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Dou H, Song C, Wang X, Feng Z, Su Y, Wang H. Integrated bioinformatics analysis of SEMA3C in tongue squamous cell carcinoma using machine-learning strategies. Cancer Cell Int 2024; 24:58. [PMID: 38321460 PMCID: PMC10845809 DOI: 10.1186/s12935-024-03247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. We aim to identify and verify potential biomarkers for TSCC using bioinformatics analysis. To begin with, we examined clinical and RNA expression information of individuals with TSCC from the Gene Expression Omnibus (GEO) database. Differential expression analysis and functional analysis were conducted. Multiple machine-learning strategies were next employed to screen and determine the hub gene, and receiver operating characteristic (ROC) analysis was used to assess diagnostic value. Semaphorin3C (SEMA3C) was identified as a critical biomarker, presenting high diagnostic accuracy for TSCC. In the validation cohorts, SEMA3C exhibited high expression levels in TSCC. The high expression of SEMA3C was a poor prognostic factor in TSCC by the Kaplan-Meier curve. Based on the Gene Ontology (GO) analysis, SEMA3C was mapped in terms related to cell adhesion, positive regulation of JAK-STAT, positive regulation of stem cell maintenance, and positive regulation of NF-κB activity. Single-cell RNA sequencing (ScRNA-seq) analysis showed cells expressing SEMA3C were predominantly tumor cells. Then, we further verified that SEMA3C had high expression in TSCC clinical samples. In addition, the knockdown of SEMA3C suppressed the proliferation, migration, and invasion of TSCC cells in vitro. This study is the first to report the involvement of SEMA3C in TSCC, suggesting that upregulated SEMA3C could be a novel and critical potential biomarker for future predictive diagnostics, prevention, prognostic assessment, and personalized medical services in TSCC.
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Affiliation(s)
- Huixin Dou
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Can Song
- Research and Development Department, Allife Medicine Inc., Beijing, China
| | - Xiaoyan Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University, Beijing, China
| | - Zhien Feng
- Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Yingying Su
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
| | - Hao Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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2
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Gao S, Song H. Integrated comparison of the mRNAome in cartilage, synovium, and macrophages in osteoarthritis. Z Rheumatol 2024; 83:62-70. [PMID: 35178608 DOI: 10.1007/s00393-022-01171-y] [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] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
The precise molecular mechanisms associated with osteoarthritis (OA), the most common musculoskeletal disorder, are poorly understood. There are currently no effective treatments to prevent the initiation and progression of the disease. In recent years, the development of mRNAome has made it possible to identify new mechanisms and therapeutic targets. However, the differentially expressed genes screened by different microarrays are not completely the same. In order to avoid this shortcoming, we integrate the different genes from different tissues and data sets, and select the commonly expressed genes for further studies.
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Affiliation(s)
- Siming Gao
- Department of Rheumatology, Beijing Jishuitan Hospital, No. 31, Xin Jie Kou East Street, Xicheng District, 100035, Beijing, China
| | - Hui Song
- Department of Rheumatology, Beijing Jishuitan Hospital, No. 31, Xin Jie Kou East Street, Xicheng District, 100035, Beijing, China.
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Sajadian M, Khademi B, Moinzadeh L, Ghaderi A, Jafarzadeh A, Razmkhah M. Modulation of semaphorin 3C & 4D expression in cancerous tissues from individuals with laryngeal squamous cell carcinoma. Indian J Med Res 2023; 158:432-438. [PMID: 38006346 DOI: 10.4103/ijmr.ijmr_3148_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND OBJECTIVES Semaphorins were initially characterized as axon guidance factors but were subsequently implicated in the regulation of immune responses, angiogenesis, organ formation and a variety of other physiological and developmental functions. Various semaphorins enhance or inhibit tumour progression through different mechanisms. The objective of this study was to assess the expression of various semaphorins and vascular endothelial growth factor (VEGF) gene transcripts as well as the serum level of Sema3A in individuals with laryngeal squamous cell carcinoma (LSCC). METHODS Tissue expression of Sema3A, Sema3C, Sema4D, Sema6D and VEGF was determined in both tumour tissues and tissues around the tumour from 30 individuals with pathologically confirmed LSCC using quantitative real-time PCR. Furthermore, the serum level of Sema3A in these individuals was assessed using enzyme-linked immunosorbent assay. RESULTS Sema3C gene transcript showed a significant increase (P=0.001), while Sema4D was observed with a significant decrease in tumour samples compared to non-tumoural tissues (P≤0.01). The expression of the Sema3C gene was found to be associated with the stage of LSCC tumour as it was statistically significant for tumours with stage IV (P<0.01). The serum level of Sema3A was not found to be significant between cases and controls. INTERPRETATION CONCLUSIONS Increased expression of Sema3C but decreased expression of Sema4D in tumour tissue of LSCC may introduce these two growth factors as crucial mediators orchestrating tumour growth in individuals with LSCC. This result could open a new vision for the treatment of this malignancy.
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Affiliation(s)
- Marzieh Sajadian
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Bijan Khademi
- Research Center of Otolaryngology Head & Neck Surgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Otolaryngology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Moinzadeh
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Tissue Engineering & Applied Cell Sciences, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Tissue Engineering & Applied Cell Sciences, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdollah Jafarzadeh
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahboobeh Razmkhah
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Tissue Engineering & Applied Cell Sciences, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Qin Y, Tu X, Huang M, Ma C, Huang Q, Huang Q, Shu H, Ou C. Novel Long Noncoding RNAs, LINC01093 and MYLK-AS1, Serve as Potential Diagnostic and Prognostic Biomarkers or Hepatocellular Carcinoma. DNA Cell Biol 2023; 42:488-497. [PMID: 37527208 DOI: 10.1089/dna.2022.0566] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal human malignancies worldwide. In this research, we aimed to identify long noncoding RNAs (lncRNAs) as biomarkers for HCC diagnosis and prognosis. lncRNA expression profiles were obtained from Gene Expression Omnibus and The Cancer Genome Atlas databases. The differentially expressed lncRNAs between HCC and adjacent tissues were analyzed with bioinformatic tools. Four lncRNAs with area under the curve of the receiver operating characteristic curve >0.9 were selected from both datasets. Univariate and Kaplan-Meier analyses were performed to obtain LINC01093, MYLK-AS1, and MCM3AP-AS1 as the optimal diagnostic and prognostic biomarkers. Finally, qPCR confirmed that LINC01093 and MYLK-AS1 were significantly differentially expressed in HCC and adjacent normal tissues. In general, we demonstrated that novel lncRNAs, LINC01093 and MYLK-AS1, could be used as potential diagnostic and prognostic biomarkers for HCC.
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Affiliation(s)
- Yanming Qin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Xin Tu
- Department of Clinical Laboratory, Liuzhou Municipal Liutie Central Hospital, Liuzhou, People's Republic of China
| | - Meifang Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Caifang Ma
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Qiongqing Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Qiqi Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
| | - Chao Ou
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning City, People's Republic of China
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5
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Bhasin S, Dusek C, Peacock JW, Cherkasov A, Wang Y, Gleave M, Ong CJ. Dependency of Tamoxifen Sensitive and Resistant ER + Breast Cancer Cells on Semaphorin 3C (SEMA3C) for Growth. Cells 2023; 12:1715. [PMID: 37443749 PMCID: PMC10341167 DOI: 10.3390/cells12131715] [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: 05/05/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Estrogen receptor positive (ER+) breast cancer (BCa) accounts for the highest proportion of breast cancer-related deaths. While endocrine therapy is highly effective for this subpopulation, endocrine resistance remains a major challenge and the identification of novel targets is urgently needed. Previously, we have shown that Semaphorin 3C (SEMA3C) is an autocrine growth factor that drives the growth and treatment resistance of various cancers, but its role in breast cancer progression and endocrine resistance is poorly understood. Here, we report that SEMA3C plays a role in maintaining the growth of ER+ BCa cells and is a novel, tractable therapeutic target for the treatment of ER+ BCa patients. Analyses of publicly available clinical datasets indicate that ER+ BCa patients express significantly higher levels of SEMA3C mRNA than other subtypes. Furthermore, SEMA3C mRNA expression was positively correlated with ESR1 mRNA expression. ER+ BCa cell lines (MCF7 and T47D) expressed higher levels of SEMA3C mRNA and protein than a normal mammary epithelial MCF10A cell line. ER siRNA knockdown was suppressed, while dose-dependent beta-estradiol treatment induced SEMA3C expression in both MCF7 and T47D cells, suggesting that SEMA3C is an ER-regulated gene. The stimulation of ER+ BCa cells with recombinant SEMA3C activated MAPK and AKT signaling in a dose-dependent manner. Conversely, SEMA3C silencing inhibited Estrogen Receptor (ER) expression, MAPK and AKT signaling pathways while simultaneously inducing apoptosis, as monitored by flow cytometry and Western blot analyses. SEMA3C silencing significantly inhibited the growth of ER+ BCa cells, implicating a growth dependency of ER+ BCa cells on SEMA3C. Moreover, the analysis of tamoxifen resistant (TamR) cell models (TamC3 and TamR3) showed that SEMA3C levels remain high despite treatment with tamoxifen. Tamoxifen-resistant cells remained dependent on SEMA3C for growth and survival. Treatment with B1SP Fc fusion protein, a SEMA3C pathway inhibitor, attenuated SEMA3C-induced signaling and growth across a panel of tamoxifen sensitive and resistant ER+ breast cancer cells. Furthermore, SEMA3C silencing and B1SP treatment were associated with decreased EGFR signaling in TamR cells. Here, our study implicates SEMA3C in a functional role in ER+ breast cancer signaling and growth that suggests ER+ BCa patients may benefit from SEMA3C-targeted therapy.
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Affiliation(s)
- Satyam Bhasin
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher Dusek
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - James W. Peacock
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher J. Ong
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
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Bica C, Tirpe A, Nutu A, Ciocan C, Chira S, Gurzau ES, Braicu C, Berindan-Neagoe I. Emerging roles and mechanisms of semaphorins activity in cancer. Life Sci 2023; 318:121499. [PMID: 36775114 DOI: 10.1016/j.lfs.2023.121499] [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: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Semaphorins are regulatory molecules that are linked to the modulation of several cancer processes, such as angiogenesis, cancer cell invasiveness and metastasis, tumor growth, as well as cancer cell survival. Semaphorin (SEMA) activity depends on the cancer histotypes and their particularities. In broad terms, the effects of SEMAs result from their interaction with specific receptors/co-receptors - Plexins, Neuropilins and Integrins - and the subsequent effects upon the downstream effectors (e.g. PI3K/AKT, MAPK/ERK). The present article serves as an integrative review work, discussing the broad implications of semaphorins in cancer, focusing on cell proliferation/survival, angiogenesis, invasion, metastasis, stemness, and chemo-resistance/response whilst highlighting their heterogeneity as a family. Herein, we emphasized that semaphorins are largely implicated in cancer progression, interacting with the tumor microenvironment components. Whilst some SEMAs (e.g. SEMA3A, SEMA3B) function widely as tumor suppressors, others (e.g. SEMA3C) act as pro-tumor semaphorins. The differences observed in terms of the biological structure of SEMAs and the particularities of each cancer histotypes require that each semaphorin be viewed as a unique entity, and its roles must be researched accordingly. A more in-depth and comprehensive view of the molecular mechanisms that promote and sustain the malignant behavior of cancer cells is of utmost importance.
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Affiliation(s)
- Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania; Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes Street, 400012 Cluj-Napoca, Romania.
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Sergiu Chira
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Eugen S Gurzau
- Cluj School of Public Health, College of Political, Administrative and Communication Sciences, Babes-Bolyai University, 7 Pandurilor Street, Cluj-Napoca, Romania; Environmental Health Center, 58 Busuiocului Street, 400240 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
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Zhang L, Wang X, Zhao W, Liu J. Overview of m 6A and circRNAs in human cancers. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04610-8. [PMID: 36807759 DOI: 10.1007/s00432-023-04610-8] [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: 10/21/2022] [Accepted: 01/27/2023] [Indexed: 02/21/2023]
Abstract
N6-methyladenosine (m6A), the richest post-transcriptional modification of RNA in eukaryotic cells, is dynamically installed/uninstalled by the RNA methylase complex ("writer") and demethylase ("eraser") and recognized by the m6A-binding protein ("reader"). M6A modification on RNA metabolism involves maturation, nuclear export, translation and splicing, thereby playing a critical role in cellular pathophysiology and disease processes. Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed loop structure. Due to its conserved and stable properties, circRNAs could participate in physiological and pathological processes through unique pathways. Despite the recent discovery of m6A and circRNAs remains in the initial stage, research has shown that m6A modifications are widespread in circRNAs and regulates circRNA metabolism, including biogenesis, cell localization, translation, and degradation. In this review, we describe the functional crosstalk between m6A and circRNAs, and illustrate their roles in cancer development. Moreover, we discuss the potential mechanisms and future research directions of m6A modification and circRNAs.
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Affiliation(s)
- Leyu Zhang
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China
| | - Xi Wang
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China.
| | - Wei Zhao
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China.
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China.
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8
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Wang C, Song D, Huang Q, Liu Q. Advances in SEMA3F regulation of clinically high-incidence cancers. Cancer Biomark 2023; 38:131-142. [PMID: 37599522 DOI: 10.3233/cbm-230085] [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] [Indexed: 08/22/2023]
Abstract
Cancer has become a leading cause of morbidity and mortality in recent years. Its high prevalence has had a severe impact on society. Researchers have achieved fruitful results in the causative factors, pathogenesis, treatment strategies, and cancer prevention. Semaphorin 3F (SEMA3F), a member of the signaling family, was initially reported in the literature to inhibit the growth, invasion, and metastasis of cancer cells in lung cancer. Later studies showed it has cancer-inhibiting effects in malignant tumors such as breast, colorectal, ovarian, oral squamous cell carcinoma, melanoma, and head and neck squamous carcinoma. In contrast, recent studies have reported that SEMA3F is expressed more in hepatocellular carcinoma than in normal tissue and promotes metastasis of hepatocellular carcinoma. We chose lung, breast, colorectal, and hepatocellular carcinomas with high clinical prevalence to review the roles and molecular mechanisms of SEMA3F in these four carcinomas. We concluded with an outlook on clinical interventions for patients targeting SEMA3F.
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Affiliation(s)
- Chaofeng Wang
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Dezhi Song
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Huang
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Liu
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
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Zou Y, Cao C, Wang Y, Zhou Y, Yao S, Zhang L, Zheng K, Zhang H, Qin W, Qin K, Xiong H, Yuan X, Fu S, Wang Y, Xiong H. Multi-omics consensus portfolio to refine the classification of lung adenocarcinoma with prognostic stratification, tumor microenvironment, and unique sensitivity to first-line therapies. Transl Lung Cancer Res 2022; 11:2243-2260. [PMID: 36519025 PMCID: PMC9742627 DOI: 10.21037/tlcr-22-775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/21/2022] [Indexed: 09/09/2023]
Abstract
BACKGROUND Molecular classification of lung adenocarcinoma (LUAD) based on transcriptomic features has been widely studied. The complementarity of data obtained from multilayer molecular biology could help the LUAD classification via combining multi-omics information. METHODS We successfully divided samples from the The Cancer Genome Atlas (TCGA) (n=437) into four subtypes (CS1, CS2, CS3 and CS4) by 10 comprehensive multi-omics clustering methods in the "movics" R package. Meanwhile, external validation sets from different sequencing technologies proved the robustness of the grouping model. The relationship between subtypes, prognosis, molecular features, tumor microenvironment and response to first-line therapy was further analyzed. Next we used univariate Cox regression analysis and Lasso regression analysis to explore the application of biomarkers in clinical prognosis and constructed a prognostic model. RESULTS CS1 showed the worst overall survival (OS) among all four clusters, possibly related to its poor immune infiltration, higher tumor mutation and worse chromosomal stability. Patients in different subtypes differed significantly in cancer stem cell characteristics, activation of cancer-related pathways, sensitivity to chemotherapy and immunotherapy. The prognostic model showed good predictive performance. The 1-, 2- and 3-year areas under the curve of risk score were 0.779, 0.742 and 0.678, respectively. Seven genes (DKK1, TSPAN7, ID1, DLGAP5, HHIPL2, CD40 and SEMA3C) used to build the model may be potential therapeutic targets for LUAD. CONCLUSIONS Four LUAD subtypes with different molecular characteristics and clinical implications were identified successfully through bioinformatic analysis. Our results may contribute to precision medicine and inform the development of rational clinical strategies for targeted and immune therapies.
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Affiliation(s)
- Yanmei Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenlin Cao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yilu Zhou
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Shuo Yao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Zheng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengling Fu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Qu X, Xie J, Zhang Y, Wang Z. Solamargine Alleviates Proliferation and Metastasis of Cervical Cancer Cells by Blocking the CXCL3-Mediated Erk Signaling Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:7634754. [PMID: 36345403 PMCID: PMC9637034 DOI: 10.1155/2022/7634754] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 07/05/2022] [Accepted: 07/23/2022] [Indexed: 07/30/2023]
Abstract
Solamargine has unique antitumor efficacy in a variety of cancers. The study is to explore the role of solamargine in cervical cancer. HeLa and SiHa cells were exposed to solamargine treatment at divergent concentrations (0, 5, 10, and 20 μM). The antitumor role of solamargine in cervical cancer cells was determined by cell counting kit 8 (CCK-8), colony formation, scratch test, transwell assay, and western blot. The expression of mRNAs regulating the extracellular regulated protein kinases (Erk) pathway in solamargine-treated cells was detected by qRT-PCR. Rescue experiments were conducted to explore the effect of C-X-C motif chemokine ligand 3 (CXCL3). Following that, we inhibited Erk1/2 by PD98059 to investigate the interplay between CXCL3 and Erk pathway in solamargine-treated cells by measuring migration, invasion, and related matrix metalloproteinase (MMP) expressions. Solamargine inhibited the viability, proliferation, migration, and invasion of cervical cancer cells in a dose-dependent manner. The expression of p-Erk1/2 was downregulated by solamargine. CXCL3 overexpression abrogated the antitumor effect of solamargine on cervical cancer cells. The inhibition of the Erk signaling pathway restored the inhibiting role of solamargine which interfered with CXCL3 overexpression, in invasion, migration, and expressions of MMP-2 and MMP-9 in cervical cancer cells. Moreover, solamargine inhibited the growth of tumor in vivo xenograft model. Solamargine alleviated proliferation and metastasis of cervical cancer cells by blocking the CXCL3-mediated Erk signaling pathway.
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Affiliation(s)
- Xiangdong Qu
- Department of Gynecology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Jirong Xie
- Department of Obstetrics and Gynecology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Youyang Zhang
- Department of Obstetrics and Gynecology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Zhimin Wang
- Department of Integrated Traditional Chinese and Western Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
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11
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Zhang G, Li T, Tan G, Song Y, Liu Q, Wang K, Ai J, Zhou Z, Li W. Identity of
MMP1
and its effects on tumor progression in head and neck squamous cell carcinoma. Cancer Med 2022; 11:2516-2530. [PMID: 35426219 PMCID: PMC9189457 DOI: 10.1002/cam4.4623] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/14/2021] [Accepted: 01/01/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Gehou Zhang
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Tieqi Li
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Guolin Tan
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Yexun Song
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Qian Liu
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Kai Wang
- Department of Otolaryngology‐Head Neck Surgery The First Affiliated Hospital of Shaoyang University Shaoyang China
| | - Jingang Ai
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Zheng Zhou
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
| | - Wei Li
- Department of Otolaryngology‐Head Neck Surgery Third Xiangya Hospital of Central South University Changsha Hunan Province China
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12
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Chen Q, Chu L, Li X, Li H, Zhang Y, Cao Q, Zhuang Q. Investigation of an FGFR-Signaling-Related Prognostic Model and Immune Landscape in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2022; 9:801715. [PMID: 35237609 PMCID: PMC8882630 DOI: 10.3389/fcell.2021.801715] [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: 10/25/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background: There is accumulating evidence on the clinical importance of the fibroblast growth factor receptor (FGFR) signal, hypoxia, and glycolysis in the immune microenvironment of head and neck squamous cell carcinoma (HNSCC), yet reliable prognostic signatures based on the combination of the fibrosis signal, hypoxia, and glycolysis have not been systematically investigated. Herein, we are committed to establish a fibrosis–hypoxia–glycolysis–related prediction model for the prognosis and related immune infiltration of HNSCC. Methods: Fibrotic signal status was estimated with microarray data of a discovery cohort from the TCGA database using the UMAP algorithm. Hypoxia, glycolysis, and immune-cell infiltration scores were imputed using the ssGSEA algorithm. Cox regression with the LASSO method was applied to define prognostic genes and develop a fibrosis–hypoxia–glycolysis–related gene signature. Immunohistochemistry (IHC) was conducted to identify the expression of specific genes in the prognostic model. Protein expression of several signature genes was evaluated in HPA. An independent cohort from the GEO database was used for external validation. Another scRNA-seq data set was used to clarify the related immune infiltration of HNSCC. Results: Six genes, including AREG, THBS1, SEMA3C, ANO1, IGHG2, and EPHX3, were identified to construct a prognostic model for risk stratification, which was mostly validated in the independent cohort. Multivariate analysis revealed that risk score calculated by our prognostic model was identified as an independent adverse prognostic factor (p < .001). Activated B cells, immature B cells, activated CD4+ T cells, activated CD8+ T cells, effector memory CD8+ T cells, MDSCs, and mast cells were identified as key immune cells between high- and low-risk groups. IHC results showed that the expression of SEMA3C, IGHG2 were slightly higher in HNSCC tissue than normal head and neck squamous cell tissue. THBS1, ANO1, and EPHX3 were verified by IHC in HPA. By using single-cell analysis, FGFR-related genes and highly expressed DEGs in low-survival patients were more active in monocytes than in other immune cells. Conclusion: A fibrosis–hypoxia–glycolysis–related prediction model provides risk estimation for better prognoses to patients diagnosed with HNSCC.
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Affiliation(s)
- Qi Chen
- Transplantation Center, Third Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Ling Chu
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xinyu Li
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Hao Li
- Transplantation Center, Third Xiangya Hospital, Central South University, Changsha, China
| | - Ying Zhang
- Transplantation Center, Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingtai Cao
- Hunan Normal University School of Medicine, Changsha, China
| | - Quan Zhuang
- Transplantation Center, Third Xiangya Hospital, Central South University, Changsha, China
- Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
- *Correspondence: Quan Zhuang,
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13
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Li M, Xu D, Xia X, Ni B, Zhu C, Zhao G, Cao H. Sema3C promotes hepatic metastasis and predicts poor prognosis in gastric adenocarcinoma. J Int Med Res 2021; 49:3000605211009802. [PMID: 33909533 PMCID: PMC8108085 DOI: 10.1177/03000605211009802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Semaphorin 3C (Sema3C) may regulate tumor metastasis and prognosis. We determined the biological roles of Sema3C in the hepatic metastasis of gastric adenocarcinoma and evaluated its clinical significance as a potential biomarker. METHODS Sema3C expression in gastric cancer (GC) cell lines and tissues was measured using RT-qPCR and western blotting. Moreover, Sema3C functions were analyzed using Transwell assays and in vitro metastasis assays in gain- and loss-of-function experiments. Furthermore, the impact of Sema3C on the prognosis of 80 randomly selected patients with GC was investigated by immunohistochemistry. Additionally, the expression of epithelial-mesenchymal transition (EMT) indicators was verified by immunohistochemistry in GC tissues. RESULTS Sema3C expression was significantly upregulated in highly metastatic GC cell lines and tissues. Additionally, Sema3C promoted invasion, migration and hepatic metastasis in GC cells. Moreover, Sema3C expression was positively correlated with clinicopathological features in GC and paired hepatic metastatic tissues, and Sema3C expression was an independent prognostic factor. Finally, Sema3C expression was associated with node metastasis, hepatic metastasis and EMT marker expression. CONCLUSIONS Sema3C may play roles in regulating the EMT and metastasis of gastric adenocarcinoma, highlighting its potential use as a prognostic factor for hepatic metastasis and poor prognosis in gastric adenocarcinoma.
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Affiliation(s)
- Maoran Li
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Danhua Xu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiang Xia
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Bo Ni
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Gang Zhao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Hui Cao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
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14
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Li M, Li H, Chen Q, Wu W, Chen X, Ran L, Si G, Tan X. A Novel and Robust Long Noncoding RNA Panel to Predict the Prognosis of Pancreatic Cancer. DNA Cell Biol 2020; 39:1282-1289. [DOI: 10.1089/dna.2019.5241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Mengying Li
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Hang Li
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Qi Chen
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Wenwen Wu
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Xuyu Chen
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Li Ran
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Guanglin Si
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Xiaodong Tan
- School of Health Sciences, Wuhan University, Wuhan, China
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15
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Zhang L, Hou C, Chen C, Guo Y, Yuan W, Yin D, Liu J, Sun Z. The role of N 6-methyladenosine (m 6A) modification in the regulation of circRNAs. Mol Cancer 2020; 19:105. [PMID: 32522202 PMCID: PMC7285594 DOI: 10.1186/s12943-020-01224-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant modification in eukaryotic cells, regulates RNA transcription, processing, splicing, degradation, and translation. Circular RNA (circRNA) is a class of covalently closed RNA molecules characterized by universality, diversity, stability and conservatism of evolution. Accumulating evidence shows that both m6A modification and circRNAs participate in the pathogenesis of multiple diseases, such as cancers, neurological diseases, autoimmune diseases, and infertility. Recently, m6A modification has been identified for its enrichment and vital biological functions in regulating circRNAs. In this review, we summarize the role of m6A modification in the regulation and function of circRNAs. Moreover, we discuss the potential applications and possible future directions in the field.
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Affiliation(s)
- Lele Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Department of Colorectal Surgery, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, 450007, Henan, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Chaofeng Hou
- Department of Colorectal Surgery, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, 450007, Henan, China
| | - Chen Chen
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yaxin Guo
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450002, Henan, China.
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