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Pan R, Zhang Y, Cheng Y, Wu Z, Liu J, Chen Z, Wang J, Zhang X, Wang H, Feng S, Zheng X. Identification of UNC5B as a novel aggressive biomarker for osteosarcoma based on basement membrane genes. Gene 2024; 930:148871. [PMID: 39154972 DOI: 10.1016/j.gene.2024.148871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/27/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND The prognosis of patients with metastatic osteosarcoma is poor, and the variation of basement membrane genes (BMGs) is associated with cancer metastasis. However, the role of BMGs in osteosarcoma has been poorly studied. METHODS BMGs were collected and differentially expressed BMGs (DE-BMGs) were found through difference analysis. DE-BMGs were further screened by univariate Cox regression and Lasso regression analyses, and six key BMGs were identified and defined as basement membrane genes signatures (BMGS). Then, BMGS was used to construct the osteosarcoma BMGS risk score system, and the osteosarcoma patients were divided into high- and low-risk groups based on the median risk score. Single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE scores were used to investigate the differences in immune infiltration between the two scoring groups. Additionally, we investigated whether UNC5B affects various features in tumors by bioinformatic analysis and whether UNC5B was involved in multiple biological functions of osteosarcoma cells by wound healing assay, transwell assay, and western blot. RESULTS The osteosarcoma BMGS risk score reliably predicts the risk of metastasis, patient prognosis, and immunity. UNC5B expression was elevated in osteosarcoma, and correlated with various characteristics such as immune infiltration, prognosis, and drug sensitivity. In vitro assays showed that UNC5B knockdown reduced osteosarcoma cells' capacity for migration and invasion, and EMT process. CONCLUSION A novel BMGS risk score system that can effectively predict the prognosis of osteosarcoma was developed and validated. The UNC5B gene in this system is one of the key aggressive biomarkers of osteosarcoma.
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Affiliation(s)
- Ruilin Pan
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Yiming Zhang
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Yanmei Cheng
- Department of Cardiothoracic Surgery ICU, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zelin Wu
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Jin Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Zihang Chen
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China; Department of Psychology, Li Ka Shing Faculty of Medicine, State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China
| | - Jinghao Wang
- Department of Pharmacy, The First Affiliated Hospital, State Key Laboratory of Frigid Zone Cardiovascular Diseases, Science and Technology Planning Project of Guangzhou, Jinan University, Guangzhou, China
| | - Xiaofang Zhang
- Department of Pharmacy, The First Affiliated Hospital, State Key Laboratory of Frigid Zone Cardiovascular Diseases, Science and Technology Planning Project of Guangzhou, Jinan University, Guangzhou, China
| | - Huajun Wang
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China.
| | - Shanshan Feng
- Key Laboratory of Regenerative Medicine, Ministry of Education, The Ministry of Science and Technology & Guangdong Province, Department of Developmental and Regenerative Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, International Base of Collaboration for Science and Technology (JNU), institute of Aging and Regenerative Medicine, School of Life Science & Technology, Jinan University, Guangzhou 510632, China.
| | - Xiaofei Zheng
- Department of Sports Medicine, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Speed Capability, The Guangzhou Key Laboratory of Precision Orthopedics and Regenerative Medicine, Jinan University, Guangzhou, China.
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Li X, Jin Y, Xue J. Unveiling Collagen's Role in Breast Cancer: Insights into Expression Patterns, Functions and Clinical Implications. Int J Gen Med 2024; 17:1773-1787. [PMID: 38711825 PMCID: PMC11073151 DOI: 10.2147/ijgm.s463649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/21/2024] [Indexed: 05/08/2024] Open
Abstract
Collagen, the predominant protein constituent of the mammalian extracellular matrix (ECM), comprises a diverse family of 28 members (I-XXVIII). Beyond its structural significance, collagen is implicated in various diseases or cancers, notably breast cancer, where it influences crucial cellular processes including proliferation, metastasis, apoptosis, and drug resistance, intricately shaping cancer progression and prognosis. In breast cancer, distinct collagens exhibit differential expression profiles, with some showing heightened or diminished levels in cancerous tissues or cells compared to normal counterparts, suggesting specific and pivotal biological functions. In this review, we meticulously analyze the expression of individual collagen members in breast cancer, utilizing Transcripts Per Million (TPM) data sourced from the GEPIA2 database. Through this analysis, we identify collagens that deviate from normal expression patterns in breast cancer, providing a comprehensive overview of their expression dynamics, functional roles, and underlying mechanisms. Our findings shed light on recent advancements in understanding the intricate interplay between these aberrantly expressed collagens and breast cancer. This exploration aims to offer valuable insights for the identification of potential biomarkers and therapeutic targets, thereby advancing the prospects of more effective interventions in breast cancer treatment.
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Affiliation(s)
- Xia Li
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou, People’s Republic of China
| | - Yue Jin
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou, People’s Republic of China
| | - Jian Xue
- Department of Emergency Medicine, Yizheng People’s Hospital, Yangzhou, People’s Republic of China
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Zhu X, Wang F, Wang M, Lv L, Fang L, Song J, Wang X, Ding F. Development of a breast cancer prognostic model based on vesicle-mediated transport-related genes to predict immune landscape and clinical drug therapy. Hum Mol Genet 2024; 33:553-562. [PMID: 38129105 DOI: 10.1093/hmg/ddad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Vesicle-mediated transport, vital for substance exchange and intercellular communication, is linked to tumor initiation and progression. This work was designed to study the role of vesicle-mediated transport-related genes (VMTRGs) in breast cancer (BC)prognosis. METHODS Univariate Cox analysis was utilized to screen prognosis-related VMTRGs. BC samples underwent unsupervised clustering based on VMTRGs to analyze survival, clinical factors, and immune cell abundance across different subtypes. We constructed a risk model using univariate Cox and LASSO regression analysis, with validation conducted using GEO datasets. Subsequently, we performed tumor mutational burden analysis, and immune landscape analysis on both groups. Ultimately, we conducted immunophenoscore (IPS) scoring to forecast immunotherapy and performed drug sensitivity analysis. RESULTS We identified 102 VMTRGs associated with BC prognosis. Using these 102 VMTRGs, BC patients were classified into 3 subtypes, with Cluster3 patients showing significantly better survival rates. We constructed a prognostic model for BC based on 12 VMTRGs that effectively predicted patient survival. Riskscore was an independent prognostic factor for BC patients. According to median risk score, high-risk group (HRG) had higher TMB values. The immune landscape of the HRG exhibited characteristics of cold tumor, with higher immune checkpoint expression levels and lower IPS scores, whereas Gemcitabine, Nilotinib, and Oxaliplatin were more suitable for treating low-risk group. CONCLUSION We classified BC subtypes and built a prognostic model based on VMTRGs. The genes in the prognostic model may serve as potential targets for BC therapy.
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Affiliation(s)
- Xiaotao Zhu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Fan Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Mingzhen Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Lin Lv
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Linghui Fang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Xiaohui Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
| | - Fengsheng Ding
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Rd, Jinhua, Zhejiang 321000, China
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4
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Wang Q, Zhang W, Guo Y, Shi F, Li Y, Kong Y, Lyu J, Wang S. A mutational signature and significantly mutated driver genes associated with immune checkpoint inhibitor response across multiple cancers. Int Immunopharmacol 2023; 116:109821. [PMID: 36753986 DOI: 10.1016/j.intimp.2023.109821] [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: 11/18/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/08/2023]
Abstract
Immune checkpoint inhibitor (ICI) treatments dramatically prolong the survival outcomes of several advanced cancers. However, as multiple studies reported, only a subset of patients could benefit from the ICI treatment. In this study, we aim to uncover novel molecular biomarkers predictive of immunotherapy efficacy across multiple cancers. Pre-treatment somatic mutational profiles and immunotherapy clinical information were obtained from 1097 samples of multiple cancers, including melanoma, non-small cell lung cancer (NSCLC), clear cell renal cell carcinoma (ccRCC), bladder carcinoma (BLCA), and head and neck squamous cell carcinoma (HNSCC). Mutational signatures, molecular subtypes, and significantly mutated genes (SMGs) were determined, and their connections with ICI response and outcome were also evaluated. We extracted a total of six mutational signatures across all samples. Among, a mutational signature featured by T > C substitutions was identified to associate with an ICI resistance. A molecular subtype determined based on mutational activities was connected with a significantly improved ICI response rate and outcome. Totaling 50 SMGs were identified, and we observed that patients with COL11A1 or COL4A6 mutations exhibited a superior ICI treatment efficacy than those without such mutations. In this study, we uncovered several novel molecular determinants of cancer immunotherapy response under a multiple-cancer setting, which provides clues for enrolling patients to receive immunotherapy and customizing personalized treatment strategies.
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Affiliation(s)
- Qinghua Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China.
| | - Wenjing Zhang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuxian Guo
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Fuyan Shi
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuting Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yujia Kong
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Juncheng Lyu
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Suzhen Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
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Feng J, Xu L, Zhang S, Geng L, Zhang T, Yu Y, Yuan R, He Y, Nan Z, Lin M, Guo H. A robust CD8+ T cell-related classifier for predicting the prognosis and efficacy of immunotherapy in stage III lung adenocarcinoma. Front Immunol 2022; 13:993187. [PMID: 36119068 PMCID: PMC9471021 DOI: 10.3389/fimmu.2022.993187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with stage III lung adenocarcinoma (LUAD) have significant survival heterogeneity, meanwhile, CD8+ T cell has a remarkable function in immunotherapy. Therefore, developing novel biomarkers based on CD8+ T cell can help evaluate the prognosis and guide the strategy of immunotherapy for patients with stage III LUAD. Thus, we abstracted twelve datasets from multiple online databases and grouped the stage III LUAD patients into training and validation sets. We then used WGCNA and CIBERSORT, while univariate Cox analysis, LASSO analysis, and multivariate Cox analysis were performed. Subsequently, a novel CD8+ T cell-related classifier including HDFRP3, ARIH1, SMAD2, and UPB1 was developed, which could divide stage III LUAD patients into high- and low-risk groups with distinct survival probability in multiple cohorts (all P < 0.05). Moreover, a robust nomogram including the traditional clinical parameters and risk signature was constructed, and t-ROC, C-index, and calibration curves confirmed its powerful predictive capacity. Besides, we detected the difference in immune cell subpopulations and evaluated the potential benefits of immunotherapy between the two risk subsets. Finally, we verified the correlation between the gene expression and CD8+ T cells included in the model by immunohistochemistry and validated the validity of the model in a real-world cohort. Overall, we constructed a robust CD8+ T cell-related risk model originally which could predict the survival rates in stage III LUAD. What’s more, this model suggested that patients in the high-risk group could benefit from immunotherapy, which has significant implications for accurately predicting the effect of immunotherapy and evaluating the prognosis for patients with stage III LUAD.
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Affiliation(s)
- Jinteng Feng
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Longwen Xu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shirong Zhang
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Luying Geng
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tian Zhang
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yang Yu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Rui Yuan
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yusheng He
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhuhui Nan
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Min Lin
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Ministry of Education of China (MOE), Xi’an, China
| | - Hui Guo
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education of China (MOE), Xi’an, China
- *Correspondence: Hui Guo,
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Huang KS, Wang YT, Byadgi O, Huang TY, Tai MH, Shaw JF, Yang CH. Screening of Specific and Common Pathways in Breast Cancer Cell Lines MCF-7 and MDA-MB-231 Treated with Chlorophyllides Composites. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123950. [PMID: 35745070 PMCID: PMC9229827 DOI: 10.3390/molecules27123950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
Our previous findings have shown that the chlorophyllides composites have anticancer activities to breast cancer cell lines (MCF-7 and MDA-MB-231). In the present study, microarray gene expression profiling was utilized to investigate the chlorophyllides anticancer mechanism on the breast cancer cells lines. Results showed that chlorophyllides composites induced upregulation of 43 and 56 differentially expressed genes (DEG) in MCF-7 and MDA-MB-231 cells, respectively. In both cell lines, chlorophyllides composites modulated the expression of annexin A4 (ANXA4), chemokine C-C motif receptor 1 (CCR1), stromal interaction molecule 2 (STIM2), ethanolamine kinase 1 (ETNK1) and member of RAS oncogene family (RAP2B). Further, the KEGG annotation revealed that chlorophyllides composites modulated DEGs that are associated with the endocrine system in MCF-7 cells and with the nervous system in MDA-MB-231 cells, respectively. The expression levels of 9 genes were validated by quantitative reverse transcription PCR (RT-qPCR). The expression of CCR1, STIM2, ETNK1, MAGl1 and TOP2A were upregulated in both chlorophyllides composites treated-MCF-7 and MDA-MB-231 cells. The different expression of NLRC5, SLC7A7 and PKN1 provided valuable information for future investigation and development of novel cancer therapy.
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Affiliation(s)
- Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan;
| | - Yi-Ting Wang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Omkar Byadgi
- International College, International Program in Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan;
| | - Ting-Yu Huang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Mi-Hsueh Tai
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Jei-Fu Shaw
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
- Correspondence: (J.-F.S.); (C.-H.Y.); Tel.: +886-7-6151100 (ext. 7310) (J.-F.S.); +886-7-6151100 (ext. 7312) (C.-H.Y.); Fax: +886-7-6151959 (J.-F.S. & C.-H.Y.)
| | - Chih-Hui Yang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
- Pharmacy Department, E-Da Hospital, No. 1, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Taipei City 106214, Taiwan
- Correspondence: (J.-F.S.); (C.-H.Y.); Tel.: +886-7-6151100 (ext. 7310) (J.-F.S.); +886-7-6151100 (ext. 7312) (C.-H.Y.); Fax: +886-7-6151959 (J.-F.S. & C.-H.Y.)
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7
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Qian Y, Zhai E, Chen S, Liu Y, Ma Y, Chen J, Liu J, Qin C, Cao Q, Chen J, Cai S. Single-cell RNA-seq dissecting heterogeneity of tumor cells and comprehensive dynamics in tumor microenvironment during lymph nodes metastasis in gastric cancer. Int J Cancer 2022; 151:1367-1381. [PMID: 35716132 DOI: 10.1002/ijc.34172] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 12/24/2022]
Abstract
Lymph node metastasis is the common metastasis route of gastric cancer. However, until now, heterogeneities of tumor cells and tumor microenvironment in primary tumors (PT) and metastatic lymph nodes (MLN) of gastric cancer (GC) remains uncharacterized. In this study, scRNA-seq was performed on tissues from PT and MLN of gastric cancer. Trajectory analysis and function enrichment analyses were conducted to decode the underlying mechanisms contributing to LN metastasis of gastric cancer. Heterogeneous composition of immune cells and distant intercellular interactions in PT and MLN were analyzed. Based on the generated single cell transcriptome profiles, dynamics of gene expressions in cancer cells between PT and MLN were characterized. Moreover, we reconstructed the developmental trajectory of GC cells' metastasis to LN and identified two sub-types of GC cells with distinct potentials of having malignant biological behaviors. We characterized the repression of neutrophil polarization associated genes, like LCN2, which would contribute to LN metastasis, and histochemistry experiments validated our findings. Additionally, heterogeneity in neutrophils, rather than macrophages, was characterized. Immune checkpoint associated interaction of SPP1 was found active in MLN. In conclusion, we decode the dynamics of tumor cells during LN metastasis in GC and to identify a sub-type of GC cells with potentials of LN metastasis. Our data indicated that the disordering the neutrophils polarization and maturation and the activation of immune checkpoint SPP1 might contribute to LN metastasis in GC, providing a novel insight on the mechanism and potential therapeutic targets of LN metastasis in GC. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yan Qian
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ertao Zhai
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sile Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinan Liu
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Ma
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junting Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianqiu Liu
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | - Qin Cao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jianhui Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shirong Cai
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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8
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Rius FE, Papaiz DD, Azevedo HFZ, Ayub ALP, Pessoa DO, Oliveira TF, Loureiro APM, Andrade F, Fujita A, Reis EM, Mason CE, Jasiulionis MG. Genome-wide promoter methylation profiling in a cellular model of melanoma progression reveals markers of malignancy and metastasis that predict melanoma survival. Clin Epigenetics 2022; 14:68. [PMID: 35606887 PMCID: PMC9128240 DOI: 10.1186/s13148-022-01291-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
The epigenetic changes associated with melanoma progression to advanced and metastatic stages are still poorly understood. To shed light on the CpG methylation dynamics during melanoma development, we analyzed the methylome profiles of a four-stage cell line model of melanoma progression: non-tumorigenic melanocytes (melan-a), premalignant melanocytes (4C), non-metastatic melanoma cells (4C11−), and metastatic melanoma cells (4C11+). We identified 540 hypo- and 37 hypermethylated gene promoters that together characterized a malignancy signature, and 646 hypo- and 520 hypermethylated promoters that distinguished a metastasis signature. Differentially methylated genes from these signatures were correlated with overall survival using TCGA-SKCM methylation data. Moreover, multivariate Cox analyses with LASSO regularization identified panels of 33 and 31 CpGs, respectively, from the malignancy and metastasis signatures that predicted poor survival. We found a concordant relationship between DNA methylation and transcriptional levels for genes from the malignancy (Pyroxd2 and Ptgfrn) and metastasis (Arnt2, Igfbp4 and Ptprf) signatures, which were both also correlated with melanoma prognosis. Altogether, this study reveals novel CpGs methylation markers associated with malignancy and metastasis that collectively could improve the survival prediction of melanoma patients.
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Affiliation(s)
- Flávia E Rius
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Debora D Papaiz
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Hatylas F Z Azevedo
- Divisão de Urologia, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Luísa P Ayub
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Diogo O Pessoa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago F Oliveira
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, São Paulo, Brazil.,Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula M Loureiro
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Andrade
- Bioinformatics Graduate Program, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil.,Department of Biology, Loyola University Chicago, Chicago, USA
| | - André Fujita
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Eduardo M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, USA
| | - Miriam G Jasiulionis
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, 04039-032, Brazil.
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Pagnotti GM, Trivedi T, Mohammad KS. Translational Strategies to Target Metastatic Bone Disease. Cells 2022; 11:1309. [PMID: 35455987 PMCID: PMC9030480 DOI: 10.3390/cells11081309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Metastatic bone disease is a common and devastating complication to cancer, confounding treatments and recovery efforts and presenting a significant barrier to de-escalating the adverse outcomes associated with disease progression. Despite significant advances in the field, bone metastases remain presently incurable and contribute heavily to cancer-associated morbidity and mortality. Mechanisms associated with metastatic bone disease perpetuation and paralleled disruption of bone remodeling are highlighted to convey how they provide the foundation for therapeutic targets to stem disease escalation. The focus of this review aims to describe the preclinical modeling and diagnostic evaluation of metastatic bone disease as well as discuss the range of therapeutic modalities used clinically and how they may impact skeletal tissue.
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Affiliation(s)
- Gabriel M. Pagnotti
- Department of Endocrine, Neoplasia and Hormonal Disorders, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA; (G.M.P.); (T.T.)
| | - Trupti Trivedi
- Department of Endocrine, Neoplasia and Hormonal Disorders, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA; (G.M.P.); (T.T.)
| | - Khalid S. Mohammad
- Department of Anatomy and Genetics, Alfaisal University, Riyadh 11533, Saudi Arabia
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10
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Hu L, Wei S, Wu Y, Li S, Zhu P, Wang X. MicroRNA regulation of the proliferation and apoptosis of Leydig cells in diabetes. Mol Med 2021; 27:104. [PMID: 34496750 PMCID: PMC8425090 DOI: 10.1186/s10020-021-00370-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/31/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The number of patients with diabetes is increasing worldwide. Diabetic testicular damage can cause spermiogenesis disorders and sexual dysfunction. We thus explored the role of miRNAs in diabetic testicular damage, and revealed that they could serve as effective prevention and treatment therapeutic targets. METHODS Streptozotocin (STZ) was used to generate a rat model of type 2 diabetes. Rat testicular tissues were used for miRNA and mRNA sequencing. Through bioinformatics analysis, we constructed an miRNA-mRNA diabetic testicular damage regulatory network and screened for key miRNAs. We also used Leydig cells to generate a diabetic cell model and detected the downstream target genes of miRNAs, secretion of testosterone, and proliferation and apoptotic levels to elucidate the role and mechanism of the selected miRNAs in diabetic testicular damage. RESULTS Using second-generation sequencing, we identified 19 differentially expressed miRNAs and 555 mRNAs in the testes of diabetic rats. Based on computational prediction of targets and negative regulation relationships, we constructed a miRNA-mRNA regulatory network, including 12 miRNAs and 215 mRNAs. KEGG enrichment analysis revealed that genes were more concentrated on the survival signalling pathway. Based on this, we screened 2 key miRNAs, miR-504 and miR-935. In vitro, glucose could induce an increase in miR-504 and miR-935, whereas a decrease in MEK5 and MEF2C in a dose-dependent manner. Overexpression of miR-504 and miR-935 led to the decreased expression of MEK5 and MEF2C, decreased proliferation rate of Leydig cells, increased apoptotic rate, and decreased secretion of testosterone. Whereas, knockdown of miR-504 and miR-935 displayed opposite tendencies. CONCLUSIONS miRNAs play important roles in diabetic testicular damage. miR-504 and miR-935 might regulate testicular damage through the classic survival pathway of MEK5-ERK5-MEF2C. Targeted inhibition of miR-504 and miR-935 could reverse the high-glucose-induced testicular complications, thus posing as a potential therapeutic approach in diabetic testicular injury.
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Affiliation(s)
- Li Hu
- Shenzhen University South China Hospital, Shenzhen University, Shenzhen, 518111, People's Republic of China
- Department of Physiology, Shantou University of Medical College, Shantou, 515041, People's Republic of China
| | - Shaochai Wei
- Department of Physiology, Shantou University of Medical College, Shantou, 515041, People's Republic of China
| | - Yuqi Wu
- Department of Urology & Carson International Cancer Center, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Center, Shenzhen University, NO.1098, Xueyuan Road, Shenzhen University City, Nanshan District, Shenzhen, 518055, People's Republic of China
| | - Shulin Li
- Department of Urology & Carson International Cancer Center, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Center, Shenzhen University, NO.1098, Xueyuan Road, Shenzhen University City, Nanshan District, Shenzhen, 518055, People's Republic of China
| | - Pei Zhu
- Department of Urology & Carson International Cancer Center, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Center, Shenzhen University, NO.1098, Xueyuan Road, Shenzhen University City, Nanshan District, Shenzhen, 518055, People's Republic of China.
| | - Xiangwei Wang
- Department of Urology & Carson International Cancer Center, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Center, Shenzhen University, NO.1098, Xueyuan Road, Shenzhen University City, Nanshan District, Shenzhen, 518055, People's Republic of China.
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11
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Berti FCB, Mathias C, Garcia LE, Gradia DF, de Araújo-Souza PS, Cipolla GA, de Oliveira JC, Malheiros D. Comprehensive analysis of ceRNA networks in HPV16- and HPV18-mediated cervical cancers reveals XIST as a pivotal competing endogenous RNA. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166172. [PMID: 34048924 DOI: 10.1016/j.bbadis.2021.166172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022]
Abstract
Cervical cancer (CC) is one of the most common cancers in women worldwide, being closely related to high-risk human papillomavirus (HR-HPVs). After a particular HR-HPV infects a cervical cell, transcriptional changes in the host cell are expected, including the regulation of lncRNAs, miRNAs, and mRNAs. Such transcripts may work independently or integrated in complex molecular networks - as in competing endogenous RNA (ceRNA) networks. In our research, we gathered transcriptome data from samples of HPV16/HPV18 cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), from The Cancer Genome Atlas (TCGA) project. Using GDCRNATools, we identified ceRNA networks that differentiate HPV16- from HPV18-mediated CESC. For HPV16-CESC, three lncRNA-mRNA co-expressed pairs were reported, all led by the X-inactive specific transcript (XIST): XIST | DLG5, XIST | LGR4, and XIST | ZNF81. The XIST | LGR4 and XIST | ZNF81 pairs shared 11 miRNAs, suggesting an increased impact on their final biological effect. XIST also stood out as an important lncRNA in HPV18-CESC, leading 35 of the 42 co-expressed pairs. Some mRNAs, such as ADAM9 and SLC38A2, emerged as important players in the ceRNA regulatory networks due to sharing a considerable amount of miRNAs with XIST. Furthermore, some XIST-associated axes, namely XIST | miR-23a-3p | LGR4 and XIST | miR-30b-5p or miR-30c-5p or miR-30e-5p I ADAM9, had a significant impact on the overall survival of HPV16- and HPV18-CESC patients, respectively. Together, these data suggest that XIST has an important role in HPV-mediated tumorigenesis, which may implicate different molecular signatures between HPV16 and HPV18-associated tumors.
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Affiliation(s)
- Fernanda Costa Brandão Berti
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Carolina Mathias
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Leandro Encarnação Garcia
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Daniela Fiori Gradia
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Patrícia Savio de Araújo-Souza
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Immunogenetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Gabriel Adelman Cipolla
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Jaqueline Carvalho de Oliveira
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil
| | - Danielle Malheiros
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil; Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-900 Curitiba, Paraná State, Brazil.
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12
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Hinz N, Jücker M. AKT in Bone Metastasis of Solid Tumors: A Comprehensive Review. Cancers (Basel) 2021; 13:cancers13102287. [PMID: 34064589 PMCID: PMC8151478 DOI: 10.3390/cancers13102287] [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: 04/16/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Bone metastasis is a frequent complication of solid tumors and leads to a reduced overall survival. Although much progress has been made in the field of tumor therapy in the last years, bone metastasis depicts a stage of the disease with a lack of appropriate therapeutical options. Hence, this review aims to present the role of AKT in bone metastasis of solid tumors to place the spotlight on AKT as a possible therapeutical approach for patients with bone metastases. Furthermore, we intended to discuss postulated underlying molecular mechanisms of the bone metastasis-promoting effect of AKT, especially in highly bone-metastatic breast, prostate, and lung cancer. To conclude, this review identified the AKT kinase as a potential therapeutical target in bone metastasis and revealed remaining questions, which need to be addressed in further research projects. Abstract Solid tumors, such as breast cancer and prostate cancer, often form bone metastases in the course of the disease. Patients with bone metastases frequently develop complications, such as pathological fractures or hypercalcemia and exhibit a reduced life expectancy. Thus, it is of vital importance to improve the treatment of bone metastases. A possible approach is to target signaling pathways, such as the PI3K/AKT pathway, which is frequently dysregulated in solid tumors. Therefore, we sought to review the role of the serine/threonine kinase AKT in bone metastasis. In general, activation of AKT signaling was shown to be associated with the formation of bone metastases from solid tumors. More precisely, AKT gets activated in tumor cells by a plethora of bone-derived growth factors and cytokines. Subsequently, AKT promotes the bone-metastatic capacities of tumor cells through distinct signaling pathways and secretion of bone cell-stimulating factors. Within the crosstalk between tumor and bone cells, also known as the vicious cycle, the stimulation of osteoblasts and osteoclasts also causes activation of AKT in these cells. As a consequence, bone metastasis is reduced after experimental inhibition of AKT. In summary, AKT signaling could be a promising therapeutical approach for patients with bone metastases of solid tumors.
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13
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Zhang J, Zhang C, Cao P, Zheng X, Yu B, Cao H, Gao Z, Zhang F, Wu J, Cao H, Hao C, Sun Z, Wang W. A zinc finger protein gene signature enables bladder cancer treatment stratification. Aging (Albany NY) 2021; 13:13023-13038. [PMID: 33962398 PMCID: PMC8148496 DOI: 10.18632/aging.202984] [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: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 12/29/2022]
Abstract
Bladder cancer (BC) is a commonly occurring malignant tumor affecting the urinary tract. Zinc finger proteins (ZNFs) constitute the largest transcription factor family in the human genome and are therefore attractive biomarker candidates for BC prognosis. In this study, we profiled the expression of ZNFs in The Cancer Genome Atlas (TCGA) BC cohort and developed a novel prognostic signature based on 7 ZNF-coding genes. After external validation of the model in the GSE48276 dataset, we integrated the 7-ZNF-gene signature with patient clinicopathological data to construct a nomogram that forecasted 1-, 2-, and 3-year OS with good predictive accuracy. We then accessed The Genomics of Drug Sensitivity in Cancer database to predict the therapeutic drug responses of signature-defined high- and low-risk BC patients in the TCGA cohort. Greater sensitivity to chemotherapy was revealed in the low-risk group. Finally, we conducted gene set enrichment analysis of the signature genes and established, by applying the ESTIMATE algorithm, distinct correlations between the two risk groups and the presence of stromal and immune cell types in the tumor microenvironment. By allowing effective risk stratification of BC patients, our novel ZNF gene signature may enable tailoring more intensive treatment for high-risk patients.
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Affiliation(s)
- Jiandong Zhang
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China.,Shanxi Bethune Hospital Affiliated Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Chen Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Cao
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Xiang Zheng
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Baozhong Yu
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Haoyuan Cao
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Zihao Gao
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Feilong Zhang
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Jiyuan Wu
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Huawei Cao
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Changzhen Hao
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Zejia Sun
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
| | - Wei Wang
- Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing 100020, China
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14
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Wang S, Qi X, Liu H. microRNA-939 Promotes the Vitality of Human Breast Cancer Cells via Inhibition of E2F1/P73 Signaling. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We assessed miR-939’s role in breast cancer (BC) and its molecular mechanism. PCR was performed to detect miRNA levels. Correlations between miR-939 and patients’ pathological information were analyzed. After transfection of E2F1 plasmid, P73 plasmid, si-E2F1, si-P73, miR-939
mimic or si-miR-939, cell proliferation and apoptosis were measured. The miR-939 target gene was proved by a luciferase assay. Protein and mRNA levels of E2F1 and P73 were detected by immunoblotting and PCR, and corresponding proliferation or apoptosis were assessed. MiR-939 expression was
significantly increased in BC and associated with TNM staging, Ki-67 enhancement, and shorter disease-free survival time. In BC clinical samples, E2F1 expression is negatively correlated with miR-939 expressions. Overexpressing miR-939 stimulated growth but suppressed cell apoptosis. Functional
analysis indicated E2F1 is the target gene of miR-939, and overexpression of miR-939 significantly downregulated E2F1 and P73. Silencing of E2F1 or P73 significantly promoted MDA-MB-231 cell proliferation and inhibited apoptosis. Overexpression of E2F1 plasmid or P73 plasmid significantly
inhibited MDA-MB-231 cell proliferation but induced apoptosis. Transfection of P73 or E2F1 plasmid abolished miR-939’s effects on proliferation and apoptosis. miR-939 promotes breast cancer progression by downregulation of E2F1 to inhibit P73 pathway, thereby promoting proliferation
and inhibiting apoptosis.
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Affiliation(s)
- Shuaibing Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China; Tianjin’s Clinical Research Center
for Cancer, Tianjin 300060, China
| | - Xiuheng Qi
- HebeiPetroChina Central Hospital, Langfang, Hebei 065000, China
| | - Hong Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China; Tianjin’s Clinical Research Center for Cancer,
Tianjin 300060, China
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15
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Ciomborowska-Basheer J, Staszak K, Kubiak MR, Makałowska I. Not So Dead Genes-Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts. Cells 2021; 10:cells10040912. [PMID: 33921034 PMCID: PMC8071448 DOI: 10.3390/cells10040912] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Retroposition is RNA-based gene duplication leading to the creation of single exon nonfunctional copies. Nevertheless, over time, many of these duplicates acquire transcriptional capabilities. In human in most cases, these so-called retrogenes do not code for proteins but function as regulatory long noncoding RNAs (lncRNAs). The mechanisms by which they can regulate other genes include microRNA sponging, modulation of alternative splicing, epigenetic regulation and competition for stabilizing factors, among others. Here, we summarize recent findings related to lncRNAs originating from retrocopies that are involved in human diseases such as cancer and neurodegenerative, mental or cardiovascular disorders. Special attention is given to retrocopies that regulate their progenitors or host genes. Presented evidence from the literature and our bioinformatics analyses demonstrates that these retrocopies, often described as unimportant pseudogenes, are significant players in the cell’s molecular machinery.
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16
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Sun N, Gao P, Li Y, Yan Z, Peng Z, Zhang Y, Han F, Qi X. Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer. Front Mol Biosci 2021; 8:619110. [PMID: 33644115 PMCID: PMC7905399 DOI: 10.3389/fmolb.2021.619110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023] Open
Abstract
Breast cancer is one of the most common cancers. Although the present molecular classification improves the treatment effect and prognosis of breast cancer, the heterogeneity of the molecular subtype remains very complex, and the applicability and effectiveness of treatment methods are still limited leading to poorer patient prognosis than expected. Further identification of more refined molecular typing based on gene expression profile will yield better understanding of the heterogeneity, improving treatment effects and prolonging prognosis of patients. Here, we downloaded the mRNA expression profiles and corresponding clinical data of patients with breast cancer from public databases and performed typical molecular typing using PAM50 (Prediction Analysis of Microarray 50) method. Comparative analyses were performed to screen the common and specific differentially expressed genes (DEGs) between cancer and corresponding para-cancerous tissues in each breast cancer subtype. The GO and KEGG analyses of the DEGs were performed to enrich the common and specific functional progress and signaling pathway involved in breast cancer subtypes. A total of 38 key common and specific DEGs were identified and selected based on the validated results, GO/KEGG enrichments, and the priority of expression, including four common DEGs and 34 specific DEGs in different subtypes. The prognostic value of these key common and specific DEGs was further analyzed to obtain useful potential markers in clinic. Finally, the potential roles and the specific prognostic values of the common and specific DEGs were speculated and summarized in total breast cancer and different subtype breast cancer based on the results of these analyses. The findings of our study provide the basis of more refined molecular typing of breast cancer, potential new therapeutic targets and prognostic markers for different breast cancer subtypes
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Affiliation(s)
- Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Pingping Gao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zexuan Yan
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of the Ministry of Education, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zaihui Peng
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
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17
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Liu Y, Xie P, Jiang D, Liu J, Zhang J, Bian T, Shi J. Molecular and Immune Characteristics for Lung Adenocarcinoma Patients With ERLIN2 Overexpression. Front Immunol 2020; 11:568440. [PMID: 33424830 PMCID: PMC7793841 DOI: 10.3389/fimmu.2020.568440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/04/2020] [Indexed: 12/25/2022] Open
Abstract
Background Endoplasmic reticulum lipid raft-associated protein 2 (ERLIN2) is protein contained in the membrane of the endoplasmic reticulum. In lung adenocarcinoma (LUAD), the molecular function of ERLIN2 and the correlation between ERLIN2 and tumor-infiltrating immune cells have been unclear. The aim of our study was to determine the role of ERLIN2 in LUAD development to provide a better understanding of the molecular pathogenesis of this disease and identify new therapeutic targets for its treatment. Methods Immunohistochemistry, Western blotting, and real-time quantitative polymerase chain reaction were used to detect protein and mRNA levels of ERLIN2 in LUAD and adjacent normal tissues. Using the A549, H1299 cell line, ERLIN2-short hairpin RNA was applied to silence ERLIN2 to determine its role in LUAD cell proliferation and invasion. Based on mRNA expression of ERLIN2 from the Cancer Genome Atlas (TCGA) database, we identified ERLIN2-related protein-coding genes and analyzed the Kyoto Encyclopedia of Genes and Genomes pathway to explore its potential biological functions and determined the correlation between ERLIN2 and tumor-infiltrating immune cells. Results ERLIN2 was abnormally expressed in a variety of tumor tissues and is highly expressed in LUAD. This overexpression was associated with histological grade (P = 0.044), TNM stage (P = 0.01), and lymph node metastasis (P = 0.038). Patient overall survival was poorer with ERLIN2 overexpression. Downregulation of ERLIN2 inhibited LUAD cell proliferation and invasion in vitro. Based on mRNA expression of ERLIN2 from the TCGA database, 13 ERLIN2-related genes and 10 pathways were identified and showed a correlation between ERLIN2 and naive B cells and neutrophils. Conclusion ERLIN2 could serve as a potential diagnostic and prognostic biomarker for LUAD and has demonstrated to be correlated with immune infiltrates, which suggests that it may represent a new therapeutic target for LUAD.
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Affiliation(s)
- Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China.,Medical School of Nantong University, Nantong, China
| | - Pengfei Xie
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Daishang Jiang
- Department of Emergency Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
| | - Jianguo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Departments of Cardio-Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
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18
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Webb MJ, Kukard C. A Review of Natural Therapies Potentially Relevant in Triple Negative Breast Cancer Aimed at Targeting Cancer Cell Vulnerabilities. Integr Cancer Ther 2020; 19:1534735420975861. [PMID: 33243021 PMCID: PMC7705812 DOI: 10.1177/1534735420975861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We reviewed the research into the mechanisms of growth of triple negative breast cancer (TNBC) based on laboratory pre-clinical studies that have shaped understanding of the disease over the past decade. In response to these findings, we propose an approach to potentially prevent cancer metabolic adaptation and recurrence. This paper collates pre-clinical results, first to determine the tumor’s mechanisms of growth and then to source natural substances that could potentially suppress those mechanisms. The results from in vivo and in vitro studies of TNBC were combined first to select 10 primary mechanisms (Hypoxia-inducible factor 1α, Hedgehog, MAPK, MTAP, NF-κ B, Notch, P13K, STAT3, and Wnt signaling pathways plus p53 and POL2A gene expression) that promote TNBC growth, and second to propose a treatment array of 21 natural compounds that suppress laboratory models of TNBC via these mechanisms. We included BRCA mutations in the review process, but only pathways with the most preclinical studies utilizing natural products were included. Then we outlined potential biomarkers to assess the changes in the micro-environment and monitor biochemical pathway suppression. This suppression-centric aim targets these mechanisms of growth with the goal of potentially halting tumor growth and preventing cancer cell metabolic adaptation. We chose TNBC to demonstrate this 5-step strategy of supplementary therapy, which may be replicated for other tumor types.
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Affiliation(s)
| | - Craig Kukard
- University of Newcastle, Newcastle, NSW, Australia
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19
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Voutsadakis IA. Amplification of 8p11.23 in cancers and the role of amplicon genes. Life Sci 2020; 264:118729. [PMID: 33166592 DOI: 10.1016/j.lfs.2020.118729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023]
Abstract
Copy number alterations are widespread in cancer genomes and are part of the genomic instability underlying the pathogenesis of neoplastic diseases. Recurrent copy number alterations of specific chromosomal loci may result in gains of oncogenes or losses of tumor suppressor genes and become entrenched in the genomic framework of certain types of cancers. The locus at chromosome 8p11.23 presents recurrent amplifications most commonly in squamous lung carcinomas, breast cancers, squamous esophageal carcinomas, and urothelial carcinomas. Amplification is rare in other cancers. The amplified segment involves several described oncogenes that may promote cancer cell survival and proliferation, as well as less well characterized genes that could also contribute to neoplastic processes. Genes proposed to be "drivers" in 8p11.23 amplifications include ZNF703, FGFR1 and PLPP5. Additional genes in the locus that could be functionally important in neoplastic networks include co-chaperone BAG4, lysine methyltransferase NSD3, ASH2L, a member of another methyltransferase complex, MLL and the mRNA processing and translation regulators LSM1 and EIF4EBP1. In this paper, genes located in the amplified segment of 8p11.23 will be examined for their role in cancer and data arguing for their importance for cancers with the amplification will be presented.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada; Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada.
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Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. Genes (Basel) 2020; 11:genes11050542. [PMID: 32408516 PMCID: PMC7290577 DOI: 10.3390/genes11050542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.
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