1
|
Eskandarion MR, Eskandarieh S, Shakoori Farahani A, Mahmoodzadeh H, Shahi F, Oghabian MA, Shirkoohi R. Prediction of novel biomarkers for gastric intestinal metaplasia and gastric adenocarcinoma using bioinformatics analysis. Heliyon 2024; 10:e30253. [PMID: 38737262 PMCID: PMC11088262 DOI: 10.1016/j.heliyon.2024.e30253] [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: 07/15/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024] Open
Abstract
Background & aim The histologic and molecular changes from intestinal metaplasia (IM) to gastric cancer (GC) have not been fully characterized. The present study sought to identify potential alterations in signaling pathways in IM and GC to predict disease progression; these alterations can be considered therapeutic targets. Materials & methods Seven gene expression profiles were selected from the GEO database. Discriminate differentially expressed genes (DEGs) were analyzed by EnrichR. The STRING database, Cytoscape, Gene Expression Profiling Interactive Analysis (GEPIA), cBioPortal, NetworkAnalyst, MirWalk database, OncomiR, and bipartite miRNA‒mRNA correlation network was used for downstream analyses of selected module genes. Results Analyses revealed that extracellular matrix-receptor interactions (ITGB1, COL1A1, COL1A2, COL4A1, FN1, COL6A3, and THBS2) in GC and PPAR signaling pathway interactions (FABP1, APOC3, APOA1, HMGCS2, and PPARA and PCK1) in IM may play key roles in both the carcinogenesis and progression of underlying GC from intestinal metaplasia. IM enrichment indicated that this is closely related to digestion and absorption. The TF-hub gene regulatory network revealed that AR, TCF4, SALL4, and ESR1 were more important for hub gene expression. It was revealed that the development and prediction of GC may be affected by hsa-miR-29. It was found that PTGR1, C1orf115, CRYL1, ALDOB, and SULT1B1 were downregulated in GC and upregulated in IM. Therefore, they might have tumor suppressor activity in GC progression. Conclusion New potential biomarkers and pathways involved in GC and IM were identified that are important for the transformation of GC from IM to adenocarcinoma and can be therapeutic targets for GC.
Collapse
Affiliation(s)
| | - Sharareh Eskandarieh
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori Farahani
- Medical Genetics Ward, IKHC Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Department of Surgery, Cancer Research Center, Cancer Institute, IKHC, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Shahi
- Department of Medical Oncology, Cancer Research Center, Cancer Institute, IKHC, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oghabian
- Medical Physics Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shirkoohi
- Cancer Research Center, Cancer Institute, IKHC, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Xiao B, Li G, Gulizeba H, Liu H, Sima X, Zhou T, Huang Y. Choline metabolism reprogramming mediates an immunosuppressive microenvironment in non-small cell lung cancer (NSCLC) by promoting tumor-associated macrophage functional polarization and endothelial cell proliferation. J Transl Med 2024; 22:442. [PMID: 38730286 PMCID: PMC11084143 DOI: 10.1186/s12967-024-05242-3] [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: 02/06/2024] [Accepted: 04/27/2024] [Indexed: 05/12/2024] Open
Abstract
INTRODUCTION Lung cancer is a prevalent malignancy globally, and immunotherapy has revolutionized its treatment. However, resistance to immunotherapy remains a challenge. Abnormal cholinesterase (ChE) activity and choline metabolism are associated with tumor oncogenesis, progression, and poor prognosis in multiple cancers. Yet, the precise mechanism underlying the relationship between ChE, choline metabolism and tumor immune microenvironment in lung cancer, and the response and resistance of immunotherapy still unclear. METHODS Firstly, 277 advanced non-small cell lung cancer (NSCLC) patients receiving first-line immunotherapy in Sun Yat-sen University Cancer Center were enrolled in the study. Pretreatment and the alteration of ChE after 2 courses of immunotherapy and survival outcomes were collected. Kaplan-Meier survival and cox regression analysis were performed, and nomogram was conducted to identify the prognostic and predicted values. Secondly, choline metabolism-related genes were screened using Cox regression, and a prognostic model was constructed. Functional enrichment analysis and immune microenvironment analysis were also conducted. Lastly, to gain further insights into potential mechanisms, single-cell analysis was performed. RESULTS Firstly, baseline high level ChE and the elevation of ChE after immunotherapy were significantly associated with better survival outcomes for advanced NSCLC. Constructed nomogram based on the significant variables from the multivariate Cox analysis performed well in discrimination and calibration. Secondly, 4 choline metabolism-related genes (MTHFD1, PDGFB, PIK3R3, CHKB) were screened and developed a risk signature that was found to be related to a poorer prognosis. Further analysis revealed that the choline metabolism-related genes signature was associated with immunosuppressive tumor microenvironment, immune escape and metabolic reprogramming. scRNA-seq showed that MTHFD1 was specifically distributed in tumor-associated macrophages (TAMs), mediating the differentiation and immunosuppressive functions of macrophages, which may potentially impact endothelial cell proliferation and tumor angiogenesis. CONCLUSION Our study highlights the discovery of ChE as a prognostic marker in advanced NSCLC, suggesting its potential for identifying patients who may benefit from immunotherapy. Additionally, we developed a prognostic signature based on choline metabolism-related genes, revealing the correlation with the immunosuppressive microenvironment and uncovering the role of MTHFD1 in macrophage differentiation and endothelial cell proliferation, providing insights into the intricate workings of choline metabolism in NSCLC pathogenesis.
Collapse
Affiliation(s)
- Bijing Xiao
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Guanjun Li
- Department of Oncology, Nanfang Hospital, Southern Medical University, No. 1023-1063, Shatai Southern Road, Baiyun District, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Haimiti Gulizeba
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Hong Liu
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Xiaoxian Sima
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Ting Zhou
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China.
| | - Yan Huang
- Medical Oncology Department, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China.
| |
Collapse
|
3
|
Agarwal S, Gupta S, Raj R. Identification of potential targetable genes in papillary, follicular, and anaplastic thyroid carcinoma using bioinformatics analysis. Endocrine 2024:10.1007/s12020-024-03836-x. [PMID: 38676768 DOI: 10.1007/s12020-024-03836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
PURPOSE To perform an extensive exploratory analysis to build a deeper insight into clinically relevant molecular biomarkers in Papillary, Follicular, and Anaplastic thyroid carcinomas (PTC, FTC, ATC). METHODS Thirteen Thyroid Cancer (THCA) datasets incorporating PTC, FTC, and ATC were derived from the Gene Expression Omnibus. Genes differentially expressed (DEGs) between THCA and normal were identified and subjected to GO and KEGG analyses. Multiple topological properties were harnessed and protein-protein interaction (PPI) networks were constructed to identify the hub genes followed by survival analysis and validation. RESULTS There were 70, 87, and 377 DEGs, and 23, 27, and 53 hub genes for PTC, FTC, and ATC samples, respectively. Survival analysis detected 39 overall and 49 relapse-free survival-relevant hub genes. Six hub genes, BCL2, FN1, ITPR1, LYVE1, NTRK2, TBC1D4, were found common to more than one THCA type. The most significant hub genes found in the study were: BCL2, CD44, DCN, FN1, IRS1, ITPR1, MFAP4, MKI67, NTRK2, PCLO, TGFA. The most enriched and significant GO terms were Melanocyte differentiation for PTC, Extracellular region for FTC, and Extracellular exosome for ATC. Prostate cancer for PTC was the most significantly enriched KEGG pathway. The results were validated using TCGA data. CONCLUSIONS The findings unravel potential biomarkers and therapeutic targets of thyroid carcinomas.
Collapse
Affiliation(s)
- Shipra Agarwal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Shikha Gupta
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India.
| | - Rishav Raj
- Department of Computer Science, S.S. College of Business Studies, University of Delhi, New Delhi, India
| |
Collapse
|
4
|
Song J, Liao H, Li H, Chen H, Si H, Wang J, Bai X. Identification of a novel cancer-associated fibroblasts gene signature based on bioinformatics analysis to predict prognosis and therapeutic responses in breast cancer. Heliyon 2024; 10:e29216. [PMID: 38601538 PMCID: PMC11004657 DOI: 10.1016/j.heliyon.2024.e29216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs) provide suitable conditions for growth of tumor cell and facilitate tumor progression. Hence, we aimed to identify a CAFs-related gene signature associated with the prognosis of patients with breast cancer (BRCA). We downloaded datasets from Gene Expression Omnibus (GEO) and confirmed the correlation between CAFs infiltration scores and prognosis. By performing weighted gene co-expression network analysis (WGCNA) and Lasso Cox regression analysis, we constructed a four-gene (COL5A3, FN1, POSTN, and RARRES2) prognostic CAFs signature model. Based on the median risk score of CAFs, patients with BRCA were divided into high- and low-risk groups. Compared with low-risk group, patients in high-risk group exhibited a poor prognosis and limited response to immunotherapy. Furthermore, patients with high CAFs risk scores were found to have a detrimental prognosis due to the induction of immunosuppressive cell infiltration, resulting in an immunosuppressive tumor microenvironment. Importantly, we found that CAFs overexpressing FN1 and POSTN significantly promoted the wound healing and invasion ability of tumor cells in vitro validation. Taking together, we identified a four-gene prognostic CAFs signature, which was proven to be a reliable indicator for prognosis and therapeutic efficacy in patients with BRCA. This study provided evidence for novel CAFs-based stromal therapy.
Collapse
Affiliation(s)
- Jin Song
- Department of General Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Huifeng Liao
- Department of General Surgery, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Huayan Li
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Hongye Chen
- Department of General Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Huiyan Si
- Department of General Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiandong Wang
- Department of General Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Xue Bai
- Department of General Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| |
Collapse
|
5
|
Qu N, Chen D, Ma B, Zhang L, Wang Q, Wang Y, Wang H, Ni Z, Wang W, Liao T, Xiang J, Wang Y, Jin S, Xue D, Wu W, Wang Y, Ji Q, He H, Piao HL, Shi R. Integrated proteogenomic and metabolomic characterization of papillary thyroid cancer with different recurrence risks. Nat Commun 2024; 15:3175. [PMID: 38609408 PMCID: PMC11014849 DOI: 10.1038/s41467-024-47581-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Although papillary thyroid cancer (PTC) has a good prognosis, its recurrence rate is high and remains a core concern in the clinic. Molecular factors contributing to different recurrence risks (RRs) remain poorly defined. Here, we perform an integrative proteogenomic and metabolomic characterization of 102 Chinese PTC patients with different RRs. Genomic profiling reveals that mutations in MUC16 and TERT promoter as well as multiple gene fusions like NCOA4-RET are enriched by the high RR. Integrative multi-omics analyses further describe the multi-dimensional characteristics of PTC, especially in metabolism pathways, and delineate dominated molecular patterns of different RRs. Moreover, the PTC patients are clustered into four subtypes (CS1: low RR and BRAF-like; CS2: high RR and metabolism type, worst prognosis; CS3: high RR and immune type, better prognosis; CS4: high RR and BRAF-like) based on the omics data. Notably, the subtypes display significant differences considering BRAF and TERT promoter mutations, metabolism and immune pathway profiles, epithelial cell compositions, and various clinical factors (especially RRs and prognosis) as well as druggable targets. This study can provide insights into the complex molecular characteristics of PTC recurrences and help promote early diagnosis and precision treatment of recurrent PTC.
Collapse
Affiliation(s)
- Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lijun Zhang
- Department of General Surgery, Ganmei Affiliated Hospital of Kunming Medical University (The First People's Hospital of Kunming), Kunming, Yunnan, China
- Department of Surgery, Kunming Medical University, Kunming, Yunnan, China
| | - Qiuping Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yuting Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongping Wang
- Department of Endocrinology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaoxian Ni
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Xiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yulong Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi Jin
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dixin Xue
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weili Wu
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Hui He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Hai-Long Piao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- Department of Biochemistry & Molecular Biology, School of Life Sciences, China Medical University, Shenyang, China.
| | - Rongliang Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
6
|
Wang Y, Song W, Li Y, Liu Z, Zhao K, Jia L, Wang X, Jiang R, Tian Y, He X. Integrated analysis of tumor microenvironment features to establish a diagnostic model for papillary thyroid cancer using bulk and single-cell RNA sequencing technology. J Cancer Res Clin Oncol 2023; 149:16837-16850. [PMID: 37733241 PMCID: PMC10645658 DOI: 10.1007/s00432-023-05420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Characterizing tumor microenvironment using single-cell RNA sequencing has been a promising strategy for cancer diagnosis and treatment. However, a few studies have focused on diagnosing papillary thyroid cancer (PTC) through this technology. Therefore, our study explored tumor microenvironment (TME) features and identified potential biomarkers to establish a diagnostic model for papillary thyroid cancer. METHODS The cell types were identified using the markers from the CellMarker database and published research. The CellChat package was conducted to analyze the cell-cell interaction. The SCEVAN package was used to identify malignant thyroid cells. The SCP package was used to perform multiple single-cell downstream analyses, such as GSEA analysis, enrichment analysis, pseudotime trajectory analysis, and differential expression analysis. The diagnostic model of PTC was estimated using the calibration curves, receiver operating characteristic curves, and decision curve analysis. RT-qPCR was performed to validate the expression of candidate genes in human papillary thyroid samples. RESULTS Eight cell types were identified in the scRNA-seq dataset by published cell markers. Extensive cell-cell interactions like FN1/ITGB1 existed in PTC tissues. We identified 26 critical genes related to PTC progression. Further, eight subgroups of PTC tumor cells were identified and exhibited high heterogeneity. The MDK/LRP1, MDK/ALK, GAS6/MERTK, and GAS6/AXL were identified as potential ligand-receptor pairs involved in the interactions between fibroblasts/endothelial cells and tumor cells. Eventually, the diagnostic model constructed by TRPC5, TENM1, NELL2, DMD, SLC35F3, and AUTS2 showed a good efficiency for distinguishing the PTC and normal tissues. CONCLUSIONS Our study comprehensively characterized the tumor microenvironment in papillary thyroid cancer. Through combined analysis with bulk RNA-seq, six potential diagnostic biomarkers were identified and validated. The diagnostic model we constructed was a promising tool for PTC diagnosis. Our findings provide new insights into the heterogeneity of thyroid cancer and the theoretical basis for diagnosing thyroid cancer.
Collapse
Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Wenbin Song
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yingxi Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Zhaoyi Liu
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Lanning Jia
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yao Tian
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| |
Collapse
|
7
|
Albaradei S, Alganmi N, Albaradie A, Alharbi E, Motwalli O, Thafar MA, Gojobori T, Essack M, Gao X. A deep learning model predicts the presence of diverse cancer types using circulating tumor cells. Sci Rep 2023; 13:21114. [PMID: 38036622 PMCID: PMC10689793 DOI: 10.1038/s41598-023-47805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Circulating tumor cells (CTCs) are cancer cells that detach from the primary tumor and intravasate into the bloodstream. Thus, non-invasive liquid biopsies are being used to analyze CTC-expressed genes to identify potential cancer biomarkers. In this regard, several studies have used gene expression changes in blood to predict the presence of CTC and, consequently, cancer. However, the CTC mRNA data has not been used to develop a generic approach that indicates the presence of multiple cancer types. In this study, we developed such a generic approach. Briefly, we designed two computational workflows, one using the raw mRNA data and deep learning (DL) and the other exploiting five hub gene ranking algorithms (Degree, Maximum Neighborhood Component, Betweenness Centrality, Closeness Centrality, and Stress Centrality) with machine learning (ML). Both workflows aim to determine the top genes that best distinguish cancer types based on the CTC mRNA data. We demonstrate that our automated, robust DL framework (DNNraw) more accurately indicates the presence of multiple cancer types using the CTC gene expression data than multiple ML approaches. The DL approach achieved average precision of 0.9652, recall of 0.9640, f1-score of 0.9638 and overall accuracy of 0.9640. Furthermore, since we designed multiple approaches, we also provide a bioinformatics analysis of the gene commonly identified as top-ranked by the different methods. To our knowledge, this is the first study wherein a generic approach has been developed to predict the presence of multiple cancer types using raw CTC mRNA data, as opposed to other models that require a feature selection step.
Collapse
Affiliation(s)
- Somayah Albaradei
- Computer Science Department, Faculty of Computing and Information Technology, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
| | - Nofe Alganmi
- Computer Science Department, Faculty of Computing and Information Technology, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | | | - Eaman Alharbi
- Computer Science Department, Faculty of Computing and Information Technology, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
| | - Olaa Motwalli
- College of Computing and Informatics, Saudi Electronic University (SEU), Madinah, Saudi Arabia
| | - Maha A Thafar
- College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
8
|
Dou F, Liu Q, Lv S, Xu Q, Wang X, Liu S, Liu G. FN1 and TGFBI are key biomarkers of macrophage immune injury in diabetic kidney disease. Medicine (Baltimore) 2023; 102:e35794. [PMID: 37960829 PMCID: PMC10637504 DOI: 10.1097/md.0000000000035794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
The pathogenesis of diabetic kidney disease (DKD) is complex, and the existing treatment methods cannot control disease progression well. Macrophages play an important role in the development of DKD. This study aimed to search for biomarkers involved in immune injury induced by macrophages in DKD. The GSE96804 dataset was downloaded and analyzed by the CIBERSORT algorithm to understand the differential infiltration of macrophages between DKD and normal controls. Weighted gene co-expression network analysis was used to explore the correlation between gene expression modules and macrophages in renal tissue of DKD patients. Protein-protein interaction network and machine learning algorithm were used to screen the hub genes in the key modules. Subsequently, the GSE30528 dataset was used to further validate the expression of hub genes and analyze the diagnostic effect by the receiver operating characteristic curve. The clinical data were applied to explore the prognostic significance of hub genes. CIBERSORT analysis showed that macrophages increased significantly in DKD renal tissue samples. A total of ten modules were generated by weighted gene co-expression network analysis, of which the blue module was closely associated with macrophages. The blue module mainly played an important role in biological processes such as immune response and fibrosis. Fibronectin 1 (FN1) and transforming growth factor beta induced (TGFBI) were identified as hub genes of DKD patients. Receiver operating characteristic curve analysis was performed in the test cohort: FN1 and TGFBI had larger area under the curve values (0.99 and 0.88, respectively). Clinical validation showed that 2 hub genes were negatively correlated with the estimated glomerular filtration rate in DKD patients. In addition, FN1 and TGFBI showed a strong positive correlation with macrophage alternative activation. FN1 and TGFBI are promising biomarkers for the diagnosis and treatment of DKD patients, which may participate in immune response and fibrosis induced by macrophages.
Collapse
Affiliation(s)
- Fulin Dou
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Qingzhen Liu
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Shasha Lv
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Qiaoying Xu
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Xueling Wang
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Shanshan Liu
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Gang Liu
- Department of Nephrology, The Second Hospital of Shandong University, Jinan, China
- Nephrology Research Institute of Shandong University, The Second Hospital of Shandong University, Jinan, China
| |
Collapse
|
9
|
Chen C, Ye L, Yi J, Liu T, Li Z. FN1 mediated activation of aspartate metabolism promotes the progression of triple-negative and luminal a breast cancer. Breast Cancer Res Treat 2023; 201:515-533. [PMID: 37458908 DOI: 10.1007/s10549-023-07032-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/28/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Breast cancer (BC) is regarded as one of the most common cancers diagnosed among the female population and has an extremely high mortality rate. It is known that Fibronectin 1 (FN1) drives the occurrence and development of a variety of cancers through metabolic reprogramming. Aspartic acid is considered to be an important substrate for nucleotide synthesis. However, the regulatory mechanism between FN1 and aspartate metabolism is currently unclear. METHODS We used RNA sequencing (RNA seq) and liquid chromatography-mass spectrometry to analyze the tumor tissues and paracancerous tissues of patients. MCF7 and MDA-MB-231 cells were used to explore the effects of FN1-regulated aspartic acid metabolism on cell survival, invasion, migration and tumor growth. We used PCR, Western blot, immunocytochemistry and immunofluorescence techniques to study it. RESULTS We found that FN1 was highly expressed in tumor tissues, especially in Lumina A and TNBC subtypes, and was associated with poor prognosis. In vivo and in vitro experiments showed that silencing FN1 inhibits the activation of the YAP1/Hippo pathway by enhancing YAP1 phosphorylation, down-regulates SLC1A3-mediated aspartate uptake and utilization by tumor cells, inhibits BC cell proliferation, invasion and migration, and promotes apoptosis. In addition, inhibition of FN1 combined with the YAP1 inhibitor or SLC1A3 inhibitor can effectively inhibit tumor growth, of which inhibition of FN1 combined with the YAP1 inhibitor is more effective. CONCLUSION Targeting the "FN1/YAP1/SLC1A3/Aspartate metabolism" regulatory axis provides a new target for BC diagnosis and treatment. This study also revealed that intratumoral metabolic heterogeneity plays an important role in the progression of different subtypes of breast cancer.
Collapse
Affiliation(s)
- Chen Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Leiguang Ye
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Jinfeng Yi
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Tang Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
| | - Zhigao Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
| |
Collapse
|
10
|
Li J, Mi L, Ran B, Sui C, Zhou L, Li F, Dionigi G, Sun H, Liang N. Identification of potential diagnostic and prognostic biomarkers for papillary thyroid microcarcinoma (PTMC) based on TMT-labeled LC-MS/MS and machine learning. J Endocrinol Invest 2022; 46:1131-1143. [PMID: 36418670 DOI: 10.1007/s40618-022-01960-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To explore the molecular mechanisms underlying aggressive progression of papillary thyroid microcarcinoma and identify potential biomarkers. METHODS Samples were collected and sequenced using tandem mass tag-labeled liquid chromatography-tandem mass spectrometry. Differentially expressed proteins (DEPs) were identified and further analyzed using Mfuzz and protein-protein interaction analysis (PPI). Parallel reaction monitoring (PRM) and immunohistochemistry (IHC) were performed to validate the DEPs. RESULTS Five thousand, two hundred and three DEPs were identified and quantified from the tumor/normal comparison group or the N1/N0 comparison group. Mfuzz analysis showed that clusters of DEPs were enriched according to progressive status, followed by normal tissue, tumors without lymphatic metastases, and tumors with lymphatic metastases. Analysis of PPI revealed that DEPs interacted with and were enriched in the following metabolic pathways: apoptosis, tricarboxylic acid cycle, PI3K-Akt pathway, cholesterol metabolism, pyruvate metabolism, and thyroid hormone synthesis. In addition, 18 of the 20 target proteins were successfully validated with PRM and IHC in another 20 paired validation samples. Based on machine learning, the five proteins that showed the best performance in discriminating between tumor and normal nodules were PDLIM4, ANXA1, PKM, NPC2, and LMNA. FN1 performed well in discriminating between patients with lymph node metastases (N1) and N0 with an AUC of 0.690. Finally, five validated DEPs showed a potential prognostic role after examining The Cancer Genome Atlas database: FN1, IDH2, VDAC1, FABP4, and TG. Accordingly, a nomogram was constructed whose concordance index was 0.685 (confidence interval: 0.645-0.726). CONCLUSIONS PDLIM4, ANXA1, PKM, NPC2, LMNA, and FN1 are potential diagnostic biomarkers. The five-protein nomogram could be a prognostic biomarker.
Collapse
Affiliation(s)
- J Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - L Mi
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - B Ran
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - C Sui
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - L Zhou
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - F Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - G Dionigi
- Division of General and Endocrine Surgery, Department of Medical Biotechnology and Translational Medicine, Istituto Auxologico Italiano IRCCS, University of Milan, Milan, Italy
| | - H Sun
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
| | - N Liang
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
| |
Collapse
|
11
|
Huang C, Liang Y, Dong Y, Huang L, Li A, Du R, Huang H. Novel prognostic matrisome-related gene signature of head and neck squamous cell carcinoma. Front Cell Dev Biol 2022; 10:884590. [PMID: 36081907 PMCID: PMC9445128 DOI: 10.3389/fcell.2022.884590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/21/2022] [Indexed: 12/09/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a common malignancy of the mucosal epithelium of the oral cavity, pharynx, and larynx. Laryngeal squamous cell carcinoma (LSCC) and oral squamous cell carcinoma are common HNSCC subtypes. Patients with metastatic HNSCC have a poor prognosis. Therefore, identifying molecular markers for the development and progression of HNSCC is essential for improving early diagnosis and predicting patient outcomes. Methods: Gene expression RNA-Seq data and patient clinical traits were obtained from The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma (TCGA-HNSC) and Gene Expression Omnibus databases. Differentially expressed gene (DEG) screening was performed using the TCGA-HNSC dataset. Intersection analysis between the DEGs and a list of core matrisome genes obtained from the Matrisome Project was used to identify differentially expressed matrisome genes. A prognostic model was established using univariate and multivariate Cox regression analyses, least absolute shrinkage, and selection operator (LASSO) regression analysis. Immune landscape analysis was performed based on the single-sample gene set enrichment analysis algorithm, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, prognostic value, receiver operating characteristic curve analysis, and gene mutation analyses. Immunohistochemical results regarding prognostic protein levels were obtained from the Human Protein Atlas. Single-gene RNA-sequencing data were obtained from GSE150321 and GSE172577 datasets. CCK-8 and Transwell assays were used to confirm cell proliferation and migration. Results: A total of 1,779 DEGs, including 939 upregulated and 840 downregulated genes, between tumor and normal samples were identified using the TCGA-HNSC microarray data. Intersection analysis revealed 52 differentially expressed matrisome-related genes. After performing univariate and multivariate Cox regression and LASSO analyses, a novel prognostic model based on six matrisome genes (FN1, LAMB4, LAMB3, DMP1, CHAD, and MMRN1) for HNSCC was established. This risk model can successfully predict HNSCC survival. The high-risk group had worse prognoses and higher enrichment of pathways related to cancer development than the low-risk group. Silencing LAMB4 in HNSCC cell lines promoted cell proliferation and migration. Conclusion: This study provides a novel prognostic model for HNSCC. Thus, FN1, LAMB4, LAMB3, DMP1, CHAD, and MMRN1 may be the promising biomarkers for clinical practice.
Collapse
Affiliation(s)
- Chao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yun Liang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Yi Dong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Li Huang
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Anlei Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Ran Du
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Hao Huang,
| |
Collapse
|
12
|
Zhang XX, Luo JH, Wu LQ. FN1 overexpression is correlated with unfavorable prognosis and immune infiltrates in breast cancer. Front Genet 2022; 13:913659. [PMID: 36035176 PMCID: PMC9417469 DOI: 10.3389/fgene.2022.913659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Objective: To investigate the correlation of fibronectin 1 (FN1) expression with prognosis and tumor-infiltrating immune cells in breast cancer (BRCA). Methods: FN1 mRNA and protein expressions were analyzed through Tumor Immune Estimation Resource (TIMER), Gene Set Cancer Analysis (GSCA), Human Protein Atlas (HPA) databases, and immunohistochemical analysis. The clinicopathological characteristics and genetic factors affecting the FN1 mRNA expression were assessed by various public databases. Then, we analyzed the prognostic value of FN1 in BRCA by Kaplan-Meier plotter, receiver operating characteristic, and Cox regression analyses. Further, the UCSC Xena database was used to retrieve TCGA-BRCA expression profiles for functional enrichment analysis and immune cell infiltration analysis. The potential drugs for the BRCA patients with high- FN1 expression were identified using the connectivity map analysis. Results: FN1 was upregulated in BRCA tissues compared with normal tissues. High FN1 mRNA expression was correlated with poor clinical outcomes and had good performance in predicting the survival status of BRCA patients. Further, Cox regression analysis showed that FN1 was an independent prognostic factor for predicting the overall survival of patients with BRCA. Moreover, hypermethylation of FN1 contributed to a better prognosis for BRCA patients. Functional enrichment analyses revealed the ECM-receptor interaction pathway and focal adhesion as the common pathways. Moreover, FN1 showed a significant association with tumor-infiltrating immune cells and immune checkpoint inhibitors. Several drugs such as telmisartan, malotilate, and seocalcitol may have therapeutic effects in BRCA patients with high FN1 expression. Conclusion: FN1 might serve as a novel prognostic biomarker and a novel therapeutic target for BRCA. Besides, the association of FN1 with immune cells and immune checkpoint inhibitors may provide assistance for BRCA treatment.
Collapse
Affiliation(s)
- Xiu-Xia Zhang
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun-Hua Luo
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li-Qiang Wu
- Department of Hematology, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Li-Qiang Wu,
| |
Collapse
|
13
|
Tracking the Molecular Scenarios for Tumorigenic Remodeling of Extracellular Matrix Based on Gene Expression Profiling in Equine Skin Neoplasia Models. Int J Mol Sci 2022; 23:ijms23126506. [PMID: 35742950 PMCID: PMC9223705 DOI: 10.3390/ijms23126506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
An important component of tissues is the extracellular matrix (ECM), which not only forms a tissue scaffold, but also provides the environment for numerous biochemical reactions. Its composition is strictly regulated, and any irregularities can result in the development of many diseases, including cancer. Sarcoid is the most common skin cancer in equids. Its formation results from the presence of the genetic material of the bovine papillomavirus (BPV). In addition, it is assumed that sarcoid-dependent oncogenic transformation arises from a disturbed wound healing process, which may be due to the incorrect functioning of the ECM. Moreover, sarcoid is characterized by a failure to metastasize. Therefore, in this study we decided to investigate the differences in the expression profiles of genes related not only to ECM remodeling, but also to the cell adhesion pathway, in order to estimate the influence of disturbances within the ECM on the sarcoid formation process. Furthermore, we conducted comparative research not only between equine sarcoid tissue bioptates and healthy skin-derived explants, but also between dermal fibroblast cell lines transfected and non-transfected with a construct encoding the E4 protein of the BP virus, in order to determine its effect on ECM disorders. The obtained results strongly support the hypothesis that ECM-related genes are correlated with sarcoid formation. The deregulated expression of selected genes was shown in both equine sarcoid tissue bioptates and adult cutaneous fibroblast cell (ACFC) lines neoplastically transformed by nucleofection with gene constructs encoding BPV1-E1^E4 protein. The identified genes (CD99, ITGB1, JAM3 and CADM1) were up- or down-regulated, which pinpointed the phenotypic differences from the backgrounds noticed for adequate expression profiles in other cancerous or noncancerous tumors as reported in the available literature data. Unravelling the molecular pathways of ECM remodeling and cell adhesion in the in vivo and ex vivo models of epidermal/dermal sarcoid-related cancerogenesis might provide powerful tools for further investigations of genetic and epigenetic biomarkers for both silencing and re-initiating the processes of sarcoid-dependent neoplasia. Recognizing those biomarkers might insightfully explain the relatively high capacity of sarcoid-descended cancerous cell derivatives to epigenomically reprogram their nonmalignant neoplastic status in domestic horse cloned embryos produced by somatic cell nuclear transfer (SCNT).
Collapse
|
14
|
Zhou WH, Du WD, Li YF, Al-Aroomi MA, Yan C, Wang Y, Zhang ZY, Liu FY, Sun CF. The Overexpression of Fibronectin 1 Promotes Cancer Progression and Associated with M2 Macrophages Polarization in Head and Neck Squamous Cell Carcinoma Patients. Int J Gen Med 2022; 15:5027-5042. [PMID: 35607361 PMCID: PMC9123938 DOI: 10.2147/ijgm.s364708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose This study aimed to investigate the biological roles of fibronectin 1 (FN1) in head and neck squamous cell carcinoma (HNSCC) and its effects on macrophage M2 polarization. Methods We analyzed FN1 expression pattern and examined its clinical relevance in HNSCC progression by bioinformatic analysis. Small interfering RNA (siRNA) was utilized to silence FN1 in HNSCC cells. Cell counting kit-8 (CCK-8) assay, colony formation assay, Transwell assay and wound healing assay were performed to reveal the effect of FN1 on malignant behaviors of HNSCC cells. Moreover, a co-culture model of macrophages and HNSCC cells was established to investigate whether FN1 induce macrophage M2 polarization. Finally, we used bioinformatic methods to explore the possible FN1-related pathways in HNSCC. Results FN1 is significantly overexpressed in HNSCC patients and has been obviously correlated with higher pathological stage and poor prognosis. Downregulation of FN1 suppressed the proliferation, migration and invasion of HNSCC cells, and inhibited macrophage M2 polarization in vitro. In addition, “PI3K-Akt” and “MAPK” signaling pathways may be involved in the malignant process of FN1 in HNSCC. Conclusion The overexpression of FN1 promotes HNSCC progression and induces macrophages M2 polarization. FN1 may serve as a promising prognostic biomarker and therapeutic target in HNSCC.
Collapse
Affiliation(s)
- Wan-Hang Zhou
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Wei-Dong Du
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Yan-Fei Li
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, 510055, People’s Republic of China
| | - Maged Ali Al-Aroomi
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Cong Yan
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Yao Wang
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Ze-Ying Zhang
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| | - Fa-Yu Liu
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
- Correspondence: Fa-Yu Liu; Chang-Fu Sun, Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110000, People’s Republic of China, Tel +86 24 22894773, Fax +86 24 86602310, Email ;
| | - Chang-Fu Sun
- Department of Oral Maxillofacial-Head and Neck Surgery, School of Stomatology, China Medical University; Oral Diseases Laboratory of Liaoning, Shenyang, 110000, People’s Republic of China
| |
Collapse
|
15
|
Tan X, Zhao J, Lou J, Zheng W, Wang P. Hsa_circ_0058129 regulates papillary thyroid cancer development via miR‐873‐5p/follistatin‐like 1 axis. J Clin Lab Anal 2022; 36:e24401. [PMID: 35373391 PMCID: PMC9102651 DOI: 10.1002/jcla.24401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/06/2023] Open
Abstract
Background Papillary thyroid cancer (PTC) is an endocrine malignancy with a high incidence. Circular RNAs (circRNAs) participate in regulating PTC. Here, we analyzed the role of hsa_circ_0058129 (circ_0058129) in PTC. Methods The expression of circ_0058129, fibronectin 1 (FN1) mRNA, microRNA‐873‐5p (miR‐873‐5p), and follistatin‐like 1 (FSTL1) was detected by qRT‐PCR and western blot. Cell proliferation was analyzed by CCK‐8, EdU, and flow cytometry analysis assays. Cell migration and invasion were evaluated by Transwell assay. The targeting relationship of miR‐873‐5p and circ_0058129 or FSTL1 was identified through dual‐luciferase reporter assay, RIP assay, and RNA pull‐down assay. Xenograft mouse model assay was implemented to determine the effect of circ_0058129 on tumor formation in vivo. Results The circ_0058129 and FSTL1 abundances were increased, while the miR‐873‐5p content was decreased in PTC tissues and cells compared with control groups. Circ_0058129 shortage inhibited PTC cell proliferation, migration, and invasion. Moreover, miR‐873‐5p repressed PTC cell malignancy by binding to FSTL1. Circ_0058129 targeted miR‐873‐5p to regulate FSTL1. Conclusion Circ_0058129 expedited PTC progression through the miR‐873‐5p/FSTL1 pathway.
Collapse
Affiliation(s)
- Xiangrong Tan
- Head and Neck Surgery 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
| | - Jiazheng Zhao
- Head and Neck Surgery 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
| | - Jianlin Lou
- Head and Neck Surgery 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
| | - Wen Zheng
- Head and Neck Surgery 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
| | - Peng Wang
- Head and Neck Surgery 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
| |
Collapse
|