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Dong Z, Dai B, Wu R, Fang K, Sui C, Geng L, Yang J. Expression Characteristics, Immune Signature, and Prognostic Value of the SOCS Family Identified by Multiomics Integrative Analysis in Liver Cancer. Cancer Rep (Hoboken) 2024; 7:e2161. [PMID: 39307915 PMCID: PMC11416904 DOI: 10.1002/cnr2.2161] [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: 11/10/2023] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a prevalent malignancy with a high mortality rate worldwide. Suppressor of cytokine signaling (SOCS) family members play important roles in the proliferation, metabolism, and immunity of HCC cells by regulating cytokines and growth factors. However, it remains uncertain whether the level of SOCS family members can affect the prognosis of HCC patients. AIMS This study aimed to comprehensively assess the role and mechanisms of SOCS family members in the development of HCC and to guide clinical selection. METHODS We investigated the expression levels of SOCS family genes in HCC patients and their associations with various clinicopathological characteristics. We also utilized a public database to analyze the changes in the expression, potential functions, transcription factors, and immune invasion of SOCS family members. Additionally, we examined the prognostic value of the SOC family for HCC and its correlation with the SOC family and ferroptosis-related genes. RESULTS This study revealed that the expression of SOCS2-7, and CISH was downregulated in HCC. The SOCS4, SOCS5, and SOCS7 genes were associated with the clinicopathological features of HCC patients. SOCS family genes are mainly related to the PIK3R3, GHR, and TNS4 pathways. Additionally, this study revealed that STAT3, PPAR-gamma 2, and IRF-2 are important transcription factors that regulate SOCS family members. The expression levels of SOCS family members are closely related to immune infiltration in liver cancer. The study also indicated that SOCS2 and SOCS4 are risk-related genes for predicting the prognosis of patients with liver cancer. Finally, this study suggested that the SOCS2 gene may be involved in the development and progression of HCC. CONCLUSION Our study enhances the current understanding of SOCS gene function in liver cancer and can help clinicians select appropriate drugs and predict the prognosis of HCC patients.
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Affiliation(s)
- Zhitao Dong
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Binghua Dai
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Rui Wu
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Kunpeng Fang
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Chengjun Sui
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Li Geng
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Jiamei Yang
- Department of Special TreatmentShanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
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Sayed Amr K, Mohamed Ezzat W, Ibrahim Saleh A, Heiba A, Amin H, Refaat Kamel R, Eltaweel N, Henery H, Omaia A, Ibrahim Siddik R, Abdelghany Abdelazeem Elhosary Y. Measuring the differential expression of the major hypermethylated tumor suppressor genes in tissues of primary hepatocellular carcinoma. J Genet Eng Biotechnol 2024; 22:100394. [PMID: 39179317 PMCID: PMC11214395 DOI: 10.1016/j.jgeb.2024.100394] [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: 08/26/2024]
Abstract
BACKGROUND Hepatocarcinogenesis is a multifactorial process that arises from a integration of genetic and epigenetic anomalies leading to abnormal gene expression and function. It is difficult to characterize HCC with a single biomarker. Our study aimed at detecting the expression of a panel of 8 methylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) as regulatory factors among Egyptian patients with HCC. METHODS This study was conducted on HCC tissue samples of 30 Egyptian patients in comparison with their non-cancerous adjacent cirrhotic tissue as a control. Tissue samples were obtained from patients who have undergone living donor liver transplantation (LDLT) or liver resection at El Sahel Teaching Hospital (Cairo, Egypt). A special Custom designed PCR Arrays was used to analyze the expression profiles of chosen methylated genes associated with HCC. RESULTS Expression of SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2 were lower in the HCC tissue compared to the cirrhotic tissue (pvalue = 0.015, 0.081, 0.004, 0.027, 0.211, 0.015, 0.025 and 0.0001 respectively). 5 genes (SOCS1, APC, GAdd45b, CDKN1B, and MSH2) showed the ability to be used as diagnostic biomarkers for HCC with high sensitivity and specificity values at cut off values: 1.05, 1.17, 0.995, 0.546, and 0.125 respectively. As for the other 3 genes (P15, PAX6, STAT1), PAX6 gene has the highest sensitivity at a cut off value of 0.3364. A significant negative correlation was shown between alpha fetoprotein (AFP) and 5 of the studied genes (SOCS1, APC, Gadd45b, STAT1, and MSH2). CONCLUSIONS Expression of the selected hypermethylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) in HCC tissue samples was lower than adjacent tissue. Their role should be further studied to solve the mystery that surrounds the pathogenesis of HCC.
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Affiliation(s)
- Khalda Sayed Amr
- Medical Molecular Genetics Dept, Human Genetics and Genome Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Wafaa Mohamed Ezzat
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Ahmed Ibrahim Saleh
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt.
| | - Ahmed Heiba
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Hend Amin
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Refaat Refaat Kamel
- Surgery Dept, Faculty Of Medicine, Ain Shams University, 38 Abbassia, Cairo 1181, Egypt
| | - Noha Eltaweel
- Medical Molecular Genetics Dept, Human Genetics and Genome Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Hoda Henery
- Surgery Dept, Elsahel Teaching Hospital, 2 Youssef Karam, Borham, El Sahel, Cairo 11697, Egypt
| | - Amr Omaia
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
| | - Reham Ibrahim Siddik
- Internal Medicine Dept, Medical Research Institute, National Research Center, 33 El Buhouth St, Dokki, Cairo 12622, Egypt
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van der Meeren PE, de Wilde RF, Sprengers D, IJzermans JNM. Benefit and harm of waiting time in liver transplantation for HCC. Hepatology 2023:01515467-990000000-00646. [PMID: 37972979 DOI: 10.1097/hep.0000000000000668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Liver transplantation is the most successful treatment for limited-stage HCC. The waiting time for liver transplantation (LT) can be a critical factor affecting the oncological prognosis and outcome of patients with HCC. Efficient strategies to optimize waiting time are essential to maximize the benefits of LT and to reduce the harm of delay in transplantation. The ever-increasing demand for donor livers emphasizes the need to improve the organization of the waiting list for transplantation and to optimize organ availability for patients with and without HCC. Current progress in innovations to expand the donor pool includes the implementation of living donor LT and the use of grafts from extended donors. By expanding selection criteria, an increased number of patients are eligible for transplantation, which necessitates criteria to prevent futile transplantations. Thus, the selection criteria for LT have evolved to include not only tumor characteristics but biomarkers as well. Enhancing our understanding of HCC tumor biology through the analysis of subtypes and molecular genetics holds significant promise in advancing the personalized approach for patients. In this review, the effect of waiting time duration on outcome in patients with HCC enlisted for LT is discussed.
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Affiliation(s)
- Pam Elisabeth van der Meeren
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Roeland Frederik de Wilde
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dave Sprengers
- Department of Gastroenterology & Hepatology, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jan Nicolaas Maria IJzermans
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Abid F, Khan K, Badshah Y, Ashraf NM, Shabbir M, Hamid A, Afsar T, Almajwal A, Razak S. Non-synonymous SNPs variants of PRKCG and its association with oncogenes predispose to hepatocellular carcinoma. Cancer Cell Int 2023; 23:123. [PMID: 37344815 PMCID: PMC10286404 DOI: 10.1186/s12935-023-02965-z] [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: 03/23/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND PRKCG encodes PKC γ, which is categorized under the classical protein kinase C family. No studies have specifically established the relationship between PRKCG nsSNPs with structural and functional variations in PKC γ in the context of hepatocellular carcinoma (HCC). The present study aims to uncover this link through in-silico and experimental studies. METHODS The 3D structure of PKC γ was predicted. Molecular Dynamic (MD) Simulations were run and estimates were made for interactions, stability, conservation and post-translational alterations between wild and mutant structures. The association of PRKCG levels with HCC survival rate was determined. Genotyping analyses were conducted to investigate the deleterious PRKCG nsSNP association with HCC. mRNA expression of PKC γ, HIF-1 alpha, AKT, SOCS3 and VEGF in the blood of controls and HCC patients was analyzed and a genetic cascade was constructed depicting these interactions. RESULTS The expression level of studied oncogenes was compared to tumour suppressor genes. Through Alphafold, the 3D structure of PKC γ was explored. Fifteen SNPs were narrowed down for in-silico analyses that were identified in exons 5, 10 and 18 and the regulatory and kinase domain of PKC γ. Root mean square deviation and fluctuation along with the radius of gyration unveiled potential changes between the wild and mutated variant structures. Mutant genotype AA (homozygous) corresponding to nsSNP, rs386134171 had more frequency in patients with OR (2.446), RR (1.564) and P-values (< 0.0029) that highlights its significant association with HCC compared to controls in which the wild genotype GG was found more prevalent. CONCLUSION nsSNP rs386134171 can be a genetic marker for HCC diagnosis and therapeutic studies. This study has laid down a road map for future studies to be conducted on HCC.
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Affiliation(s)
- Fizzah Abid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan.
| | - Arslan Hamid
- LIMES Institute (AG-Netea), University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Xue C, Yao Q, Gu X, Shi Q, Yuan X, Chu Q, Bao Z, Lu J, Li L. Evolving cognition of the JAK-STAT signaling pathway: autoimmune disorders and cancer. Signal Transduct Target Ther 2023; 8:204. [PMID: 37208335 DOI: 10.1038/s41392-023-01468-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/22/2023] [Indexed: 05/21/2023] Open
Abstract
The Janus kinase (JAK) signal transducer and activator of transcription (JAK-STAT) pathway is an evolutionarily conserved mechanism of transmembrane signal transduction that enables cells to communicate with the exterior environment. Various cytokines, interferons, growth factors, and other specific molecules activate JAK-STAT signaling to drive a series of physiological and pathological processes, including proliferation, metabolism, immune response, inflammation, and malignancy. Dysregulated JAK-STAT signaling and related genetic mutations are strongly associated with immune activation and cancer progression. Insights into the structures and functions of the JAK-STAT pathway have led to the development and approval of diverse drugs for the clinical treatment of diseases. Currently, drugs have been developed to mainly target the JAK-STAT pathway and are commonly divided into three subtypes: cytokine or receptor antibodies, JAK inhibitors, and STAT inhibitors. And novel agents also continue to be developed and tested in preclinical and clinical studies. The effectiveness and safety of each kind of drug also warrant further scientific trials before put into being clinical applications. Here, we review the current understanding of the fundamental composition and function of the JAK-STAT signaling pathway. We also discuss advancements in the understanding of JAK-STAT-related pathogenic mechanisms; targeted JAK-STAT therapies for various diseases, especially immune disorders, and cancers; newly developed JAK inhibitors; and current challenges and directions in the field.
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Affiliation(s)
- Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qinfan Yao
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingmiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengyi Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Cabrera-Galván JJ, Araujo E, de Mirecki-Garrido M, Pérez-Rodríguez D, Guerra B, Aranda-Tavío H, Guerra-Rodríguez M, Brito-Casillas Y, Melián C, Martínez-Martín MS, Fernández-Pérez L, Recio C. SOCS2 protects against chemical-induced hepatocellular carcinoma progression by modulating inflammation and cell proliferation in the liver. Biomed Pharmacother 2023; 157:114060. [PMID: 36455458 DOI: 10.1016/j.biopha.2022.114060] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers worldwide, but the precise intracellular mechanisms underlying the progression of this inflammation associated cancer are not well established. SOCS2 protein plays an important role in the carcinogenesis of different tumors by regulating cytokine signalling through the JAK/STAT axis. However, its role in HCC is unclear. Here, we investigate the role of SOCS2 in HCC progression and its potential as HCC biomarker. The effects of SOCS2 in HCC progression were evaluated in an experimental model of diethylnitrosamine (DEN)-induced HCC in C57BL/6 and SOCS2 deficient mice, in cultured hepatic cells, and in liver samples from HCC patients. Mice lacking SOCS2 showed higher liver tumor burden with increased malignancy grade, inflammation, fibrosis, and proliferation than their controls. Protein and gene expression analysis reported higher pSTAT5 and pSTAT3 activation, upregulation of different proteins involved in survival and proliferation, and increased levels of proinflammatory and pro-tumoral mediators in the absence of SOCS2. Clinically relevant, downregulated expression of SOCS2 was found in neoplasia from HCC patients compared to healthy liver tissue, correlating with the malignancy grade. In summary, our data show that lack of SOCS2 increases susceptibility to chemical-induced HCC and suggest the tumor suppressor role of this protein by regulating the oncogenic and inflammatory responses mediated by STAT5 and STAT3 in the liver. Hence, SOCS2 emerges as an attractive target molecule and potential biomarker to deepen in the study of HCC treatment.
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Affiliation(s)
- Juan José Cabrera-Galván
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain; Departamento Morfología, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Eduardo Araujo
- Departamento Morfología, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Mercedes de Mirecki-Garrido
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - David Pérez-Rodríguez
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Borja Guerra
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain; Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain and Instituto de Investigaciones Biomédicas "Alberto Sols" Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
| | - Haidée Aranda-Tavío
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Miguel Guerra-Rodríguez
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Yeray Brito-Casillas
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Carlos Melián
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - María Soledad Martínez-Martín
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain; Departamento Morfología, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain; Servicio Anatomía Patológica, Complejo Hospitalario Universitario Insular - Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - Leandro Fernández-Pérez
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain; Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain and Instituto de Investigaciones Biomédicas "Alberto Sols" Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlota Recio
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain.
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Yamazaki M, Hosokawa M, Matsunaga H, Arikawa K, Takamochi K, Suzuki K, Hayashi T, Kambara H, Takeyama H. Integrated spatial analysis of gene mutation and gene expression for understanding tumor diversity in formalin-fixed paraffin-embedded lung adenocarcinoma. Front Oncol 2022; 12:936190. [PMID: 36505794 PMCID: PMC9731154 DOI: 10.3389/fonc.2022.936190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction A deeper understanding of intratumoral heterogeneity is essential for prognosis prediction or accurate treatment plan decisions in clinical practice. However, due to the cross-links and degradation of biomolecules within formalin-fixed paraffin-embedded (FFPE) specimens, it is challenging to analyze them. In this study, we aimed to optimize the simultaneous extraction of mRNA and DNA from microdissected FFPE tissues (φ = 100 µm) and apply the method to analyze tumor diversity in lung adenocarcinoma before and after erlotinib administration. Method Two magnetic beads were used for the simultaneous extraction of mRNA and DNA. The decross-linking conditions were evaluated for gene mutation and gene expression analyses of microdissected FFPE tissues. Lung lymph nodes before treatment and lung adenocarcinoma after erlotinib administration were collected from the same patient and were preserved as FFPE specimens for 4 years. Gene expression and gene mutations between histologically classified regions of lung adenocarcinoma (pre-treatment tumor in lung lymph node biopsies and post-treatment tumor, normal lung, tumor stroma, and remission stroma, in resected lung tissue) were compared in a microdissection-based approach. Results Using the optimized simultaneous extraction of DNA and mRNA and whole-genome amplification, we detected approximately 4,000-10,000 expressed genes and the epidermal growth factor receptor (EGFR) driver gene mutations from microdissected FFPE tissues. We found the differences in the highly expressed cancer-associated genes and the positive rate of EGFR exon 19 deletions among the tumor before and after treatment and tumor stroma, even though they were collected from tumors of the same patient or close regions of the same specimen. Conclusion Our integrated spatial analysis method would be applied to various FFPE pathology specimens providing area-specific gene expression and gene mutation information.
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Affiliation(s)
- Miki Yamazaki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Koji Arikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Kazuya Takamochi
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hideki Kambara
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Frontier BioSystems Inc., Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan,*Correspondence: Haruko Takeyama,
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Analysis of SOCS3 gene genotype in patients with acute cerebral infarction and its relationship with disease progression. Clin Neurol Neurosurg 2022; 224:107518. [PMID: 36434897 DOI: 10.1016/j.clineuro.2022.107518] [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: 09/19/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE This reseaech aimed to analyze the polymorphism of SOCS3 gene in patients with acute cerebral infarction (ACI), and to explore its relationship with disease progression. METHODS A total of 310 patients with ACI were categorized into mild stroke group and moderate to severe stroke group according to the National Institute of Stroke Scale (NIHSS) score at admission. Based on NIHSS scores at 7 days after admission, patients were further divided into advanced group and non-advanced group. According to the results of SOCS3 gene detection, three genotypes of rs8064821 were detected: CC, CA and AA. The distribution difference of the genotypes and their predictive possibility were reckoned. RESULTS The distribution of SOCS3 genotype at rs8064821 in patients with ACI was CC (161 cases), CA (127 cases), and AA (22 cases), with frequencies of 51.93 %, 40.97 %, and 7.10 %, respectively. Compared with mild group, the proportion of CC genotype was lower, while the proportion of CA and AA genotypes was higher in moderate-severe stroke group (P < 0.01). Compared with non-advanced group, patients who advanced to neurological deficit had a lower proportion of CC genotype, and a higher proportion of CA and AA genotype (P < 0.01). CONCLUSION CA and AA genotypes were the main genotypes of SOCS3 in patients with ACI in northern Anhui of China. The disease was more severe in patients with CA and AA, who are more likely to develop neurological deficits.
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Ashfaq I, Sheikh N, Fatima N, Tayyeb A. Inhibition of anti-inflammatory pathway through suppressors of cytokine signalling (Socs2/Socs3) in the initiation of hepatocellular carcinoma. Saudi J Biol Sci 2022; 29:103348. [PMID: 35800143 PMCID: PMC9253924 DOI: 10.1016/j.sjbs.2022.103348] [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: 01/05/2022] [Revised: 04/30/2022] [Accepted: 06/10/2022] [Indexed: 11/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC), a leading cause of cancer related deaths is predominantly driven by chronic inflammatory responses. Due to asymptomatic nature and lack of early patient biopsies, precise involvement of inflammation in hepatic injury initiation remains unidentified. Aim of the study was to elucidate the regulation patterns of inflammatory signalling from initiation of hepatic injury to development of HCC. HCC mice model was established using DEN followed by repeated doses of CCl4 and sacrificed at three different stages of disease comprising 7, 14 and 21 weeks. Serum biochemical tests, hepatic lipids quantification, histopathology and qPCR analyses were conducted to characterize the initiation and progression of liver injury and inflammatory signalling. Notably, at 7 weeks, we observed hepatocyte damage and periportal necrotic bodies coupled with induction of Socs2/Socs3 and anti-inflammatory cytokine Il-10. At 14 weeks, mice liver showed advancement of liver injury with micro-vesicular steatosis and moderate collagen deposition around portal zone. With progression of injury, the expression of Socs3 was declined with further reduction of Il-10 and Tgf-β indicating the disturbance of anti-inflammatory mechanism. In contrast, pro-inflammatory cytokines Il1-β, Il6 and Tnf-α were upregulated contributing inflammation. Subsequently, at 21 weeks severe liver damage was estimated as characterized by macro-vesicular steatosis, perisinusoidal collagen bridging, immune cell recruitment and significant upregulation of Col-1α and α-Sma. In parallel, there was significant upregulation of pro/anti-inflammatory cytokines highlighting the commencement of chronic inflammation. Findings of the study suggest that differential regulation of cytokine suppressors and inflammatory cytokines might play role in the initiation and progression of hepatic injury leading towards HCC.
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Affiliation(s)
- Isbah Ashfaq
- Cell & Molecular Biology Lab, Institute of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
- School of Biological Sciences (SBS), University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Nadeem Sheikh
- Cell & Molecular Biology Lab, Institute of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Naz Fatima
- Cell & Molecular Biology Lab, Institute of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
- Department of Zoology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Asima Tayyeb
- School of Biological Sciences (SBS), University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
- Corresponding author at: School of Biological Sciences (SBS), University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan.
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10
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Lin ZL, Liu YC, Gao YL, Chen XS, Wang CL, Shou ST, Chai YF. S100A9 and SOCS3 as diagnostic biomarkers of acute myocardial infarction and their association with immune infiltration. Gene 2022; 97:67-79. [PMID: 35675985 DOI: 10.1266/ggs.21-00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Acute myocardial infarction (AMI) is one of the leading causes of death globally, with a mortality rate of over 20%. However, the diagnostic biomarkers frequently used in current clinical practice have limitations in both sensitivity and specificity, likely resulting in delayed diagnosis. This study aimed to identify potential diagnostic biomarkers for AMI and explored the possible mechanisms involved. Datasets were retrieved from the Gene Expression Omnibus. First, we identified differentially expressed genes (DEGs) and preserved modules, from which we identified candidate genes by LASSO (least absolute shrinkage and selection operator) regression and the SVM-RFE (support vector machine-recursive feature elimination) algorithm. Subsequently, we used ROC (receiver operating characteristic) analysis to evaluate the diagnostic accuracy of the candidate genes. Thereafter, functional enrichment analysis and an analysis of immune infiltration were implemented. Finally, we assessed the association between biomarkers and biological processes, infiltrated cells, clinical traits, tissues and time points. We identified nine preserved modules containing 1,016 DEGs and managed to construct a diagnostic model with high accuracy (GSE48060: AUC = 0.923; GSE66360: AUC = 0.973) incorporating two genes named S100A9 and SOCS3. Functional analysis revealed the pivotal role of inflammation; immune infiltration analysis indicated that eight cell types (monocytes, epithelial cells, neutrophils, CD8+ T cells, Th2 cells, NK cells, NKT cells and platelets) were likely involved in AMI. Furthermore, we observed that S100A9 and SOCS3 were correlated with inflammation, variably infiltrated cells, clinical traits of patients, sampling tissues and sampling time points. In conclusion, we suggested S100A9 and SOCS3 as diagnostic biomarkers of AMI and discovered their association with inflammation, infiltrated immune cells and other factors.
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Affiliation(s)
- Ze-Liang Lin
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Yan-Cun Liu
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Yu-Lei Gao
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Xin-Sen Chen
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Chao-Lan Wang
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Song-Tao Shou
- Department of Emergency Medicine, Tianjin Medical University General Hospital
| | - Yan-Fen Chai
- Department of Emergency Medicine, Tianjin Medical University General Hospital
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11
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Fan X, Ou Y, Liu H, Zhan L, Zhu X, Cheng M, Li Q, Yin D, Liao L. A Ferroptosis-Related Prognostic Signature Based on Antitumor Immunity and Tumor Protein p53 Mutation Exploration for Guiding Treatment in Patients With Head and Neck Squamous Cell Carcinoma. Front Genet 2021; 12:732211. [PMID: 34616431 PMCID: PMC8488345 DOI: 10.3389/fgene.2021.732211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/24/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Due to the lack of accurate guidance of biomarkers, the treatment of head and neck squamous cell carcinoma (HNSCC) has not been ideal. Ferroptosis plays an important role in tumor suppression and treatment of patients. However, tumor protein p53 (TP53) mutation may promote tumor progression through ferroptosis. Therefore, it is particularly important to mine prognostic-related differentially expressed ferroptosis-related genes (PR-DE-FRGs) in HNSCC to construct a prognostic model for accurately guiding clinical treatment. Methods: First, the HNSCC data obtained from The Cancer Genome Atlas (TCGA) was used to identify PR-DE-FRGs for screening candidate genes to construct a prognostic model. We not only used a variety of methods to verify the accuracy of the model for predicting prognosis but also explored the role of ferroptosis in the development of HNSCC from the perspective of the immune microenvironment and mutation. Finally, we explored the correlation between the prognostic model and clinical treatment and drew a high-precision nomogram to predict the prognosis. Results: Seventeen of the 29 PR-DE-FRGs were selected to construct a prognostic model with good predictive performance. Patients in the low-risk group were found to have a greater number of CD8 + T cells, follicular helper T cells, regulatory T cells, mast cells, T-cell costimulations, and type II interferon responses. A higher tumor mutation burden (TMB) was observed in the low-risk group and was associated with a better prognosis. A higher risk score was found in the TP53 mutation group and was associated with a worse prognosis. The risk score is closely related to the expression of immune checkpoint inhibitors (ICIs)-related genes such as PD-L1 and the IC50 of six chemotherapeutic drugs. The nomogram we constructed performs well in predicting prognosis. Conclusion: Ferroptosis may participate in the progression of HNSCC through the immune microenvironment and TP53 mutation. The model we built can be used as an effective predictor of immunotherapy and chemotherapy effects and prognosis of HNSCC patients.
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Affiliation(s)
- Xin Fan
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - YangShaobo Ou
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - Huijie Liu
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | | | - Xingrong Zhu
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - Mingyang Cheng
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - Qun Li
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - Dongmei Yin
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
| | - Lan Liao
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China.,The Key Laboratory of Oral Biomedicine, Jiangxi Province, Nanchang, China
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12
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The Relevance of SOCS1 Methylation and Epigenetic Therapy in Diverse Cell Populations of Hepatocellular Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11101825. [PMID: 34679523 PMCID: PMC8534387 DOI: 10.3390/diagnostics11101825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
The suppressor of cytokine signaling 1 (SOCS1) is a tumor suppressor gene found to be hypermethylated in cancers. It is involved in the oncogenic transformation of cirrhotic liver tissues. Here, we investigated the clinical relevance of SOCS1 methylation and modulation upon epigenetic therapy in diverse cellular populations of hepatocellular carcinoma (HCC). HCC clinical specimens were evaluated for SOCS1 methylation and mRNA expression. The effect of 5-Azacytidine (5-AZA), a demethylation agent, was assessed in different subtypes of HCC cells. We demonstrated that the presence of SOCS1 methylation was significantly higher in HCC compared to peri-HCC and non-tumoral tissues (52% vs. 13% vs. 14%, respectively, p < 0.001). In vitro treatment with a non-toxic concentration of 5-AZA significantly reduced DNMT1 protein expression for stromal subtype lines (83%, 73%, and 79%, for HLE, HLF, and JHH6, respectively, p < 0.01) compared to cancer stem cell (CSC) lines (17% and 10%, for HepG2 and Huh7, respectively), with the strongest reduction in non-tumoral IHH cells (93%, p < 0.001). 5-AZA modulated the SOCS1 expression in different extents among the cells. It was restored in CSC HCC HepG2 and Huh7 more efficiently than sorafenib. This study indicated the relevance of SOCS1 methylation in HCC and how cellular heterogeneity influences the response to epigenetic therapy.
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13
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Hu ZW, Wen YH, Ma RQ, Chen L, Zeng XL, Wen WP, Sun W. Ferroptosis Driver SOCS1 and Suppressor FTH1 Independently Correlate With M1 and M2 Macrophage Infiltration in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:727762. [PMID: 34527677 PMCID: PMC8437260 DOI: 10.3389/fcell.2021.727762] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
Objective To investigate the role of ferroptosis, an iron-dependent form of non-apoptotic cell death, in the head and neck squamous cell carcinoma (HNSCC) immune microenvironment. Materials and Methods A list of ferroptosis-related genes was obtained from the FerrDb database. Gene expression data were acquired from the cancer genome atlas (TCGA) and analyzed using the R language. Protein–protein interaction analysis was conducted using STRING and GeneMANIA. The correlations between gene expression levels and a patient’s survival were analyzed using GEPIA, the Kaplan–Meier estimate, and a multivariate Cox proportional hazards model. The expression results were verified using Oncomine and Human Protein Atlas data. We used the TIMER, GEPIA2, GEPIA2021, and TIMER2 databases to investigate the relationships between gene expression and infiltrating immune cells. Results Analysis of differentially expressed genes (DEGs) identified nine each ferroptosis drivers and ferroptosis suppressors, among which four genes correlated with survival as follows: two drivers (SOCS1, CDKN2A) associated with better survival and two suppressors (FTH1, CAV1) associated with poorer survival. Multivariate Cox survival analysis identified SOCS1 and FTH1 as independent prognostic factors for HNSCC, and their higher expression levels were verified using Oncomine and HPA data. The results acquired using TIMER, GEPIA2, GEPIA2021, and TIMER2 data revealed that the driver SOCS1 and the suppressor FTH1 independently correlated with M1 and M2 macrophage infiltration. Conclusions The ferroptosis driver SOCS1 and suppressor FTH1 are independent prognostic factors and that correlate with M1 and M2 macrophage infiltration in HNSCC. Targeting ferroptosis-immunomodulation may serve as a strategy to enhance the activity of immunotherapy.
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Affiliation(s)
- Zhang-Wei Hu
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Yi-Hui Wen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Ren-Qiang Ma
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Xue-Lan Zeng
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Wei-Ping Wen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China.,Department of Otolaryngology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Sun
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
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14
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Umer HM, Smolinska K, Komorowski J, Wadelius C. Functional annotation of noncoding mutations in cancer. Life Sci Alliance 2021; 4:4/9/e201900523. [PMID: 34282050 PMCID: PMC8321657 DOI: 10.26508/lsa.201900523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Recurrent regulatory mutations affecting transcription factor binding sites in 2,500 cancer samples. In a cancer genome, the noncoding sequence contains the vast majority of somatic mutations. While very few are expected to be cancer drivers, those affecting regulatory elements have the potential to have downstream effects on gene regulation that may contribute to cancer progression. To prioritize regulatory mutations, we screened somatic mutations in the Pan-Cancer Analysis of Whole Genomes cohort of 2,515 cancer genomes on individual bases to assess their potential regulatory roles in their respective cancer types. We found a highly significant enrichment of regulatory mutations associated with the deamination signature overlapping a CpG site in the CCAAT/Enhancer Binding Protein β recognition sites in many cancer types. Overall, 5,749 mutated regulatory elements were identified in 1,844 tumor samples from 39 cohorts containing 11,962 candidate regulatory mutations. Our analysis indicated 20 or more regulatory mutations in 5.5% of the samples, and an overall average of six per tumor. Several recurrent elements were identified, and major cancer-related pathways were significantly enriched for genes nearby the mutated regulatory elements. Our results provide a detailed view of the role of regulatory elements in cancer genomes.
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Affiliation(s)
- Husen M Umer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karolina Smolinska
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Swedish Collegium for Advanced Study, Uppsala, Sweden.,Washington National Primate Research Center, Seattle, WA, USA
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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15
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Liu ZK, Li C, Zhang RY, Wei D, Shang YK, Yong YL, Kong LM, Zheng NS, Liu K, Lu M, Liu M, Hu CX, Yang XZ, Chen ZN, Bian H. EYA2 suppresses the progression of hepatocellular carcinoma via SOCS3-mediated blockade of JAK/STAT signaling. Mol Cancer 2021; 20:79. [PMID: 34044846 PMCID: PMC8157759 DOI: 10.1186/s12943-021-01377-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Somatic mutations are involved in hepatocellular carcinoma (HCC) progression, but the genetic mechanism associated to hepatocarcinogenesis remains poorly understood. We report that Eyes absent homolog 2 (EYA2) suppresses the HCC progression, while EYA2(A510E) mutation identified by exome sequencing attenuates the tumor-inhibiting effect of EYA2. METHODS Whole-exome sequencing was performed on six pairs of human HCC primary tumors and matched adjacent tissues. Focusing on EYA2, expression level of EYA2 in human HCC samples was evaluated by quantitative real-time PCR, western blot and immunohistochemistry. Loss- and gain-of-function studies, hepatocyte-specific deletion of EYA2 (Eya2-/-) in mice and RNA sequencing analysis were used to explore the functional effect and mechanism of EYA2 on HCC cell growth and metastasis. EYA2 methylation status was evaluated using Sequenom MassARRAY and publicly available data analysis. RESULTS A new somatic mutation p.Ala510Glu of EYA2 was identified in HCC tissues. The expression of EYA2 was down-regulated in HCC and associated with tumor size (P = 0.001), Barcelona Clinic Liver Cancer stage (P = 0.016) and tumor differentiation (P = 0.048). High level of EYA2 was correlated with a favorable prognosis in HCC patients (P = 0.003). Results from loss-of-function and gain-of-function experiments suggested that knockdown of EYA2 enhanced, while overexpression of EYA2 attenuated, the proliferation, clone formation, invasion, and migration of HCC cells in vitro. Delivery of EYA2 gene had a therapeutic effect on inhibition of orthotopic liver tumor in nude mice. However, EYA2(A510E) mutation led to protein degradation by unfolded protein response, thus weakening the inhibitory function of EYA2. Hepatocyte-specific deletion of EYA2 in mice dramatically promoted diethylnitrosamine-induced HCC development. EYA2 was also down-regulated in HCC by aberrant CpG methylation. Mechanically, EYA2 combined with DACH1 to transcriptionally regulate SOCS3 expression, thus suppressing the progression of HCC via SOCS3-mediated blockade of the JAK/STAT signaling pathway. CONCLUSIONS In our study, we identified and validated EYA2 as a tumor suppressor gene in HCC, providing a new insight into HCC pathogenesis.
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Affiliation(s)
- Ze-Kun Liu
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Can Li
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Ren-Yu Zhang
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Ding Wei
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yu-Kui Shang
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yu-Le Yong
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Ling-Min Kong
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Nai-Shan Zheng
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Ke Liu
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Meng Lu
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Man Liu
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Cai-Xia Hu
- Oncology and Hepatobiliary Minimally Invasive Interventional Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiao-Zhen Yang
- Oncology and Hepatobiliary Minimally Invasive Interventional Center, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Zhi-Nan Chen
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China.
| | - Huijie Bian
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China.
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