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Rezapour M, Wesolowski R, Gurcan MN. Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS. Int J Mol Sci 2024; 25:7306. [PMID: 39000413 PMCID: PMC11242629 DOI: 10.3390/ijms25137306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/23/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.
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Affiliation(s)
- Mostafa Rezapour
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Robert Wesolowski
- Division of Medical Oncology, James Cancer Hospital and the Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Metin Nafi Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
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Wu X, Chan L, Zhu D, Pang Y, Jin M, Wang Y, Wang W. Mitosis targeting in non-small lung cancer cells by inhibition of PAD4. Heliyon 2024; 10:e27313. [PMID: 38496857 PMCID: PMC10944192 DOI: 10.1016/j.heliyon.2024.e27313] [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: 02/04/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
PAD4 expression and activity were significantly up-regulated in lung cancer tissues suggesting that PAD4 could be a possible target for lung cancer treatment. In this study we had demonstrated that PAD4 expression was higher in lung cancer patients whom with lymphnode metastasis and pleural invasion. Inhibiting PAD4 with a small molecular inhibitor could induce apoptosis and suppress growth in lung cancer cells. We used RNA-sequencing to further investigate transcriptional changes that induced by PAD4 inhibition, and results suggested its affected mostly on the cell cycle, mitotic cell cycle process, p53 signaling pathway. By using image flow cytometry analysis, we found that PAD4 inhibited by YW3-56 could accumulate cells in the G1/G0 phases and reducing the fraction of G2/M and S phase cells. Quantification of different phase of mitosis in cells treated with YW3-56 revealed an increasing trend of telophase and prophase cells. Taken together, our data indicated that PAD4 inhibitor could affect cell cycle and mitosis of lung cancer cells, and targeting PAD4 could be a promising strategy for discovery novel anti-NSCLC treatments.
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Affiliation(s)
- Xiangmei Wu
- Department of Pathology, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 150086, China
- Department of Pathology, Beijing Geriatric Hospital, Beijing, 100095, China
| | - Liujia Chan
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, 100069, China
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yuheng Pang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, 100069, China
| | - Mulan Jin
- Department of Pathology, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 150086, China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, 100069, China
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Carter T, Valenzuela RK, Yerukala Sathipati S, Medina-Flores R. Gene signatures associated with prognosis and chemotherapy resistance in glioblastoma treated with temozolomide. Front Genet 2023; 14:1320789. [PMID: 38259614 PMCID: PMC10802164 DOI: 10.3389/fgene.2023.1320789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background: Glioblastoma (GBM) prognosis remains extremely poor despite standard treatment that includes temozolomide (TMZ) chemotherapy. To discover new GBM drug targets and biomarkers, genes signatures associated with survival and TMZ resistance in GBM patients treated with TMZ were identified. Methods: GBM cases in The Cancer Genome Atlas who received TMZ (n = 221) were stratified into subgroups that differed by median overall survival (mOS) using network-based stratification to cluster patients whose somatic mutations affected genes in similar modules of a gene interaction network. Gene signatures formed from differentially mutated genes in the subgroup with the longest mOS were used to confirm their association with survival and TMZ resistance in independent datasets. Somatic mutations in these genes also were assessed for an association with OS in an independent group of 37 GBM cases. Results: Among the four subgroups identified, subgroup four (n = 71 subjects) exhibited the longest mOS at 18.3 months (95% confidence interval: 16.2, 34.1; p = 0.0324). Subsets of the 86 genes that were differentially mutated in this subgroup formed 20-gene and 8-gene signatures that predicted OS in two independent datasets (Spearman's rho of 0.64 and 0.58 between actual and predicted OS; p < 0.001). Patients with mutations in five of the 86 genes had longer OS in a small, independent sample of 37 GBM cases, but this association did not reach statistical significance (p = 0.07). Thirty-one of the 86 genes formed signatures that distinguished TMZ-resistant GBM samples from controls in three independent datasets (area under the curve ≥ 0.75). The prognostic and TMZ-resistance signatures had eight genes in common (ANG, BACH1, CDKN2C, HMGA1, IFI16, PADI4, SDF4, and TP53INP1). The latter three genes have not been associated with GBM previously. Conclusion: PADI4, SDF4, and TP53INP1 are novel therapy and biomarker candidates for GBM. Further investigation of their oncologic functions may provide new insight into GBM treatment resistance mechanisms.
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Affiliation(s)
- Tonia Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Robert K. Valenzuela
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | | | - Rafael Medina-Flores
- Department of Pathology (Neuropathology), Marshfield Clinic, Marshfield, WI, United States
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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Identification and Interaction Analysis of Molecular Markers in Pancreatic Ductal Adenocarcinoma by Bioinformatics and Next-Generation Sequencing Data Analysis. Bioinform Biol Insights 2023; 17:11779322231186719. [PMID: 37529485 PMCID: PMC10387711 DOI: 10.1177/11779322231186719] [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: 01/12/2023] [Accepted: 06/18/2023] [Indexed: 08/03/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the molecular pathogenesis, but the molecular mechanisms of PDAC are still not well understood. The purpose of this study is to further explore the molecular mechanism of PDAC through integrated bioinformatics analysis. Methods To identify the candidate genes in the carcinogenesis and progression of PDAC, next-generation sequencing (NGS) data set GSE133684 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and Gene Ontology (GO) and pathway enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using Integrated Interactions Database (IID) interactome database and Cytoscape. Subsequently, miRNA-DEG regulatory network and TF-DEG regulatory network were constructed using miRNet database, NetworkAnalyst database, and Cytoscape software. The expression levels of hub genes were validated based on Kaplan-Meier analysis, expression analysis, stage analysis, mutation analysis, protein expression analysis, immune infiltration analysis, and receiver operating characteristic (ROC) curve analysis. Results A total of 463 DEGs were identified, consisting of 232 upregulated genes and 233 downregulated genes. The enriched GO terms and pathways of the DEGs include vesicle organization, secretory vesicle, protein dimerization activity, lymphocyte activation, cell surface, transferase activity, transferring phosphorus-containing groups, hemostasis, and adaptive immune system. Four hub genes (namely, cathepsin B [CCNB1], four-and-a-half LIM domains 2 (FHL2), major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) and tubulin beta 1 class VI (TUBB1)) were obtained via taking interaction of different analysis results. Conclusions On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of PDAC and provide potential targets for further investigation.
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Affiliation(s)
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Society’s College of Pharmacy, Gadag, India
| | - Rajeshwari Horakeri
- Department of Computer Science, Government First Grade College, Hubballi, India
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Luo X, Chang S, Xiao S, Peng Y, Gao Y, Hu F, Liang J, Xu Y, Du K, Chen Y, Qin J, Meltzer SJ, Deng S, Feng X, Fan X, Hou G, Jin Z, Zhang X. PAD4-dependent citrullination of nuclear translocation of GSK3β promotes colorectal cancer progression via the degradation of nuclear CDKN1A. Neoplasia 2022; 33:100835. [PMID: 36113195 PMCID: PMC9483803 DOI: 10.1016/j.neo.2022.100835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/06/2022]
Abstract
Peptidylarginine deiminase 4 (PAD4), a Ca2+-dependent enzyme, catalyzes the conversion of arginine to citrulline and has been strongly associated with many malignant tumors. However, the molecular mechanisms of PAD4 in the development and progression of colorectal cancer (CRC) remain unclearly defined. In our study, PAD4 expression was increased in CRC tissues and cells, and was closely related to tumor size, lymph node metastasis. Moreover, the transcription factor KLF9 directly bound to PADI4 gene promoter, leading to overexpression of PAD4 in CRC cells, which augmented cell growth and migration. We revealed that PAD4 interacted with and citrullinated glycogen synthase kinase-3β (GSK3β) in CRC cells, and GSK3β Arg-344 was the dominating PAD4-citrullination site. Furthermore, IgL2 and catalytic domains of PAD4 directly bound to the kinase domain of GSK3β in CRC cells. Mechanistically, PAD4 promoted the transport of GSK3β from the cytoplasm to the nucleus, thereby increasing the ubiquitin-dependent proteasome degradation of nuclear cyclin-dependent kinase inhibitor 1 (CDKN1A). Our study is the first to reveal the details of a critical PAD4/GSK3β/CDKN1A signaling axis for CRC progression, and provides evidence that PAD4 is a potential diagnosis biomarker and therapeutic target in CRC.
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Affiliation(s)
- Xiaonuan Luo
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Shanshan Chang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Siyu Xiao
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yin Peng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yuli Gao
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Fan Hu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Jianxue Liang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yidan Xu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Kaining Du
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Jiequan Qin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Stephen J Meltzer
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Ki-mmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Shiqi Deng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xianling Feng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xinmin Fan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Gangqiang Hou
- Department of Medical Image Center, Kangning Hospital of Shenzhen, Shenzhen, Guangdong Province, People's Republic of China
| | - Zhe Jin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China.
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Lesbon JCC, Garnica TK, Xavier PLP, Rochetti AL, Reis RM, Müller S, Fukumasu H. A Screening of Epigenetic Therapeutic Targets for Non-Small Cell Lung Cancer Reveals PADI4 and KDM6B as Promising Candidates. Int J Mol Sci 2022; 23:ijms231911911. [PMID: 36233212 PMCID: PMC9570250 DOI: 10.3390/ijms231911911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/23/2022] Open
Abstract
Despite advances in diagnostic and therapeutic approaches for lung cancer, new therapies targeting metastasis by the specific regulation of cancer genes are needed. In this study, we screened a small library of epigenetic inhibitors in non-small-cell lung cancer (NSCLC) cell lines and evaluated 38 epigenetic targets for their potential role in metastatic NSCLC. The potential candidates were ranked by a streamlined approach using in silico and in vitro experiments based on publicly available databases and evaluated by real-time qPCR target gene expression, cell viability and invasion assays, and transcriptomic analysis. The survival rate of patients with lung adenocarcinoma is inversely correlated with the gene expression of eight epigenetic targets, and a systematic review of the literature confirmed that four of them have already been identified as targets for the treatment of NSCLC. Using nontoxic doses of the remaining inhibitors, KDM6B and PADI4 were identified as potential targets affecting the invasion and migration of metastatic lung cancer cell lines. Transcriptomic analysis of KDM6B and PADI4 treated cells showed altered expression of important genes related to the metastatic process. In conclusion, we showed that KDM6B and PADI4 are promising targets for inhibiting the metastasis of lung adenocarcinoma cancer cells.
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Affiliation(s)
- Jéssika Cristina Chagas Lesbon
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Duque de Caxias, 225-Jardim Elite, Pirassununga 13635-900, SP, Brazil
| | - Taismara Kustro Garnica
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Duque de Caxias, 225-Jardim Elite, Pirassununga 13635-900, SP, Brazil
| | - Pedro Luiz Porfírio Xavier
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Duque de Caxias, 225-Jardim Elite, Pirassununga 13635-900, SP, Brazil
| | - Arina Lázaro Rochetti
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Duque de Caxias, 225-Jardim Elite, Pirassununga 13635-900, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Hospital de Amor, Antenor Duarte Viléla, 1331-Dr. Paulo Prata, Barretos 14784-400, SP, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4805-017 Guimarães, Portugal
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str 15-60438, 60438 Frankfurt am Main, Germany
| | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Duque de Caxias, 225-Jardim Elite, Pirassununga 13635-900, SP, Brazil
- Correspondence:
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Jiao J, Ji L, Li X, Gao Z, Wang G, Qin J, Wang Y, Wang Y. Dynamic proteomic change of tumor and immune organs in an immune-competent hepatocellular carcinoma mouse model. Am J Cancer Res 2022; 12:1621-1634. [PMID: 35530287 PMCID: PMC9077077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023] Open
Abstract
Subcutaneous implantation of a human cancer cell line in immune-deficient mice (CDX) is a commonly used tool in preclinical studies for the assessment of potential anti-cancer drugs. As immunotherapy is transforming cancer treatment, tumor models in immunocompetent mice are necessary for us to understand the immune aspects of tumor biology. However, the systemic immune response to the implantation of cancer cells at proteome level is unclear. In this study, we characterized the dynamic proteomic changes of subcutaneous tumors and 5 immune organs (draining lymph node, mesenteric lymph node, spleen, thymus and marrow) at six time points after implantation using a Hepa1-6 derived allograft mouse model. Our data suggest that interaction of the implanted tumor cells with mouse immune system followed the trajectory of "tumor rejection" to "immune evasion" in that the tumor gained the ability to evade the immune system for growth. Furthermore, anti-PDL2 antibody was validated here as an optional immunotherapy strategy to inhibit the growth of Hepa1-6 subcutaneous tumors. These findings from our study provided valuable information for the understanding of tumor and immune interaction and shed light on the rational design for clinical cancer treatment and other preclinical experiments.
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Affiliation(s)
- Jiaqi Jiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Linlin Ji
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical UniversityTianjin 300000, China
| | - Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Zhan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Guangshun Wang
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical UniversityTianjin 300000, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Yini Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
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Miura Y, Ohkubo H, Niimi A, Kanazawa S. Suppression of epithelial abnormalities by nintedanib in induced-rheumatoid arthritis-associated interstitial lung disease mouse model. ERJ Open Res 2021; 7:00345-2021. [PMID: 34881329 PMCID: PMC8646002 DOI: 10.1183/23120541.00345-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/19/2021] [Indexed: 12/20/2022] Open
Abstract
Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is relevant for the prognosis in patients with RA. Nintedanib, which inhibits both receptor and non-receptor type tyrosine kinases, is an antifibrotic drug for the treatment of progressive fibrosing ILDs, such as idiopathic pulmonary fibrosis and systemic sclerosis-associated interstitial lung disease. Little is known about the effects of nintedanib on RA-ILD. We examined the characteristics of a novel induced RA-ILD (iRA-ILD) mouse model and the effects of nintedanib on the model. D1CC×D1BC mice are highly susceptible to arthritogenic antigens, such as bovine type II collagen, resulting in severe inflammatory arthritis. ILD develops after joint inflammation is alleviated. Serum surfactant protein D levels were monitored as an ILD marker. Nintedanib was orally administered to iRA-ILD mice for 2 months. The iRA-ILD model showed similar symptoms to those in patients with RA-ILD. The histopathological features of pulmonary disorder resembled nonspecific interstitial pneumonia, but with metaplastic epithelium. Histopathological analysis revealed that in addition to reducing fibrosis, nintedanib suppressed M2 macrophage polarisation and hyperplasia of Type 2 alveolar epithelial cells. The metaplastic epithelium acquired invasiveness because of the expression of E-cadherin, MMP7, Tgf-β, Col1a1, Padi2 and Padi4. Moreover, citrullinated peptides were detected in these invasive epithelial cells as well as in the bronchiolar epithelium. Administration of nintedanib reduced the expression of Pad4 and citrullinated peptides and eliminated invasive epithelial cells. The broad inhibitory effects of nintedanib on tyrosine kinases may contribute to the overall improvement in RA-ILD, including epithelial abnormalities associated with progressive lung fibrosis.
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Affiliation(s)
- Yoko Miura
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hirotsugu Ohkubo
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akio Niimi
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Satoshi Kanazawa
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Dai P, Tang Z, Ruan P, Bajinka O, Liu D, Tan Y. Gimap5 Inhibits Lung Cancer Growth by Interacting With M6PR. Front Oncol 2021; 11:699847. [PMID: 34604035 PMCID: PMC8479171 DOI: 10.3389/fonc.2021.699847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Objective Several studies have demonstrated the impacts of GTPases of immunity-associated proteins (GIMAPs) on malignant cells. However, the mechanisms through which Gimap5 regulates lung cancer cells are yet to be thoroughly investigated in the literature. Our study aimed to investigate the function of Gimap5 in the development of lung cancer. Methods The expression levels of the GIMAP family were analyzed in lung cancer patients of various cancer databases and lung cancer cell lines. After the survival rates of the cells were analyzed, we constructed Gimap5 over-expressed lung cancer cell lines and assessed the effects of Gimap5 on cell migration, cell invasion, cell proliferation and the epithelial-mesenchymal transition (EMT). We later screened the interacting proteins of Gimap5 using Co-IP combined with mass spectrometry and then analyzed the expression and distribution of M6PR, including its impacts on protein-arginine deiminase type-4 (PADI4). Results Findings indicated that GIMAP family expression decreased significantly in lung cancer cell lines. We also noticed that the downregulation of the GIMAP family was related to the poor prognosis of lung cancer patients. Our experimental results showed that Gimap5 could inhibit the migration, invasion, proliferation and EMT of lung cancer cell lines. Moreover, we found that Gimap5 promoted the transport of M6PR from the cytoplasm to the cell membrane, thereby inhibiting the enhancement of EMT-related PADI4. Conclusion Our research suggested that Gimap5 could inhibit the growth of lung cancer by interacting with M6PR and that it could be a potential biomarker for the diagnosis and prognosis of lung cancer.
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Affiliation(s)
- Pei Dai
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Zhongxiang Tang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Pinglang Ruan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Ousman Bajinka
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China.,China-Africa Research Centre of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Dan Liu
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yurong Tan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China.,China-Africa Research Centre of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, China
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Ji T, Ma K, Chen L, Cao T. PADI1 contributes to EMT in PAAD by activating the ERK1/2-p38 signaling pathway. J Gastrointest Oncol 2021; 12:1180-1190. [PMID: 34295566 DOI: 10.21037/jgo-21-283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 11/06/2022] Open
Abstract
Background Peptidylarginine deiminase 1 (PADI1) has been reported to promote tumorigenesis in breast cancer. However, the functional role of PADI1 in pancreatic ductal adenocarcinoma (PAAD) has remained elusive until now. Methods The expression pattern of PADI1 in PAAD tissues and normal tissues was analyzed using The Cancer Genome Atlas (TCGA) dataset. A Kaplan-Meier curve analysis was performed to evaluate the prognostic value of PADI1 in PAAD patients. PADI1 was knocked down in CFPAN-1 and HPAC cells, and overexpressed in PANC-1 and Bxpc-3 cells by RNA interference. A wound-healing assay was performed to analyze relative cell migration distance. Cell migration and invasion were assessed by a Transwell assay. Related protein expression levels were measured by western blot and immunofluorescence. Results The bioinformatics analysis showed that PADI1 was overexpressed in PAAD tissues and associated with a poor survival prognosis. The knockdown of PADI1 suppressed cell migration and invasion, and activated the ERK1/2-p38 signaling pathway in CFPAN-1 and HPAC cells. The overexpression of PADI1 produced the opposite results in PANC-1 and Bxpc-3 cells. Additionally, treatment with an MEK1/2 inhibitor significantly attenuated the effects of PADI1 knockdown on cell migration, invasion, the epithelial-mesenchymal transition (EMT) process, and p-ERK1/2 and p38 expression in CFPAN-1 and HPAC cells. Conclusions Our data suggested that PADI1 may function as an oncogene in regulating metastasis in vitro in PAAD.
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Affiliation(s)
- Tengfei Ji
- Department of Hepatobiliary Surgery, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangzhou, China
| | - Keqiang Ma
- Department of Hepatobiliary Surgery, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangzhou, China
| | - Liang Chen
- Department of Hepatobiliary Surgery, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangzhou, China
| | - Tiansheng Cao
- Department of Hepatobiliary Surgery, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangzhou, China
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11
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Chen H, Luo M, Wang X, Liang T, Huang C, Huang C, Wei L. Inhibition of PAD4 enhances radiosensitivity and inhibits aggressive phenotypes of nasopharyngeal carcinoma cells. Cell Mol Biol Lett 2021; 26:9. [PMID: 33726680 PMCID: PMC7962337 DOI: 10.1186/s11658-021-00251-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a tumor deriving from nasopharyngeal epithelium. Peptidyl-arginine deiminase 4 (PAD4) is a vital mediator of histone citrullination and plays an essential role in regulating disease process. Radiotherapy is an essential method to treat NPC. In this research, we explored the effect of PAD4 on NPC radiosensitivity. METHODS We enrolled 50 NPC patients, established mice xenograft model, and purchased cell lines for this study. Statistical analysis and a series of experiments including RT-qPCR, clonogenic survival, EdU, Transwell, and wound healing assays were done. RESULTS Our data manifested that PAD4 (mRNA and protein) presented a high expression in NPC tissues and cells. GSK484, an inhibitor of PAD4, could inhibit activity of PAD4 in NPC cell lines. PAD4 overexpression promoted the radioresistance, survival, migration, and invasion of NPC cells, whereas treatment of GSK484 exerted inhibitory effects on radioresistance and aggressive phenotype of NPC cells. Additionally, GSK484 could attenuate the effect of PAD4 of NPC cell progression. More importantly, we found that GSK484 significantly inhibited tumor size, tumor weight and tumor volume in mice following irradiation. CONCLUSIONS PAD4 inhibitor GSK484 attenuated the radioresistance and cellular progression in NPC.
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Affiliation(s)
- Hao Chen
- Department of Endoscopy, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Min Luo
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China
| | - Xiangping Wang
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China
| | - Ting Liang
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China
| | - Chaoyuan Huang
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China
| | - Changjie Huang
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China.
| | - Lining Wei
- Department of Oncology, The Second Nanning People's Hospital, No.13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China.
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Musiani D, Massignani E, Cuomo A, Yadav A, Bonaldi T. Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Curr Protein Pept Sci 2021; 21:725-739. [PMID: 32338214 DOI: 10.2174/1389203721666200426232531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/27/2022]
Abstract
The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.
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Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
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Arisan ED, Uysal-Onganer P, Lange S. Putative Roles for Peptidylarginine Deiminases in COVID-19. Int J Mol Sci 2020; 21:E4662. [PMID: 32629995 PMCID: PMC7370447 DOI: 10.3390/ijms21134662] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023] Open
Abstract
Peptidylarginine deiminases (PADs) are a family of calcium-regulated enzymes that are phylogenetically conserved and cause post-translational deimination/citrullination, contributing to protein moonlighting in health and disease. PADs are implicated in a range of inflammatory and autoimmune conditions, in the regulation of extracellular vesicle (EV) release, and their roles in infection and immunomodulation are known to some extent, including in viral infections. In the current study we describe putative roles for PADs in COVID-19, based on in silico analysis of BioProject transcriptome data (PRJNA615032 BioProject), including lung biopsies from healthy volunteers and SARS-CoV-2-infected patients, as well as SARS-CoV-2-infected, and mock human bronchial epithelial NHBE and adenocarcinoma alveolar basal epithelial A549 cell lines. In addition, BioProject Data PRJNA631753, analysing patients tissue biopsy data (n = 5), was utilised. We report a high individual variation observed for all PADI isozymes in the patients' tissue biopsies, including lung, in response to SARS-CoV-2 infection, while PADI2 and PADI4 mRNA showed most variability in lung tissue specifically. The other tissues assessed were heart, kidney, marrow, bowel, jejunum, skin and fat, which all varied with respect to mRNA levels for the different PADI isozymes. In vitro lung epithelial and adenocarcinoma alveolar cell models revealed that PADI1, PADI2 and PADI4 mRNA levels were elevated, but PADI3 and PADI6 mRNA levels were reduced in SARS-CoV-2-infected NHBE cells. In A549 cells, PADI2 mRNA was elevated, PADI3 and PADI6 mRNA was downregulated, and no effect was observed on the PADI4 or PADI6 mRNA levels in infected cells, compared with control mock cells. Our findings indicate a link between PADI expression changes, including modulation of PADI2 and PADI4, particularly in lung tissue, in response to SARS-CoV-2 infection. PADI isozyme 1-6 expression in other organ biopsies also reveals putative links to COVID-19 symptoms, including vascular, cardiac and cutaneous responses, kidney injury and stroke. KEGG and GO pathway analysis furthermore identified links between PADs and inflammatory pathways, in particular between PAD4 and viral infections, as well as identifying links for PADs with a range of comorbidities. The analysis presented here highlights roles for PADs in-host responses to SARS-CoV-2, and their potential as therapeutic targets in COVID-19.
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Affiliation(s)
- Elif Damla Arisan
- Gebze Technical University, Institute of Biotechnology, Gebze, 41400 Kocaeli, Turkey;
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
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