future trends in developing market-competitive recombinant collagens.
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Affiliation(s)
- Zilong Zhao
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianjun Deng
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
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6
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Huang J, Zhao P, Shi J, Ning J, Wang Z, Luo Y, Qin J, Huang X. Prognostic Value and Immunological Role of P4HA3 in Colon Adenocarcinoma. Int J Gen Med 2023; 16:1953-1971. [PMID: 37251280 PMCID: PMC10224728 DOI: 10.2147/ijgm.s407068] [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: 02/03/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
Purpose Prolyl 4-hydroxylase subunit alpha 3 (P4HA3) has been proven to participate in the occurrence and development of multiple cancers. However, the functional role of P4HA3 in the tumor immune microenvironment (TIME) of colon adenocarcinoma (COAD) and the prognosis of COAD patients has not been clarified. This study aimed to elucidate the immunological role and prognostic value of P4HA3 in COAD. Methods P4HA3 expression in COAD tissues was analyzed via experiments and a bioinformatics algorithm. Based on the COAD patients in The Cancer Genome Atlas database, we comprehensively evaluated whether the expression levels of P4HA3 affected clinical prognosis, TIME, and immunotherapy of COAD using the R platforms and several public databases, including GEPIA, TIMER, TISIDB, and TCIA. Results The results of the pan-cancer analysis indicated that P4HA3 expression was significantly different in most tumor tissues compared with normal tissues. P4HA3 was overexpressed in COAD tissues, and overexpression of P4HA3 was associated with a worse overall survival and a shorted progression-free interval in COAD patients. The expression of P4HA3 was positively correlated with pathological stage, T stage, N stage, perineural infiltration, and lymphatic infiltration. There were significant correlations of P4HA3 expression levels with immune cell infiltration and their makers, as well as immunomodulators, chemokines, and microsatellite status. Moreover, overexpression of P4HA3 was associated with a lower response rate to immunotherapy in the IMvigor210 cohort. Conclusion Overexpression of P4HA3 is closely related to the poor prognosis of COAD patients, and P4HA3 is a potential target for immunotherapy in COAD patients.
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Affiliation(s)
- Jun Huang
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Peizhuang Zhao
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Jialing Shi
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Jiajia Ning
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zhen Wang
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yihua Luo
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Jingqian Qin
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Xue Huang
- Department of Geriatrics and Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
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Wang F, Yu Z, Liu X, Hu F, Liu X, Fu X, Liu Y, Zou Z. A meta-analysis and bioinformatics analysis of P4HB expression levels in the prognosis of cancer patients. Pathol Res Pract 2023; 245:154474. [PMID: 37119730 DOI: 10.1016/j.prp.2023.154474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND P4HB (prolyl 4-hydroxylase, beta polypeptide) is a human chromosomal gene that encodes an endoplasmic reticulum (ER) molecular chaperone protein with oxidoreductase, chaperone and isomerase activities. Recent studies indicated that P4HB may have clinical significance, with elevated P4HB expression reported in cancer patients, but its impact on tumor prognosis is not yet clear. To our knowledge, this is the first meta-analysis to show an association between P4HB expression and the prognosis of various cancers. METHODS We conducted a systematic literature search in the PubMed, PubMed Central, Web of Science, Embase, CNKI, Wanfang and Weipu databases, followed by a quantitative meta-analysis using Stata SE14.0 and R statistics software 4.2.1. The hazard ratio (HR) and relative risk (RR) were analyzed to evaluate the relationships of P4HB expression levels with overall survival (OS), disease-free survival (DFS), and clinicopathological parameters of cancer patients. Subsequently, P4HB expression in various cancer types was validated using the Gene Expression Profiling Interactive Analysis (GEPIA) online database. RESULTS Ten articles containing the data of 4121 cancer patients were included in the analysis, and a significant correlation of high P4HB expression with apparently shorter OS was found (HR, 1.90; 95% CI, 1.50-2.40; P < 0.01), while there was no significant correlation with gender (RR, 1.06; 95% CI, 0.91-1.22; P = 0.084), or age. Additionally, GEPIA online analysis revealed significant upregulation of P4HB in 13 types of cancer. Among them, P4HB overexpression was associated with shorter OS in 9 and worse DFS in 11 cancer types. CONCLUSIONS Upregulation of P4HB is correlated with worse prognosis in various cancers, which could provide new ideas for the development of P4HB-related diagnostic biomarkers and new therapeutic targets.
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Affiliation(s)
- Feiyang Wang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Zhixiang Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China
| | - Xiaohan Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The Second School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Feng Hu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Xiangjun Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China
| | - Xinyi Fu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Yan Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The Second School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Zhenhong Zou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China.
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8
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Wang S, Wu J, Zhao W, Li M, Li S. CEBPB upregulates P4HA2 to promote the malignant biological behavior in IDH1 wildtype glioma. FASEB J 2023; 37:e22848. [PMID: 36906285 DOI: 10.1096/fj.202201244rrrr] [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: 08/03/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 03/13/2023]
Abstract
Temozolomide (TMZ), the primary drug for glioma treatment, has limited treatment efficacy. Additionally, considerable evidence shows that isocitrate dehydrogenase 1 mutation-type (IDH1 mut) gliomas have a better response to TMZ than isocitrate dehydrogenase 1 wildtype (IDH1 wt) gliomas. Here, we aimed to identify potential mechanisms underlying this phenotype. Herein, the Cancer Genome Atlas bioinformatic data and 30 clinical samples from patients were analyzed to reveal the expression level of cytosine-cytosine-adenosine-adenosine-thymidine (CCAAT) Enhancer Binding Protein Beta (CEBPB) and prolyl 4-hydroxylase subunit alpha 2 (P4HA2) in gliomas. Next, cellular and animal experiments, including cell proliferation, colony formation, transwell, CCK-8, and xenograft assays, were performed to explore the tumor-promoting effects of P4HA2 and CEBPB. Then, chromatin immunoprecipitation (ChIP) assays were used to confirm the regulatory relationships between them. Finally, a co-immunoprecipitation (Co-IP) assay was performed to confirm the effect of IDH1-132H to CEBPB proteins. We found that CEBPB and P4HA2 expression was significantly upregulated in IDH1 wt gliomas and associated with poor prognosis. CEBPB knockdown inhibited the proliferation, migration, invasion, and temozolomide resistance of glioma cells and hindered the growth of glioma xenograft tumors. CEBPE, as a transcription factor, exerted its function by transcriptionally upregulating P4HA2 expression in glioma cells. Importantly, CEBPB is prone to ubiquitin-proteasomal degradation in IDH1 R132H glioma cells. We also demonstrated that both genes are related to collagen synthesis, as confirmed by in vivo experiments. Thus, CEBPE promotes proliferation and TMZ resistance by inducing P4HA2 expression in glioma cells and offers a potential therapeutic target for glioma treatment.
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Affiliation(s)
- Shuai Wang
- Department of Functional Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Jingheng Wu
- Department of Functional Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Wujun Zhao
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China.,Department of Neurosurgery of the First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Miaomiao Li
- Department of Functional Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Shaoyi Li
- Department of Functional Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
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Wilhelm D, Wurtz A, Abouelfarah H, Sanchez G, Bui C, Vincourt JB. Tissue-specific collagen hydroxylation at GEP/GDP triplets mediated by P4HA2. Matrix Biol 2023; 119:141-153. [PMID: 37003347 DOI: 10.1016/j.matbio.2023.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Collagen, the most abundant organic compound of vertebrate organisms, is a supramolecular, protein-made polymer. Details of its post-translational maturation largely determine the mechanical properties of connective tissues. Its assembly requires massive, heterogeneous prolyl-4-hydroxylation (P4H), catalyzed by Prolyl-4-hydroxylases (P4HA1-3), providing thermostability to its elemental, triple helical building block. So far, there was no evidence of tissue-specific regulation of P4H, nor of a differential substrate repertoire of P4HAs. Here, the post-translational modifications of collagen extracted from bone, skin, and tendon were compared, revealing lower hydroxylation of most GEP/GDP triplets, together with fewer other residue positions along collagen α chains, in the tendon. This regulation is mostly conserved in two distant homeotherm species, mouse and chicken. The comparison of detailed P4H patterns in both species suggests a two-step mechanism of specificity. P4ha2 expression is low in tendon and its genetic invalidation in the ATDC5 cellular model of collagen assembly specifically mimics the tendon-related P4H profile. Therefore, P4HA2 has a better ability than other P4HAs to hydroxylate the corresponding residue positions. Its local expression participates in determining the P4H profile, a novel aspect of the tissue specificities of collagen assembly. Data availability: Proteomics data are available via ProteomeXchange with the identifier PXD039221. Reviewer account details.
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Affiliation(s)
- Dafné Wilhelm
- Université de Lorraine, CNRS, IMoPA, UMR 7365, F-54000 Nancy, France
| | - Alison Wurtz
- Université de Lorraine, CNRS, IMoPA, UMR 7365, F-54000 Nancy, France
| | | | - Guillaume Sanchez
- Université de Lorraine, CNRS, IMoPA, UMR 7365, F-54000 Nancy, France
| | - Catherine Bui
- Université de Lorraine, CNRS, IMoPA, UMR 7365, F-54000 Nancy, France
| | - Jean-Baptiste Vincourt
- Université de Lorraine, CNRS, IMoPA, UMR 7365, F-54000 Nancy, France.; Proteomics core facility of the University of Lorraine, CNRS, INSERM, IBSLor, UMS2008/US40, F-54000 Nancy, France..
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Zhang Z, Zhang Y, Zhang R. P4HA3 promotes clear cell renal cell carcinoma progression via the PI3K/AKT/GSK3β pathway. Med Oncol 2023; 40:70. [PMID: 36588128 DOI: 10.1007/s12032-022-01926-2] [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: 09/18/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma. P4HA3 is a key enzyme in collagen biosynthesis and has emerged as important molecules in regulation of proliferation, invasion, and metastasis in various tumor types. The role of P4HA3 in the development of ccRCC has remained to be elucidated. Genes expression, prognostic, and enrichment analyses were carried out with bioinformatics analysis. The efficiency of P4HA3 knockdown was confirmed by real-time quantitative PCR and Western blotting. The cellular functions were analyzed by CCK-8, EdU, wound healing, and transwell assays. The levels of related proteins expression were analyzed by Western blotting. P4HA3 was highly expressed in ccRCC compared with normal tissue samples from the TCGA database. Kaplan-Meier curves results showed that the expression level of P4HA3 was significantly negatively correlated with overall survival of patients. P4HA3 expression knockdown inhibited the proliferation, migration, and invasion of ccRCC cells, as demonstrated by in vitro experiments. In addition, GSEA results revealed that P4HA3 may be related to EMT and involved in the PI3K-AKT-GSK3β pathway in ccRCC; this was tentatively confirmed through Western blotting. P4HA3 may induce ccRCC progression via the PI3K-AKT-GSK3β signaling pathway and could represent a potential therapeutic target.
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Affiliation(s)
- Zhechuan Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong District, Chongqing, China
- The Second Clinical College, Chongqing Medical University, Chongqing, China
| | - Yuanfeng Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong District, Chongqing, China.
| | - Ronggui Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong District, Chongqing, China.
- Department of Urology, Chongqing University Central Hospital, Chongqing University, 1 Jiankang Road, Yuzhong District, Chongqing, China.
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11
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Shi R, Xu M, Ye H, Gao S, Li J, Li H, Li C. Cycloheximide promotes type I collagen maturation mainly via collagen prolyl 4-hydroxylase subunit α2. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1832-1840. [PMID: 36789685 PMCID: PMC10157532 DOI: 10.3724/abbs.2022191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aberrant deposition of collagen is associated with cancer development and tissue fibrosis. Proline hydroxylation, catalyzed by collagen prolyl 4-hydroxylases (C-P4Hs), is necessary for collagen maturation and secretion. Here, we try to evaluate the mechanism of the regulation of CHX on collagen maturation. Using pepsin digestion, liquid chromatograph mass spectrometry and gene knockout, we find that treatment of mouse embryonic fibroblasts with cycloheximide (CHX) increases type I collagen proline hydroxylation partially via P4HA1 and mainly via P4HA2. Western blot analysis results show that CHX treatment reduces type I collagen but does not obviously impact the level of P4HA1/2 protein in the endoplasmic reticulum, which enhances the molar ratio of P4HA1/2 to type I collagen, and coimmunoprecipitation results confirm that more P4HA1/2 can bind to each type I collagen. Since C-P4Hs possess the capability to hydroxylate proline independent of ascorbate for a few cycles, this enhanced binding between P4HA1/2 and type I collagen can partially explain how CHX stimulates type I collagen maturation.
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12
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Crystal structure of the collagen prolyl 4-hydroxylase (C-P4H) catalytic domain complexed with PDI: Toward a model of the C-P4H α 2β 2 tetramer. J Biol Chem 2022; 298:102614. [PMID: 36265586 PMCID: PMC9676403 DOI: 10.1016/j.jbc.2022.102614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4H) are α2β2 tetramers, which catalyze the prolyl 4-hydroxylation of procollagen, allowing for the formation of the stable triple-helical collagen structure in the endoplasmic reticulum. The C-P4H α-subunit provides the N-terminal dimerization domain, the middle peptide-substrate-binding (PSB) domain, and the C-terminal catalytic (CAT) domain, whereas the β-subunit is identical to the enzyme protein disulfide isomerase (PDI). The structure of the N-terminal part of the α-subunit (N-terminal region and PSB domain) is known, but the structures of the PSB-CAT linker region and the CAT domain as well as its mode of assembly with the β/PDI subunit, are unknown. Here, we report the crystal structure of the CAT domain of human C-P4H-II complexed with the intact β/PDI subunit, at 3.8 Å resolution. The CAT domain interacts with the a, b', and a' domains of the β/PDI subunit, such that the CAT active site is facing bulk solvent. The structure also shows that the C-P4H-II CAT domain has a unique N-terminal extension, consisting of α-helices and a β-strand, which is the edge strand of its major antiparallel β-sheet. This extra region of the CAT domain interacts tightly with the β/PDI subunit, showing that the CAT-PDI interface includes an intersubunit disulfide bridge with the a' domain and tight hydrophobic interactions with the b' domain. Using this new information, the structure of the mature C-P4H-II α2β2 tetramer is predicted. The model suggests that the CAT active-site properties are modulated by α-helices of the N-terminal dimerization domains of both subunits of the α2-dimer.
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Baldari S, Di Modugno F, Nisticò P, Toietta G. Strategies for Efficient Targeting of Tumor Collagen for Cancer Therapy. Cancers (Basel) 2022; 14:cancers14194706. [PMID: 36230627 PMCID: PMC9563908 DOI: 10.3390/cancers14194706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The tumor microenvironment encompasses the cellular and extracellular matrix components that support and shape the three-dimensional framework in which solid tumors develop and grow. The extracellular matrix of the tumor is characterized by increased deposition and aberrant architecture of collagen fibers. Therefore, as a key mechanical component of the tumor microenvironment, collagen plays a critical role in cancer progression, metastasis, and therapeutic response. To boost the efficacy of current anticancer therapies, including immunotherapy, innovative approaches should take into account strategies directed against the dysregulated non-cancer cell stromal components. In the current review, we provide an overview of the principal approaches to target tumor collagen to provide therapeutic benefits. Abstract The tumor stroma, which comprises stromal cells and non-cellular elements, is a critical component of the tumor microenvironment (TME). The dynamic interactions between the tumor cells and the stroma may promote tumor progression and metastasis and dictate resistance to established cancer therapies. Therefore, novel antitumor approaches should combine anticancer and anti-stroma strategies targeting dysregulated tumor extracellular matrix (ECM). ECM remodeling is a hallmark of solid tumors, leading to extensive biochemical and biomechanical changes, affecting cell signaling and tumor tissue three-dimensional architecture. Increased deposition of fibrillar collagen is the most distinctive alteration of the tumor ECM. Consequently, several anticancer therapeutic strategies have been developed to reduce excessive tumor collagen deposition. Herein, we provide an overview of the current advances and challenges of the main approaches aiming at tumor collagen normalization, which include targeted anticancer drug delivery, promotion of degradation, modulation of structure and biosynthesis of collagen, and targeting cancer-associated fibroblasts, which are the major extracellular matrix producers.
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Zhang T, Yuan L, Sheng M, Chen Y, Wang J, Lan Q. Identifying α-KG-dependent prognostic signature for lower-grade glioma based on transcriptome profiles. Front Oncol 2022; 12:840394. [PMID: 35965532 PMCID: PMC9363673 DOI: 10.3389/fonc.2022.840394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
The inhibition of alpha-ketoglutarate (α-KG)-dependent dioxygenases is thought to contribute to isocitrate dehydrogenase (IDH) mutation-derived malignancy. Herein, we aim to thoroughly investigate the expression pattern and prognostic significance of genes encoding α-KG-dependent enzymes for lower-grade glioma (LGG) patients. In this retrospective study, a total of 775 LGG patients were enrolled. The generalized linear model, least absolute shrinkage and selection operator Cox regression, and nomogram were applied to identify the enzyme-based signature. With the use of gene set enrichment analysis and Gene Ontology, the probable molecular abnormalities underlying high-risk patients were investigated. By comprehensively analyzing mRNA data, we observed that 41 genes were differentially expressed between IDHMUT and IDHWT LGG patients. A risk signature comprising 10 genes, which could divide samples into high- and low-risk groups of distinct prognoses, was developed and independently validated. This enzyme-based signature was indicative of a more malignant phenotype. The nomogram model incorporating the risk signature, molecular biomarkers, and clinicopathological parameters proved the incremental utility of the α-KG-dependent signature by achieving a more accurate prediction impact. Our study demonstrates that the α-KG-dependent enzyme-encoding genes were differentially expressed in relation to the IDH phenotype and may serve as a promising indicator for clinical outcomes of LGG patients.
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Niu X, Ren L, Wang S, Gao D, Ma M, Hu A, Qi H, Zhang S. High Prolyl 4-Hydroxylase Subunit Alpha 3 Expression as an Independent Prognostic Biomarker and Correlated With Immune Infiltration in Gastric Cancer. Front Genet 2022; 13:952335. [PMID: 35846138 PMCID: PMC9283575 DOI: 10.3389/fgene.2022.952335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Gastric cancer (GC) has a high mortality rate and is particularly prevalent in China. The extracellular matrix protein, prolyl 4-hydroxylase subunit alpha 3 (P4HA3), has been implicated in various cancers. We aimed to assess the diagnostic and prognostic value of P4HA3 in GC and investigate its correlation with immune cell infiltration. Methods: The present study used microarray data from the Cancer Genome Atlas (TCGA) to analyze the association of P4HA3 expression with clinicopathological features. Data from the Gene Expression Omnibus (GEO) were used for validation. Receiver operating characteristic (ROC) and Kaplan–Meier curves were constructed to determine the diagnostic and prognostic value of P4HA3 in GC. Univariate and multivariate regression analyses were performed to assess the impact of P4HA3 on overall survival (OS) rates. A protein–protein interaction (PPI) network was generated and functional enrichment evaluated. Single-sample gene set enrichment analysis (ssGSEA) was conducted to correlate P4HA3 expression with immune cell infiltration. The correlation between P4HA3 and immune check point genes was studied. Results: P4HA3 was over-expressed in GC, along with 15 other types of cancer, including breast invasive carcinoma and cholangiocarcinoma. P4HA3 showed high diagnostic and prognostic value in GC and was an independent prognostic factor. P4HA3, TNM (tumor, node, metastases) stage, pathological stage and age all correlated with OS rates. Genes related to P4HA3 were enriched in the lumen of the endoplasmic reticulum and included procollagen-proline 3-dioxygenase activity. P4HA3 expression correlated with numbers of macrophages, natural killer (NK) cells, immature dendritic cells (iDC), mast cells, eosinophils, effective memory T cells (Tem), T-helper 1 (Th1) cells and dendritic cells (DC). P4HA3 was positively correlated with hepatitis A virus cellular receptor 2 (HAVCR2) and programmed cell death 1 ligand 2 (PDCD1LG2). Conclusion: P4HA3 is a potential independent biomarker for prognosis of GC and may be an immunotherapy target in the treatment of GC.
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Affiliation(s)
- Xiaoji Niu
- Department of Gastroenterology of Traditional Chinese Medicine, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liman Ren
- Department of Endocrinology, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
| | - Shoumei Wang
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dong Gao
- Department of Gastroenterology of Traditional Chinese Medicine, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
| | - Mingyue Ma
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Aiyan Hu
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongjun Qi
- Department of Gastroenterology of Traditional Chinese Medicine, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
- *Correspondence: Hongjun Qi, ; Shuhui Zhang,
| | - Shuhui Zhang
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Hongjun Qi, ; Shuhui Zhang,
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16
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Niu X, Ren L, Hu A, Zhang S, Qi H. Identification of Potential Diagnostic and Prognostic Biomarkers for Gastric Cancer Based on Bioinformatic Analysis. Front Genet 2022; 13:862105. [PMID: 35368700 PMCID: PMC8966486 DOI: 10.3389/fgene.2022.862105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Gastric cancer (GC) is one of the most prevalent cancers all over the world. The molecular mechanisms of GC remain unclear and not well understood. GC cases are majorly diagnosed at the late stage, resulting in a poor prognosis. Advances in molecular biology techniques allow us to get a better understanding of precise molecular mechanisms and enable us to identify the key genes in the carcinogenesis and progression of GC. Methods: The present study used datasets from the GEO database to screen differentially expressed genes (DEGs) between GC and normal gastric tissues. GO and KEGG enrichments were utilized to analyze the function of DEGs. The STRING database and Cytoscape software were applied to generate protein–protein network and find hub genes. The expression levels of hub genes were evaluated using data from the TCGA database. Survival analysis was conducted to evaluate the prognostic value of hub genes. The GEPIA database was involved to correlate key gene expressions with the pathological stage. Also, ROC curves were constructed to assess the diagnostic value of key genes. Results: A total of 607 DEGs were identified using three GEO datasets. GO analysis showed that the DEGs were mainly enriched in extracellular structure and matrix organization, collagen fibril organization, extracellular matrix (ECM), and integrin binding. KEGG enrichment was mainly enriched in protein digestion and absorption, ECM-receptor interaction, and focal adhesion. Fifteen genes were identified as hub genes, one of which was excluded for no significant expression between tumor and normal tissues. COL1A1, COL5A2, P4HA3, and SPARC showed high values in prognosis and diagnosis of GC. Conclusion: We suggest COL1A1, COL5A2, P4HA3, and SPARC as biomarkers for the diagnosis and prognosis of GC.
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Affiliation(s)
- Xiaoji Niu
- Department of Gastroenterology of Traditional Chinese Medicine, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liman Ren
- Department of Endocrinology, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
| | - Aiyan Hu
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuhui Zhang
- Department of Pathology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Shuhui Zhang, ; Hongjun Qi,
| | - Hongjun Qi
- Department of Gastroenterology of Traditional Chinese Medicine, Qinghai Province Hospital of Traditional Chinese Medicine, Xining, China
- *Correspondence: Shuhui Zhang, ; Hongjun Qi,
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17
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Barnum CE, Shetye SS, Fazelinia H, Garcia BA, Fang S, Alzamora M, Li H, Brown LM, Tang C, Myers K, Wapner R, Soslowsky LJ, Vink JY. The Non-pregnant and Pregnant Human Cervix: a Systematic Proteomic Analysis. Reprod Sci 2022; 29:1542-1559. [PMID: 35266109 DOI: 10.1007/s43032-022-00892-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 02/13/2022] [Indexed: 10/18/2022]
Abstract
Appropriate timing of cervical remodeling (CR) is key to normal term parturition. To date, mechanisms behind normal and abnormal (premature or delayed) CR remain unclear. Recent studies show regional differences exist in human cervical tissue structure. While the entire cervix contains extracellular matrix (ECM), the internal os is highly cellular containing 50-60% cervical smooth muscle (CSM). The external os contains 10-20% CSM. Previously, we reported ECM rigidity and different ECM proteins influence CSM cell function, highlighting the importance of understanding not only how cervical cells orchestrate cervical ECM remodeling in pregnancy, but also how changes in specific ECM proteins can influence resident cellular function. To understand this dynamic process, we utilized a systematic proteomic approach to understand which soluble ECM and cellular proteins exist in the different regions of the human cervix and how the proteomic profiles change from the non-pregnant (NP) to the pregnant (PG) state. We found the human cervix proteome contains at least 4548 proteins and establish the types and relative abundance of cellular and soluble matrisome proteins found in the NP and PG human cervix. Further, we report the relative abundance of proteins involved with elastic fiber formation and ECM organization/degradation were significantly increased while proteins involved in RNA polymerase I/promoter opening, DNA methylation, senescence, immune system, and compliment activation were decreased in the PG compared to NP cervix. These findings establish an initial platform from which we can further comprehend how changes in the human cervix proteome results in normal and abnormal CR.
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Affiliation(s)
- Carrie E Barnum
- McKay Orthopedic Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Snehal S Shetye
- McKay Orthopedic Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shuyang Fang
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Maria Alzamora
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hongyu Li
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chuanning Tang
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kristin Myers
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Louis J Soslowsky
- McKay Orthopedic Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Joy Y Vink
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA. .,Preterm Birth Prevention Center, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Shi R, Zhang Z, Zhu A, Xiong X, Zhang J, Xu J, Sy MS, Li C. Targeting Type I Collagen for Cancer Treatment. Int J Cancer 2022; 151:665-683. [PMID: 35225360 DOI: 10.1002/ijc.33985] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/07/2022]
Abstract
Collagen is the most abundant protein in animals. Interactions between tumor cells and collagen influence every step of tumor development. Type I collagen is the main fibrillar collagen in the extracellular matrix and is frequently up-regulated during tumorigenesis. The binding of type I collagen to its receptors on tumor cells promotes tumor cell proliferation, epithelial-mesenchymal transition, and metastasis. Type I collagen also regulates the efficacy of tumor therapies, such as chemotherapy, radiotherapy, and immunotherapy. Furthermore, type I collagen fragments are diagnostic markers of metastatic tumors and have prognostic value. Inhibition of type I collagen synthesis has been reported to have anti-tumor effects in animal models. However, collagen has also been shown to possess anti-tumor activity. Therefore, the roles that type I collagen plays in tumor biology are complex and tumor type-dependent. In this review, we discuss the expression and regulation of synthesis of type I collagen, as well as the role up-regulated type I collagen plays in various stages of cancer progression. We also discuss the role of collagen in tumor therapy. Finally, we highlight several recent approaches targeting type I collagen for cancer treatment. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Run Shi
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Zhe Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Ankai Zhu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Xingxing Xiong
- Department of Operating Room, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Jie Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
| | - Jiang Xu
- Department of Stomatology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Man-Sun Sy
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chaoyang Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong High Education Institute, Guangzhou, China
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Zhou H, Zou J, Shao C, Zhou A, Yu J, Chen S, Xu C. Prolyl 4-hydroxylase subunit alpha 3 facilitates human colon cancer growth and metastasis through the TGF-β/Smad signaling pathway. Pathol Res Pract 2022; 230:153749. [PMID: 34959098 DOI: 10.1016/j.prp.2021.153749] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023]
Abstract
Prolyl 4-hydroxylase subunit alpha 3 (P4HA3) has been known to be associated with a variety of human cancers. However, the role of P4HA3 on colon cancer growth and metastasis is unclear. In this study, we investigated the effect of P4HA3 on the growth and metastasis of colon cancer and its possible molecular mechanism. First of all, we demonstrated that P4HA3 expression was greatly higher in cells and tissues of colon cancer than that in non-tumor tissues and cells, and the prognosis of patients who had higher P4HA3 was distinctively poorer than patients who had lower level of P4HA3. Second, it was shown that P4HA3 knockdown strongly inhibited the migration, proliferation and invasion ability of colon cancer cells. However, P4HA3 over-expression accelerated the abilities. Meanwhile, P4HA3 could promote subcutaneous tumorigenesis in nude mice in vivo. In addition, P4HA3 knockdown significantly decreased mesenchymal markers Vimentin, N-cadherin and Snail expression and increased epithelial marker E-cadherin expression. And conversely, over-expression of P4HA3 produced the opposite effects. In the current study, there was further evidence that down-regulating P4HA3 significantly reduced both TGF-β and its following molecules including p-Smad2 as well as p-Smad3. However, overexpression of P4HA3 showed the opposite effect. In conclusion, this study shows that P4HA3 promotes the human colon cancer growth and metastasis by affecting TGF-β/Smad signaling pathway. P4HA3 may become a new target for early diagnosis, treatment and prognosis assessment of colon cancer.
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Affiliation(s)
- Hailang Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, PR China; Department of Gastroenterology, Lianshui People's Hospital Affiliated to Kangda College of Nanjing Medical University, Huaian, Jiangsu 223400, PR China
| | - Junwei Zou
- Department of General Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Changjiang Shao
- Department of Gastroenterology, The Second People's Hospital of Lianyungang, Lianyungang, Jiangsu 222006, PR China
| | - Aijun Zhou
- Department of Gastroenterology, Lianshui People's Hospital Affiliated to Kangda College of Nanjing Medical University, Huaian, Jiangsu 223400, PR China
| | - Jiufeng Yu
- Department of Traditional Chinese Medicine, Lianshui People's Hospital Affiliated to Kangda College of Nanjing Medical University, Huaian, Jiangsu 223400, PR China
| | - Song Chen
- The Institute of Life Sciences, Jiangsu College of Nursing,Huaian, Jiangsu 223300, PR China
| | - Chunfang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, PR China.
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20
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The Regulation of Collagen Processing by miRNAs in Disease and Possible Implications for Bone Turnover. Int J Mol Sci 2021; 23:ijms23010091. [PMID: 35008515 PMCID: PMC8745169 DOI: 10.3390/ijms23010091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
This article describes several recent examples of miRNA governing the regulation of the gene expression involved in bone matrix construction. We present the impact of miRNA on the subsequent steps in the formation of collagen type I. Collagen type I is a main factor of mechanical bone stiffness because it constitutes 90–95% of the organic components of the bone. Therefore, the precise epigenetic regulation of collagen formation may have a significant influence on bone structure. We also describe miRNA involvement in the expression of genes, the protein products of which participate in collagen maturation in various tissues and cancer cells. We show how non-collagenous proteins in the extracellular matrix are epigenetically regulated by miRNA in bone and other tissues. We also delineate collagen mineralisation in bones by factors that depend on miRNA molecules. This review reveals the tissue variability of miRNA regulation at different levels of collagen maturation and mineralisation. The functionality of collagen mRNA regulation by miRNA, as proven in other tissues, has not yet been shown in osteoblasts. Several collagen-regulating miRNAs are co-expressed with collagen in bone. We suggest that collagen mRNA regulation by miRNA could also be potentially important in bone metabolism.
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21
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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