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Dong YY, Wang MY, Jing JJ, Wu YJ, Li H, Yuan Y, Sun LP. Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:13-29. [PMID: 37923250 DOI: 10.1016/j.ajpath.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/22/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Gastric cancer (GC) is a major global health concern with poor outcomes. Heterogeneous nuclear ribonucleoprotein U (HNRNPU) is a multifunctional protein that participates in pre-mRNA packaging, alternative splicing regulation, and chromatin remodeling. Its potential role in GC remains unclear. In this study, the expression characteristics of HNRNPU were analyzed by The Cancer Genome Atlas data, Gene Expression Omnibus data, and then further identified by real-time quantitative PCR and immunohistochemistry using tissue specimens. From superficial gastritis, atrophic gastritis, and hyperplasia to GC, the in situ expression of HNRNPU protein gradually increased, and the areas under the curve for diagnosis of GC and its precancerous lesions were 0.911 and 0.847, respectively. A nomogram integrating HNRNPU expression, lymph node metastasis, and other prognostic indicators exhibited an area under the curve of 0.785 for predicting survival risk. Knockdown of HNRNPU significantly inhibited GC cell proliferation, migration, and invasion and promoted apoptosis in vitro. In addition, RNA-sequencing analysis showed that HNRNPU could affect alternative splicing events in GC cells, with functional enrichment analysis revealing that HNRNPU may exert malignant biological function in GC progression through alternative splicing regulation. In summary, the increased expression of HNRNPU was significantly associated with the development of GC, with a good performance in diagnosing and predicting the prognostic risk of GC. Functionally, HNRNPU may play an oncogenic role in GC by regulating alternative splicing.
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Affiliation(s)
- Ying-Ying Dong
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Meng-Ya Wang
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Department of Radiotherapy, Zhumadian Central Hospital, Zhumadian, China
| | - Jing-Jing Jing
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yi-Jun Wu
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Hao Li
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China.
| | - Li-Ping Sun
- Tumor Etiology and Screening Department of Cancer Institute and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China; Key Laboratory of Gastrointestinal Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China.
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Liu Z, Xie Y, Liu S, Shen S, Zhu Y, Gou Q. Identification of the ferroptosis regulator HELLS with prognostic value for adrenocortical carcinoma based on integrated analysis and experimental validation. Gland Surg 2023; 12:1251-1270. [PMID: 37842529 PMCID: PMC10570968 DOI: 10.21037/gs-22-736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/27/2023] [Indexed: 10/17/2023]
Abstract
Background For adrenocortical carcinoma (ACC), a rare endocrine malignancy with a high rate of mortality and recurrence, it is difficult for clinicians to predict overall survival and select the most effective treatment. Targeting ferroptosis, a form of cell death, has been reported to be a promising therapeutic strategy for ACC; however, the core ferroptosis regulator and its prognostic value in ACC remain unknown. Methods RNA sequencing data and clinical information were downloaded from public databases. Differentially expressed gene and survival analyses were performed to identify candidate ferroptosis regulators. A multivariate Cox regression model was used to construct a gene signature, and a nomogram was constructed to predict the overall survival of patients with ACC. Gene set variation analysis (GSVA) was used to identify underlying aberrant pathways and the relative immune cell infiltration levels of each ACC sample. Immunohistochemistry staining was performed in formalin-fixed paraffin-embedded tumor tissue sections. Results Ultimately, 23 differentially expressed ferroptosis regulators were identified between normal adrenal gland and ACC tissues, and 50 ferroptosis regulators were related to prognosis, with 13 ferroptosis regulators being simultaneously found to satisfy the differential expression and prognostic value. According to the multivariate Cox regression model, a ferroptosis regulator signature was constructed from 3 genes in The Cancer Genome Atlas (TCGA; hazard ratio =9.01; P=1.39×10-10), and the area under the curve (AUC) values of 3-, 5-, 8-year overall survival were 0.924, 0.906, and 0.866, respectively. The survival analysis and the receiver operating characteristic (ROC) analysis validated the prognostic value of the ferroptosis regulator signature in 3 validation datasets. Moreover, metabolism-, E2F-, MYC-, and G2/M checkpoint-related pathways and aberrant immune cell infiltration levels were identified as being responsible for the different prognosis of risk groups in ACC. HELLS was found to be a significantly differentially expressed ferroptosis-suppressor gene with a prognostic value in ACC and to be highly associated with immune cell infiltration levels and multiple biological functions. Conclusions A ferroptosis regulator signature showed promising power for predicting the prognosis of ACC, and HELLS was identified as a hub ferroptosis regulator in the initiation and progression of ACC.
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Affiliation(s)
- Zijian Liu
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Xie
- Breast Disease Center, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Medical Oncology of Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shengzhuo Liu
- Urology Department, West China Hospital, Sichuan University, Chengdu, China
| | - Sikui Shen
- Urology Department, West China Hospital, Sichuan University, Chengdu, China
| | - Yuchun Zhu
- Urology Department, West China Hospital, Sichuan University, Chengdu, China
| | - Qiheng Gou
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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Zhang L, Ren BC, Wei F, Liu Y, Gao Y, Yuan B. Ferroptosis regulator NOS2 is closely associated with the prognosis and cell malignant behaviors of hepatoblastoma: a bioinformatic and in vitro study. Front Oncol 2023; 13:1228199. [PMID: 37795447 PMCID: PMC10546316 DOI: 10.3389/fonc.2023.1228199] [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: 05/24/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
Background Hepatoblastoma (HB) is the most common liver tumor in children with easy metastasis. The emergence of ferroptosis as a novel form of cell death has gained increased attention in various human cancers. However, the roles of ferroptosis-related (FR) genes in HB remain elusive. Methods The GSE133039, GSE131329, and GSE81928 datasets were utilized for screening core FR genes in HB. Through Lasso regression analysis and using the support vector machine recursive feature elimination (SVM-RFE) algorithm, three candidate FR genes were obtained for characterizing HB. Their expression patterns and their clinical associations were explored through the 'Limma' R package, and their diagnostic potential was evaluated using ROC curves. Nitric oxide synthase 2 (NOS2) emerged as a candidate for further analyses. The CIBERSORT algorithm and GSEA dataset were used to respectively investigate the immune and metabolism effects of NOS2; the former was validated through immunofluorescence. The GSDC database was employed to analyze the correlation between NOS2 expression and the therapeutic efficacy of multiple drugs. PCR, Western blotting, colony formation assays, and Transwell experiments, were used to determine biological functions of NOS2 in HB cells. Potential upstream transcription factors of NOS2 were predicted through the TRRUST, hTFtarget, GeneCards, and JASPAR databases. Results NQO1, SLC1A4, and NOS2 were identified as potential genes in HB and found to be significantly upregulated in tumor samples. Nevertheless, only NOS2 was closely associated with HB clinicopathological characteristics; high NOS2 expression indicated poor prognosis, metastatic tendency, and late clinical stage. Immune analyses indicated that high NOS2 expression was concomitant with decreased infiltration levels of CD8+ T cells but increased infiltration levels of macrophages. GSEA revealed that NOS2 failed to affect the enrichments of glycolysis, fatty acid metabolism, and cholesterol biosynthesis in HB. Moreover, NOS2 was positively correlated with the IC50 values of trametinib, lapatinib, and cisplatin. NOS2 overexpression promoted the proliferation, migration and invasion of HepG2 and HuH-6 cells. JUND was identified as a potential transcriptional regulator of NOS2 by binding to its promoter (5'-TTCTGACTCTTTT-3'). Conclusion NOS2 plays a significant role in HB clinical assessments and holds promise as a novel therapeutic target.
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Affiliation(s)
- Lan Zhang
- Department of Pediatrics, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Bin-cheng Ren
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Fei Wei
- Department of Pediatrics, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yan Liu
- Department of Pediatrics, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ya Gao
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Bo Yuan
- Department of General Surgery, Xi’an Central Hospital, Xi’an, China
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Chen L, He Y, Zhu J, Zhao S, Qi S, Chen X, Zhang H, Ni Z, Zhou Y, Chen G, Liu S, Xie T. The roles and mechanism of m 6A RNA methylation regulators in cancer immunity. Biomed Pharmacother 2023; 163:114839. [PMID: 37156113 DOI: 10.1016/j.biopha.2023.114839] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
N6-methyladenosine (m6A), the most common internal modification in RNA, can be regulated by three types of regulators, including methyltransferases (writers), demethylases (erasers), and m6A binding proteins (readers). Recently, immunotherapy represented by immune checkpoint blocking has increasingly become an effective cancer treatment, and increasing shreds of evidence show that m6A RNA methylation affects cancer immunity in various cancers. Until now, there have been few reviews about the role and mechanism of m6A modification in cancer immunity. Here, we first summarized the regulation of m6A regulators on the expression of target messenger RNAs (mRNA) and their corresponding roles in inflammation, immunity response, immune process and immunotherapy in various cancer cells. Meanwhile, we described the roles and mechanisms of m6A RNA modification in tumor microenvironment and immune response by affecting the stability of non-coding RNA (ncRNA). Moreover, we also discussed the m6A regulators or its target RNAs which might be used as predictor of cancer diagnosis and prognosis, and shed light on the potentiality of m6A methylation regulators as therapeutic targets in cancer immunity.
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Affiliation(s)
- Lu Chen
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Ying He
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Jinyu Zhu
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Shujuan Zhao
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Shasha Qi
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xudong Chen
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Hao Zhang
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Ziheng Ni
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yuan Zhou
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Gongxing Chen
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| | - Shuiping Liu
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| | - Tian Xie
- School of Pharmacy and Department of Respiratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; 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, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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RBM15 Promates the Proliferation, Migration and Invasion of Pancreatic Cancer Cell Lines. Cancers (Basel) 2023; 15:cancers15041084. [PMID: 36831430 PMCID: PMC9954619 DOI: 10.3390/cancers15041084] [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: 01/02/2023] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
(1) Background: Pancreatic cancer is increasingly becoming the leading cause of cancer deaths worldwide. In eukaryotic cells, m6A is the most abundant mRNA methylation modification. (2) Methods: We performed a bioinformatic multidimensional analysis using files containing the clinical data of patients and m6A-related gene expression differences downloaded from web-based databases, and performed a statistical analysis and image mapping mainly using R-package. Next, we studied the RBM15 expression in cancer and paracancerous tissues. We then validated these findings in two cell lines by western blot, PCR, Transwell, CCK-8, and EDU animal models. (3) Results: We discovered that RBM15 was highly expressed in pancreatic cancer patients and that it is a significant cause of poor prognosis. Its association with lymphatic T cell family aggregation was established through immune infiltration analysis. A retrospective analysis of data from clinical patient specimens revealed that high expression of RBM15 in patients was closely and positively correlated with preoperative glucose values, gender, and lymphocyte counts. Results from cellular experiments and animal experiments indicated that when the RBM15 gene was silenced, cell proliferation, migration, and metastasis were inhibited. (4) Conclusions: We propose that RBM15 plays a key role in the progression of pancreatic cancer by promoting tumor proliferation, migration and metastasis.
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Gu Y, Wang Z, Wang R, Yang Y, Tong P, Lv S, Xiao L, Wang Z. N6-methyladenine regulator-mediated RNA methylation modification patterns in immune microenvironment regulation of osteoarthritis. Front Genet 2023; 14:1113515. [PMID: 36777725 PMCID: PMC9908960 DOI: 10.3389/fgene.2023.1113515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
Background: Osteoarthritis is a common chronic degenerative disease, and recently, an increasing number of studies have shown that immunity plays an important role in the progression of osteoarthritis, which is exacerbated by local inflammation. The role of N6-methyladenine (m6A) modification in immunity is being explored. However, the role of m6A modification in regulating the immune microenvironment of osteoarthritis remains unknown. In this study, we sought to discuss the association between the N6-methyladenine (m6A) modification and the immune microenvironment of osteoarthritis. Methods: First, the data and gene expression profiles of 139 samples, including 33 healthy samples and 106 osteoarthritis samples, were obtained from the Genetics osteoARthritis and Progression (GARP) study. Then the differences in m6A regulators between healthy individuals and osteoarthritis patients were analyzed. The correlation between m6A regulators and immune characteristics was also investigated by single-sample gene set enrichment analysis (ssGSEA). Principal component analysis (PCA), Gene Set Variation Analysis (GSVA) enrichment analysis, weighted gene coexpression network analysis (WGCNA), and Associated R packages were used to identify the m6A phenotype and its biological functions. Results: A total of 23 m6A regulators were involved in this study. We found a close correlation between most m6A regulators in all samples as well as in osteoarthritis samples. VIRMA and LRPPRC were the most highly correlated m6A regulators and showed a positive correlation, whereas VIRMA and RBM15B were the most negatively correlated. M6A regulators are associated with osteoarthritis immune characteristics. For example, MDSC cell abundance was strongly correlated with RBM15B and HNRNPC. Meanwhile, RBM15B and HNRNPC were important effectors of natural killer cell immune responses. IGFBP3 is an important regulator of cytolytic activity immune function. We performed an unsupervised consensus cluster analysis of the osteoarthritis samples based on the expression of 23 m6A regulators. Three different m6A subtypes of osteoarthritis were identified, including 27 samples in subtype C1, 21 samples in subtype C2, and 58 samples in subtype C3. Different m6A subtypes have unique biological pathways and play different roles in the immune microenvironment of osteoarthritis. Conclusion: The m6A modification plays a crucial role in the diversity and complexity of the immune microenvironment in osteoarthritis.
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Affiliation(s)
- Yong Gu
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Zhengming Wang
- Shi’s Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China,Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Rui Wang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China
| | - Yunshang Yang
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Peijian Tong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China
| | - Shuaijie Lv
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
| | - Long Xiao
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
| | - Zhirong Wang
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
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Ke C, Dai S, Xu F, Yuan J, Fan S, Chen Y, Yang L, Li Y. Cuproptosis regulatory genes greatly contribute to clinical assessments of hepatocellular carcinoma. BMC Cancer 2023; 23:25. [PMID: 36611155 PMCID: PMC9824945 DOI: 10.1186/s12885-022-10461-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common abdominal cancer with dissatisfactory therapeutic effects. The discovery of cuproptosis lights on new approach for cancer treatment and assessment. So far, there is extremely limited research investigating the roles of cuproptosis-related (CR) genes in cancers. METHODS A novel CR risk signature was constructed using the Lasso regression analysis. Its prognostic value was assessed via a series of survival analyses and validated in three GEO cohorts. The effects of CR risk signature on tumor immune microenvironment (TIM) were explored through CIBERSORT, ESTIMATE, and ssGSEA algorithms. Using GESA, we investigated its impacts on various metabolism process. The somatic mutation features of CR signature genes were also explored via cBioPortal database. Using tumor mutation burden, expressions of immune checkpoints, TIDE score, IMvigor 210 cohort, and GSE109211 dataset, we explored the potential associations of CR risk score with the efficacy of immune checkpoint inhibitors (ICIs) and sorafenib. Finally, the biofunctions of DLAT in HCC cells were ascertained through qPCR, immunohistochemistry, colony formation, and Transwell assays. RESULTS FDX1, DLAT, CDKN2A and GLS constituted the CR risk signature. CR risk signature possessed high prognostic value and was also applicable to three validation cohorts. Meanwhile, it could improve the accuracy and clinical making-decision benefit of traditional prognostic model. Moreover, high CR risk was indicative of unfavorable anti-tumor immune response and active metabolisms of glycolysis and nucleotide. As for therapeutic correlation, CR risk score was a potential biomarker for predicting the efficacy of ICIs and sorafenib. Through qPCR and immunohistochemistry detection in clinical samples, we reconfirmed DLAT was significantly upregulated in HCC samples. Overexpression of DLAT could promote the proliferation, migration, and invasion of HepG2 and HuH-7 cells. CONCLUSIONS The novel CR risk signature greatly contributed to the clinical assessment of HCC. Cuproptosis regulatory gene DLAT possessed cancer-promoting capacities and was expected to be a promising therapeutic target for HCC.
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Affiliation(s)
- Changwei Ke
- grid.452672.00000 0004 1757 5804Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province China
| | - Shejiao Dai
- grid.452672.00000 0004 1757 5804Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, No. 157, West Five Road, Xi’an, 710004 Shaanxi China
| | - Fangshi Xu
- grid.43169.390000 0001 0599 1243Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province China
| | - Jia Yuan
- grid.452672.00000 0004 1757 5804Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, No. 157, West Five Road, Xi’an, 710004 Shaanxi China
| | - Shuting Fan
- grid.452672.00000 0004 1757 5804Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, No. 157, West Five Road, Xi’an, 710004 Shaanxi China
| | - Yang Chen
- grid.43169.390000 0001 0599 1243Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Five Road, Xi'an, 710004, Shaanxi, China. .,Department of Outpatient, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China.
| | - Yong Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Five Road, Xi'an, 710004, Shaanxi, China. .,Department of Outpatient, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China.
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Xu F, Cai D, Liu S, He K, Chen J, Qu L, Chong T, Li X, Ren B. N7-methylguanosine regulatory genes well represented by METTL1 define vastly different prognostic, immune and therapy landscapes in adrenocortical carcinoma. Am J Cancer Res 2023; 13:538-568. [PMID: 36895966 PMCID: PMC9989616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
Although N7-methylguanosine (m7G) is one of the most frequent RNA modifications, it has received little attention. Adrenocortical carcinoma (ACC) is a highly malignant and easily metastatic tumor, eagerly needing for novel therapeutic strategy. Herein, a novel m7G risk signature (METTL1, NCBP1, NUDT1 and NUDT5) was constructed using the Lasso regression analysis. It possessed highly prognostic value and could improve the predictive accuracy and clinical making-decision benefit of traditional prognostic model. Its prognostic value was also successfully validated in GSE19750 cohort. Through CIBERSORT, ESTIMATE, ssGSEA and GSEA analyzes, high-m7G risk score was found to be closely associated with increased enrichment of glycolysis and suppression of anti-cancer immune response. Therapeutic correlation of m7G risk signature was also investigated using tumor mutation burden, the expressions of immune checkpoints, TIDE score, IMvigor 210 cohort and TCGA cohort. m7G risk score was a potential biomarker for predicting the efficacy of ICBs and mitotane. Furthermore, we explored the biofunctions of METTL1 in ACC cells through a series of experimentations. Overexpression of METTL1 stimulated the proliferation, migration and invasion of H295R and SW13 cells. Immunofluorescence assays revealed that the infiltrating levels of CD8+ T cells was lower and that of macrophages was higher in clinical ACC samples with high METTL1 expression compared to that in low expression ones. Silencing METTL1 could significantly inhibited tumor growth in mouse xenograft model. Western blot assays showed that METTL1 positively regulated the expression of glycolysis rate-limiting enzyme HK1. Finally, miR-885-5p and CEBPB were predicted as the upstream regulators of METTL1 through data mining of the public databases. In conclusions, m7G regulatory genes well represented by METTL1 profoundly affected the prognosis, tumor immune, therapeutic outcomes, and malignant progression of ACC.
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Affiliation(s)
- Fangshi Xu
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University No. 157, West Five Road, Xi'an 710004, Shaanxi, China.,Department of Urology, Shaanxi Provincial People's Hospital No. 256, Friendship West Road, Xi'an 710068, Shaanxi, China
| | - Danrui Cai
- Department of Ophthalmology, Second Affiliated Hospital of Xi'an Jiaotong University No. 157, West Five Road, Xi'an 710004, Shaanxi, China
| | - Shanshan Liu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
| | - Kaini He
- Department of Gastroenterology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
| | - Jing Chen
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
| | - Li Qu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
| | - Tie Chong
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University No. 157, West Five Road, Xi'an 710004, Shaanxi, China
| | - Xueyi Li
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
| | - Bincheng Ren
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University Xi'an, Shaanxi, China
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9
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Gao J, Wang D, Yang Q, Tang M, Du J, He L, Liu W. The signature of pyroptosis-related gene prognostic and immune microenvironment in adrenocortical carcinoma. Front Mol Biosci 2023; 10:1131402. [PMID: 36911522 PMCID: PMC9998516 DOI: 10.3389/fmolb.2023.1131402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Adrenocortical carcinoma (ACC) has a low incidence but a poor prognosis. And ACC has complex clinical manifestations and limited treatment. Pyroptosis has a dual character and has both positive and negative effects on cancer. However, the role of pyroptosis-related genes (PRGs) in ACC and the impact on ACC progression remains unelucidated. This study performed systematic bioinformatics analysis and basic experimental validation to enable the establishment of prognostic models and demonstrate levels of immune infiltration. Pearson's correlation analysis was used to assess the association of PRGs with tumor immune infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and immune checkpoints. There 4 PRGs were upregulated, and 25 PRGs were downregulated in ACC. At the same time, we analyzed and reviewed the genetic mutation variation landscape of PRGs. Functional enrichment analysis was also performed to clarify the function of PRGs. Pyroptosis, the inflammatory response, the Toll-like receptor signaling pathway, and the NOD-like receptor signaling pathway are the functions and pathways mainly involved and exerted effects by these 33 PRGs. The results of the prognosis analysis revealed high expression of CASP3, CASP9, GSDMB, GSDMD, NLRC4, PRKACA, and SCAF11 caused a poor survival rate for ACC patients. The above seven PRGs were screened by the optimal λ value of LASSO Cox analysis, and the five selected genes (CASP3, CASP9, GSDMB, GSDMD, NLRC4) were involved in constructing a prognostic PRGs model which enables the overall survival in ACC patients can be predicted with moderate to high accuracy. Prognostic PRGs, especially CASP9, which is the independent factor of ACC prognosis, may be closely correlated with immune-cell infiltration, tumor mutation burden, microsatellite instability, and immune checkpoints. Quantitative Real-Time PCR (qRT-PCR), Western blot and immunohistochemical were performed to validate the mRNA expression levels of CASP9 in adjacent normal tissues and ACC tissues. According to the result of immune checkpoints analysis, NLRC4 and GSDMB may be identified as potential therapeutic targets. In conclusion, we established a prognostic model of PRG characteristics in ACC and analyzed the relationship between PRGs and immune infiltration. Through our study, it may be helpful to find the mechanism of pyroptosis in ACC.
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Affiliation(s)
- Jun Gao
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Dai Wang
- Xiangya School of Pharmacy, Central South University, Changsha, China
| | - Qingping Yang
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Mengjie Tang
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiayi Du
- Department of Pharmacy, Fuqing City Hospital of Fujian, Fuqing, China
| | - Leye He
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wei Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
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10
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Zhou K, Yang J, Li X, Xiong W, Zhang P, Zhang X. N7-Methylguanosine Regulatory Genes Profoundly Affect the Prognosis, Progression, and Antitumor Immune Response of Hepatocellular Carcinoma. Front Surg 2022; 9:893977. [PMID: 35784919 PMCID: PMC9246272 DOI: 10.3389/fsurg.2022.893977] [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: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a common abdominal cancer with poor survival outcomes. Although there is growing evidence that N7-methylguanosine (m7G) is closely associated with tumor prognosis, development, and immune response, few studies focus on this topic. Methods The novel m7G risk signature was constructed through the Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC-LIRI, GSE14520, and GSE116174 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were applied to explore the effects of the m7G risk score on tumor immune microenvironment (TIM). The GSEA method was used to evaluate the impacts of the m7G risk score on glycolysis, ferroptosis, and pyroptosis. The human protein atlas (HPA) database was used to clarify the histological expression levels of five m7G signature genes. The biofunctions of NCBP2 in hepatocellular cancer (HC) cells were confirmed through qPCR, CCK8, and transwell assays. Results Five m7G regulatory genes comprised the novel risk signature. The m7G risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of traditional prognostic models. Besides, we established a nomogram containing the clinical stage and m7G risk score to predict the survival rates of HCC patients. The prognostic value of the m7G model was successfully validated in ICGC and GSE116174 cohorts. Moreover, high m7G risk led to a decreased infiltration level of CD8+ T cells, whereas it increased the infiltration levels of Tregs and macrophages. The glycolysis and pyroptosis processes were found to be enriched in the HCC patients with high m7G risk. Finally, overexpression of NCBP2 could promote the proliferation, migration, and invasion of HC cells. Conclusions The m7G risk score was closely related to the prognosis, antitumor immune process, glycolysis, and malignant progression of HCC. NCBP2 has pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Kexiang Zhou
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
- ChongQing Medical University, Chongqing, China
| | - Jiaqun Yang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xiaoyan Li
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Wei Xiong
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Pengbin Zhang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xuqing Zhang
- ChongQing Medical University, Chongqing, China
- Department of Infectious Diseases, The Third Affiliated Hospital of ChongQing Medical University, China
- Correspondence: Xuqing Zhang
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11
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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12
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Zhao Y, Song Q, Xu F, Zhou Y, Zuo X, Zhang Z. Pyroptosis-Related Risk Signature Exhibits Distinct Prognostic, Immune, and Therapeutic Landscapes in Hepatocellular Carcinoma. Front Genet 2022; 13:823443. [PMID: 35368686 PMCID: PMC8965507 DOI: 10.3389/fgene.2022.823443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a common abdominal cancer. The existing therapeutic approaches often fail to achieve satisfactory results. Pyroptosis, an inflammatory form of programmed cell death, provides new ideas for anticancer treatment. However, the roles of pyroptosis-related (PR) genes (PRGs) in HCC remain elusive. Methods: Differentially expressed genes (DEGs) (n = 22) were screened out using TCGA and GTEx databases. A novel PR risk signature was constructed through Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC and GSE14520 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were employed to determine the effects of the PR risk score on the tumor immune microenvironment (TIM). The TIDE scoring system, IMvigor210 cohort, GSE109211 dataset, and GSDC database were applied to explore the associations of the PR risk score with therapeutic effects. The biofunctions of WNK1 in hepatocellular cancer (HC) cells were confirmed through qPCR, colony formation, and Transwell assays. Results: Overall, 22 of 45 PRGs (48.9%) were abnormally expressed in HCC samples. Then, a PR risk signature consisting of eight PRGs was constructed. A high PR risk score led to an unfavorable prognosis. The PR risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of the traditional TNM model. In addition, we established a nomogram containing the clinical stage and PR risk score to predict the survival rates of HCC patients. The prognostic value of the PR model was successfully validated in ICGC and GSE14520 cohorts. Moreover, high PR risk conferred the decreased infiltration level of CD8+ T cells and weakened the activities of "cytolytic activity" pathways. As for therapeutic correlation, a high PR risk score seemed to imply a poor efficacy of PD-1/L1 inhibitors and sorafenib. Finally, the overexpression of WNK1 could promote the proliferation, migration, and invasion of HC cells. Conclusions: The PR risk score was closely related to the prognosis, antitumor immune process, therapeutic outcomes, and malignant progression of HCC. WNK1, the core regulator of pyroptosis, possesses pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Yidi Zhao
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qingya Song
- Xi'an Medical Emergency Center, Xi'an, China
| | - Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yang Zhou
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoli Zuo
- Department of Orthopedics, Second Affiliated Hospital of Xi'a Jiaotong University, Xi'an, China
| | - Zhengliang Zhang
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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13
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Grisanti S, Cosentini D, Sigala S, Berruti A. Molecular genotyping of adrenocortical carcinoma: a systematic analysis of published literature 2019-2021. Curr Opin Oncol 2022; 34:19-28. [PMID: 34669649 PMCID: PMC10863665 DOI: 10.1097/cco.0000000000000799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW comprehensive molecular characterization of adrenocortical carcinoma (ACC) through next-generation sequencing and bioinformatics analyses is expanding the number of targets with potential prognostic and therapeutic value. We performed a critical review of recent published literature on genotyping of ACC. RECENT FINDINGS 423 studies were published between 2019 and 2021. After manual curation we summarized selected evidence in two thematic areas: germline deoxyribonucleic acid (DNA) variations, genomic alterations and prognosis. SUMMARY the evolving genomic landscape of ACC requires target validation in terms of prognostic and predictive value within scientific consortia. Although the existing multiple driver genes are difficult targets in the perspective of precision oncology, alterations in DNA damage repair genes or in promoter hypermethylation could open new venues for repurposing of existing drugs in ACC.
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Affiliation(s)
- Salvatore Grisanti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
| | - Sandra Sigala
- Section of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
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Babenko V, Redina O, Smagin D, Kovalenko I, Galyamina A, Babenko R, Kudryavtseva N. Dorsal Striatum Transcriptome Profile Profound Shift in Repeated Aggression Mouse Model Converged to Networks of 12 Transcription Factors after Fighting Deprivation. Genes (Basel) 2021; 13:genes13010021. [PMID: 35052361 PMCID: PMC8774333 DOI: 10.3390/genes13010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/11/2021] [Accepted: 12/18/2021] [Indexed: 01/18/2023] Open
Abstract
Both aggressive and aggression-deprived (AD) species represent pathologic cases intensely addressed in psychiatry and substance abuse disciplines. Previously, we reported that AD mice displayed a higher aggressive behavior score than the aggressive group, implying the manifestation of a withdrawal effect. We employed an animal model of chronic social conflicts, curated in our lab for more than 30 years. In the study, we pursued the task of evaluating key events in the dorsal striatum transcriptome of aggression experienced mice and AD species compared to controls using RNA-Seq profiling. Aggressive species were subjected to repeated social conflict encounters (fights) with regular positive (winners) experience in the course of 20 consecutive days (A20 group). This led to a profoundly shifted transcriptome expression profile relative to the control group, outlined by more than 1000 differentially expressed genes (DEGs). RNA-Seq cluster analysis revealed that elevated cyclic AMP (cAMP) signaling cascade and associated genes comprising 170 differentially expressed genes (DEGs) in aggressive (A20) species were accompanied by a downturn in the majority of other metabolic/signaling gene networks (839 DEGs) via the activation of transcriptional repressor DEGs. Fourteen days of a consecutive fighting deprivation period (AD group) featured the basic restoration of the normal (control) transcriptome expression profile yielding only 62 DEGs against the control. Notably, we observed a network of 12 coordinated DEG Transcription Factor (TF) activators from 62 DEGs in total that were distinctly altered in AD compared to control group, underlining the distinct transcription programs featuring AD group, partly retained from the aggressive encounters and not restored to normal in 14 days. We found circadian clock TFs among them, reported previously as a withdrawal effect factor. We conclude that the aggressive phenotype selection with positive reward effect (winning) manifests an addiction model featuring a distinct opioid-related withdrawal effect in AD group. Along with reporting profound transcriptome alteration in A20 group and gaining some insight on its specifics, we outline specific TF activator gene networks associated with transcriptional repression in affected species compared to controls, outlining Nr1d1 as a primary candidate, thus offering putative therapeutic targets in opioid-induced withdrawal treatment.
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Affiliation(s)
- Vladimir Babenko
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
- Correspondence:
| | - Olga Redina
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
| | - Dmitry Smagin
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
| | - Irina Kovalenko
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
| | - Anna Galyamina
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
| | - Roman Babenko
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
| | - Natalia Kudryavtseva
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.R.); (D.S.); (I.K.); (A.G.); (R.B.); (N.K.)
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
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