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Huang CG, Liu Q, Zheng ST, Liu T, Tan YY, Peng TY, Chen J, Lu XM. Chemokines and Their Receptors: Predictors of Therapeutic Potential in Tumor Microenvironment on Esophageal Cancer. Dig Dis Sci 2024; 69:1562-1570. [PMID: 38580886 PMCID: PMC11098888 DOI: 10.1007/s10620-024-08392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Esophageal carcinoma (ESCA) is an aggressive solid tumor. The 5-year survival rate for patients with ESCA is estimated to be less than 20%, mainly due to tumor invasion and metastasis. Therefore, it is urgent to improve early diagnostic tools and effective treatments for ESCA patients. Tumor microenvironment (TME) enhances the ability of tumor cells to proliferate, migrate, and escape from the immune system, thus promoting the occurrence and development of tumor. TME contains chemokines. Chemokines consist of four major families, which are mainly composed of CC and CXC families. The main purpose of this review is to understand the CC and CXC chemokines and their receptors in ESCA, to improve the understanding of tumorigenesis of ESCA and determine new biomarkers for the diagnosis and prognosis of ESCA. We reviewed the literature on CC and CXC chemokines and their receptors in ESCA identified by PubMed database. This article introduces the general structures and functions of CC, CXC chemokines and their receptors in TME, as well as their roles in the progress of ESCA. Chemokines are involved in the development of ESCA, such as cancer cell invasion, metastasis, angiogenesis, and radioresistance, and are key determinants of disease progression, which have a great impact on patient prognosis and treatment response. In addition, a full understanding of their mechanism of action is essential to further verify that these chemokines and their receptors may serve as biomarkers or therapeutic targets of ESCA.
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Affiliation(s)
- Cong-Gai Huang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
- Precision Pathology Diagnosis for Serious Diseases Key Laboratory of Luzhou, Luzhou, People's Republic of China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Shu-Tao Zheng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Tao Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Yi-Yi Tan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Tian-Yuan Peng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Jiao Chen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Xiao-Mei Lu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China.
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Dai CL, Yang HX, Liu QP, Rahman K, Zhang H. CXCL6: A potential therapeutic target for inflammation and cancer. Clin Exp Med 2023; 23:4413-4427. [PMID: 37612429 DOI: 10.1007/s10238-023-01152-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/23/2023] [Indexed: 08/25/2023]
Abstract
Chemokines were originally defined as cytokines that affect the movement of immune cells. In recent years, due to the increasing importance of immune cells in the tumor microenvironment (TME), the role of chemokines has changed from a single "chemotactic agent" to a key factor that can regulate TME and affect the tumor phenotype. CXCL6, also known as granulocyte chemoattractant protein-2 (GCP-2), can recruit neutrophils to complete non-specific immunity in the process of inflammation. Cancer-related genes and interleukin family can promote the abnormal secretion of CXCL6, which promotes tumor growth, metastasis, epithelial mesenchymal transformation (EMT) and angiogenesis in the TME. CXCL6 also has a role in promoting fibrosis and tissue damage repair. In this review, we focus on the regulatory network affecting CXCL6 expression, its role in the progress of inflammation and how it affects tumorigenesis and progression based on the TME, in an attempt to provide a potential target for the treatment of diseases such as inflammation and cancer.
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Affiliation(s)
- Chun-Lan Dai
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Xuan Yang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiu-Ping Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Khalid Rahman
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
| | - Hong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Zhang X, Cai X, Yan C. Opportunities and challenges in combining immunotherapy and radiotherapy in esophageal cancer. J Cancer Res Clin Oncol 2023; 149:18253-18270. [PMID: 37985502 PMCID: PMC10725359 DOI: 10.1007/s00432-023-05499-z] [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: 10/11/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Immunotherapy has shown promise in the treatment of esophageal cancer, but using it alone only benefits a small number of patients. Most patients either do not have a significant response or develop secondary drug resistance. The combination of radiotherapy and immunotherapy appears to be a promising approach to treating esophageal cancer. PURPOSE We reviewed milestone clinical trials of radiotherapy combined with immunotherapy for esophageal cancer. We then discussed potential biomarkers for radiotherapy combined with immunotherapy, including programmed cell death-ligand 1 (PD-L1) status, tumor mutation burden (TMB), tumor-infiltrating lymphocytes, ct-DNA, imaging biomarkers, and clinical factors. Furthermore, we emphasize the key mechanisms of radiation therapy-induced immune stimulation and immune suppression in order to propose strategies for overcoming immune resistance in radiation therapy (RT). Lastly, we discussed the emerging role of low-dose radiotherapy (LDRT) , which has become a promising approach to overcome the limitations of high-dose radiotherapy. CONCLUSION Radiotherapy can be considered a triggering factor for systemic anti-tumor immune response and, with the assistance of immunotherapy, can serve as a systemic treatment option and potentially become the standard treatment for cancer patients.
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Affiliation(s)
- Xinyu Zhang
- Weifang Hospital of Traditional Chinese Medicine, 666 Weizhou Road, Weifang, 261000, Shandong, China
- Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Xinsheng Cai
- Weifang Hospital of Traditional Chinese Medicine, 666 Weizhou Road, Weifang, 261000, Shandong, China
| | - Chaoguang Yan
- Weifang Hospital of Traditional Chinese Medicine, 666 Weizhou Road, Weifang, 261000, Shandong, China.
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Xu J, Pang B, Lan Y, Dou R, Wang S, Kang S, Zhang W, Liu Y, Zhang Y, Ping Y. Identifying the personalized driver gene sets maximally contributing to abnormality of transcriptome phenotype in glioblastoma multiforme individuals. Mol Oncol 2023; 17:2472-2490. [PMID: 37491836 PMCID: PMC10620122 DOI: 10.1002/1878-0261.13499] [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: 12/02/2022] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
High heterogeneity in genome and phenotype of cancer populations made it difficult to apply population-based common driver genes to the diagnosis and treatment of cancer individuals. Characterizing and identifying the personalized driver mechanism for glioblastoma multiforme (GBM) individuals were pivotal for the realization of precision medicine. We proposed an integrative method to identify the personalized driver gene sets by integrating the profiles of gene expression and genetic alterations in cancer individuals. This method coupled genetic algorithm and random walk to identify the optimal gene sets that could explain abnormality of transcriptome phenotype to the maximum extent. The personalized driver gene sets were identified for 99 GBM individuals using our method. We found that genomic alterations in between one and seven driver genes could maximally and cumulatively explain the dysfunction of cancer hallmarks across GBM individuals. The driver gene sets were distinct even in GBM individuals with significantly similar transcriptomic phenotypes. Our method identified MCM4 with rare genetic alterations as previously unknown oncogenic genes, the high expression of which were significantly associated with poor GBM prognosis. The functional experiments confirmed that knockdown of MCM4 could significantly inhibit proliferation, invasion, migration, and clone formation of the GBM cell lines U251 and U118MG, and overexpression of MCM4 significantly promoted the proliferation, invasion, migration, and clone formation of the GBM cell line U87MG. Our method could dissect the personalized driver genetic alteration sets that are pivotal for developing targeted therapy strategies and precision medicine. Our method could be extended to identify key drivers from other levels and could be applied to more cancer types.
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Affiliation(s)
- Jinyuan Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Bo Pang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yujia Lan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Renjie Dou
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Shuai Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Shaobo Kang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Wanmei Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yuanyuan Liu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yijing Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yanyan Ping
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
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Ashrafizadeh M, Mohan CD, Rangappa S, Zarrabi A, Hushmandi K, Kumar AP, Sethi G, Rangappa KS. Noncoding RNAs as regulators of STAT3 pathway in gastrointestinal cancers: Roles in cancer progression and therapeutic response. Med Res Rev 2023; 43:1263-1321. [PMID: 36951271 DOI: 10.1002/med.21950] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/09/2022] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
Gastrointestinal (GI) tumors (cancers of the esophagus, gastric, liver, pancreas, colon, and rectum) contribute to a large number of deaths worldwide. STAT3 is an oncogenic transcription factor that promotes the transcription of genes associated with proliferation, antiapoptosis, survival, and metastasis. STAT3 is overactivated in many human malignancies including GI tumors which accelerates tumor progression, metastasis, and drug resistance. Research in recent years demonstrated that noncoding RNAs (ncRNAs) play a major role in the regulation of many signaling pathways including the STAT3 pathway. The major types of endogenous ncRNAs that are being extensively studied in oncology are microRNAs, long noncoding RNAs, and circular RNAs. These ncRNAs can either be tumor-promoters or tumor-suppressors and each one of them imparts their activity via different mechanisms. The STAT3 pathway is also tightly modulated by ncRNAs. In this article, we have elaborated on the tumor-promoting role of STAT3 signaling in GI tumors. Subsequently, we have comprehensively discussed the oncogenic as well as tumor suppressor functions and mechanism of action of ncRNAs that are known to modulate STAT3 signaling in GI cancers.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chakrabhavi D Mohan
- Department of Studies in Molecular Biology, University of Mysore, Manasagangotri, India
| | - Shobith Rangappa
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri University, Nagamangala Taluk, India
| | - Ali Zarrabi
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul, Sariyer, Turkey
| | - Kiavash Hushmandi
- Division of Epidemiology, Faculty of Veterinary Medicine, Department of Food Hygiene and Quality Control, University of Tehran, Tehran, Iran
| | - Alan Prem Kumar
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gautam Sethi
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Wu L, Yan J, Bai Y, Chen F, Zou X, Xu J, Huang A, Hou L, Zhong Y, Jing Z, Yu Q, Zhou X, Jiang Z, Wang C, Cheng M, Ji Y, Hou Y, Luo R, Li Q, Wu L, Cheng J, Wang P, Guo D, Huang W, Lei J, Liu S, Yan Y, Chen Y, Liao S, Li Y, Sun H, Yao N, Zhang X, Zhang S, Chen X, Yu Y, Li Y, Liu F, Wang Z, Zhou S, Yang H, Yang S, Xu X, Liu L, Gao Q, Tang Z, Wang X, Wang J, Fan J, Liu S, Yang X, Chen A, Zhou J. An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte-tumor cell crosstalk, local immunosuppression and tumor progression. Cell Res 2023; 33:585-603. [PMID: 37337030 PMCID: PMC10397313 DOI: 10.1038/s41422-023-00831-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/22/2023] [Indexed: 06/21/2023] Open
Abstract
Dissecting and understanding the cancer ecosystem, especially that around the tumor margins, which have strong implications for tumor cell infiltration and invasion, are essential for exploring the mechanisms of tumor metastasis and developing effective new treatments. Using a novel tumor border scanning and digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq), we identified a 500 µm-wide zone centered around the tumor border in patients with liver cancer, referred to as "the invasive zone". We detected strong immunosuppression, metabolic reprogramming, and severely damaged hepatocytes in this zone. We also identified a subpopulation of damaged hepatocytes with increased expression of serum amyloid A1 and A2 (referred to collectively as SAAs) located close to the border on the paratumor side. Overexpression of CXCL6 in adjacent malignant cells could induce activation of the JAK-STAT3 pathway in nearby hepatocytes, which subsequently caused SAAs' overexpression in these hepatocytes. Furthermore, overexpression and secretion of SAAs by hepatocytes in the invasive zone could lead to the recruitment of macrophages and M2 polarization, further promoting local immunosuppression, potentially resulting in tumor progression. Clinical association analysis in additional five independent cohorts of patients with primary and secondary liver cancer (n = 423) showed that patients with overexpression of SAAs in the invasive zone had a worse prognosis. Further in vivo experiments using mouse liver tumor models in situ confirmed that the knockdown of genes encoding SAAs in hepatocytes decreased macrophage accumulation around the tumor border and delayed tumor growth. The identification and characterization of a novel invasive zone in human cancer patients not only add an important layer of understanding regarding the mechanisms of tumor invasion and metastasis, but may also pave the way for developing novel therapeutic strategies for advanced liver cancer and other solid tumors.
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Affiliation(s)
- Liang Wu
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Southwest, BGI-Shenzhen, Chongqing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Jiayan Yan
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Yinqi Bai
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- BGI-Hangzhou, Hangzhou, Zhejiang, China
| | - Feiyu Chen
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Xuanxuan Zou
- BGI-Southwest, BGI-Shenzhen, Chongqing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangshan Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ao Huang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Liangzhen Hou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Zehua Jing
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qichao Yu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhifeng Jiang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Chunqing Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengnan Cheng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ji
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qinqin Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Wu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianwen Cheng
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Pengxiang Wang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Dezhen Guo
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Waidong Huang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Lei
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shang Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Yizhen Yan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Yiling Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Sha Liao
- BGI-Southwest, BGI-Shenzhen, Chongqing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Yuxiang Li
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Haixiang Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Na Yao
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Xiangyu Zhang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Shiyu Zhang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Xi Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Yang Yu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yao Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Fengming Liu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Zheng Wang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Shaolai Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Shuang Yang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xun Xu
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, Guangdong, China
| | - Longqi Liu
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Hangzhou, Hangzhou, Zhejiang, China
| | - Qiang Gao
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Zhaoyou Tang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Xiangdong Wang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Wang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Science, Hangzhou, Zhejiang, China
| | - Jia Fan
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Shiping Liu
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, Guangdong, China.
| | - Xinrong Yang
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China.
| | - Ao Chen
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China.
- BGI-Southwest, BGI-Shenzhen, Chongqing, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, Chongqing, China.
| | - Jian Zhou
- Zhongshan-BGI Precision Medical Center, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
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7
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Liu Y, Li D, Chen Y, Liu Y, Lin Y, Huang X, Wu T, Wang C, Ding J. Integrated bioinformatics analysis for conducting a prognostic model and identifying immunotherapeutic targets in gastric cancer. BMC Bioinformatics 2023; 24:191. [PMID: 37161430 PMCID: PMC10170748 DOI: 10.1186/s12859-023-05312-1] [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: 12/04/2022] [Accepted: 04/28/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Gastric cancer is the third leading cause of death from cancer worldwide and has a poor prognosis. Practical risk scores and prognostic models for gastric cancer are lacking. While immunotherapy has succeeded in some cancers, few gastric cancer patients benefit from immunotherapy. Immune genes and the tumor microenvironment (TME) are essential for cancer progression and immunotherapy response. However, the roles of immune genes and the tumor microenvironment in immunotherapy remain unclear. The study aimed to construct a prognostic prediction model and identify immunotherapeutic targets for gastric cancer (GC) patients by exploring immune genes and the tumor microenvironment. RESULTS An immune-related risk score (IRRS) model, including APOH, RNASE2, F2R, DEFB126, CXCL6, and CXCL3 genes, was constructed for risk stratification. Patients in the low-risk group, which was characterized by elevated tumor mutation burden (TMB) have higher survival rate. The risk level was remarkably correlated with tumor-infiltrating immune cells (TIICs), the immune checkpoint molecule expression, and immunophenoscore (IPS). CXCL3 and CXCL6 were significantly upregulated in gastric cancer tissues compared with normal tissues using the UALCAN database and RT-qPCR. The nomogram showed good calibration and moderate discrimination in predicting overall survival (OS) at 1-, 3-, and 5- year for gastric cancer patients using risk-level and clinical characteristics. CONCLUSION Our findings provided a risk stratification and prognosis prediction tool for gastric cancer patients and further the research into immunotherapy in gastric cancer.
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Affiliation(s)
- YaLing Liu
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Dan Li
- Department of Gastroenterology, Fujian Medical University Union Hospital, Fuzhou, 350212, China
| | - Yong Chen
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - YiJuan Liu
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - YiJuan Lin
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - XunRu Huang
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ting Wu
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - ChengDang Wang
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Jian Ding
- Department of Gastroenterology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
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Chen X, Tian F, Wu Z. A Genomic Instability-Associated Prognostic Signature for Glioblastoma Patients. World Neurosurg 2022; 167:e515-e526. [PMID: 35977679 DOI: 10.1016/j.wneu.2022.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Genomic instability and aberrant tumor mutation burden are widely accepted hallmarks of cancer. Glioblastoma (GBM) is a common brain tumor in adults, and survival of patients with GBM is poor. This study aimed to investigate the prognostic value of genomic instability-derived genes in GBM. METHODS GBM data were downloaded from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases. Differential expression analysis of all samples with different tumor mutation burden was performed. Univariate Cox and LASSO Cox regression analyses were integrated to determine the optimal genes for constructing a risk score model. Multivariate Cox regression analysis and survival analysis determined independent prognostic indicators. Immune cell infiltration was analyzed by CIBERSORT algorithm. RESULTS In GMB patients with high and low tumor mutation burden, we identified 154 differentially expressed genes, which were significantly enriched in 47 Gene Ontology terms and 6 Kyoto Encyclopedia of Genes and Genomes pathways. To establish a risk score, 9 genes were further screened, including SDC1, CXCL1, CXCL6, RGS4, PCDHGB2, CA9, ZAR1, CHRM3, and SLN. High-risk patients had worse prognosis in two databases. The performance of a nomogram including prognostic factors (risk score and age) was good. Moreover, mast cells resting was significantly differentially infiltrated between high- and low-risk GBM samples. CONCLUSIONS The risk score constructed by 9 genomic instability-derived genes could reliably predict prognosis of GBM patients. The nomogram based on age and risk score also had a good prognostic predictive value.
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Affiliation(s)
- Xiaodong Chen
- Neurosurgery Department, The Affiliated Hospital of Qingdao University, Shandong, China
| | - Fen Tian
- Nephrology Department, The Affiliated Hospital of Qingdao University, Shandong, China.
| | - Zeyu Wu
- Neurosurgery Department, The Affiliated Hospital of Qingdao University, Shandong, China
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Ou Z, Lin S, Qiu J, Ding W, Ren P, Chen D, Wang J, Tong Y, Wu D, Chen A, Deng Y, Cheng M, Peng T, Lu H, Yang H, Wang J, Jin X, Ma D, Xu X, Wang Y, Li J, Wu P. Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203040. [PMID: 35986392 PMCID: PMC9561780 DOI: 10.1002/advs.202203040] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/10/2022] [Indexed: 05/07/2023]
Abstract
The effective treatment of advanced cervical cancer remains challenging. Herein, single-nucleus RNA sequencing (snRNA-seq) and SpaTial enhanced resolution omics-sequencing (Stereo-seq) are used to investigate the immunological microenvironment of cervical squamous cell carcinoma (CSCC). The expression levels of most immune suppressive genes in the tumor and inflammation areas of CSCC are not significantly higher than those in the non-cancer samples, except for LGALS9 and IDO1. Stronger signals of CD56+ NK cells and immature dendritic cells are found in the hypermetabolic tumor areas, whereas more eosinophils, immature B cells, and Treg cells are found in the hypometabolic tumor areas. Moreover, a cluster of pro-tumorigenic cancer-associated myofibroblasts (myCAFs) are identified. The myCAFs may support the growth and metastasis of tumors by inhibiting lymphocyte infiltration and remodeling of the tumor extracellular matrix. Furthermore, these myCAFs are associated with poorer survival probability in patients with CSCC, predict resistance to immunotherapy, and might be present in a small fraction (< 30%) of patients with advanced cancer. Immunohistochemistry and multiplex immunofluorescence staining are conducted to validate the spatial distribution and potential function of myCAFs. Collectively, these findings enhance the understanding of the immunological microenvironment of CSCC and shed light on the treatment of advanced CSCC.
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10
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Patankar M, Li M, Khalatbari A, Castle JD, Hu L, Zhang C, Shaker A. Inflammatory and Proliferative Pathway Activation in Human Esophageal Myofibroblasts Treated with Acidic Bile Salts. Int J Mol Sci 2022; 23:ijms231810371. [PMID: 36142285 PMCID: PMC9498994 DOI: 10.3390/ijms231810371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022] Open
Abstract
Subepithelial human esophageal myofibroblasts (HEMFs) in gastroesophageal reflux disease (GERD) are exposed to luminal contents via impaired squamous epithelium barrier integrity. The supernatant of HEMFs treated with acidic bile salts reflective of in vivo reflux increases squamous epithelial thickness. We aimed to identify the involved mechanisms using an unbiased approach. Acidic-bile-salt-treated primary HEMF cultures (n = 4) were submitted for RNA-Seq and analyzed with Partek Flow followed by Ingenuity Pathway Analysis (IPA). A total of 1165 molecules (579 downregulated, 586 upregulated) were differentially expressed, with most top regulated molecules either extracellular or in the plasma membrane. Increases in HEMF CXCL-8, IL-6, AREG, and EREG mRNA, and protein secretion were confirmed. Top identified canonical pathways were agranulocyte and granulocyte adhesion and diapedesis, PI3K/AKT signaling, CCR5 signaling in macrophages, and the STAT3 pathway. Top diseases and biological functions were cellular growth and development, hematopoiesis, immune cell trafficking, and cell-mediated response. The targets of the top upstream regulator ErbB2 included CXCL-8, IL-6, and AREG and the inhibition of CXCL-8 in the HEMF supernatant decreased squamous epithelial proliferation. Our work shows an inflammatory/immune cell and proliferative pathways activation in HEMFs in the GERD environment and identifies CXCL-8 as a HEMF-derived chemokine with paracrine proliferative effects on squamous epithelium.
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Affiliation(s)
- Madhura Patankar
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Meng Li
- USC Libraries Bioinformatics Services, University of Southern California, Los Angeles, CA 90007, USA
| | - Atousa Khalatbari
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Joshua D. Castle
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Liping Hu
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Chunying Zhang
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Anisa Shaker
- Department of Internal Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
- Correspondence: ; Tel.: +1-323-442-2084
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11
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Cheng C, Zhuge L, Xiao X, Luan S, Yuan Y. Overcoming resistance to PD-1/PD-L1 inhibitors in esophageal cancer. Front Oncol 2022; 12:955163. [PMID: 36132136 PMCID: PMC9483164 DOI: 10.3389/fonc.2022.955163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
As the predominant treatment option of the immunotherapy for advanced esophageal cancer (EC), the application of programmed death 1 (PD-1) and programmed death-ligand 1 (PD-L1) inhibitors brings new hope to clinical practice. However, a considerable portion of patients do not response to this therapy, meanwhile most patients sensitive to PD-1 or PD-L1 antibody initially will develop resistance to the treatment eventually. To break through the limits of clinical effect, it is of critical importance to make a profound understanding of the mechanisms of so called primary resistance and acquired resistance. Subsequently, exploring potent predictors to identify suitable patients for anti-PD-1/PD-L1 treatment and investigating efficient strategies to overcome drug resistance will be helpful to expend the benefit of immunotherapy. In the present view, we summarized the potential predictive factors for anti-PD-1/PD-L1 immunotherapy in EC, and demonstrated the plausible mechanisms of resistance to PD-1/PD-L1 blockade as well as its feasible solutions.
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Affiliation(s)
- Chao Cheng
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Lingdun Zhuge
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Xiao
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Siyuan Luan
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Yong Yuan
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Yong Yuan,
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12
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Su X, Jin H, Du N, Wang J, Lu H, Xiao J, Li X, Yi J, Gu T, Dan X, Gao Z, Li M. A Novel Computational Framework for Predicting the Survival of Cancer Patients With PD-1/PD-L1 Checkpoint Blockade Therapy. Front Oncol 2022; 12:930589. [PMID: 35832540 PMCID: PMC9271954 DOI: 10.3389/fonc.2022.930589] [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: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) induce durable responses, but only a minority of patients achieve clinical benefits. The development of gene expression profiling of tumor transcriptomes has enabled identifying prognostic gene expression signatures and patient selection with targeted therapies. Methods Immune exclusion score (IES) was built by elastic net-penalized Cox proportional hazards (PHs) model in the discovery cohort and validated via four independent cohorts. The survival differences between the two groups were compared using Kaplan-Meier analysis. Both GO and KEGG analyses were performed for functional annotation. CIBERSORTx was also performed to estimate the relative proportion of immune-cell types. Results A fifteen-genes immune exclusion score (IES) was developed in the discovery cohort of 65 patients treated with anti-PD-(L)1 therapy. The ROC efficiencies of 1- and 3- year prognosis were 0.842 and 0.82, respectively. Patients with low IES showed a longer PFS (p=0.003) and better response rate (ORR: 43.8% vs 18.2%, p=0.03). We found that patients with low IES enriched with high expression of immune eliminated cell genes, such as CD8+ T cells, CD4+ T cells, NK cells and B cells. IES was positively correlated with other immune exclusion signatures. Furthermore, IES was successfully validated in four independent cohorts (Riaz’s SKCM, Liu’s SKCM, Nathanson’s SKCM and Braun’s ccRCC, n = 367). IES was also negatively correlated with T cell–inflamed signature and independent of TMB. Conclusions This novel IES model encompassing immune-related biomarkers might serve as a promising tool for the prognostic prediction of immunotherapy.
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Affiliation(s)
- Xiaofan Su
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Haoxuan Jin
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Ning Du
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jiaqian Wang
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Huiping Lu
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Jinyuan Xiao
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Xiaoting Li
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Jian Yi
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Tiantian Gu
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Xu Dan
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Zhibo Gao
- Department of Translational Medicine, YuceBioTechnology Co., Ltd., Shenzhen, China
- Department of Translational Medicine, YuceNeo Technology Co., Ltd., Shenzhen, China
| | - Manxiang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Manxiang Li,
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13
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Mu L, Hu S, Li G, Wu P, Ren C, Lin T, Zhang S. Characterization of the Prognostic Values of CXCL Family in Epstein-Barr Virus Associated Gastric Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2218140. [PMID: 35693706 PMCID: PMC9177340 DOI: 10.1155/2022/2218140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022]
Abstract
Background CXCL family is a class of secreted growth factors signaling through G-protein-coupled receptors, and abnormal expression is associated with the growth and progression of many tumors. However, their prognostic value has been poorly studied in Epstein-Barr virus- (EBV-) associated gastric cancer (EBVaGC). Therefore, it is of great significance to explore the prognostic value of the CXCL family in EBVaGC. Methods CXCL family mRNA expression was analyzed in STAD data from The Cancer Genome Atlas (TCGA). Kaplan-Meier Plotter was used to assess the prognostic value of the CXCL family. Transcription factors (TFs) and miRNAs associated with the CXCL family were identified by TFCheckpoint, miRWalk, and ViRBase databases. The prognostic model was evaluated using the EBVaGC patient cohort GSE51575. Results The mRNA expression of CXCL1/3/5/6/8/9/10/11/16 was significantly upregulated, while the expression of CXCL12/14 was downregulated in EBVaGC compared with normal tissues from TCGA-STAD. The mRNA expressions of CXCL9, CXCL10, CXCL11, and CXCL17 in EBVaGCs were higher than those in EBVnGCs, but the mRNA expressions of CXCL6, CXCL12, and CXCL17 were lower than those in EBVnGCs. The mRNA expression levels of CXCL9, CXCL10, and CXCL11 in EBVaGCs were higher than those in EBVnGCs regardless of the tumor stage. High mRNA expression of CXCL8 was associated with better OS in patients with EBVaGC, while high expression of CXCL9 was associated with better OS in patients with EBVnGC. We obtained 10 candidate potential transcription factors (TFs) associated with CXCLs: OTOP3, NKX6-2, NKX2-2, FEV, SMYD1, TRIMSO, TBX10, CDX1, SLC26A3, and ARC. 576 miRNA-mRNA interactions were obtained. Among them, 65 miRNAs were predicted to be correlated with CXCL6, CXCL9, CXCL10, and CXCL11. Similar to the results of TCGA-STAD, the GSE51575 dataset also showed that the mRNA expression levels of CXCL1/3/9/10/11/16 were markedly enhanced in EBVaGC tissues compared with corresponding normal gastric mucosa tissues, while the mRNA expression levels of CXCL12/14 were significantly reduced. The mRNA expression levels of CXCL3/9/10/11/13/17 were increased in EBVaGC compared with EBVnGC tissues. Conclusions The expression differences of CXCL family members are closely associated with the progression of EBVaGC. Expression of CXCL9/10/11/17 mRNA may be a promising prognostic indicator for EBVaGC patients.
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Affiliation(s)
- Li Mu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Shun Hu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Guoping Li
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Ping Wu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Caihong Ren
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Taiyu Lin
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Sheng Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
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14
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Zhang R, Jin Y, Chang C, Xu L, Bian Y, Shen Y, Sun Y, Sun S, Schrodi SJ, Guo S, He D. RNA-seq and Network Analysis Reveal Unique Chemokine Activity Signatures in the Synovial Tissue of Patients With Rheumatoid Arthritis. Front Med (Lausanne) 2022; 9:799440. [PMID: 35602512 PMCID: PMC9116426 DOI: 10.3389/fmed.2022.799440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/16/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose This study aimed to provide a comprehensive understanding of the genome-wide expression patterns in the synovial tissue samples of patients with rheumatoid arthritis (RA) to investigate the potential mechanisms regulating RA occurrence and development. Methods Transcription profiles of the synovial tissue samples from nine patients with RA and 15 patients with osteoarthritis (OA) (control) from the East Asian population were generated using RNA sequencing (RNA-seq). Gene set enrichment analysis (GSEA) was used to analyze all the detected genes and the differentially expressed genes (DEGs) were identified using DESeq. To further analyze the DEGs, the Gene Ontology (GO) functional enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. The protein-protein interaction (PPI) network of the DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the hub genes were identified by topology clustering with the Molecular Complex Detection (MCODE)-Cytoscape. The most important hub genes were validated using quantitative real-time PCR (qRT-PCR). Results Of the 17,736 genes detected, 851 genes were identified as the DEGs (474 upregulated and 377 downregulated genes) using the false discovery rate (FDR) approach. GSEA revealed that the significantly enriched gene sets that positively correlated with RA were CD40 signaling overactivation, Th1 cytotoxic module, overactivation of the immune response, adaptive immune response, effective vs. memory CD8+ T cells (upregulated), and naïve vs. effective CD8+ T cells (downregulated). Biological process enrichment analysis showed that the DEGs were significantly enriched for signal transduction (P = 3.01 × 10-6), immune response (P = 1.65 × 10-24), and inflammatory response (P = 5.76 × 10-10). Molecule function enrichment analysis revealed that the DEGs were enriched in calcium ion binding (P = 1.26 × 10-5), receptor binding (P = 1.26 × 10-5), and cytokine activity (P = 2.01 × 10-3). Cellular component enrichment analysis revealed that the DEGs were significantly enriched in the plasma membrane (P = 1.91 × 10-31), an integral component of the membrane (P = 7.39 × 10-13), and extracellular region (P = 7.63 × 10-11). The KEGG pathway analysis showed that the DEGs were enriched in the cytokine-cytokine receptor interaction (P = 3.05 × 10-17), chemokine signaling (P = 3.50 × 10-7), T-cell receptor signaling (P = 5.17 × 10-4), and RA (P = 5.17 × 10-4) pathways. We confirmed that RA was correlated with the upregulation of the PPI network hub genes, such as CXCL13, CXCL6, CCR5, CXCR5, CCR2, CXCL3, and CXCL10, and the downregulation of the PPI network hub gene such as SSTR1. Conclusion This study identified and validated the DEGs in the synovial tissue samples of patients with RA, which highlighted the activity of a subset of chemokine genes, thereby providing novel insights into the molecular mechanisms of RA pathogenesis and identifying potential diagnostic and therapeutic targets for RA.
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Affiliation(s)
- Runrun Zhang
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yehua Jin
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanqin Bian
- Guanghua Integrative Medicine Hospital, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yu Shen
- Guanghua Integrative Medicine Hospital, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yang Sun
- Guanghua Integrative Medicine Hospital, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Songtao Sun
- Department of Orthopedics, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Steven J. Schrodi
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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15
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Lin D, Zhao W, Yang J, Wang H, Zhang H. Integrative Analysis of Biomarkers and Mechanisms in Adamantinomatous Craniopharyngioma. Front Genet 2022; 13:830793. [PMID: 35432485 PMCID: PMC9006448 DOI: 10.3389/fgene.2022.830793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
Craniopharyngioma is a benign tumor, and the predominant treatment methods are surgical resection and radiotherapy. However, both treatments may lead to complex complications, seriously affecting patients’ survival rate and quality of life. Adamantinomatous craniopharyngioma (ACP), as one of the histological subtypes of craniopharyngioma, is associated with a high incidence and poor prognosis, and there is a gap in the targeted therapy of immune-related genes for ACP. In this study, two gene expression profiles of ACP, namely GSE68015 and GSE94349, were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by the Limma package, and 271 differentially expressed immune-related genes (DEIRGs) were obtained from the Immport database. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Five hub genes, including CXCL6, CXCL10, CXCL11, CXCL13, and SAA1, were screened out through protein-protein interaction (PPI) network interaction construction. Two diagnostic markers, namely S100A2 and SDC1 (both of which have the Area Under Curve value of 1), were screened by the machine learning algorithm. CIBERSORT analysis showed that M2 macrophages, activated NK cells, and gamma delta T cells had higher abundance in ACP infiltration, while CD8+ T cells, regulatory T cells, and Neutrophils had less abundance in ACP infiltration. The expression of gamma delta T cells was positively correlated with CXCL6, S100A2, SDC1, and SAA1, while CD8+ T cells expression was negatively correlated with CXCL6, S100A2, SDC1, and CXCL10. ACP with high CXCL6 showed remarkable drug sensitivity to Pentostatin and Wortmannin via CellMiner database analysis. Our results deepened the understanding of the molecular immune mechanism in ACP and provided potential biomarkers for the precisely targeted therapy for ACP.
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Affiliation(s)
- Da Lin
- Department of Neurosurgery, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Wenyue Zhao
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jun Yang
- Department of Neurosurgery, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Hao Wang
- Department of Neurosurgery, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Hongbing Zhang
- Department of Neurosurgery, Beijing Luhe Hospital, Capital Medical University, Beijing, China
- *Correspondence: Hongbing Zhang,
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Qiu R, Wang W, Li J, Wang Y. Roles of PTEN inactivation and PD-1/PD-L1 activation in esophageal squamous cell carcinoma. Mol Biol Rep 2022; 49:6633-6645. [PMID: 35301651 DOI: 10.1007/s11033-022-07246-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 02/07/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most common type of esophageal cancer in China and developing countries. The purpose of this review is to summarize the roles of inactivation of the tumor suppressor gene, phosphatase and tensin homolog (PTEN), and activation of the programmed cell death protein 1 (PD-1) upon binding to its ligand (PD-L1) in the promotion of ESCC. Studies of ESCC performed in vitro and in vivo indicated that PTEN and PD-L1 function in the regulation of cell proliferation, invasion, and migration; the epithelial-mesenchymal transition; resistance to chemotherapy and radiotherapy; and the PI3K/AKT signaling pathway. Certain genetic variants of PTEN are related to susceptibility to ESCC, and PTEN and PD-L1 also function in ESCC progression and affect the prognosis of patients with ESCC. There is also evidence that the expression of PD-L1 and PTEN are associated with the progression of certain other cancers. Future studies should further examine the relationship of PD-L1 and PTEN and their possible interactions in ESCC.
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Affiliation(s)
- Rong Qiu
- Department of Radiation Oncology, Fourth Hospital of Hebei Medical University, No. 12 Jian Kang Road, Shijiazhuang, Hebei Province, P. R. China
| | - Wenxi Wang
- Department of Oncology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan Province, China
| | - Juan Li
- Department of Radiation Oncology, Fourth Hospital of Hebei Medical University, No. 12 Jian Kang Road, Shijiazhuang, Hebei Province, P. R. China
| | - Yuxiang Wang
- Department of Radiation Oncology, Fourth Hospital of Hebei Medical University, No. 12 Jian Kang Road, Shijiazhuang, Hebei Province, P. R. China.
- , No.12, Jiankang Road, 050011, Shijiazhuang, Hebei Province, China.
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SOX8 promotes cetuximab resistance via HGF/MET bypass pathway activation in colorectal cancer. Cancer Chemother Pharmacol 2022; 89:441-449. [PMID: 35195773 DOI: 10.1007/s00280-021-04378-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/16/2021] [Indexed: 01/15/2023]
Abstract
AIM Cetuximab is an essential drug for the treatment of wild-type K-RAS colorectal cancer (CRC). It improves the overall survival of patients. However, acquired resistance prevents its clinical efficacy. Tumor heterogeneity may be a nonnegligible reason for cetuximab resistance. We attempted to explore the corresponding molecular mechanism. METHODS Cetuximab-resistant CRC cell RKO and cetuximab-sensitive CRC cell Caco-2 were applied in this study. Cells were centrifuged to determine the concentration in the culture supernatant (CS). MTT, EdU, and colony formation assays were utilized to evaluate cell survival and proliferation. Chromatin immunoprecipitation (ChIP) and promoter-luciferase reporter assays were employed to confirm the direct binding of transcription factors. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) assays were used to detect the expression of molecular markers in the pathway. RESULTS Hepatocyte growth factor (HGF) was up-regulated in RKO cell culture supernatant and induced cetuximab resistance in Caco-2 cells. SRY-Box Transcription Factor 8 (SOX8) bound to the promoter sequence of HGF. HGF activated the HGF/MET bypass pathway and induced cetuximab resistance in Caco-2 cells. CONCLUSION The SOX8/HGF/MET axis played a crucial role in the communication between cetuximab-resistant cells and cetuximab-sensitive cells, inducing treatment resistance.
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Shao Y, Li F, Liu H. Circ-DONSON Facilitates the Malignant Progression of Gastric Cancer Depending on the Regulation of miR-149-5p/LDHA Axis. Biochem Genet 2021; 60:640-655. [PMID: 34409524 DOI: 10.1007/s10528-021-10120-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/02/2021] [Indexed: 12/11/2022]
Abstract
Earlier studies have shown that circular RNA (circRNA) expression is closely related to the malignant progression of cancer, but the role of circ-DONSON in gastric cancer (GC) has not been fully elucidated. The expression of circ-DONSON, miR-149-5p and lactate dehydrogenase A (LDHA) was measured via qRT-PCR. CCK8 assay was used to assess cell viability, and colony formation assay was performed to detect the number of colonies and the radiosensitivity of cells. Besides, flow cytometry, transwell assay and tube formation assay were employed to determine cell apoptosis, migration, invasion and angiogenesis. Western blot analysis was used to assess the protein expression. The interaction between miR-149-5p and circ-DONSON or LDHA was confirmed by dual-luciferase reporter assay. The influence of circ-DONSON on GC tumor growth in vivo was explored through constructing mice xenograft models. Our results suggested that circ-DONSON was highly expressed in GC tissues and cells. Loss-functional assay results confirmed that silenced circ-DONSON could inhibit the proliferation, metastasis and angiogenesis, while enhance the apoptosis and radiosensitivity of GC cells. In terms of mechanism, circ-DONSON could sponge miR-149-5p, which could target LDHA in GC. MiR-149-5p inhibitor or LDHA overexpression could reverse the suppression effect of circ-DONSON knockdown on GC progression. Additionally, our results also suggested that circ-DONSON silencing could restrain the tumor growth of GC in vivo. These results demonstrated that circ-DONSON could facilitate GC progression by increasing LDHA expression via sponging miR-149-5p, indicating that circ-DONSON might be a novel biomarker for GC treatment.
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Affiliation(s)
- Yingying Shao
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, No.150 Ximen Street, Linhai, Taizhou City, 317000, Zhejiang Province, China.,Emergency Department, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou City, 317000, Zhejiang, China
| | - Fangshun Li
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, No.150 Ximen Street, Linhai, Taizhou City, 317000, Zhejiang Province, China
| | - Hanlin Liu
- Department of anorectal and gastrointestinal surgery, Taizhou Municipal Hospital, Taizhou City, 317000, Zhejiang, China.
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