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Chu X, Li X, Zhang Y, Dang G, Miao Y, Xu W, Wang J, Zhang Z, Cheng S. Integrative single-cell analysis of human colorectal cancer reveals patient stratification with distinct immune evasion mechanisms. NATURE CANCER 2024:10.1038/s43018-024-00807-z. [PMID: 39147986 DOI: 10.1038/s43018-024-00807-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
The tumor microenvironment (TME) considerably influences colorectal cancer (CRC) progression, therapeutic response and clinical outcome, but studies of interindividual heterogeneities of the TME in CRC are lacking. Here, by integrating human colorectal single-cell transcriptomic data from approximately 200 donors, we comprehensively characterized transcriptional remodeling in the TME compared to noncancer tissues and identified a rare tumor-specific subset of endothelial cells with T cell recruitment potential. The large sample size enabled us to stratify patients based on their TME heterogeneity, revealing divergent TME subtypes in which cancer cells exploit different immune evasion mechanisms. Additionally, by associating single-cell transcriptional profiling with risk genes identified by genome-wide association studies, we determined that stromal cells are major effector cell types in CRC genetic susceptibility. In summary, our results provide valuable insights into CRC pathogenesis and might help with the development of personalized immune therapies.
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Affiliation(s)
| | | | - Yu Zhang
- Changping Laboratory, Beijing, China
| | - Guohui Dang
- Changping Laboratory, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Wenbin Xu
- Changping Laboratory, Beijing, China
| | | | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Lin YY, Lee SY, Cheng YJ. Low-Level Laser Therapy Induces Melanoma Tumor Growth by Promoting Angiogenesis. Life (Basel) 2023; 13:life13020320. [PMID: 36836677 PMCID: PMC9962383 DOI: 10.3390/life13020320] [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: 12/26/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
The effects of low-level laser therapy (LLLT) on tumor growth are inconsistent. In this study, we investigated the effects of LLLT on melanoma tumor growth and angiogenesis. C57/BL6 mice were challenged with B16F10 melanoma cells and treated with LLLT for 5 consecutive days; untreated mice were used as controls. Tumor weight, angiogenesis, immunohistochemistry, and protein levels were compared between the treated and untreated mice. In an in vitro experiment, B16F10 cells were treated with LLLT. Proteins were extracted and subjected to Western blot analysis for analyzing signaling pathways. Compared with the findings in the untreated mice, tumor weight substantially increased in the treated mice. Both immunohistochemical and Western blot analyses revealed markedly increased levels of CD31, a biomarker of vascular differentiation, in the LLLT group. In B16F10 cells, LLLT considerably induced the phosphorylation of extracellular signal-regulated kinase (ERK), which, in turn, phosphorylated p38 mitogen-activated protein kinase (MAPK). Furthermore, LLLT induced the expression of vascular endothelial growth factor, but not hypoxia-inducible factor-1α, through the ERK/p38 MAKP signaling pathways. Our findings indicate that LLLT induces melanoma tumor growth by promoting angiogenesis. Therefore, it should be avoided in patients with melanoma.
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Affiliation(s)
- Yi-Yuan Lin
- Department of Exercise and Health Science, National Taipei University of Nursing and Health Sciences, Taipei 112303, Taiwan
| | - Shin-Yi Lee
- General Education Center, China Medical University, Taichung 406, Taiwan
- Foreign Language Center, Feng Chia University, Taichung 407, Taiwan
| | - Yu-Jung Cheng
- Department of Physical Therapy and Graduate Institute of Rehabilitation Science, China Medical University, Taichung 406, Taiwan
- Department of Rehabilitation, China Medical University Hospital, Taichung 404, Taiwan
- Correspondence: ; Tel.: +886-422053366 (ext. 7308)
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Tiwari A, Trivedi R, Lin SY. Tumor microenvironment: barrier or opportunity towards effective cancer therapy. J Biomed Sci 2022; 29:83. [PMID: 36253762 PMCID: PMC9575280 DOI: 10.1186/s12929-022-00866-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed by tumor cells for successful development and metastasis of tumor. With the advent of 3D culture and advanced bioinformatic methodologies, it is now possible to study TME’s individual components and their interplay at higher resolution. Deeper understanding of the immune cell’s diversity, stromal constituents, repertoire profiling, neoantigen prediction of TMEs has provided the opportunity to explore the spatial and temporal regulation of immune therapeutic interventions. The variation of TME composition among patients plays an important role in determining responders and non-responders towards cancer immunotherapy. Therefore, there could be a possibility of reprogramming of TME components to overcome the widely prevailing issue of immunotherapeutic resistance. The focus of the present review is to understand the complexity of TME and comprehending future perspective of its components as potential therapeutic targets. The later part of the review describes the sophisticated 3D models emerging as valuable means to study TME components and an extensive account of advanced bioinformatic tools to profile TME components and predict neoantigens. Overall, this review provides a comprehensive account of the current knowledge available to target TME.
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Affiliation(s)
- Aadhya Tiwari
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Lindgren M, Rask G, Jonsson J, Berglund A, Lundin C, Jonsson P, Ljuslinder I, Nyström H. Type IV Collagen in Human Colorectal Liver Metastases—Cellular Origin and a Circulating Biomarker. Cancers (Basel) 2022; 14:cancers14143396. [PMID: 35884455 PMCID: PMC9325127 DOI: 10.3390/cancers14143396] [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: 05/18/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Patients with colorectal liver metastases (CLM) can be cured through surgery if metastases are detected early in disease progression. Today, CLM diagnosis relies heavily on diagnostic imaging, and cheap, non-invasive, and efficiently measurable biomarkers are needed. Circulating type IV collagen (COL IV) is a potential biomarker for detecting CLM. Patients with CLM show elevated circulating levels of COL IV and increased tissue expression of COL IV in CLM tissue, which could result from enhanced production and degradation of COL IV. This study aimed to establish the cellular source behind enhanced COL IV levels, which is helpful in the evaluation of the biomarker potential of COL IV. We show that fibroblasts express COL IV both in vitro and in the stromal tissue of CLM. We also found that CLM tissue expresses COL IV-degrading proteases. Lastly, CLM patients have higher circulating COL IV levels than healthy controls. Abstract Circulating type IV collagen (cCOL IV) is a potential biomarker for patients with colorectal liver metastases (CLM) who present with elevated levels of COL IV in both CLM tissue and circulation. This study aimed to establish the cellular origin of elevated levels of COL IV and analyze circulating COL IV in CLM patients. The cellular source was established through in situ hybridization, immunohistochemical staining, and morphological evaluation. Cellular expression in vitro was assessed by immunofluorescence. Tissue expression of COL IV-degrading matrix metalloproteinases (MMPs)-2, -7, -9, and -13 was studied with immunohistochemical staining. Plasma levels of COL IV in CLM patients and healthy controls were analyzed with ELISA. This study shows that cancer-associated fibroblasts (CAFs) express COL IV in the stroma of CLM and that COL IV is expressed in vitro by fibroblasts but not by tumor cells. MMP-2, -7, -9, and -13 are expressed in CLM tissue, mainly by hepatocytes and immune cells, and circulating COL IV is significantly elevated in CLM patients compared with healthy controls. Our study shows that stromal cells, not tumor cells, produce COL IV in CLM, and that circulating COL IV is elevated in patients with CLM.
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Affiliation(s)
- Moa Lindgren
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
- Correspondence:
| | - Gunilla Rask
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
- Department of Medical Biosciences/Pathology, Umeå University, SE-901 87 Umeå, Sweden
| | - Josefin Jonsson
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
| | - Anette Berglund
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
| | - Christina Lundin
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
| | - Pär Jonsson
- Department of Chemistry, Umeå University, SE-907 36 Umeå, Sweden;
| | - Ingrid Ljuslinder
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87 Umeå, Sweden;
| | - Hanna Nyström
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, SE-901 85 Umeå, Sweden; (G.R.); (J.J.); (A.B.); (C.L.); (H.N.)
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87 Umeå, Sweden
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Yin W, Zhu H, Tan J, Xin Z, Zhou Q, Cao Y, Wu Z, Wang L, Zhao M, Jiang X, Ren C, Tang G. Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma. Cancer Cell Int 2021; 21:276. [PMID: 34034744 PMCID: PMC8147444 DOI: 10.1186/s12935-021-01982-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 05/13/2021] [Indexed: 01/05/2023] Open
Abstract
Background Gliomas account for the majority of fatal primary brain tumors, and there is much room for research in the underlying pathogenesis, the multistep progression of glioma, and how to improve survival. In our study, we aimed to identify potential biomarkers or therapeutic targets of glioma and study the mechanism underlying the tumor progression. Methods We downloaded the microarray datasets (GSE43378 and GSE7696) from the Gene Expression Omnibus (GEO) database. Then, we used weighted gene co-expression network analysis (WGCNA) to screen potential biomarkers or therapeutic targets related to the tumor progression. ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) algorithm and TIMER (Tumor Immune Estimation Resource) database were used to analyze the correlation between the selected genes and the tumor microenvironment. Real-time reverse transcription polymerase chain reaction was used to measure the selected gene. Transwell and wound healing assays were used to measure the cell migration and invasion capacity. Western blotting was used to test the expression of epithelial-mesenchymal transition (EMT) related markers. Results We identified specific module genes that were positively correlated with the WHO grade but negatively correlated with OS of glioma. Importantly, we identified that 6 collagen genes (COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, and COL5A2) could regulate the immunosuppressive microenvironment of glioma. Moreover, we found that these collagen genes were significantly involved in the EMT process of glioma. Finally, taking COL3A1 as a further research object, the results showed that knockdown of COL3A1 significantly inhibited the migration, invasion, and EMT process of SHG44 and A172 cells. Conclusions In summary, our study demonstrated that collagen genes play an important role in regulating the immunosuppressive microenvironment and EMT process of glioma and could serve as potential therapeutic targets for glioma management. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01982-0.
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Affiliation(s)
- Wen Yin
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, Hunan, 410205, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Zhaoqi Xin
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Quanwei Zhou
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Yudong Cao
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Zhaoping Wu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China
| | - Lei Wang
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, The Key Laboratory for Carcinogenesis of Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, Hunan, People's Republic of China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, Hunan, 410205, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan Province, 410008, China.
| | - Caiping Ren
- Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, The Key Laboratory for Carcinogenesis of Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, Hunan, People's Republic of China.
| | - Guihua Tang
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The first affiliated hospital of Hunan Normal University, The college of clinical medicine of Human Normal University), Changsha, Hunan Province, 410005, China.
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SRC Signaling in Cancer and Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1270:57-71. [PMID: 33123993 DOI: 10.1007/978-3-030-47189-7_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pioneering experiments performed by Harold Varmus and Mike Bishop in 1976 led to one of the most influential discoveries in cancer research and identified the first cancer-causing oncogene called Src. Later experimental and clinical evidence suggested that Src kinase plays a significant role in promoting tumor growth and progression and its activity is associated with poor patient survival. Thus, several Src inhibitors were developed and approved by FDA for treatment of cancer patients. Tumor microenvironment (TME) is a highly complex and dynamic milieu where significant cross-talk occurs between cancer cells and TME components, which consist of tumor-associated macrophages, fibroblasts, and other immune and vascular cells. Growth factors and chemokines activate multiple signaling cascades in TME and induce multiple kinases and pathways, including Src, leading to tumor growth, invasion/metastasis, angiogenesis, drug resistance, and progression. Here, we will systemically evaluate recent findings regarding regulation of Src and significance of targeting Src in cancer therapy.
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Gu J, Hu W, Liu Y, Zhang X, Yuan L, Du L, Bai M. Role of Platelet-Derived Growth Factor on the Fibrosis Process in Thyroid Carcinoma: Evaluation by Shear Wave Elastography. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2020; 39:1709-1719. [PMID: 32191354 DOI: 10.1002/jum.15269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVES We aimed to determine the correlation between fibrosis and elastic values in papillary thyroid carcinoma (PTC) by shear wave elastography and to evaluate the effect of platelet-derived growth factor (PDGF) on the fibrosis process. METHODS Small interfering RNA (siRNA)-PDGF and normal BCPAP cell lines were injected subcutaneously into the backs of nude mice. The elastic values of all tumors were measured by shear wave elastography. The content of collagen fibers and the expression of PDGF and type IV collagen (COL4) were evaluated by Masson staining and western blotting. RESULTS There were 32 tumors in the control group and 30 tumors in the siRNA-PDGF group. The tumors were divided into 4 subgroups based on maximum diameters of the tumors. The mean elastic values ± SD (Emean , 29.79 ± 11.04 kPa; Emin , 16.98 ± 7.51 kPa, Emax , 39.99 ± 15.30 kPa; and SD, 5.92 ± 2.00 kPa) in the siRNA-PDGF group were lower than in the control group (Emean , 35.73 ± 18.49 kPa; Emin , 23.65 ± 14.92 kPa, Emax , 45.73 ± 22.88 kPa; and SD, 6.02 ± 3.38 kPa). The content of collagen fibers and the expression of platelet-derived growth factor B (PDGFB) and COL4 proteins in the siRNA-PDGF group were lower than in the control group (11.43% ± 6.99% and 19.80% ± 11.70%; P = .010; 0.14 ± 0.06 and 0.27 ± 0.10; P = .002; and 0.11 ± 0.06 and 0.15 ± 0.07; P = .101). The elastic values, collagen fiber content, and PDGFB and COL4 in the 4 subgroups gradually increased with the maximum diameter of tumors. CONCLUSIONS There was a positive correlation among PDGF, tumor stiffness, and fibrosis in the growth of PTC. Thus, PDGF might play an important role in the development of PTC.
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Affiliation(s)
- Jiying Gu
- Department of Ultrasound, Shanghai Fourth People's Hospital, affiliated to Tongji University School of Medicine, Shanghai, China
| | - Wenjie Hu
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Liu
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuemei Zhang
- Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Yuan
- Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianfang Du
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Bai
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Kim K, Jung JH, Yoo HJ, Hyun JK, Park JH, Na D, Yeon JH. Anti-Metastatic Effects of Plant Sap-Derived Extracellular Vesicles in a 3D Microfluidic Cancer Metastasis Model. J Funct Biomater 2020; 11:jfb11030049. [PMID: 32650517 PMCID: PMC7563847 DOI: 10.3390/jfb11030049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Natural medicinal plants have attracted considerable research attention for their potential as effective drugs. The roots, leaves and stems of the plant, Dendropanax morbifera, which is endemic to southern regions of Asia, have long been used as a folk medicine to treat variety of diseases. However, the sap of this plant has not been widely studied and its bioactive properties have yet to be clearly elucidated. Here, we isolated extracellular vesicles from D. morbifera sap with the goal of improving the intracellular delivery efficiency and clinical effectiveness of bioactive compounds in D. morbifera sap. We further investigated the anti-metastatic effects of D. morbifera sap-derived extracellular vesicles (DMS-EVs) using a cancer metastasis model based on 3D microfluidic system that closely mimics the in vivo tumor environment. We found that DMS-EVs exerted a concentration-dependent suppressive effect on cancer-associated fibroblasts (CAFs), which are important mediators of cancer metastasis. DMS-EVs also altered expression level of genes, especially growth factor and extracellular matrix (ECM)-related genes, including integrin and collagen. Our findings suggest that DMS-EVs can act as anti-CAF agents to reduce CAFs in the tumor microenvironment. They further indicate the utility of our 3D microfluidic model for various drug-screening assays as a potential alternative to animal testing for use in validating therapeutic effects on cancer metastasis.
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Affiliation(s)
- Kimin Kim
- Department of Integrative Biosciences, University of Brain Education, Cheonan 31228, Korea; (K.K.); (H.J.Y.)
| | - Jik-Han Jung
- Department of Bio and Brain engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (J.-H.J.); (J.-H.P.)
| | - Hye Ju Yoo
- Department of Integrative Biosciences, University of Brain Education, Cheonan 31228, Korea; (K.K.); (H.J.Y.)
| | - Jae-Kyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju 28119, Korea;
| | - Ji-Ho Park
- Department of Bio and Brain engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (J.-H.J.); (J.-H.P.)
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul 06911, Korea;
| | - Ju Hun Yeon
- Department of Integrative Biosciences, University of Brain Education, Cheonan 31228, Korea; (K.K.); (H.J.Y.)
- Correspondence: ; Tel.: +82-41-529-2621; Fax: +82-41-529-2674
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Liu Q, Zhang W, Wu Z, Liu H, Hu H, Shi H, Li S, Zhang X. Construction of a circular RNA-microRNA-messengerRNA regulatory network in stomach adenocarcinoma. J Cell Biochem 2019; 121:1317-1331. [PMID: 31486138 DOI: 10.1002/jcb.29368] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 08/20/2019] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Circular RNAs (circRNAs) can interact with microRNAs (miRNAs) to regulate gene expression in cancer cells. However, the roles of competitive endogenous RNA (ceRNA) networks consisting of differentially expressed circRNAs (DECs), miRNAs, and messenger RNAs (mRNAs) in stomach adenocarcinoma (STAD) remain unclear. This study was performed to explore novel regulatory networks in STAD. METHODS The circRNA expression profiles, as well as miRNA and mRNA sequence data of STAD, were retrieved from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Candidates were identified to construct a network through a comprehensive bioinformatics strategy. The expression of hub-genes identified by protein-protein interactions (PPI) was validated by quantitative reverse transcription (RT) polymerase chain reaction. RESULTS A total of 51 DECs were identified in the GSE83521 and GSE89143 datasets of GEO. A total of 11 448 differentially expressed mRNAs (DEMs) and 458 differentially expressed miRNAs (DEMIs) were obtained by RNA sequencing of TCGA-STAD. Prediction by using five online databases (Cancer-Specific CircRNA, CircInteractome, miRTarBase, miRDB, and TargetScan) resulted in the selection of 6 DECs, 6 DEMIs, and 36 DEMs to establish a circRNA-miRNA-mRNA regulatory network based on the interactions of circRNA-miRNA and miRNA-mRNA. Through PPI analysis, four hub-genes (COL10A1, COL5A2, COL4A1, and COL3A1) were discovered. Moreover, overexpressions of COL10A1, COL5A1, and COL4A1 were associated with a poor overall survival rate of patients with STAD. On the basis of TNM staging, we found that the expressions of COL10A1, COL5A2, and COL3A1 in T2, T3, and T4 was significantly higher than in T1. Hub-genes expressions were validated in STAD tissues and cell lines. CONCLUSIONS Our study provides a novel perspective on the regulatory mechanism of STAD involving ceRNAs including DECs, DEMIs, and DEMs.
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Affiliation(s)
- Qincheng Liu
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Wei Zhang
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhenqian Wu
- The Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Haijun Liu
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Huiqiong Hu
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Huisen Shi
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shaohua Li
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xueli Zhang
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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Amini P, Nassiri S, Ettlin J, Malbon A, Markkanen E. Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma. Dis Model Mech 2019; 12:dmm.040444. [PMID: 31308057 PMCID: PMC6737962 DOI: 10.1242/dmm.040444] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
Spontaneous canine simple mammary carcinomas (mCA) are often viewed as models of human mCA. Cancer-associated stroma (CAS) is central for initiation and progression of human cancer, and is likely to play a key role in canine tumours as well. However, canine CAS lacks characterisation and it remains unclear how canine and human CAS compare. Formalin-fixed paraffin embedded (FFPE) tissue constitutes a valuable resource of patient material, but chemical crosslinking has largely precluded its analysis by next-generation RNA sequencing (RNAseq). We have recently established a protocol to isolate CAS and normal stroma from archival FFPE tumours using laser-capture microdissection followed by RNAseq. Using this approach, we have analysed stroma from 15 canine mCA. Our data reveal strong reprogramming of canine CAS. We demonstrate a high-grade molecular homology between canine and human CAS, and show that enrichment of upregulated canine CAS genes strongly correlates with the enrichment of an independently derived human stromal signature in the TCGA breast tumour dataset. Relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Finally, we establish the prognostic potential of the canine CAS signature in human samples, emphasising the relevance of studying canine CAS as a model of the human disease. In conclusion, we provide a proof-of-principle to analyse specific subsections of FFPE tissue by RNAseq, and compare stromal gene expression between human and canine mCA to reveal molecular drivers in CAS supporting tumour growth and malignancy. Summary: This study offers proof-of-principle for a novel protocol to analyse gene expression in subsections of FFPE patient tissue, supporting the use of spontaneous canine mammary tumours as models for the human disease.
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Affiliation(s)
- Parisa Amini
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Sina Nassiri
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Julia Ettlin
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Alexandra Malbon
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
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Abstract
Fibrosis is part of a tissue repair response to injury, defined as increased deposition of extracellular matrix. In some instances, fibrosis is beneficial; however, in the majority of diseases fibrosis is detrimental. Virtually all chronic progressive diseases are associated with fibrosis, representing a huge number of patients worldwide. Fibrosis occurs in all organs and tissues, becomes irreversible with time and further drives loss of tissue function. Various cells types initiate and perpetuate pathological fibrosis by paracrine activation of the principal cellular executors of fibrosis, i.e. stromal mesenchymal cells like fibroblasts, pericytes and myofibroblasts. Multiple pathways are involved in fibrosis, platelet-derived growth factor (PDGF)-signaling being one of the central mediators. Stromal mesenchymal cells express both PDGF receptors (PDGFR) α and β, activation of which drives proliferation, migration and production of extracellular matrix, i.e. the principal processes of fibrosis. Here, we review the role of PDGF signaling in organ fibrosis, with particular focus on the more recently described ligands PDGF-C and -D. We discuss the potential challenges, opportunities and open questions in using PDGF as a potential target for anti-fibrotic therapies.
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Affiliation(s)
| | - Jürgen Floege
- Division of Nephrology, RWTH University of Aachen, Germany
| | - Peter Boor
- Institute of Pathology, RWTH University of Aachen, Germany; Division of Nephrology, RWTH University of Aachen, Germany.
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12
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Li H, Wang Y, Liu H, Shi Q, Li H, Wu W, Zhu D, Amos CI, Fang S, Lee JE, Li Y, Han J, Wei Q. Genetic variants of PDGF signaling pathway genes predict cutaneous melanoma survival. Oncotarget 2017; 8:74595-74606. [PMID: 29088810 PMCID: PMC5650365 DOI: 10.18632/oncotarget.20245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022] Open
Abstract
To investigate whether genetic variants of platelet-derived growth factor (PDGF) signaling pathway genes are associated with survival of cutaneous melanoma (CM) patients, we assessed associations of single-nucleotide polymorphisms in PDGF pathway with melanoma-specific survival in 858 CM patients of M.D. Anderson Cancer Center (MDACC). Additional data of 409 cases from Harvard University were also included for further analysis. We identified 13 SNPs in four genes (COL6A3, NCK2, COL5A1 and PRKCD) with a nominal P < 0.05 and false discovery rate (FDR) < 0.2 in MDACC dataset. Based on linkage disequilibrium, functional prediction and minor allele frequency, a representative SNP in each gene was selected. In the meta-analysis using MDACC and Harvard datasets, there were two SNPs associated with poor survival of CM patients: rs6707820 C>T in NCK2 (HR = 1.87, 95% CI = 1.35-2.59, Pmeta= 1.53E-5); and rs2306574 T>C in PRKCD (HR = 1.73, 95% CI = 1.33-2.24, Pmeta= 4.56E-6). Moreover, CM patients in MDACC with combined risk genotypes of these two loci had markedly poorer survival (HR = 2.47, 95% CI = 1.58-3.84, P < 0.001). Genetic variants of rs6707820 C>T in NCK2 and rs2306574 T>C in PRKCD of the PDGF signaling pathway may be biomarkers for melanoma survival.
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Affiliation(s)
- Hong Li
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China.,Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yanru Wang
- Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qiong Shi
- Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongyu Li
- Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wenting Wu
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Dakai Zhu
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Christopher I Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
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13
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NMU signaling promotes endometrial cancer cell progression by modulating adhesion signaling. Oncotarget 2016; 7:10228-42. [PMID: 26849234 PMCID: PMC4891116 DOI: 10.18632/oncotarget.7169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/21/2016] [Indexed: 11/25/2022] Open
Abstract
Neuromedin U (NMU) was originally named based on its strong uterine contractile activity, but little is known regarding its signaling/functions in utero. We identified that NMU and one of its receptors, NMUR2, are not only present in normal uterine endometrium but also co-expressed in endometrial cancer tissues, where the NMU level is correlated with the malignant grades and survival of patients. Cell-based assays further confirmed that NMU signaling can promote cell motility and proliferation of endometrial cancer cells derived from grade II tumors. Activation of NMU pathway in these endometrial cancer cells is required in order to sustain expression of various adhesion molecules, such as CD44 and integrin alpha1, as well as production of their corresponding extracellular matrix ligands, hyaluronan and collagen IV; it also increased the activity of SRC and its downstream proteins RHOA and RAC1. Thus, it is concluded that NMU pathway positively controls the adhesion signaling-SRC-Rho GTPase axis in the tested endometrial cancer cells and that changes in cell motility and proliferation can occur when there is manipulation of NMU signaling in these cells either in vitro or in vivo. Intriguingly, this novel mechanism also explains how NMU signaling promotes the EGFR-driven and TGFβ receptor-driven mesenchymal transitions. Through the above axis, NMU signaling not only can promote malignancy of the tested endometrial cancer cells directly, but also helps these cells to become more sensitive to niche growth factors in their microenvironment.
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14
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Paolillo M, Serra M, Schinelli S. Integrins in glioblastoma: Still an attractive target? Pharmacol Res 2016; 113:55-61. [PMID: 27498157 DOI: 10.1016/j.phrs.2016.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 02/08/2023]
Abstract
Integrin-mediated signaling pathways have been found to promote the invasiveness and survival of glioma cells by modifying the brain microenvironment to support the formation of the tumoral niche. A variety of cells in the niche express integrin receptors, including tumor-associated macrophages, fibroblasts, endothelial cells and pericytes. In particular, RGD-binding integrins have been demonstrated to have an important role in the epithelial-mesenchymal transition process, considered the first step in the infiltration of tissue by cancer cells and molecular markers of which have been found in glioma cells. In simultaneous research, Small Molecule Integrin Antagonists (SMIA) yielded initially promising results in in vitro and in vivo studies, leading to clinical trials to test their safety and efficacy in combination with other anticancer drugs in the treatment of several tumor types. The initially high expectations, especially because of their antiangiogenic activity, which appeared to be a winning strategy against GBM, were not confirmed and this cast serious doubts on the real benefits to be gained from the use of SMIA for the treatment of cancer in humans. In this review, we provide an overview of recent findings concerning the functional roles of integrins, especially RGD-binding integrins, in the processes related to glioma cells survival and brain tissue infiltration. These findings disclose a new scenario in which recently developed SMIA might become useful tools to hinder glioblastoma cell dissemination.
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Affiliation(s)
- Mayra Paolillo
- Department of Drug Sciences, University of Pavia, Pavia, Italy.
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, Pavia, Italy
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15
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Som A, Bloch S, Ippolito JE, Achilefu S. Acidic extracellular pH of tumors induces octamer-binding transcription factor 4 expression in murine fibroblasts in vitro and in vivo. Sci Rep 2016; 6:27803. [PMID: 27302093 PMCID: PMC4908587 DOI: 10.1038/srep27803] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022] Open
Abstract
Octamer-binding transcription factor 4 (OCT-4) is an important marker of cellular de-differentiation that can be induced by environmental stressors, such as acidity. Here we demonstrate that chronic acidic stress in solid tumors induced OCT-4 expression in fibroblasts and other stromal cells in four tumor models. The results have implications for how tumors utilize pH modulation to recruit associated stromal cells, induce partial reprogramming of tumor-associated stromal cells, and respond to therapy.
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Affiliation(s)
- Avik Som
- Department of Radiology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA
| | - Sharon Bloch
- Department of Radiology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA
| | - Joseph E Ippolito
- Department of Radiology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA.,Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA
| | - Samuel Achilefu
- Department of Radiology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA.,Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, 63110, USA
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16
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Lee JS, Kim W, Cho S, Jun J, Cho KH, Jang J. Multidimensional hybrid conductive nanoplate-based aptasensor for platelet-derived growth factor detection. J Mater Chem B 2016; 4:4447-4454. [PMID: 32263427 DOI: 10.1039/c6tb00726k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the development of disease diagnoses, rapid responses to and accurate selectivity for target analytes are critical aspects. As one diagnostic approach, biosensors with high sensitivity and selectivity are investigated to detect disorder factors (e.g., endocrine disruptors and cancer oncoproteins). In this report, we demonstrate an aptamer-functionalized multidimensional hybrid conducting-polymer (3-carboxylated polypyrrole) plate (A_MHCPP) based field-effect transistor (FET) sensor to detect a platelet-derived growth factor (PDGF-BB). The multidimensional hybrid conducting-polymer plates (MHCPPs) are formed on the graphene surface by using electrodeposition and vapor deposition polymerization (VDP) steps. The amine-functionalized PDGF-B binding aptamers are then immobilized on the carboxylated polypyrrole surface by means of covalent bond formation (-CONH). The prepared FET sensors present high sensing ability toward PDGF-BB - as low as 1.78 fM among interfering biomolecules at room temperature.
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Affiliation(s)
- Jun Seop Lee
- School of Chemical and Biological Engineering, College of Engineering, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 151-742, Korea.
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