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Zhou Y, Zhang X, Gao Y, Peng Y, Liu P, Chen Y, Guo C, Deng G, Ouyang Y, Zhang Y, Han Y, Cai C, Shen H, Gao L, Zeng S. Neuromedin U receptor 1 deletion leads to impaired immunotherapy response and high malignancy in colorectal cancer. iScience 2024; 27:110318. [PMID: 39055918 PMCID: PMC11269305 DOI: 10.1016/j.isci.2024.110318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/27/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Colorectal cancer (CRC) exhibits significant heterogeneity, impacting immunotherapy efficacy, particularly in immune desert subtypes. Neuromedin U receptor 1 (NMUR1) has been reported to perform a vital function in immunity and inflammation. Through comprehensive multi-omics analyses, we have systematically characterized NMUR1 across various tumors, assessing expression patterns, genetic alterations, prognostic significance, immune infiltration, and pathway associations at both the bulk sequencing and single-cell scales. Our findings demonstrate a positive correlation between NMUR1 and CD8+ T cell infiltration, with elevated NMUR1 levels in CD8+ T cells linked to improved immunotherapy outcomes in patients with CRC. Further, we have validated the NMUR1 expression signature in CRC cell lines and patient-derived tissues, revealing its interaction with key immune checkpoints, including lymphocyte activation gene 3 and cytotoxic T-lymphocyte-associated protein 4. Additionally, NMUR1 suppression enhances CRC cell proliferation and invasiveness. Our integrated analyses and experiments open new avenues for personalized immunotherapy strategies in CRC treatment.
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Affiliation(s)
- Yulai Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiangyang Zhang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yan Gao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Cao Guo
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Gongping Deng
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan 570311, China
| | - Yanhong Ouyang
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan 570311, China
| | - Yan Zhang
- Department of Oncology, Yueyang People’s Hospital, Yueyang Hospital Affiliated to Hunan Normal University, Yueyang, Hunan 414000, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Le Gao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Li Z, Fan Y, Ma Y, Meng N, Li D, Wang D, Lian J, Hu C. Identification of Crucial Genes and Signaling Pathways in Alectinib-Resistant Lung Adenocarcinoma Using Bioinformatic Analysis. Mol Biotechnol 2023:10.1007/s12033-023-00973-y. [PMID: 38142454 DOI: 10.1007/s12033-023-00973-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/27/2023] [Indexed: 12/26/2023]
Abstract
Alectinib, a second-generation anaplastic lymphoma kinase (ALK) inhibitor, has been shown to be effective for patients with ALK-positive non-small cell lung cancer (NSCLC). However, alectinib resistance is a serious problem worldwide. To the best of our knowledge, little information is available on its molecular mechanisms using the Gene Expression Omnibus (GEO) database. In this study, the differentially expressed genes (DEGs) were selected from the gene expression profile GSE73167 between parental and alectinib-resistant human lung adenocarcinoma (LUAD) cell samples. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) annotation enrichment analyses were conducted using Database for Annotation, Visualization and Integrated Discovery (DAVID). The construction of protein-protein interaction (PPI) network was performed to visualize DEGs. The hub genes were extracted based on the analysis of the PPI network using plug-in cytoHubba of Cytoscape software. The functional roles of the key genes were investigated using Gene Expression Profiling Interactive Analysis (GEPIA), University of Alabama at Birmingham Cancer (UALCAN), Gene Set Enrichment Analysis (GSEA), and Tumor Immune Estimation Resource (TIMER) analysis. The networks of kinase, miRNA, and transcription-factor targets of SFTPD were explored using LinkedOmics. The drug sensitivity analysis of SFTPD was analyzed using the RNAactDrug database. Results showed a total of 144 DEGs were identified. Five hub genes were extracted, including mucin 5B (MUC5B), surfactant protein D (SFTPD), deleted in malignant brain tumors 1 (DMBT1), surfactant protein A2 (SFTPA2), and trefoil factor 3 (TFF3). The survival analysis using GEPIA displayed that low expression of SFTPD had a significantly negative effect on the prognosis of patients with LUAD. GSEA revealed that low expression of SFTPD was positively correlated with the pathways associated with drug resistance, such as DNA replication, cell cycle, drug metabolism, and DNA damage repair, including mismatch repair (MMR), base excision repair (BER), homologous recombination (HR), and nucleotide excision repair (NER). The SFTPD expression was negatively correlated with the drug sensitivity of alectinib according to RNAactDrug database. The expression of SFTPD was further validated in parental H3122 cells and alectinib-resistant H3122 cells by quantitative reverse transcription PCR (RT-qPCR). In conclusion, our study found that the five hub genes, especially low expression of SFTPD, are closely related to alectinib resistance in patients with LUAD.
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Affiliation(s)
- Zhilong Li
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China
| | - Yafeng Fan
- Respiratory Department, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China
| | - Yong Ma
- Thoracic Surgery Department II, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China
| | - Nan Meng
- Department of Translational Medicine, ChosenMed Technology (Zhejiang) Co., Ltd, Beijing, 100176, China
| | - Dongbing Li
- Department of Translational Medicine, ChosenMed Technology (Zhejiang) Co., Ltd, Beijing, 100176, China
| | - Dongliang Wang
- Department of Translational Medicine, ChosenMed Technology (Zhejiang) Co., Ltd, Beijing, 100176, China
| | - Jianhong Lian
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China.
| | - Chengguang Hu
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, China.
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Rahim NS, Wu YS, Sim MS, Velaga A, Bonam SR, Gopinath SCB, Subramaniyan V, Choy KW, Teow SY, Fareez IM, Samudi C, Sekaran SD, Sekar M, Guad RM. Three Members of Transmembrane-4-Superfamily, TM4SF1, TM4SF4, and TM4SF5, as Emerging Anticancer Molecular Targets against Cancer Phenotypes and Chemoresistance. Pharmaceuticals (Basel) 2023; 16:ph16010110. [PMID: 36678607 PMCID: PMC9867095 DOI: 10.3390/ph16010110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
There are six members of the transmembrane 4 superfamily (TM4SF) that have similar topology and sequence homology. Physiologically, they regulate tissue differentiation, signal transduction pathways, cellular activation, proliferation, motility, adhesion, and angiogenesis. Accumulating evidence has demonstrated, among six TM4SF members, the regulatory roles of transmembrane 4 L6 domain family members, particularly TM4SF1, TM4SF4, and TM4SF5, in cancer angiogenesis, progression, and chemoresistance. Hence, targeting derailed TM4SF for cancer therapy has become an emerging research area. As compared to others, this review aimed to present a focused insight and update on the biological roles of TM4SF1, TM4SF4, and TM4SF5 in the progression, metastasis, and chemoresistance of various cancers. Additionally, the mechanistic pathways, diagnostic and prognostic values, and the potential and efficacy of current anti-TM4SF antibody treatment were also deciphered. It also recommended the exploration of other interactive molecules to be implicated in cancer progression and chemoresistance, as well as potential therapeutic agents targeting TM4SF as future perspectives. Generally, these three TM4SF members interact with different integrins and receptors to significantly induce intracellular signaling and regulate the proliferation, migration, and invasion of cancer cells. Intriguingly, gene silencing or anti-TM4SF antibody could reverse their regulatory roles deciphered in different preclinical models. They also have prognostic and diagnostic value as their high expression was detected in clinical tissues and cells of various cancers. Hence, TM4SF1, TM4SF4, and TM4SF5 are promising therapeutic targets for different cancer types preclinically and deserve further investigation.
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Affiliation(s)
- Nur Syafiqah Rahim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Department of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Perlis Branch, Arau Campus, Arau 02600, Malaysia
- Collaborative Drug Discovery Research (CDDR) Group, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, Bandar Puncak Alam 42300, Malaysia
| | - Yuan Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia
- Correspondence: (Y.S.W.); (R.M.G.)
| | - Maw Shin Sim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Appalaraju Velaga
- Department of Medicinal Chemistry, Faculty of Pharmacy, MAHSA University, Jenjarom 42610, Malaysia
| | - Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Subash C. B. Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), Arau 02600, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar 01000, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, Arau 02600, Malaysia
| | - Vetriselvan Subramaniyan
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Malaysia
| | - Ker Woon Choy
- Department of Anatomy, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh 47000, Malaysia
| | - Sin-Yeang Teow
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Quhai, Wenzhou 325060, China
| | - Ismail M. Fareez
- Collaborative Drug Discovery Research (CDDR) Group, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, Bandar Puncak Alam 42300, Malaysia
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor Branch, Shah Alam Campus, 40450 Shah Alam, Malaysia
| | - Chandramathi Samudi
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Shamala Devi Sekaran
- Faculty of Medical and Health Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Malaysia
| | - Rhanye Mac Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
- Correspondence: (Y.S.W.); (R.M.G.)
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Ruan P, Gao L, Jiang H, Chu T, Ge J, Kong X. Identification of PTPN22 as a potential genetic biomarker for abdominal aortic aneurysm. Front Cardiovasc Med 2022; 9:1061771. [PMID: 36588574 PMCID: PMC9797128 DOI: 10.3389/fcvm.2022.1061771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is a severe life-threatening disease that is generally asymptomatic and is diagnosed at a very late stage. The genetic component underpinning AAA is considerable, with an estimated heritability of up to 70%. Therefore, identifying genetic biomarkers for AAA is valuable for predicting high-risk populations. We used integrative bioinformatics and cellular AAA model-based validation to reveal that the gene encoding protein tyrosine phosphatase non-receptor type 22 (PTPN22) may be a potentially useful diagnostic biomarker for AAA. Integrative bioinformatics analyses of clinical specimens showed that PTPN22 expression was consistently upregulated in aortic tissues and peripheral blood mononuclear cells (PBMCs) derived from patients with AAA. Moreover, transcriptomics data revealed that PTPN22 is a potential biomarker for AAA with limited diagnostic value in patients with thoracic aortic aneurysm/dissection. Single-cell RNA sequencing-based findings further highlight PTPN22 expression in aortic immune cells and vascular smooth muscle cells (VSMCs) is consistently upregulated in patients with AAA. A cellular AAA model was eventually employed to verify the increase in PTPN22 expression. Collectively, the results indicate that PTPN22 could be a potentially useful diagnostic biomarker for AAA.
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Zhu X, Zhou R, Lu Y, Zhang Y, Chen Q, Li Y. Identification and Validation of Afatinib Potential Drug Resistance Gene BIRC5 in Non-Small Cell Lung Cancer. Front Oncol 2021; 11:763035. [PMID: 34804966 PMCID: PMC8595596 DOI: 10.3389/fonc.2021.763035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/13/2021] [Indexed: 01/11/2023] Open
Abstract
Introduction Resistance to second-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), afatinib, is the most significant challenge in the clinical management of non-small cell lung cancer (NSCLC), and the underlying mechanisms remain unclear. Methods Genomic signatures that may confer afatinib resistance in NSCLC were identified via data mining of public databases and integrative bioinformatic analyses. Furthermore, acquired afatinib-resistant lung adenocarcinoma cell lines (HCC827 AR) were established by long-term exposure under afatinib in vitro for stepwise escalation. The expression of baculovirus IAP repeat protein 5 (BIRC5) was detected by western blot, and cellular viability of HCC827 AR was determined by CCK8. Results Through integrative bioinformatic analyses of public datasets, overexpression of baculovirus IAP repeat protein 5 (BIRC5) was identified in both afatinib-resistant NSCLC cells and tissues, and BIRC5 overexpression was positively correlated with lymph node metastasis as well as pathological stage in NSCLC. Furthermore, NSCLC patients with BIRC5 overexpression showed poor survival outcomes. Immune infiltration analysis suggested that BIRC5 expression was significantly inversely correlated with tumor-infiltrating cell numbers and immune biomarker expression in NSCLC. The functions of genes co-expressed with BIRC5 were mainly enriched in cell cycle mitotic phase transition, double-strand break repair, and negative regulation of the cell cycle process signaling pathway. In addition, overexpression of BIRC5 protein was detected in afatinib-resistant cells by western blot, while BIRC5-expressing cells treated with BIRC5 inhibitor, YM155, were sensitive to afatinib. Conclusions In this study, we showed that overexpression of BIRC5 resulted in resistance to afatinib in NSCLC and BIRC5-specific inhibitors may overcome the resistant phenotype, indicating that dysregulation of the apoptotic cell death pathway may be the key mechanism underlying TKI resistance in the development of NSCLC.
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Affiliation(s)
- Xiaoxi Zhu
- Department of Oncology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Renyu Zhou
- Department of Clinical Pathology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuanzhi Lu
- Department of Clinical Pathology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ying Zhang
- Department of Oncology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qiang Chen
- Department of Oncology, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yin Li
- Department of Oncology, First Affiliated Hospital of Jinan University, Guangzhou, China
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Pan Y, Deng C, Qiu Z, Cao C, Wu F. The Resistance Mechanisms and Treatment Strategies for ALK-Rearranged Non-Small Cell Lung Cancer. Front Oncol 2021; 11:713530. [PMID: 34660278 PMCID: PMC8517331 DOI: 10.3389/fonc.2021.713530] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a validated molecular target for non-small-cell lung cancer (NSCLC). The use of tyrosine kinase inhibitors (TKIs) has led to significantly improved survival benefits. However, the clinical benefits of targeting ALK using TKIs are limited due to the emergence of drug resistance. The landscape of resistance mechanisms and treatment decisions has become increasingly complex. Therefore, continued research into new drugs and combinatorial therapies is required to improve outcomes in NSCLC. In this review, we explore the resistance mechanisms of ALK TKIs in advanced NSCLC in order to provide a theoretical basis and research ideas for solving the problem of ALK drug resistance.
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Affiliation(s)
- Yue Pan
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Chao Deng
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Qiu
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China
| | | | - Fang Wu
- Department of Oncology, Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, China
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Tian J, Bai Y, Liu A, Luo B. Identification of key biomarkers for thyroid cancer by integrative gene expression profiles. Exp Biol Med (Maywood) 2021; 246:1617-1625. [PMID: 33899546 DOI: 10.1177/15353702211008809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Thyroid cancer is a frequently diagnosed malignancy and the incidence has been increased rapidly in recent years. Despite the favorable prognosis of most thyroid cancer patients, advanced patients with metastasis and recurrence still have poor prognosis. Therefore, the molecular mechanisms of progression and targeted biomarkers were investigated for developing effective targets for treating thyroid cancer. Eight chip datasets from the gene expression omnibus database were selected and the inSilicoDb and inSilicoMerging R/Bioconductor packages were used to integrate and normalize them across platforms. After merging the eight gene expression omnibus datasets, we obtained one dataset that contained the expression profiles of 319 samples (188 tumor samples plus 131 normal thyroid tissue samples). After screening, we identified 594 significantly differentially expressed genes (277 up-regulated genes plus 317 down-regulated genes) between the tumor and normal tissue samples. The differentially expressed genes exhibited enrichment in multiple signaling pathways, such as p53 signaling. By building a protein-protein interaction network and module analysis, we confirmed seven hub genes, and they were all differentially expressed at all the clinical stages of thyroid cancer. A diagnostic seven-gene signature was established using a logistic regression model with the area under the receiver operating characteristic curve (AUC) of 0.967. Seven robust candidate biomarkers predictive of thyroid cancer were identified, and the obtained seven-gene signature may serve as a useful marker for thyroid cancer diagnosis and prognosis.
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Affiliation(s)
- Jinyi Tian
- Department of General Surgery, School of Clinical Medicine, Tsinghua University, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Yizhou Bai
- Department of General Surgery, School of Clinical Medicine, Tsinghua University, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Anyang Liu
- Department of General Surgery, School of Clinical Medicine, Tsinghua University, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Bin Luo
- Department of General Surgery, School of Clinical Medicine, Tsinghua University, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
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Islam R, Ahmed L, Paul BK, Ahmed K, Bhuiyan T, Moni MA. Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective. J Genet Eng Biotechnol 2021; 19:43. [PMID: 33742334 PMCID: PMC7979844 DOI: 10.1186/s43141-021-00134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 02/14/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Worldwide, more than 80% of identified lung cancer cases are associated to the non-small cell lung cancer (NSCLC). We used microarray gene expression dataset GSE10245 to identify key biomarkers and associated pathways in NSCLC. RESULTS To collect Differentially Expressed Genes (DEGs) from the dataset GSE10245, we applied the R statistical language. Functional analysis was completed using the Database for Annotation Visualization and Integrated Discovery (DAVID) online repository. The DifferentialNet database was used to construct Protein-protein interaction (PPI) network and visualized it with the Cytoscape software. Using the Molecular Complex Detection (MCODE) method, we identify clusters from the constructed PPI network. Finally, survival analysis was performed to acquire the overall survival (OS) values of the key genes. One thousand eighty two DEGs were unveiled after applying statistical criterion. Functional analysis showed that overexpressed DEGs were greatly involved with epidermis development and keratinocyte differentiation; the under-expressed DEGs were principally associated with the positive regulation of nitric oxide biosynthetic process and signal transduction. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway investigation explored that the overexpressed DEGs were highly involved with the cell cycle; the under-expressed DEGs were involved with cell adhesion molecules. The PPI network was constructed with 474 nodes and 2233 connections. CONCLUSIONS Using the connectivity method, 12 genes were considered as hub genes. Survival analysis showed worse OS value for SFN, DSP, and PHGDH. Outcomes indicate that Stratifin may play a crucial role in the development of NSCLC.
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Affiliation(s)
- Rakibul Islam
- Department of Software Engineering, Daffodil International University (DIU), Ashulia, Savar, Dhaka, 1342, Bangladesh
| | - Liton Ahmed
- Department of Software Engineering, Daffodil International University (DIU), Ashulia, Savar, Dhaka, 1342, Bangladesh
| | - Bikash Kumar Paul
- Department of Software Engineering, Daffodil International University (DIU), Ashulia, Savar, Dhaka, 1342, Bangladesh.,Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh.,Group of Bio-photomatiχ, Mawlana Bhashani Science and Technology University (MBSTU), Santosh, Tangail, 1902, Bangladesh
| | - Kawsar Ahmed
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh. .,Group of Bio-photomatiχ, Mawlana Bhashani Science and Technology University (MBSTU), Santosh, Tangail, 1902, Bangladesh.
| | - Touhid Bhuiyan
- Department of Software Engineering, Daffodil International University (DIU), Ashulia, Savar, Dhaka, 1342, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, School of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney, Australia
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Gao L, Wu X, Zhang L, Dai Y, Zhu Z, Zhi Y, Wang K. REG4 is a Potential Biomarker for Radiochemotherapy Sensitivity in Colorectal Cancer. Onco Targets Ther 2021; 14:1605-1611. [PMID: 33688207 PMCID: PMC7936684 DOI: 10.2147/ott.s296031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is one of the most common types of malignancies, and radiochemotherapy (RCT) followed by surgery is the recommended approach for CRC treatment. However, some cases do not respond to first-line conventional chemotherapy or even progress further after treatment. Moreover, there is a risk of severe side effects, such as radiodermatitis. Therefore, identifying predictors for RCT sensitivity is an essential step toward predicting and eventually overcoming resistance. Materials and Methods We used integrative bioinformatics analysis and experimental validation to show that regenerating family member 4 (REG4) may be a potential biomarker for RCT sensitivity in CRC. Results REG4, whose expression is upregulated in some CRC tissues and downregulated in RCT-sensitive CRC cells, was identified as a potential genetic marker for RCT sensitivity in CRC. Immunohistochemistry-based tissue microarray of human CRC was used to experimentally validate REG4 data obtained from the bioinformatics analysis. Conclusion Collectively, these results indicate that REG4 may be a potential biomarker for RCT sensitivity in CRC.
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Affiliation(s)
- Lei Gao
- Department of Thoracic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, 230001, People's Republic of China
| | - Xingjun Wu
- Department of Oncology, Jiangsu Taizhou NO. 2 People Hospital, Jiangsu, People's Republic of China
| | - Libo Zhang
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Yang Dai
- Department of Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Zhe Zhu
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Yunqing Zhi
- Department of Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Gynecology, Shanghai Changning Maternity and Infant Health Hospital, Shanghai, People's Republic of China
| | - Kaijing Wang
- Department of Hepatological Surgery, General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
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Abstract
BACKGROUNDS Lung adenocarcinoma (LUAD) is one of the most common malignancies, and is a serious threat to human health. The aim of the present study was to assess potential biomarkers for the prognosis of LUAD through the analysis of gene expression microarrays. METHODS The gene expression data for GSE118370 was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between normal lung and LUAD samples were screened using the R language. The DAVID database was used to analyze the functions and pathways of DEGs. The STRING database was used to the map protein-protein interaction (PPI) networks, and these were visualized with the Cytoscape software. Finally, the prognostic analysis of the hub gene in the PPI network was performed using the Kaplan-Meier tool. RESULTS A total of 406 downregulated and 203 upregulated DEGs were identified. The GO analysis results revealed that downregulated DEGs were significantly enriched in angiogenesis, calcium ion binding and cell adhesion. The upregulated DEGs were significantly enriched in the extracellular matrix disassembly, collagen catabolic process, chemokine-mediated signaling pathway and endopeptidase inhibitor activity. The KEGG pathway analysis revealed that downregulated DEGs were enriched in neuroactive ligand-receptor interaction, hematopoietic cell lineage and vascular smooth muscle contraction, while upregulated DEGs were enriched in phototransduction. In addition, the top 10 hub genes and the most closely interacting modules of the top 3 proteins in the PPI network were screened. Finally, the independent prognostic value of each hub gene in LUAD patients was analyzed through the Kaplan-Meier plotter. Seven hub genes (ADCY4, S1PR1, FPR2, PPBP, NMU, PF4, and GCG) were closely correlated to overall survival time. CONCLUSION The discovery of these candidate genes and pathways reveals the etiology and molecular mechanisms of LUAD, providing ideas and guidance for the development of new therapeutic approaches to LUAD.
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Identification of Potential Biomarkers for Thyroid Cancer Using Bioinformatics Strategy: A Study Based on GEO Datasets. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9710421. [PMID: 32337286 PMCID: PMC7152968 DOI: 10.1155/2020/9710421] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/29/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
Abstract
Background The molecular mechanisms and genetic markers of thyroid cancer are unclear. In this study, we used bioinformatics to screen for key genes and pathways associated with thyroid cancer development and to reveal its potential molecular mechanisms. Methods The GSE3467, GSE3678, GSE33630, and GSE53157 expression profiles downloaded from the Gene Expression Omnibus database (GEO) contained a total of 164 tissue samples (64 normal thyroid tissue samples and 100 thyroid cancer samples). The four datasets were integrated and analyzed by the RobustRankAggreg (RRA) method to obtain differentially expressed genes (DEGs). Using these DEGs, we performed gene ontology (GO) functional annotation, pathway analysis, protein-protein interaction (PPI) analysis and survival analysis. Then, CMap was used to identify the candidate small molecules that might reverse thyroid cancer gene expression. Results By integrating the four datasets, 330 DEGs, including 154 upregulated and 176 downregulated genes, were identified. GO analysis showed that the upregulated genes were mainly involved in extracellular region, extracellular exosome, and heparin binding. The downregulated genes were mainly concentrated in thyroid hormone generation and proteinaceous extracellular matrix. Pathway analysis showed that the upregulated DEGs were mainly attached to ECM-receptor interaction, p53 signaling pathway, and TGF-beta signaling pathway. Downregulation of DEGs was mainly involved in tyrosine metabolism, mineral absorption, and thyroxine biosynthesis. Among the top 30 hub genes obtained in PPI network, the expression levels of FN1, NMU, CHRDL1, GNAI1, ITGA2, GNA14 and AVPR1A were associated with the prognosis of thyroid cancer. Finally, four small molecules that could reverse the gene expression induced by thyroid cancer, namely ikarugamycin, adrenosterone, hexamethonium bromide and clofazimine, were obtained in the CMap database. Conclusion The identification of the key genes and pathways enhances the understanding of the molecular mechanisms for thyroid cancer. In addition, these key genes may be potential therapeutic targets and biomarkers for the treatment of thyroid cancer.
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Jinru XMS, Yu YMS, Bo JMD, Linxue QMD, Xian-Quan SP. Identification of Key Genes Between Lung Adenocarcinoma and Lung Squamous Cell Carcinoma by Bioinformatics Analysis. ADVANCED ULTRASOUND IN DIAGNOSIS AND THERAPY 2020. [DOI: 10.37015/audt.2020.200011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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13
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Dai B, Ren LQ, Han XY, Liu DJ. Bioinformatics analysis reveals 6 key biomarkers associated with non-small-cell lung cancer. J Int Med Res 2019; 48:300060519887637. [PMID: 31775549 PMCID: PMC7783251 DOI: 10.1177/0300060519887637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Objective Non-small-cell lung cancer (NSCLC) accounts for >85% of lung cancers, and
its incidence is increasing. We explored expression differences between
NSCLC and normal cells and predicted potential target sites for detection
and diagnosis of NSCLC. Methods Three microarray datasets from the Gene Expression Omnibus database were
analyzed using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and
Genomes enrichment analysis were conducted. Then, the String database,
Cytoscape, and MCODE plug-in were used to construct a protein–protein
interaction (PPI) network and screen hub genes. Overall and disease-free
survival of hub genes were analyzed using Kaplan-Meier curves, and the
relationship between expression patterns of target genes and tumor grades
were analyzed and validated. Gene set enrichment analysis and receiver
operating characteristic curves were used to verify enrichment pathways and
diagnostic performance of hub genes. Results In total, 293 differentially expressed genes were identified and mainly
enriched in cell cycle, ECM–receptor interaction, and malaria. In the PPI
network, 36 hub genes were identified, of which 6 were found to play
significant roles in carcinogenesis of NSCLC: CDC20,
ECT2, KIF20A, MKI67,
TPX2, and TYMS. Conclusion The identified target genes can be used as biomarkers for the detection and
diagnosis of NSCLC.
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Affiliation(s)
- Bai Dai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, P. R. China
| | - Li-Qing Ren
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, P. R. China
| | - Xiao-Yu Han
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, P. R. China
| | - Dong-Jun Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, P. R. China
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Huang R, Wang K, Gao L, Gao W. TIMP1 Is A Potential Key Gene Associated With The Pathogenesis And Prognosis Of Ulcerative Colitis-Associated Colorectal Cancer. Onco Targets Ther 2019; 12:8895-8904. [PMID: 31802901 PMCID: PMC6826183 DOI: 10.2147/ott.s222608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is the third most frequently diagnosed cancer worldwide. As a high-risk factor for CRC, ulcerative colitis (UC) has been demonstrated to lead to epithelial dysplasia, DNA damage, and eventually cancer. There are approximately 18% of patients with UC may develop CRC. Patients and methods The gene expression profiles were retrieved from the Gene Expression Omnibus. The Database for Annotation, Visualization and Integrated Discovery was employed to conduct gene annotations. Protein-protein interaction network was constructed by the Search Tool for the Retrieval of Interacting Genes, and further analysed by the Molecular Complex Detection. The correlation between TIMP1 and prognosis was evaluated by the Gene Expression Profiling Interactive Analysis. To predict the potential functions of TIMP1, the GeneMANIA, Coremine, and FunRich were employed. After transfection with small interfering RNA targeting TIMP1, cell proliferation, migration, and apoptosis were determined by CCK-8, scratch wound, and Annexin V-FITC/PI assays, respectively. Results TIMP1, consistently overexpressed in the initiation and progression of UC-associated CRC (ucaCRC), was identified to be a potential biomarker for the prognosis of patients with CRC. Experimental results showed knockdown of TIMP1 could increase the migration, while did not affect the proliferation and apoptosis of RKO cells. The role of TIMP1 in the malignant transformation of ucaCRC was confirmed by using the protein/gene interactions and biological process annotation and validated by analysing the transcription factors targeting TIMP1. Conclusion TIMP1 is consistently upregulated in the pathological process of ucaCRC and can be a potential biomarker for the worse prognosis of CRC.
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Affiliation(s)
- Ru Huang
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kaijing Wang
- Department of Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Lei Gao
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Wei Gao
- Department of Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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Lebedev TD, Vagapova ER, Popenko VI, Leonova OG, Spirin PV, Prassolov VS. Two Receptors, Two Isoforms, Two Cancers: Comprehensive Analysis of KIT and TrkA Expression in Neuroblastoma and Acute Myeloid Leukemia. Front Oncol 2019; 9:1046. [PMID: 31681584 PMCID: PMC6813278 DOI: 10.3389/fonc.2019.01046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/26/2019] [Indexed: 01/04/2023] Open
Abstract
Pediatric cancers represent a wide variety of different tumors, though they have unique features that distinguish them from adult cancers. Receptor tyrosine kinases KIT and TrkA functions in AML and NB, respectively, are well-characterized. Though expression of these receptors is found in both tumors, little is known about KIT function in NB and TrkA in AML. By combining gene enrichment analysis with multidimensional scaling we showed that pediatric AMLs with t(8;21) or inv16 and high KIT expression levels stand out from other AML subtypes as they share prominent transcriptomic features exclusively with KIT-overexpressing NBs. We showed that AML cell lines had a predominant expression of an alternative TrkAIII isoform, which reportedly has oncogenic features, while NB cell lines had dominating TrkAI-II isoforms. NB cells, on the other hand, had an abnormal ratio of KIT isoforms as opposed to AML cells. Both SCF and NGF exerted protective action against doxorubicin and cytarabine for t(8;21) AML and NB cells. We identified several gene sets both unique and common for pediatric AML and NB, and this expression is associated with KIT or TrkA levels. NMU, DUSP4, RET, SUSD5, NOS1, and GABRA5 genes are differentially expressed in NBs with high KIT expression and are associated with poor survival in NB. We identified HOXA10, BAG3, and MARCKS genes that are connected with TrkA expression and are marker genes of poor outcome in AML. We also report that SLC18A2, PLXNC1, and MRPL33 gene expression is associated with TrkA or KIT expression levels in both AML and NB, and these genes have a prognostic value for both cancers. Thus, we have provided a comprehensive characterization of TrkA and KIT expression along with the oncogenic signatures of these genes across two pediatric tumors.
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Affiliation(s)
- Timofey D Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Elmira R Vagapova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Vladimir I Popenko
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Olga G Leonova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Pavel V Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Vladimir S Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
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Przygodzka P, Soboska K, Sochacka E, Boncela J. Neuromedin U: A Small Peptide in the Big World of Cancer. Cancers (Basel) 2019; 11:cancers11091312. [PMID: 31492042 PMCID: PMC6770777 DOI: 10.3390/cancers11091312] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/19/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Neuromedin U (NMU), a neuropeptide isolated from porcine spinal cord and named because of its activity as a rat uterus smooth muscle contraction inducer, is emerging as a new player in the tumorigenesis and/or metastasis of many types of cancers. Expressed in a variety of tissues, NMU has been shown to possess many important activities in the central nervous system as well as on the periphery. Along with the main structural and functional features of NMU and its currently known receptors, we summarized a growing number of recently published data from different tissues and cells that associate NMU activity with cancer development and progression. We ask if, based on current reports, NMU can be included as a marker of these processes and/or considered as a therapeutic target.
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Affiliation(s)
- Patrycja Przygodzka
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str, 93-232 Lodz, Poland.
| | - Kamila Soboska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str, 93-232 Lodz, Poland
- Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska Str, 90-236 Lodz, Poland
| | - Ewelina Sochacka
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str, 93-232 Lodz, Poland
- Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska Str, 90-236 Lodz, Poland
| | - Joanna Boncela
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str, 93-232 Lodz, Poland.
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Tu J, Chen J, He M, Tong H, Liu H, Zhou B, Liao Y, Wang Z. Bioinformatics analysis of molecular genetic targets and key pathways for hepatocellular carcinoma. Onco Targets Ther 2019; 12:5153-5162. [PMID: 31303768 PMCID: PMC6612290 DOI: 10.2147/ott.s198802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second leading cause of death among cancers worldwide. In this study, we aimed to identify the molecular target genes and detect the key mechanisms of HCC. Three gene expression profiles (GSE84006, GSE14323, GSE14811) and two miRNA expression profiles (GSE40744, GSE36915) were analyzed to determine the molecular target genes, microRNAs (miRNAs) and the potential molecular mechanisms in HCC. Methods All profiles were extracted from the Gene Expression Omnibus database. The identification of the differentially expressed genes (DEGs) was analyzed by the GEO2R method. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO) enrichment analysis performed database for Integrated Discovery, Visualization and Annotation. The miRNA-gene network and protein–protein interaction (PPI) network were correlated by the Cytoscape software. The key target genes were identified by the CytoHubba plugin, Molecular Complex Detection (MCODE) plugin and miRNA-gene network. The identified hub genes were testified for survival curve using the Kaplan–Meier plotter database. Results Expression profiles had 592 overlapped DEGs. The majority of the DEGs were enriched in membrane-bounded organelles and intracellular membrane-bounded organelles. These DEGs were significantly enriched in metabolic, protein processing in the endoplasmic reticulum and thyroid cancer pathways. PPI network analysis showed these genes were mostly involved in the pathogenic Escherichia coli infection and the regulation of actin cytoskeleton pathways. Combining these results, we identified 10 key genes involving in the progression of HCC. Finally, PLK1, PRCC, PRPF4 and PSMA7 exhibited higher expression levels in HCC patients with poor prognosis than those for lower expression via Kaplan–Meier plotter database. Conclusion PLK1, PRCC, PRPF4 and PSMA7 could be potential biomarkers or therapeutic targets for HCC. Meanwhile, the metabolic pathway, protein processing in the endoplasmic reticulum and the thyroid cancer pathway may play vital roles in the progression of HCC.
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Affiliation(s)
- Junxue Tu
- Department of Pharmacy, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Jingjing Chen
- Department of Breast Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Meimei He
- Department of Pharmacy, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Hongfei Tong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Haibin Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Bin Zhou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Yi Liao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Zhaohong Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
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