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Sultana S, Banerjee P, Ganai I, Laha A, Sultana N, Biswas H, Saha NC, Moitra S, Podder S. Polymorphism in ADAM33 gene associated with asthmatics in West Bengal, India - An investigation by in-silico analysis. World Allergy Organ J 2023; 16:100834. [PMID: 38020285 PMCID: PMC10663682 DOI: 10.1016/j.waojou.2023.100834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Asthma is one of the common chronic polygenic inflammatory diseases. Genome wide association studies have identified ADAM33 as an asthma candidate gene. The present study investigated possible association of rs2280090 (T1), rs2280091 (T2) and rs3918396 (S1) single nucleotide polymorphisms (SNPs) of ADAM33 with aeroallergen induced asthma in West Bengal population, India. In addition, in-silico analysis was performed to find out changes in protein function. Methods Forced expiratory volume in 1 second (FEV1)/Forced vital capacity (FVC), peak expiratory flow rate (PEFR) were assessed using spirometry in 1039 participants. Allergic sensitivity of 619 spirometry positive asthma patients was assessed by skin prick test (SPT) against 22 aeroallergens. For genotyping of T1, T2, and S1 SNPs in 540 allergic asthma patient and 420 control subjects, polymerase chain reaction-based restriction fragment length polymorphism was performed. Total Immunoglobulin-E (IgE) level was measured in both patients and controls. ADAM333 haplotype blocks were constructed using Haploview software v.4.2. Structural model of transmembrane and cytoplasmic domains of ADAM33 was generated using RaptorX. Protein-protein interaction was analysed using the STRING server. Results Highest number of patient sensitivity was observed towards Cocos nusifera (n = 215) and Dermatophagoides farinae (n = 229). Significant difference in sensitivity was observed between child and late adult (P = 0.03), child and early adult (P = 0.02), adolescent and late adult (P = 0.02) and adolescent and early adult (P = 0.01). Genotypic frequencies differed significantly between patients and controls (P < 0.05). rs2280090 GG, rs2280091GG and AG genotype, and rs3918396 AA carried significant risk for asthma (P = 0.02, P = 0.008, P = 0.04, P = 0.01 respectively). ADAM33 T1, T2, and S1 polymorphisms were in high Linkage Disequilibrium (D = 0.98). Haplotype consisting of rs2280090G, rs2280091G and rs3918396A alleles were found significantly higher in patient population in comparison with controls (OR = 2.03). IgE level differed significantly among different genotypes for T1, T2, and S1 SNPs analysed in pair (P < 0.0001). FEV1/FVC ratio differed significantly among different genotypes for T1, T2 and S1 SNPs analysed in pair (P < 0.0001). Significant difference of FEV1/FVC was also found between GGA and AAG haplotype (P < 0.0001). In-silico analysis revealed T1 and T2 polymorphisms are located in cytoplasmic domain of ADAM33 may cause bronchial smooth muscle cell mobility and cellular hyperplasia as well as cytoskeletal remodelling by altered interaction with different cytoplasmic proteins found by string analysis. Conclusion Present study showed significant association of T1, T2, and S1 polymorphisms of ADAM33 with aeroallergen-induced asthma in West Bengal, India. These polymorphisms may be used as prognostic markers and possible targets for therapeutics in future.
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Affiliation(s)
- Saheen Sultana
- Ecology and Allergology Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Priyajit Banerjee
- Fishery and Eco-toxicology Research Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Indranil Ganai
- Ecology and Allergology Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Arghya Laha
- Ecology and Allergology Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Nasima Sultana
- Ecology and Allergology Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Himani Biswas
- Post Graduate Department of Zoology, Krishnagar Government College, Krishnagar, West Bengal, 741101, India
| | - Nimai Chandra Saha
- Post Graduate Department of Zoology, Bidhannagar College, Kolkata, West Bengal-700064, India
| | - Saibal Moitra
- Apollo Multispecialty Hospitals, Kolkata, West Bengal, 700054, India
| | - Sanjoy Podder
- Ecology and Allergology Lab, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
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Yan L, Zheng J, Pan Q, Liang Y, Yu P, Chen Q. Novel PPFIA1- ALK, ALK- C2orf91(intergenic) double-fusion responded well to alectinib in an advanced lung adenocarcinoma patient: a case report. Front Oncol 2023; 13:1264820. [PMID: 37706178 PMCID: PMC10497211 DOI: 10.3389/fonc.2023.1264820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023] Open
Abstract
Non-small cell lung cancers (NSCLCs) with anaplastic lymphoma kinase (ALK)-rearrangement have favorable responses to ALK inhibitors. However, ALK fusion mutations harbored approximately 90 distinct fusion partners. Patients with different ALK fusions might respond distinctly to different-generation ALK inhibitors. In this case report, we identified a novel non-reciprocal ALK fusion, ALK-C2orf91(intergenic) (A19: intergenic) and PPFIA1-ALK (P2:A20), by next-generation DNA sequencing in an advanced lung adenocarcinoma patient. After 2 months of alectinib, the targeted lung lesion regressed significantly, and evaluation of therapeutic efficiency indicated partial response. To date, the patient had achieved 12 months of progression-free survival from alectinib treatment. Our study extended the spectrum of ALK fusion partners in ALK-positive NSCLC, and we reported a new ALK fusion, PPFIA1-ALK and ALK-C2orf91(intergenic), and its sensitivity to alectinib firstly in lung cancer. We believe that this case report has an important clinical reference.
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Affiliation(s)
- Lingxin Yan
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiayu Zheng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qingyun Pan
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuxian Liang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Pengli Yu
- Geneplus-Beijing Institute, Beijing, China
| | - Quanfang Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Gao Y, Guan L, Jia R, Xiao W, Han Y, Li Y, Tang P, Yu Z, Zhang H. High expression of PPFIA1 in human esophageal squamous cell carcinoma correlates with tumor metastasis and poor prognosis. BMC Cancer 2023; 23:417. [PMID: 37158817 PMCID: PMC10169376 DOI: 10.1186/s12885-023-10872-9] [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: 12/28/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND PTPRF interacting protein alpha 1 (PPFIA1) is reportedly related to the occurrence and progression of several kinds of malignancies. However, its role in esophageal squamous cell carcinoma (ESCC) is unclear. This current study investigated the prognostic significance and biological functions of PPFIA1 in ESCC. METHODS Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), and Gene Expression Omnibus (GEO) were used to investigate PPFIA1 expression in esophageal cancer. The relationship between PPFIA1 expression and clinicopathological characteristics and patient survival was evaluated in GSE53625 dataset, and verified in the cDNA array based on qRT-PCR and tissue microarray (TMA) dataset based on immunohistochemistry. The impact of PPFIA1 on the migration and invasion of cancer cells were investigated by wound-healing and transwell assays, respectively. RESULTS The expression of PPFIA1 was obviously increased in ESCC tissues versus adjacent esophageal tissues according to online database analyses (all P < 0.05). High PPFIA1 expression was closely related to several clinicopathological characteristics, including tumor location, histological grade, tumor invasion depth, lymph node metastasis, and tumor-node-metastasis (TNM) stage. High PPFIA1 expression was related to worse outcomes and was identified as an independent prognostic factor of overall survival in ESCC patients (GSE53625 dataset, P = 0.019; cDNA array dataset, P < 0.001; TMA dataset, P = 0.039). Downregulation of PPFIA1 expression can significantly reduce the migration and invasion ability of ESCC cells. CONCLUSION PPFIA1 is related to the migration and invasion of ESCC cells, and can be used as a potential biomarker to evaluate the prognosis of ESCC patients.
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Affiliation(s)
- Yongyin Gao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Lizhao Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ran Jia
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China
| | - Wanyi Xiao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Youming Han
- Binhai Hospital of Tianjin Medical University General Hospital, Tianjin, 300456, China
| | - Yue Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Peng Tang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China.
| | - Zhentao Yu
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China.
| | - Hongdian Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China.
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Chu J, Min KW, Kim DH, Son BK, Kim HS, Jung US, Kwon MJ, Do SI. High PPFIA1 expression promotes cancer survival by suppressing CD8+ T cells in breast cancer: drug discovery and machine learning approach. Breast Cancer 2023; 30:259-270. [PMID: 36478321 DOI: 10.1007/s12282-022-01419-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND PTPRF-interacting protein alpha 1 (PPFIA1) plays an important role as a regulator of cell motility and tumor cell invasion and is frequently amplified in breast cancer. The aim of this study was to investigate the clinicopathologic features, survival, anticancer immunities and specific gene sets related to high PPFIA1 expression in patients with breast cancer. We verified the importance of PPFIA1 and survival rates using machine learning and identified drugs that can effectively reduce breast cancer cells with high PPFIA1 expression. METHODS This study analyzed clinicopathologic factors, survival rates, immune profiles and gene sets according to PPFIA1 expression in 3457 patients with breast cancer from the Kangbuk Samsung Medical Center cohort (456 cases), Molecular Taxonomy of Breast Cancer International Consortium (1904 cases) and The Cancer Genome Atlas (1097 cases). We applied gene set enrichment analysis (GSEA), in silico cytometry, pathway network analyses, in vitro drug screening, and gradient boosting machine (GBM) analysis. RESULTS High PPFIA1 expression in breast cancer was associated with worse prognosis, with reduced tumor-infiltrating lymphocytes, especially CD8+ T cells, and increased PD-L1 expression. In pathway network analysis, PPFIA1 was linked directly to the tyrosine-protein phosphatase pathway and indirectly to immune pathways. The importance of PPFIA1's association with survival in GBM analysis was higher than that of perineural and lymphovascular invasion. In in vitro drug screening, expression of PPFIA1 on mRNA level positively correlated with sensitivity of cell lines to erlotinib. CONCLUSION High PPFIA1 in patients with breast cancer is related to poor prognosis and decreased anticancer immune response, and erlotinib may be promising for development of therapeutic approaches in patients with tumors overexpressing PPFIA1.
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Affiliation(s)
- Jinah Chu
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, 29 Saemunanro, Jongno-gu, Seoul, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea.
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, 29 Saemunanro, Jongno-gu, Seoul, Republic of Korea.
| | - Byoung Kwan Son
- Department of Internal Medicine, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu, Gyeonggi-do, Republic of Korea
| | - Hyung Suk Kim
- Division of Breast Surgery, Department of Surgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Un Suk Jung
- Department of Obstetrics and Gynecology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Gyeonggi-do, Republic of Korea
| | - Sung-Im Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, 29 Saemunanro, Jongno-gu, Seoul, Republic of Korea
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Fu F, Niu R, Zheng M, Yang X, Fan L, Fu W, Zhang S. Clinicopathological Significances and Prognostic Value of PPFIA4 in Colorectal Cancer. J Cancer 2023; 14:24-34. [PMID: 36605492 PMCID: PMC9809326 DOI: 10.7150/jca.78634] [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: 09/04/2022] [Accepted: 11/06/2022] [Indexed: 01/04/2023] Open
Abstract
Purpose: The PPFIA gene family (PPFIA1, PPFIA2, PPFIA3, and PPFIA4) is associated with multiple human diseases, particularly malignant tumors. However, the expression and prognostic value of the PPFIA family in human colorectal cancers (CRCs) have not been reported. Materials and methods: In this study, several databases, including Oncomine, UALCAN, and the cancer cell line encyclopedia, were used to compare differences in PPFIA1, PPFIA2, PPFIA3, and PPFIA4 expression between normal colon samples and CRCs. The expression levels of these four proteins were used to evaluate the survival of patients with CRC, as determined by the Cancer Genome Atlas Program (TCGA) portal and gene expression profiling interactive analysis (GEPIA) databases. Western blotting and reverse transcription-polymerase chain reaction were performed to detect protein and mRNA levels of PPFIA1, PPFIA3, and PPFIA4, respectively. Immunohistochemical (IHC) staining was used to detect the correlation between PPFIA4 expression and the degree of CRC malignancy. Furthermore, potential miRNAs targeting PPFIA4 in CRCs were studied and confirmed. Results: Bioinformatic analysis showed that the mRNA levels of PPFIA1, PPFIA3, and PPFIA4 were higher in CRC tissue samples than in normal colon tissue. Both mRNA and protein expression of PPFIA1, PPFIA3, and PPFIA4 were increased in the CRC cell lines LoVo and Hct116 compared with the normal colon epithelial cell line. Only PPFIA4 was associated with the prognosis of patients with CRC, which was confirmed by TCGA portal and GEPIA. IHC staining confirmed that the expression of PPFIA4 was higher in CRC tissues than in normal colon tissues and also increased in poorly differentiated CRC tissues and lymph node metastatic foci in comparison with well-differentiated CRC tissues and moderately differentiated CRC tissues. Functional annotation enrichment analysis indicated that the top 100 genes co-expressed with PPFIA4 were enriched in the G-protein coupled peptide receptor activity, leukotrience B4 receptor activity, and peroxisome proliferator-activated receptors and hypoxia-inducible factor-1 signaling pathways. In addition, miR-485-5p negatively regulates the expression of PPFIA4. Conclusion: PPFIA4 expression is associated with the development of CRCs and may be a novel potential prognostic marker for human CRCs.
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Affiliation(s)
- Fangmei Fu
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin, 300121, P.R. China
| | - Rui Niu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P.R. China
| | - Minying Zheng
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin, 300121, P.R. China
| | - Xiaohui Yang
- Nankai University School of Medicine, Nankai University, Tianjin, 300071, P.R. China
| | - Linlin Fan
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P.R. China
| | - Wenzheng Fu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin, 300121, P.R. China.,✉ Corresponding author: Shiwu Zhang, M.D., Ph.D., Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, China; Tel: (086)13652136865; Fax: (86)022-87721989; E-mail:
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Liprins in oncogenic signaling and cancer cell adhesion. Oncogene 2021; 40:6406-6416. [PMID: 34654889 PMCID: PMC8602034 DOI: 10.1038/s41388-021-02048-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022]
Abstract
Liprins are a multifunctional family of scaffold proteins, identified by their involvement in several important neuronal functions related to signaling and organization of synaptic structures. More recently, the knowledge on the liprin family has expanded from neuronal functions to processes relevant to cancer progression, including cell adhesion, cell motility, cancer cell invasion, and signaling. These proteins consist of regions, which by prediction are intrinsically disordered, and may be involved in the assembly of supramolecular structures relevant for their functions. This review summarizes the current understanding of the functions of liprins in different cellular processes, with special emphasis on liprins in tumor progression. The available data indicate that liprins may be potential biomarkers for cancer progression and may have therapeutic importance.
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Cao Z, Jin Z, Zeng L, He H, Chen Q, Zou Q, Ouyang D, Luo N, Zhang Y, Yuan Y, Yi W. Prognostic and tumor-immune infiltration cell signatures in tamoxifen-resistant breast cancers. Gland Surg 2021; 10:2766-2779. [PMID: 34733726 PMCID: PMC8514308 DOI: 10.21037/gs-21-566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND The cumulative risk of distant recurrence of hormone receptor-positive (HR+) breast cancer in the past 20 years has ranged from 22% to 52% after 5 years of endo-therapy. The TNM stage, histological grade, and age are important clinical factors related to recurrence, however the exact mechanism of tamoxifen resistance is still unclear. METHODS Differentially expressed genes (DEGs) were identified in 10 pairs of patients who had relapsed and non-relapsed after tamoxifen treatment based on matching their clinicopathological factors. After analysis of the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, 10 hub genes were identified using Cytoscape software. Next, real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database were used to verify the expression and overall survival (OS) of the 10 hub genes respectively, and GSE96058 and Kaplan-Meier Plotter website were used to further verify the OS of C3, CX3CL1, CXCL2, and SAA1. Finally, Immune Cell Abundance Identifier (ImmuCellAI) and the TIMER database were used to estimate immune cell infiltration and the expression of prognostic genes. RESULTS The DEGs were mainly enriched in the inflammatory response and cytokine-receptor interaction. The expression and the survival analysis identified CX3CL1, CXCL2, and SAA1 as prognostic factors, whose overexpression in HR+/human epidermal growth factor receptor 2 (HER-2) negative breast cancer possibly predicted a longer disease-free survival. The expression levels of these 3 genes are positively correlated with immune cell infiltration. Their high expression levels may predict longer disease-free survival in breast cancer after tamoxifen treatment and may be biomarkers for tamoxifen-resistant therapy. CONCLUSIONS In conclusion, the high expression of CX3CL1, CXCL2, and SAA1 may predict longer disease-free survival in breast cancer after tamoxifen treatment and may be a biomarker for tamoxifen therapy.
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Affiliation(s)
- Zhenyu Cao
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Ziwei Jin
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Liyun Zeng
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Hongye He
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Qitong Chen
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Qiongyan Zou
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Dengjie Ouyang
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Na Luo
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Yulong Zhang
- Department of Glandular Surgery, Baise People’s Hospital, Baise, China
| | - Yunchang Yuan
- Department of Thoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
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Han S, Zhu W, Yang W, Guan Q, Chen C, He Q, Zhong Z, Zhao R, Xiong H, Han H, Li Y, Sun Z, Hu X, Tian J. A Prognostic Signature Constructed by CTHRC1 and LRFN4 in Stomach Adenocarcinoma. Front Genet 2021; 12:646818. [PMID: 34512711 PMCID: PMC8427509 DOI: 10.3389/fgene.2021.646818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Stomach adenocarcinoma (STAD) is the most common histological type of stomach cancer, which causes a considerable number of deaths worldwide. This study aimed to identify its potential biomarkers with the notion of revealing the underlying molecular mechanisms. METHODS Gene expression profile microarray data were downloaded from the Gene Expression Omnibus (GEO) database. The "limma" R package was used to screen the differentially expressed genes (DEGs) between STAD and matched normal tissues. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for function enrichment analyses of DEGs. The STAD dataset from The Cancer Genome Atlas (TCGA) database was used to identify a prognostic gene signature, which was verified in another STAD dataset from the GEO database. CIBERSORT algorithm was used to characterize the 22 human immune cell compositions. The expression of LRFN4 and CTHRC1 in tissues was determined by quantitative real-time PCR from the patients recruited to the present study. RESULTS Three public datasets including 90 STAD patients and 43 healthy controls were analyzed, from which 44 genes were differentially expressed in all three datasets. These genes were implicated in biological processes including cell adhesion, wound healing, and extracellular matrix organization. Five out of 44 genes showed significant survival differences. Among them, CTHRC1 and LRFN4 were selected for construction of prognostic signature by univariate Cox regression and stepwise multivariate Cox regression in the TCGA-STAD dataset. The fidelity of the signature was evaluated in another independent dataset and showed a good classification effect. The infiltration levels of multiple immune cells between high-risk and low-risk groups had significant differences, as well as two immune checkpoints. TIM-3 and PD-L2 were highly correlated with the risk score. Multiple signaling pathways differed between the two groups of patients. At the same time, the expression level of LRFN4 and CTHRC1 in tissues analyzed by quantitative real-time PCR were consistent with the in silico findings. CONCLUSION The present study constructed the prognostic signature by expression of CTHRC1 and LRFN4 for the first time via comprehensive bioinformatics analysis, which provided the potential therapeutic targets of STAD for clinical treatment.
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Affiliation(s)
- Songling Han
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Changshu Qiushi Technology Co., Ltd., Suzhou, China
| | - Weili Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qijie Guan
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Chao Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang He
- Department of Nephrology, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Zhuoheng Zhong
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Ruoke Zhao
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Hangming Xiong
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Haote Han
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yaohan Li
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Zijian Sun
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Xingjiang Hu
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
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Masisi BK, El Ansari R, Alfarsi L, Craze ML, Jewa N, Oldfield A, Cheung H, Toss M, Rakha EA, Green AR. The Biological and Clinical Significance of Glutaminase in Luminal Breast Cancer. Cancers (Basel) 2021; 13:cancers13163963. [PMID: 34439127 PMCID: PMC8391318 DOI: 10.3390/cancers13163963] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/23/2021] [Accepted: 08/02/2021] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Certain nutrients are needed by cancers to grow. Some breast cancers need the nutrient glutamine to grow and without it they don’t grow as quickly. In this study, we wanted to know the role of an enzyme, glutaminase, which is a substance produced by the body that breaks down glutamine so it can be used by cancers to grow. This enzyme occurs as two different types but we don’t know what their roles are in breast cancer. We therefore looked at the two types of enzyme in over 7000 breast cancers. We found that patients with high amounts of enzyme in early forms of breast cancer died earlier. Therefore, this enzyme has an important role in breast cancer and could be used to identify cancers which will get worse. We also think that using a drug to stop this enzyme will stop cancers growing. More studies are needed to confirm this. Abstract The glutamine metabolism has a key role in the regulation of uncontrolled tumour growth. This study aimed to evaluate the expression and prognostic significance of glutaminase in luminal breast cancer (BC). The glutaminase isoforms (GLS/GLS2) were assessed at genomic/transcriptomic levels, using METABRIC (n = 1398) and GeneMiner datasets (n = 4712), and protein using immunohistochemistry in well-characterised cohorts of Oestrogen receptor-positive/HER2-negative BC patients: ductal carcinoma in situ (DCIS; n = 206) and invasive breast cancer (IBC; n = 717). Glutaminase expression was associated with clinicopathological features, patient outcome and glutamine-metabolism-related genes. In DCIS, GLS alone and GLS+/GLS2- expression were risk factors for shorter local recurrence-free interval (p < 0.0001 and p = 0.001, respectively) and remained prognostic factors independent of tumour size, grade and comedo necrosis (p = 0.0008 and p = 0.003, respectively). In IBC, GLS gene copy number gain with high mRNA expression was associated with poor patient outcome (p = 0.011), whereas high GLS2 protein was predictive of a longer disease-free survival (p = 0.006). Glutaminase plays a role in the biological function of luminal BC, particularly GLS in the early non-invasive stage, which could be used as a potential biomarker to predict disease progression and a target for inhibition. Further validation is required to confirm these observations, and functional assessments are needed to explore their specific roles.
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Affiliation(s)
- Brendah K. Masisi
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Rokaya El Ansari
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Lutfi Alfarsi
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Madeleine L. Craze
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Natasha Jewa
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Andrew Oldfield
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Hayley Cheung
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Michael Toss
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
| | - Emad A. Rakha
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
- Cellular Pathology, Nottingham University Hospitals NHS Trust, Hucknall Road, Nottingham NG5 1PB, UK
| | - Andrew R. Green
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (B.K.M.); (R.E.A.); (L.A.); (M.L.C.); (N.J.); (A.O.); (H.C.); (M.T.); (E.A.R.)
- Correspondence: ; Tel.: +44-1158231407
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Li F, Zhang W, Wang M, Jia P. IL1RAP regulated by PRPRD promotes gliomas progression via inducing neuronal synapse development and neuron differentiation in vitro. Pathol Res Pract 2020; 216:153141. [PMID: 32829106 DOI: 10.1016/j.prp.2020.153141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Glioma is a common fatal brain tumor that affects the central nervous system of the brain and spinal cord. METHODS This is an original research. The morphology of M059 J cells and U373 cells were detected by microscope, cell neurite outgrowth was observed by immunofluorescence, and the expression of PRPRD and its downstream genes in HMC3 cells, M059 J cells and U373 cells were evaluated and compared with flow cytometry, immunofluorescence and Western blotting assay. RESULTS Here we show that the expression of FBP17 on the surface of glioma cells M059 J and U373 cells is more than normal cells. Overexpression of protein tyrosine phosphatase receptor-δ (PTPRD) in M059 J and U373 cells resulted in a significant increase in the S phase of the cells, while the G2 phase of the cells decreased significantly after interference with PTPRD. And PTPRD protein is mainly distributed in HMC3 cells, M059 J and U373 cytoplasm. Moreover, overexpression of PTPRD resulted in a significant increase in the expression of interleukin 1 receptor accessory protein (IL1RAP), PPFIA1 and SLITRK2, and these genes were significantly suppressed after interference with PTPRD. CONCLUSION This study shows that PRPRD can be used as a potential biomarker for glioma treatment. These results indicate that the PRPRD protein affects the development of neuronal synapses and neuronal differentiation by regulating IL1RAP, thereby promoting the progression of gliomas, indicating that PRPRD can be used as a potential biomarker for the treatment of gliomas.
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Affiliation(s)
- Feng Li
- Department of Neurosurgery, Rui Jin Hospital North, Shanghai Jiao Tong University School of Medicine, No.999, Xi Wang Road, Jia Ding District, Shanghai, 201801, China
| | - Weifeng Zhang
- Department of Neurosurgery, Rui Jin Hospital North, Shanghai Jiao Tong University School of Medicine, No.999, Xi Wang Road, Jia Ding District, Shanghai, 201801, China
| | - Ming Wang
- Department of Neurosurgery, Rui Jin Hospital North, Shanghai Jiao Tong University School of Medicine, No.999, Xi Wang Road, Jia Ding District, Shanghai, 201801, China
| | - Pifeng Jia
- Department of Neurosurgery, Rui Jin Hospital North, Shanghai Jiao Tong University School of Medicine, No.999, Xi Wang Road, Jia Ding District, Shanghai, 201801, China.
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