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Deng Y, Liu L, Xiao X, Zhao Y. A four-gene-based methylation signature associated with lymph node metastasis predicts overall survival in lung squamous cell carcinoma. Genes Genet Syst 2023; 98:209-219. [PMID: 37839873 DOI: 10.1266/ggs.22-00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
We aimed to identify prognostic methylation genes associated with lymph node metastasis (LNM) in lung squamous cell carcinoma (LUSC). Bioinformatics methods were used to obtain optimal prognostic genes for risk model construction using data from the Cancer Genome Atlas database. ROC curves were adopted to predict the prognostic value of the risk model. Multivariate regression was carried out to identify independent prognostic factors and construct a prognostic nomogram. The differences in overall survival, gene mutation and pathways between high- and low-risk groups were analyzed. Finally, the expression and methylation level of the optimal prognostic genes among different LNM stages were analyzed. FGA, GPR39, RRAD and TINAGL1 were identified as the optimal prognostic genes and were applied to establish a prognostic risk model. Significant differences were found among the different LNM stages. The risk model could predict overall survival, showing a moderate performance with AUC of 0.64-0.68. The model possessed independent prognostic value, and could accurately predict 1-, 3- and 5-year survival. Patients with a high risk score showed poorer survival. Lower gene mutation frequencies and enrichment of leukocyte transendothelial migration and the VEGF signaling pathway in the high-risk group may lead to the poor prognosis. This study identified several specific methylation markers associated with LNM in LUSC and generated a prognostic model to predict overall survival for LUSC patients.
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Affiliation(s)
- Yufei Deng
- Department of Pharmacy, Wuxi No.2 People's Hospital
| | - Lifeng Liu
- Department of Pharmacy, Wuxi No.2 People's Hospital
| | - Xia Xiao
- Department of Oncology, Wuxi No.2 People's Hospital
| | - Yin Zhao
- Department of Pharmacy, Wuxi No.2 People's Hospital
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2
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Han S, Liu X, Ju S, Mu W, Abulikemu G, Zhen Q, Yang J, Zhang J, Li Y, Liu H, Chen Q, Cui B, Wu S, Zhang Y. New mechanisms and biomarkers of lymph node metastasis in cervical cancer: reflections from plasma proteomics. Clin Proteomics 2023; 20:35. [PMID: 37689639 PMCID: PMC10492398 DOI: 10.1186/s12014-023-09427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/21/2023] [Indexed: 09/11/2023] Open
Abstract
OBJECTIVE Lymph node metastasis (LNM) and lymphatic vasculature space infiltration (LVSI) in cervical cancer patients indicate a poor prognosis, but satisfactory methods for diagnosing these phenotypes are lacking. This study aimed to find new effective plasma biomarkers of LNM and LVSI as well as possible mechanisms underlying LNM and LVSI through data-independent acquisition (DIA) proteome sequencing. METHODS A total of 20 cervical cancer plasma samples, including 7 LNM-/LVSI-(NC), 4 LNM-/LVSI + (LVSI) and 9 LNM + /LVSI + (LNM) samples from a cohort, were subjected to DIA to identify differentially expressed proteins (DEPs) for LVSI and LNM. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for DEP functional annotation. Protein-protein interaction (PPI) and weighted gene coexpression network analysis (WGCNA) were used to detect new effective plasma biomarkers and possible mechanisms. RESULTS A total of 79 DEPs were identified in the cohort. GO and KEGG analyses showed that DEPs were mainly enriched in the complement and coagulation pathway, lipid and atherosclerosis pathway, HIF-1 signal transduction pathway and phagosome and autophagy. WGCNA showed that the enrichment of the green module differed greatly between groups. Six interesting core DEPs (SPARC, HPX, VCAM1, TFRC, ERN1 and APMAP) were confirmed to be potential plasma diagnostic markers for LVSI and LNM in cervical cancer patients. CONCLUSION Proteomic signatures developed in this study reflected the potential plasma diagnostic markers and new possible pathogenesis mechanisms in the LVSI and LNM of cervical cancer.
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Affiliation(s)
- Sai Han
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Xiaoli Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Shuang Ju
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Wendi Mu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Gulijinaiti Abulikemu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Qianwei Zhen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Jiaqi Yang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Jingjing Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Yi Li
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Hongli Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Qian Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Baoxia Cui
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Shuxia Wu
- Department of Obstetrics and Gynecology, the Fifth People's Hospital of Jinan, Jinan, Shandong, 250012, People's Republic of China.
| | - Youzhong Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
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Tong X, Yang X, Tong X, Zhai D, Liu Y. Complement system-related genes in stomach adenocarcinoma: Prognostic signature, immune landscape, and drug resistance. Front Genet 2022; 13:903421. [PMID: 36159981 PMCID: PMC9493128 DOI: 10.3389/fgene.2022.903421] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Stomach adenocarcinoma (STAD) is one of the most common malignant tumors of the digestive tract, and its survival predictors are critical for precision medicine but have not been fully investigated. The complement system is a complex multistep cascade at the interface of innate and adaptive immunity, which augments the function of antibodies and phagocytes. This study aimed to construct and validate a CSRG signature based on TCGA (The Cancer Genome Atlas) STAD dataset and revalidated it in an external GEO (Gene Expression Omnibus) STAD cohort. Subsequently, we assessed the association of risk levels with the stromal and immune cell infiltration level in STAD using the ESTIMATE, single-sample Gene Set Enrichment Analysis (ssGSEA), and Microenvironment Cell Populations-counter (MCP-counter) algorithm. It was found that the CSRG signature, based on three genes (SERPINE1, PROC, and CFHR3), was significantly and independently associated with the OS in TCGA STAD patients (p < 0.001). Subsequently, we found that the high-risk STAD harbors more immune cell infiltration than the low-risk group, and the ESTIMATE results indicated that there exists a more stromal component in the tumor microenvironment of the high-risk groups. Compared to the low-risk group, the high-risk STAD patients had higher expressions of marker genes for immune checkpoint inhibitors (ICIs) and showed higher sensitivity to the chemotherapy agents (rapamycin, nilotinib, 5-fluorouracil, axitinib, DMOG, and JNK inhibitor VIII). The prognostic value of the CSRGs was further validated by nomogram plots, which revealed that it was superior to tumor TNM and pathologic stage. Finally, the three expression levels were evaluated in GES-1, HGC27, and AGS cells by qRT-PCR.
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Affiliation(s)
- Xiaoxia Tong
- Experimental Research Center, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
| | - Xiaohu Yang
- Experimental Research Center, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
| | - Xiaojuan Tong
- Department of General Family Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Dong Zhai
- The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yonglei Liu
- Experimental Research Center, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
- *Correspondence: Yonglei Liu,
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Abdelal H, Chatterjee D. The Clinical and Pathologic Features of Intracholecystic Papillary-Tubular Neoplasms of the Gallbladder. Surg Pathol Clin 2022; 15:565-577. [PMID: 36049837 DOI: 10.1016/j.path.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Intracholecystic papillary-tubular neoplasm denotes a discrete mucosal-based neoplastic proliferation into the gallbladder lumen. It is diagnosed incidentally during cholecystectomy or radiologically during a workup for abdominal pain. The majority of polypoid lesions in the gallbladder are non-neoplastic; therefore, pathologic examination is the gold standard to establish this diagnosis. Intracholecystic papillary-tubular neoplasm is considered as premalignant, although associated invasive carcinomas may be present in the specimen. Invasive carcinoma arising from intracholecystic papillary-tubular neoplasm have a better prognosis than de novo gallbladder carcinomas. The pathology of intracholecystic papillary-tubular neoplasm, including the challenges involved in the diagnosis of this entity, is discussed.
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Affiliation(s)
- Heba Abdelal
- Department of Pathology, Yale School of Medicine, 310 Cedar Street, New Haven, CT, USA
| | - Deyali Chatterjee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Wan Z, Li X, Luo X, Wang B, Zhou X, Chen A. The miR-590-3p/CFHR3/STAT3 signaling pathway promotes cell proliferation and metastasis in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:5783-5799. [PMID: 35852862 PMCID: PMC9365569 DOI: 10.18632/aging.204178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/08/2022] [Indexed: 12/24/2022]
Abstract
Accumulating evidence has indicated that Complement factor H-related 3 (CFHR3) plays an essential role in various diseases. However, the biological functions of CFHR3 in hepatocellular carcinoma (HCC) remain largely unclear. Therefore, we perform a further study on CFHR3 in HCC. In this article, we report the suppressive role of CFHR3 in the proliferation and metastasis of HCC cells. CFHR3 downregulation is closely associated with large (T3-T4) HCC, tumor recurrence, and advanced (stage III-IV) clinical stage, functioning as an independent factor for the prognoses of HCC patients. Knockdown of CFHR3 promotes proliferation, migration, and invasion of HCC cells. Mechanistically, downregulation of CFHR3 is induced by miR-590-3p binding to the 3’ untranslated region (UTR) of CFHR3. CFHR3 downregulation promotes the phosphorylation of STAT3 protein, thereby suppressing p53 expression. The promotional effect upon downregulation of CFHR3 induced by CFHR3 stable knockdown or miR-590-3p on HCC cell malignant phenotypes is attenuated by STAT3 inhibitor, S3I-201. In conclusion, our results reveal that CFHR3 is a protective biomarker for HCC patients, and targeting the miR-590-3p/CFHR3/p-STAT3/p53 signaling axis provides a promising strategy for HCC therapeutics.
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Affiliation(s)
- Zhongzhong Wan
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
| | - Xingrun Li
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
| | - Xinru Luo
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
| | - Bofan Wang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
| | - Xiang Zhou
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
| | - Ao Chen
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei Province, People’s Republic of China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong 0000, People’s Republic of China
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 0000, People’s Republic of China
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Zeng Z, Lei S, Wang J, Yang Y, Lan J, Tian Q, Chen T, Hao X. A novel hypoxia-driven gene signature that can predict the prognosis of hepatocellular carcinoma. Bioengineered 2022; 13:12193-12210. [PMID: 35549979 PMCID: PMC9276011 DOI: 10.1080/21655979.2022.2073943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hypoxia environment exists in already started hepatocellular carcinoma (HCC) and promotes its progression by driving changes in the gene expression profiles of cells. However, the status of hypoxia-driven genes in HCC is largely unknown. In the present study, 368 HCC tissues from The Cancer Genome Atlas were divided into high and low hypoxia groups according to their hypoxia signatures. A total of 1,142 differentially expressed genes (DEGs) were identified between the two groups, and 34 of these DEGs were highly expressed in HCC tissues compared with adjacent tissues, especially in HCC tissues from patients with stage III-IV HCC. After constructing a protein-protein interaction network and applying the least absolute shrinkage and selection operator Cox regression method for 34 DEGs, a three-gene signature (complement factor H related 3 [CFHR3], egl-9 family hypoxia inducible factor 3 [EGLN3], and chromogranin A [CHGA]) was constructed and had prognostic value to predicted outcome of patients with HCC. This three-gene signature was suitable for classifying patients with HCC in the International Cancer Genome Consortium. CFHR3 shows remarkable diagnostic value in HCC. Hypoxia decreased CFHR3 expression, but increased HCC cell proliferation and motility. Overexpression of CFHR3 in HCC cells under hypoxia reversed the stimulatory effects of hypoxia and suppressed cell proliferation and metastasis in vivo. In conclusion, we identified a novel hypoxia-driven gene signature (CFHR3, EGLN3, and CHGA) for reliable prognostic prediction of HCC, and demonstrated that overexpression of CFHR3 may be a potential strategy to overcome hypoxia and treat HCC.
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Affiliation(s)
- Zhirui Zeng
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
| | - Shan Lei
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Jingya Wang
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Yushi Yang
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jinzhi Lan
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Qianting Tian
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Tengxiang Chen
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Precision Medicine Research Institute of Guizhou Medical University, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiaojiang Hao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
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Manne A, Woods E, Tsung A, Mittra A. Biliary Tract Cancers: Treatment Updates and Future Directions in the Era of Precision Medicine and Immuno-Oncology. Front Oncol 2021; 11:768009. [PMID: 34868996 PMCID: PMC8634105 DOI: 10.3389/fonc.2021.768009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
The effective management of biliary tract cancers (BTCs) has been hampered by limited options for systemic therapy. In recent years, the focus on precision medicine has made technologies such as next-generation sequencing (NGS) accessible to clinicians to identify targetable mutations in BTCs in tumor tissue (primarily) as well as blood, and to treat them with targeted therapies when possible. It has also expanded our understanding of functional pathways associated with genetic alterations and opened doors for identifying novel targets for treatment. Recent advances in the precision medicine approach allowed us to identify new molecular markers in BTCs, such as epigenetic changes (methylation and histone modification) and non-DNA markers such as messenger RNA, microRNA, and long non-coding RNA. It also made detecting these markers from non-traditional sources such as blood, urine, bile, and cytology (from fine-needle aspiration and biliary brushings) possible. As these tests become more accessible, we can see the integration of different molecular markers from all available sources to aid physicians in diagnosing, assessing prognosis, predicting tumor response, and screening BTCs. Currently, there are a handful of approved targeted therapies and only one class of immunotherapy agents (immune checkpoint inhibitors or ICIs) to treat BTCs. Early success with new targets, vascular endothelial growth factor receptor (VEGFR), HER2, protein kinase receptor, and Dickkopf-1 (DKK1); new drugs for known targets, fibroblast growth factor receptors (FGFRs) such as futabatinib, derazantinib, and erdafitinib; and ICIs such as durvalumab and tremelimumab is encouraging. Novel immunotherapy agents such as bispecific antibodies (bintrafusp alfa), arginase inhibitors, vaccines, and cellular therapy (chimeric antigen receptor-T cell or CAR-T, natural killer cells, tumor-infiltrating lymphocytes) have the potential to improve outcomes of BTCs in the coming years.
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Affiliation(s)
- Ashish Manne
- Department of Internal Medicine, Division of Medical Oncology at the Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Edward Woods
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Allan Tsung
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Cancer Hospital and Solove Research Institute, Columbus, OH, United States
| | - Arjun Mittra
- Department of Internal Medicine, Division of Medical Oncology at the Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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