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Chang C, Li L, Su L, Yang F, Zha Q, Sun M, Tao L, Wang M, Song K, Jiang L, Gao H, Liang Y, Xu C, Yong C, Wang M, Huang J, Liu J, Jin W, Lv W, Dong H, Li Q, Bu F, Yan S, Qi H, Zhao S, Zhu Y, Wang Y, Shi J, Qiao Y, Xu J, Chabot B, Chen J. Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403387. [PMID: 39018261 DOI: 10.1002/advs.202403387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/03/2024] [Indexed: 07/19/2024]
Abstract
RNA splicing is a dynamic molecular process in response to environmental stimuli and is strictly regulated by the spliceosome. Sm proteins, constituents of the spliceosome, are key components that mediate splicing reactions; however, their potential role in hepatocellular carcinoma (HCC) is poorly understood. In the study, SNRPD2 (PD2) is found to be the most highly upregulated Sm protein in HCC and to act as an oncogene. PD2 modulates DDX39A intron retention together with HNRNPL to sustain the DDX39A short variant (39A_S) expression. Mechanistically, 39A_S can mediate MYC mRNA nuclear export to maintain high MYC protein expression, while MYC in turn potentiates PD2 transcription. Importantly, digitoxin can directly interact with PD2 and has a notable cancer-suppressive effect on HCC. The study reveals a novel mechanism by which DDX39A senses oncogenic MYC signaling and undergoes splicing via PD2 to form a positive feedback loop in HCC, which can be targeted by digitoxin.
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Affiliation(s)
- Cunjie Chang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Lina Li
- Medical Molecular Biology Laboratory, Medical College, Jinhua University of Vocational Technology, Jinhua, 321016, P.R. China
| | - Ling Su
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Fan Yang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Quanxiu Zha
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Mengqing Sun
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Lin Tao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Menglan Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Kangli Song
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Liangyu Jiang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Haojin Gao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yexin Liang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Chao Xu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Caiyu Yong
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Minmin Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Jiacheng Huang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Jing Liu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Weiwei Jin
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Wenyuan Lv
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Heng Dong
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Qian Li
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Fangtian Bu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Shuanghong Yan
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Haoxiang Qi
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Shujuan Zhao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yingshuang Zhu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- School of Public Health, Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yu Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore
| | - Junping Shi
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yiting Qiao
- The First Affiliated Hospital, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, 310003, P. R. China
| | - Jian Xu
- Hepatobiliary and Liver transplantation Department of Hainan Digestive Disease Center, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, P. R. China
| | - Benoit Chabot
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Jianxiang Chen
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, P. R. China
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Liu Z, Lai S, Qu Q, Liu X, Zhang W, Zhao D, He S, Sun Y, Bao H. Analysis of weighted gene co-expression networks and clinical validation identify hub genes and immune cell infiltration in the endometrial cells of patients with recurrent implantation failure. Front Genet 2024; 15:1292757. [PMID: 38645487 PMCID: PMC11026622 DOI: 10.3389/fgene.2024.1292757] [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: 09/14/2023] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Background About 10% of individuals undergoing in vitro fertilization encounter recurrent implantation failure (RIF), which represents a worldwide social and economic concern. Nevertheless, the critical genes and genetic mechanisms underlying RIF are largely unknown. Methods We first obtained three comprehensive microarray datasets "GSE58144, GSE103465 and GSE111974". The differentially expressed genes (DEGs) evaluation, enrichment analysis, as well as efficient weighted gene co-expression network analysis (WGCNA), were employed for distinguishing RIF-linked hub genes, which were tested by RT-qPCR in our 30 independent samples. Next, we studied the topography of infiltration of 22 immune cell subpopulations and the association between hub genes and immune cells in RIF using the CIBERSORT algorithm. Finally, a novel ridge plot was utilized to exhibit the potential function of core genes. Results The enrichment of GO/KEGG pathways reveals that Herpes simplex virus 1 infection and Salmonella infection may have an important role in RIF. After WGCNA, the intersected genes with the previous DEGs were obtained using both variance and association. Notably, the subsequent nine hub genes were finally selected: ACTL6A, BECN1, SNRPD1, POLR1B, GSK3B, PPP2CA, RBBP7, PLK4, and RFC4, based on the PPI network and three different algorithms, whose expression patterns were also verified by RT-qPCR. With in-depth analysis, we speculated that key genes mentioned above might be involved in the RIF through disturbing endometrial microflora homeostasis, impairing autophagy, and inhibiting the proliferation of endometrium. Furthermore, the current study revealed the aberrant immune infiltration patterns and emphasized that uterine NK cells (uNK) and CD4+ T cells were substantially altered in RIF endometrium. Finally, the ridge plot displayed a clear and crucial association between hub genes and other genes and key pathways. Conclusion We first utilized WGCNA to identify the most potential nine hub genes which might be associated with RIF. Meanwhile, this study offers insights into the landscape of immune infiltration status to reveal the underlying immune pathogenesis of RIF. This may be a direction for the next study of RIF etiology. Further studies would be required to investigate the involved mechanisms.
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Affiliation(s)
- Zhenteng Liu
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Shoucui Lai
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Qinglan Qu
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Xuemei Liu
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Wei Zhang
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Dongmei Zhao
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Shunzhi He
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Yuxia Sun
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
| | - Hongchu Bao
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
- Shandong Provincial Key Medical and Health Laboratory of Reproductive Health and Genetics (Yantai Yuhuangding Hospital), Yantai, Shandong, China
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Wang X, Luo L, Zhang Y, Liu G, Fang Z, Xu Z, Hu X. CENPB promotes the proliferation of hepatocellular carcinoma and is directly regulated by miR-29a. Aging (Albany NY) 2023; 15:12171-12191. [PMID: 37925172 PMCID: PMC10683605 DOI: 10.18632/aging.205171] [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: 06/20/2023] [Accepted: 10/03/2023] [Indexed: 11/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a significant global health concern as it ranks as the sixth most common malignant tumor and the third leading cause of cancer-related deaths. In this study, we analyzed the expression of centromere protein B (CENPB) mRNA in HCC using TCGA and GEO datasets. Immunohistochemistry (IHC) was performed to determine CENPB protein levels in 490 HCC patients. Our findings revealed higher expression of CENPB mRNA in HCC tissues across the three datasets. Additionally, as the pathological stage and histological grade advanced, CENPB expression increased. Patients with elevated levels of CENPB mRNA and protein demonstrated shorter overall survival (OS) and recurrence-free survival (OS). Notably, CENPB protein showed prognostic value in patients with stage I/II, AFP levels below 400 ng/ml, and tumor size less than 5 cm. Using multivariate regression analysis in 490 HCC patients, we developed nomograms to predict 1-year, 3-year, and 5-year OS and RFS. Knockdown of CENPB in Hep3B and MHCC97 cell lines resulted in significant inhibition of cell proliferation and invasion. Furthermore, bioinformatics analysis identified miR-29a as a potential negative regulator of CENPB expression, which was validated through a dual-luciferase reporter assay. In conclusion, our findings suggest that CENPB may serve as an oncogenic factor in HCC and is directly regulated by miR-29a, highlighting its potential as a promising therapeutic target.
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Affiliation(s)
- Xuyang Wang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Laibang Luo
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Youfu Zhang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Gang Liu
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Zehong Fang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Zhidan Xu
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Xuguang Hu
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
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Wang H, Wang R, Fang J. A spliceosome-associated gene signature aids in predicting prognosis and tumor microenvironment of hepatocellular carcinoma. Aging (Albany NY) 2023; 15:204765. [PMID: 37301543 PMCID: PMC10292887 DOI: 10.18632/aging.204765] [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: 03/11/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
Splicing alterations have been shown to be key tumorigenesis drivers. In this study, we identified a novel spliceosome-related genes (SRGs) signature to predict the overall survival (OS) of patients with hepatocellular carcinoma (HCC). A total of 25 SRGs were identified from the GSE14520 dataset (training set). Univariate and least absolute shrinkage and selection operator (LASSO) regression analyses were utilized to construct the signature using genes with predictive significance. We then constructed a risk model using six SRGs (BUB3, IGF2BP3, RBM3, ILF3, ZC3H13, and CCT3). The reliability and predictive power of the gene signature were validated in two validation sets (TCGA and GSE76427 dataset). Patients in training and validation sets were divided into high and low-risk groups based on the gene signature. Patients in high-risk groups exhibited a poorer OS than in low-risk groups both in the training set and two validation sets. Next, risk score, BCLC staging, TNM staging, and multinodular were combined in a nomogram for OS prediction, and the decision curve analysis (DCA) curve exhibited the excellent prediction performance of the nomogram. The functional enrichment analyses demonstrated high-risk score patients were closely related to multiple oncology characteristics and invasive-related pathways, such as Cell cycle, DNA replication, and Spliceosome. Different compositions of the tumor microenvironment and immunocyte infiltration ratio might contribute to the prognostic difference between high and low-risk score groups. In conclusion, a spliceosome-related six-gene signature exhibited good performance for predicting the OS of patients with HCC, which may aid in clinical decision-making for individual treatment.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ruling Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third People’s Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou 350108, Fujian, China
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Wang H, Chen M, Yang C, Hu H, Jiang Y, Yang F, Lv L. SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway. Arch Biochem Biophys 2023; 743:109661. [PMID: 37268273 DOI: 10.1016/j.abb.2023.109661] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Small nuclear ribonucleoprotein Sm D1 (SNRPD1) has been reported as an oncogene in some solid cancers. Our previous study suggested that SNRPD1 has diagnostic and prognostic value in hepatocellular carcinoma (HCC), but its role in tumor growth and biological behavior remains unknown. In this study, we aimed to unravel the role and mechanism of SNRPD1 in HCC. METHODS We investigated the SNRPD1 mRNA level in adjacent normal liver tissues and HCC tissues with different tumor stages in the UALCAN database. The associations between SNRPD1 mRNA expression and HCC prognosis were investigated in TCGA database. Then, 52 pairs of frozen HCC tissues and corresponding adjacent normal liver tissues were collected to perform qPCR and immunohistochemistry assay. Next, we carried out a series of experiments in vitro and in vivo to investigate the effects of SNRPD1 expression on cell invasion, migration, proliferation, autophagy, and the PI3K/AKT/mTOR pathway. RESULTS The bioinformatics analysis and qPCR in our patient cohort demonstrated that the SNRPD1 mRNA level in HCC tissues was higher than in adjacent normal tissues. In addition, the immunohistochemistry assay exhibited an increased SNRPD1 protein level with the tumor stage increase. Survival analysis suggested that higher expression of SNRPD1 was significantly associated with unfavorable prognosis of patients with HCC. The functional experiments in vitro indicated that SNRPD1 knockdown suppressed the cellular proliferation, migration, and invasion capacities. Furthermore, SNRPD1 inhibition induced cellular apoptosis and arrested the HCC cells at the G0/G1 phase of the cell cycle. Mechanistic analyses demonstrated that SNRPD1 knockdown induced the increase of autophagic vacuoles and the expression of autophagy-related genes (ATG5, ATG7, and ATG12) and blocked the PI3K/AKT/mTOR/4EBP1 pathway in vitro. Moreover, SNRPD1 inhibition suppressed tumor growth and expression of the Ki67 protein in vivo. CONCLUSIONS SNRPD1 may serve as an oncogene in HCC and promote tumor proliferation via inhibiting autophagy induced through the PI3K/Akt/mTOR/4EBP1 pathway.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China; Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian, 350025, China.
| | - Minyong Chen
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, 350014, Fuzhou, Fujian, 350025, China
| | - Chengkai Yang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Huanzhang Hu
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Yi Jiang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Fang Yang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Lizhi Lv
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China.
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Wang H, Yu M, Yang C, Li Q. Upregulation of HCFC1 expression promoted hepatocellular carcinoma progression through inhibiting cell cycle arrest and correlated with immune infiltration. J Cancer 2023; 14:1381-1397. [PMID: 37283799 PMCID: PMC10240668 DOI: 10.7150/jca.84579] [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: 03/23/2023] [Accepted: 04/29/2023] [Indexed: 06/08/2023] Open
Abstract
Background: Host cell factor 1 (HCFC1) was reported associated with the progression of a variety of cancers. However, its role in the prognosis and immunological characteristics of hepatocellular carcinoma (HCC) patients has not been revealed. Methods: The expression and prognostic value of HCFC1 in HCC were investigated from the Cancer Genome Atlas (TCGA) dataset and a cohort of 150 HCC patients. The associations between HCFC1 expression with somatic mutational signature, tumor mutational burden (TMB), and microsatellite instability (MSI) were investigated. Next, the correlation of HCFC1 expression with immune cell infiltration was investigated. In vitro, cytological experiments were conducted to verify the role of HCFC1 in HCC. Results: HCFC1 mRNA and protein upregulated in HCC tissues and correlated to poor prognosis. Multivariate regression analysis based on a cohort of 150 HCC patients revealed that high HCFC1 protein expression was an independent risk factor for prognosis. Upregulation of HCFC1 expression was associated with TMB, MSI, and tumor purity. HCFC1 expression showed a significant positive association with B cell memory, T cell CD4 memory, macrophage M0, and a significant positive association with immune checkpoint-related gene expression in the tumor microenvironment. HCFC1 expression negatively correlated to ImmuneScore, EstimateScore, and StromalScore. The single-cell RNA sequencing analysis demonstrated that the malignant cells and immune cells (B cells, T cells, and macrophages) represented high HCFC1 expression in HCC tissues. Functional analysis revealed that HCFC1 was remarkably correlated with cell cycle signaling. HCFC1 knockdown inhibited the proliferation, migration, and invasion capacity while promoting the apoptosis of HCC cells. At the same time, the cell-cycle-related proteins such as Cyclin D1 (CCND1), Cyclin A2 (CCNA2), cyclin-dependent kinase 4 (CDK4), and cyclin-dependent kinase 6 (CDK6) were downregulated. Conclusion: Upregulation of HCFC1 predicted undesirable prognosis of HCC patients and promoted tumor progression through inhibiting cell cycle arrest.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
| | - Meng Yu
- Department of Critical Care Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, China
| | - Chengkai Yang
- Department of Gastroenterology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, China
| | - Qingsong Li
- Department of Gastroenterology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, China
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Wang H, Yang C, Li D, Wang R, Li Y, Lv L. Bioinformatics analysis and experimental validation of a novel autophagy-related signature relevant to immune infiltration for recurrence prediction after curative hepatectomy. Aging (Albany NY) 2023; 15:2610-2630. [PMID: 37014321 PMCID: PMC10120910 DOI: 10.18632/aging.204632] [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: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/05/2023]
Abstract
Hepatocellular carcinoma (HCC) remains imposing an enormous economic and healthcare burden worldwide. In this present study, we constructed and validated a novel autophagy-related gene signature to predict the recurrence of HCC patients. A total of 29 autophagy-related differentially expressed genes were identified. A five-gene signature (CLN3, HGF, TRIM22, SNRPD1, and SNRPE) was constructed for HCC recurrence prediction. Patients in high-risk groups exhibited a significantly poor prognosis compared with low-risk patients both in the training set (GSE14520 dataset) and the validation set (TCGA and GSE76427 dataset). Multivariate cox regression analysis demonstrated that the 5-gene signature was an independent risk factor for recurrence-free survival (RFS) in HCC patients. The nomograms incorporating 5-gene signature and clinical prognostic risk factors were able to effectively predict RFS. KEGG and GSEA analysis revealed that the high-risk group was enriched with multiple oncology characteristics and invasive-related pathways. Besides, the high-risk group had a higher level of immune cells and higher levels of immune checkpoint-related gene expression in the tumor microenvironment, suggesting that they might be more likely to benefit from immunotherapy. Finally, the immunohistochemistry and cell experiments confirmed the role of SNRPE, the most significant gene in the gene signature. SNRPE was significantly overexpressed in HCC. After SNRPE knockdown, the proliferation, migration and invasion ability of the HepG2 cell line were significantly inhibited. Our study established a novel five-gene signature and nomogram to predict RFS of HCC, which may help in clinical decision-making for individual treatment.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Chengkai Yang
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
| | - Dong Li
- Department of Anesthesiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, China
| | - Ruling Wang
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Yanbing Li
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Lizhi Lv
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
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Yu M, Wang H, Xu H, Lv Y, Li Q. High MCM8 expression correlates with unfavorable prognosis and induces immune cell infiltration in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:10027-10049. [PMID: 36575045 PMCID: PMC9831725 DOI: 10.18632/aging.204440] [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: 10/08/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND MCM8 has been reported highly expressed in several human malignancies. However, its role in HCC has not yet been researched. METHODS The prognostic significance of MCM8 mRNA expression was analyzed using datasets from TCGA and GEO databases. Immunohistochemistry (IHC) assay was used to detect the MCM8 protein expression in HCC tissues. The Cox regression analysis was employed to determine the independent prognostic value of MCM8. Then, we established a nomogram for OS and RFS prediction based on MCM8 protein expression. We analyzed the DNA methylation and genetic alteration of MCM8 in HCC. Moreover, GO, KEGG and GSEA were utilized to explore the potential biological functions of MCM8. Subsequently, we evaluate the correlations between MCM8 expression and composition of the tumor microenvironment as well as immunocyte infiltration ratio in HCC. RESULTS MCM8 mRNA and protein were significantly overexpressed in HCC tissues. High MCM8 protein expression was an independent risk factor for OS and RFS of HCC patients. MCM8 expression is altered in 60% of queried HCC patients. In addition, higher methylation of the CpG site cg03098629, cg10518808, and 17230679 correlated with lower MCM8 levels. MCM8 expression correlated with cell cycle and DNA replication signaling. Moreover, MCM8 may be correlated with different compositions of the tumor microenvironment and immunocyte infiltration ratio in HCC. CONCLUSIONS MCM8 was highly expressed in HCC tissues and was associated with poor prognosis. Meanwhile, high expression of MCM8 may induce immune cell infiltration and may be a promising prognostic biomarker for HCC.
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Affiliation(s)
- Meng Yu
- Department of Critical Care Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China
| | - Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Hongyang Xu
- Department of Critical Care Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China
| | - Yuhang Lv
- Department of Critical Care Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China
| | - Qingsong Li
- Department of Gastroenterology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China
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Yang Y, Huang T, Fan Y, Lu H, Shao J, Wang Y, Shen A. Significance of Spliceosome-Related Genes in the Prediction of Prognosis and Treatment Strategies for Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1753563. [PMID: 36389112 PMCID: PMC9652092 DOI: 10.1155/2022/1753563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/18/2022] [Indexed: 08/25/2023]
Abstract
BACKGROUND The leading cause of cancer-related fatalities globally is lung cancer; lung adenocarcinoma (LUAD) is the most common histological type in it. The spliceosome plays an important role in a majority of malignancies. However, it is yet unclear how spliceosome-related genes affect patients with LUAD in terms of treatment course and prognosis. METHODS Spliceosome-related genes were assessed from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database to obtain clinical information and gene expression in patients with LUAD. A spliceosome-related gene signature and prognostic model were constructed by using the least absolute shrinkage and selection operator (LASSO), time-dependent receiver operating characteristic (ROC), and nomogram. Immune infiltrate levels, mutation analysis, and pathway enrichment were predicted potential mechanisms of the signature by using single-sample gene set enrichment analysis (ssGSEA), Gene Set Cancer Analysis (GSCA) database, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) database. Then, a protein-protein interaction (PPI) network and transcription factor- (TF-) hub gene and drug mining network were also established by Cytoscape software. RESULTS Firstly, we constructed a prognostic model for 11 spliceosome signature genes. Based on the prognostic risk score, we stratified patients with LUAD into high- and low-risk groups. The high- and low-risk groups were closely related to the OS, tumor immune infiltration level, immune checkpoint molecules, and tumor mutation burden (TMB) of LUAD patients. Based on PPI networks, we also predict relevant TF genes that may regulate signature prognostic genes. Finally, drugs including oxaliplatin, arsenic trioxide, cisplatin, and sunitinib were excavated for the treatment of the 11 spliceosome signature genes in LUAD patients. CONCLUSION In conclusion, this study is the first to explore the importance of spliceosome-related genes in the prognosis and treatment of LUAD. Through our study, we have innovatively provided potential prognosis genes and new therapeutic drug targets for the treatment of LUAD patients.
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Affiliation(s)
- Ying Yang
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Tianyi Huang
- Department of Pharmacy, Nantong University Xinling College, Nantong, China
| | - Yihui Fan
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Haimin Lu
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Jingjing Shao
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Yilang Wang
- Department of Oncology, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Aiguo Shen
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
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Zhang Y, Wang X, Wang H, Jiang Y, Xu Z, Luo L. Elevated Small Nuclear Ribonucleoprotein Polypeptide an Expression Correlated With Poor Prognosis and Immune Infiltrates in Patients With Hepatocellular Carcinoma. Front Oncol 2022; 12:893107. [PMID: 35860579 PMCID: PMC9290672 DOI: 10.3389/fonc.2022.893107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundElevated Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA) can enhance tumor cell growth and proliferation in various cancers. However, rarely studies focus on the comprehensive analysis of SNRPA in hepatocellular carcinoma (HCC).MethodsTCGA and GEO databases were used to analyze the mRNA expression of SNRPA in HCC. Protein expression of SNAPA was validated using immunohistochemistry. Stably transfected HCC cells were used to investigate the role of SNRPA in the progression of HCC. The functional enrichment analysis was utilized for the biological function prediction. The CIBERSORT and ssGSEA algorithms were used to evaluate the composition of the tumor microenvironment and immunocyte infiltration ratio.ResultsThe SNRPA expression was upregulated in HCC and positively correlated with tumor stage and grade. SNRPA overexpression were independent risk factors for poor overall survival (OS) and recurrence-free survival (RFS). In patients with early-stage disease, low alpha-fetoprotein expression, and better differentiation, SNRPA still exhibited the excellent prognostic value. Knockdown of SNRPA inhibited the proliferation and migration while promoting the apoptosis of HCC cells. Higher methylation of the CpG site cg16596691 correlated with longer OS in HCC patients. Genes co-expressed with SNRPA were overexpressed in HCC and correlated with shorter OS. The GO and KEGG enrichment analysis showed that SNRPA expression was related to mRNA splicing, spliceosome signaling. GSEA demonstrated that the main enrichment pathway of SNRPA-related differential genes was spliceosome signaling, cell cycle signaling, P53 signaling pathway, T cell receptor signaling pathway, natural killer cell-mediated signaling. CIBERSORT and ssGSEA algorithm revealed that SNRPA was mainly associated with the higher proportion of CD8+T cells, T cells follicular helper, T cells regulatory, Macrophages M0, and the lower proportion of T cells CD4 memory resting, NK cells resting, Monocytes, and Mast cells resting.ConclusionElevated SNRPA enhances tumor cell proliferation and correlated with poor prognosis and immune infiltrates in patients with HCC.
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Affiliation(s)
- Youfu Zhang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Xuyang Wang
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Huaxiang Wang
- Department of Hepatobiliary Surgery, The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, China
| | - Yi Jiang
- Department of Hepatobiliary Surgery, The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, China
| | - Zhidan Xu
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- *Correspondence: Laibang Luo, ; Zhidan Xu,
| | - Laibang Luo
- Department of Organ Transplantation, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- *Correspondence: Laibang Luo, ; Zhidan Xu,
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Wang H, Yang C, Jiang Y, Hu H, Fang J, Yang F. A novel ferroptosis-related gene signature for clinically predicting recurrence after hepatectomy of hepatocellular carcinoma patients. Am J Cancer Res 2022; 12:1995-2011. [PMID: 35693077 PMCID: PMC9185608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
High recurrence rate in HCC is the primary cause of the poor prognosis after hepatectomy. Therefore, in this study, we aimed to construct a gene signature for predicting the recurrence rate in HCC. The mRNA expression profiles and clinical information of HCC patients from GEO and TCGA databases were used, and ferroptosis-related gene list was obtained from the FerrDb database. We identified 39 ferroptosis-related genes (FDEGs) that were differentially expressed between HCC samples and normal tissues from the GSE14520 dataset. The univariate and multivariate Cox regression analyses were employed to construct a prognostic signature. Seven FDEGs (MAPK9, SLC1A4, PCK2, ACSL3, STMN1, CDO1, and CXCL2) were included to construct a risk model, which was validated in the TCGA dataset. Patients in high-risk groups exhibited a significantly poor prognosis compared with patients in low-risk groups in both the training set (GSE14520 cohort) and the validation set (TCGA cohort). Multivariate cox regression analyses demonstrated that the 7-gene signature was an independent risk factor for RFS in HCC patients. KEGG analysis showed that FDEGs were mainly enriched in Ferroptosis, Hepatocellular carcinoma pathway, and MAPK signaling pathway. GSEA analysis suggested that the high-risk group was correlated with multiple oncogenic signatures and invasive-related pathways. These results indicated that this risk model can accurately predict recurrence after hepatectomy and offer novel research directions for personalized treatment in HCC patients.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of MedicineShiyan, Hubei 442000, China
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Chengkai Yang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Yi Jiang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
| | - Huanzhang Hu
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third People’s Hospital of Fujian University of Traditional Chinese MedicineFuzhou 350108, Fujian, China
| | - Fang Yang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
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