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Ma H, Qu J, Pang Z, Luo J, Yan M, Xu W, Zhuang H, Liu L, Qu Q. Super-enhancer omics in stem cell. Mol Cancer 2024; 23:153. [PMID: 39090713 PMCID: PMC11293198 DOI: 10.1186/s12943-024-02066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
The hallmarks of stem cells, such as proliferation, self-renewal, development, differentiation, and regeneration, are critical to maintain stem cell identity which is sustained by genetic and epigenetic factors. Super-enhancers (SEs), which consist of clusters of active enhancers, play a central role in maintaining stemness hallmarks by specifically transcriptional model. The SE-navigated transcriptional complex, including SEs, non-coding RNAs, master transcriptional factors, Mediators and other co-activators, forms phase-separated condensates, which offers a toggle for directing diverse stem cell fate. With the burgeoning technologies of multiple-omics applied to examine different aspects of SE, we firstly raise the concept of "super-enhancer omics", inextricably linking to Pan-omics. In the review, we discuss the spatiotemporal organization and concepts of SEs, and describe links between SE-navigated transcriptional complex and stem cell features, such as stem cell identity, self-renewal, pluripotency, differentiation and development. We also elucidate the mechanism of stemness and oncogenic SEs modulating cancer stem cells via genomic and epigenetic alterations hijack in cancer stem cell. Additionally, we discuss the potential of targeting components of the SE complex using small molecule compounds, genome editing, and antisense oligonucleotides to treat SE-associated organ dysfunction and diseases, including cancer. This review also provides insights into the future of stem cell research through the paradigm of SEs.
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Affiliation(s)
- Hongying Ma
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
- Hunan key laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, 410219, China
| | - Zicheng Pang
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jian Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Min Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Weixin Xu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Haihui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Linxin Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China.
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.
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Chen J, Hu Q, Zhou C, Jin D. CCT2 prevented β-catenin proteasomal degradation to sustain cancer stem cell traits and promote tumor progression in epithelial ovarian cancer. Mol Biol Rep 2024; 51:54. [PMID: 38165547 DOI: 10.1007/s11033-023-09047-3] [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: 03/26/2023] [Accepted: 10/25/2023] [Indexed: 01/04/2024]
Abstract
BACKGROUND Epithelial ovarian cancer (EOC) is featured by rapid progression and dismal outcomes clinically. Chaperonin Containing TCP1 Subunit 2 (CCT2) was identified as a crucial regulator for tumor progression, however, its exact role in EOC remained largely unknown. METHODS CCT2 expression and prognostic value in EOC samples were assessed according to TCGA dataset. Proliferation and mobility potentials were assessed by CCK8, colony-formation, wound healing, and Transwell assays. Cancer stem cell (CSC) traits were evaluated by RT-PCR, WB assays, sphere-forming assay and chemoresistance analysis. Bioinformatic analysis, co-IP assays and ubiquitin assays were performed to explore the mechanisms of CCT2 on EOC cells. RESULTS CCT2 highly expressed in EOC tissues and predicted poor prognosis of EOC patients by TCGA analysis. Silencing CCT2 significantly restrained cell proliferation, migration, and invasion. Moreover, CCT2 could effectively trigger epithelial-mesenchymal transition to confer extensive invasion potentials to EOC cells, Importantly, CCT2 positively correlated with CSC markers in EOC, and CCT2 knockdown impaired CSC traits and sensitize EOC cells to conventional chemotherapy regimens. Contrarily, overexpressing CCT2 achieved opposite results. Mechanistically, CCT2 exerted its pro-oncogene function by triggering Wnt/β-catenin signaling. Specifically, CCT2 could recruit HSP105-PP2A complex, a well-established dephosphorylation complex, to β-catenin via direct physical interaction to prevent phosphorylation-induced proteasomal degradation of β-catenin, resulting in intracellular accumulation of active β-catenin and increased signaling activity. CONCLUSIONS CCT2 was a novel promotor for EOC progression and a crucial sustainer for CSC traits mainly by preventing β-catenin degradation. Targeting CCT2 may represent a promising therapeutic strategy for EOC.
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Affiliation(s)
- Jiayao Chen
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, 316021, Zhejiang, China.
| | - Qiong Hu
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, 316021, Zhejiang, China
| | - Chenhao Zhou
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, 316021, Zhejiang, China
| | - Danwen Jin
- Pathological Diagnosis Center, Zhoushan Hospital of Zhejiang Province, Zhoushan, 316021, Zhejiang, China
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Shen J, Li M. Gastric Cancer Immune Subtypes and Prognostic Modeling: Insights from Aging-Related Gene Analysis. Crit Rev Immunol 2024; 44:1-13. [PMID: 38618724 DOI: 10.1615/critrevimmunol.2024052391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Gastric cancer (GC) is highly heterogeneous and influenced by aging-related factors. This study aimed to improve individualized prognostic assessment of GC by identifying aging-related genes and subtypes. Immune scores of GC samples from GEO and TCGA databases were calculated using ESTIMATE and scored as high immune (IS_high) and low immune (IS_low). ssGSEA was used to analyze immune cell infiltration. Univariate Cox regression was employed to identify prognosis-related genes. LASSO regression analysis was used to construct a prognostic model. GSVA enrichment analysis was applied to determine pathways. CCK-8, wound healing, and Transwell assays tested the proliferation, migration, and invasion of the GC cell line (AGS). Cell cycle and aging were examined using flow cytometry, β-galactosidase staining, and Western blotting. Two aging-related GC subtypes were identified. Subtype 2 was characterized as lower survival probability and higher risk, along with a more immune-responsive tumor microenvironment. Three genes (IGFBP5, BCL11B, and AKR1B1) screened from aging-related genes were used to establish a prognosis model. The AUC values of the model were greater than 0.669, exhibiting strong prognostic value. In vitro, IGFBP5 overexpression in AGS cells was found to decrease viability, migration, and invasion, alter the cell cycle, and increase aging biomarkers (SA-β-galactosidase, p53, and p21). This analysis uncovered the immune characteristics of two subtypes and aging-related prognosis genes in GC. The prognostic model established for three aging-related genes (IGFBP5, BCL11B, and AKR1B1) demonstrated good prognosis performance, providing a foundation for personalized treatment strategies aimed at GC.
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Affiliation(s)
- Jian Shen
- Beijing Chao-Yang Hospital, Capital Medical University
| | - Minzhe Li
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
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Shehab-Eldeen S, Essa A, Arafat ES, Sleem AS, Alhosary AA, Darwish E, Essa A, Al-Omair OA, Al-Khoufi EA, Al Abdulqader AK, Nada A. Serum LINC00152 and UCA1 in HCV-Induced Hepatocellular Carcinoma: Clinical Significance and Prognostic Value. Biologics 2023; 17:137-149. [PMID: 37854341 PMCID: PMC10581015 DOI: 10.2147/btt.s433872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/07/2023] [Indexed: 10/20/2023]
Abstract
Background Despite significant advancements in the molecular characterization of hepatocellular carcinoma (HCC), no oncogene addiction has been discovered. Long noncoding RNAs (lncRNAs) have a lot of promise as cancer biomarkers. LINC00152 and UCA1 have shown potential as diagnostic, prognostic, and therapeutic targets for human cancers. Aim To investigate the diagnostic and prognostic potential of serum LINC00152 and UCA1 in hepatocellular carcinoma (HCC). Methods The expression levels of LINC00152 and UCA1 in blood samples from 120 patients (60 with HCC, 60 with liver cirrhosis) and 40 healthy subjects were assessed using real-time qRT-PCR. Results Serum LINC00152 and UCA1 expression were considerably higher in HCC patients compared to patients with liver cirrhosis and the healthy controls (p<0.001 and p<0.001 respectively). And their expressions in the liver cirrhosis group were significantly higher than in healthy controls. Both lncRNAs performed well in the ROC analysis, distinguishing HCC patients from patients with liver cirrhosis. Higher levels of LINC00152 expression were linked to lesions in both lobes of the liver (p=0.02), while higher levels of UCA1 expression were linked to vascular invasion and the late stage (p=0.01, p=0.03 respectively). The multivariate analysis showed that a high level of LINC00152 in the blood was an independent indicator of a bad outcome for HCC patients (HR=2.23, 95% CI= 1.30-5.29, p=0.03). Conclusion Serum LINC00152 and UCA1 expression were upregulated in patients with HCC, suggesting their use as non-invasive biomarkers for HCC. Furthermore, LINC00152 has the potential to serve as a prognostic indicator.
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Affiliation(s)
- Somaia Shehab-Eldeen
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Abdallah Essa
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Eman Salah Arafat
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Asmaa Shaaban Sleem
- Medical Microbiology and Immunology Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | | | - Ehab Darwish
- Tropical Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
- Gastroenterology and Infectious Diseases Unit, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Ali Essa
- Medical Student, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Omar Ahmed Al-Omair
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Emad Ali Al-Khoufi
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | | | - Ali Nada
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Shebin Elkom, Egypt
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Abe H, Kamimura K, Okuda S, Watanabe Y, Inoue J, Aoyagi Y, Wakai T, Kominami R, Terai S. BCL11B expression in hepatocellular carcinoma relates to chemosensitivity and clinical prognosis. Cancer Med 2023; 12:15650-15663. [PMID: 37293953 PMCID: PMC10417273 DOI: 10.1002/cam4.6167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
INTRODUCTION B-cell lymphoma/leukemia 11B (BCL11B) is a subunit of SWI/SNF chromatin remodeling complexes and functions in cell cycle regulation and apoptosis upon DNA replication stress and damages via transcription. Many malignancies were reported to exhibit changes in BCL11B gene expression; however, no study has focused on the relationship between BCL11B and hepatocellular carcinoma, which potentially exhibits DNA replication stress and damages upon its oncogenesis. Thus, in this study, we examined the molecular characterization of BCL11B expression in hepatocellular carcinoma. METHODS AND RESULTS The cumulative progression-free survival and overall survival were significantly longer in the clinical cases of BCL11B-negative hepatocellular carcinoma than BCL11B-positve cases. Microarray and real-time PCR analyses in hepatocellular carcinoma cell lines indicated a correlation between BCL11B and GATA6, a gene reported to be correlated with oncogenic activities and resistance to anthracycline, which is often used for hepatocellular carcinoma chemotherapy. Consequently, BCL11B-overexpressing cell lines exhibited resistance to anthracycline in cell growth assays and the resistance has been evidenced by the increased expression of BCL-xL in cell lines. The results were supported by the analyses of human HCC samples showing the correlation between BCL11B and GATA6 expressions. DISCUSSIONS AND CONCLUSION Our results indicated that overexpression of BCL11B amplifies GATA6 expression in hepatocellular carcinoma in vitro and in vivo that leads to anti-apoptotic signal activation, and induces resistance to chemotherapy, which influenced the postoperative prognosis.
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Affiliation(s)
- Hiroyuki Abe
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Kenya Kamimura
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
- Department of General MedicineNiigata University School of MedicineNiigataNiigataJapan
| | - Shujiro Okuda
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Yu Watanabe
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Jun Inoue
- Department of Agricultural Chemistry, Faculty of Applied BiosciencesTokyo University of AgricultureTokyoJapan
| | - Yutaka Aoyagi
- Department of Gastroenterology and HepatologyNiigata Medical CenterNiigataNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Ryo Kominami
- Department of Molecular Genetics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
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Johansson P, Laguna T, Ossowski J, Pancaldi V, Brauser M, Dührsen U, Keuneke L, Queiros A, Richter J, Martín-Subero JI, Siebert R, Schlegelberger B, Küppers R, Dürig J, Murga Penas EM, Carillo-de Santa Pau E, Bergmann AK. Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker. Clin Epigenetics 2022; 14:148. [PMID: 36376973 PMCID: PMC9664638 DOI: 10.1186/s13148-022-01362-z] [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: 04/24/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8+ memory cytotoxic T cells, is only partly understood. The role of deregulated methylation in T-LGLL is not well known. We analyzed the epigenetic profile of T-LGLL cells of 11 patients compared to their normal counterparts by array-based DNA methylation profiling. For identification of molecular events driving the pathogenesis of T-LGLL, we compared the differentially methylated loci between the T-LGLL cases and normal T cells with chromatin segmentation data of benign T cells from the BLUEPRINT project. Moreover, we analyzed gene expression data of T-LGLL and benign T cells and validated the results by pyrosequencing in an extended cohort of 17 patients, including five patients with sequential samples. RESULTS We identified dysregulation of DNA methylation associated with altered gene expression in T-LGLL. Since T-LGLL is a rare disease, the samples size is low. But as confirmed for each sample, hypermethylation of T-LGLL cells at various CpG sites located at enhancer regions is a hallmark of this disease. The interaction of BLC11B and C14orf64 as suggested by in silico data analysis could provide a novel pathogenetic mechanism that needs further experimental investigation. CONCLUSIONS DNA methylation is altered in T-LGLL cells compared to benign T cells. In particular, BCL11B is highly significant differentially methylated in T-LGLL cells. Although our results have to be validated in a larger patient cohort, BCL11B could be considered as a potential biomarker for this leukemia. In addition, altered gene expression and hypermethylation of enhancer regions could serve as potential mechanisms for treatment of this disease. Gene interactions of dysregulated genes, like BLC11B and C14orf64, may play an important role in pathogenic mechanisms and should be further analyzed.
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Affiliation(s)
- Patricia Johansson
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Teresa Laguna
- grid.482878.90000 0004 0500 5302Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, 28049 Madrid, Spain
| | - Julio Ossowski
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany ,grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
| | - Vera Pancaldi
- grid.468186.5Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, INSERM U1037, 31037 Toulouse, France ,grid.10097.3f0000 0004 0387 1602Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Martina Brauser
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Ulrich Dührsen
- grid.5718.b0000 0001 2187 5445Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lara Keuneke
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - Ana Queiros
- grid.5841.80000 0004 1937 0247Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Julia Richter
- grid.9764.c0000 0001 2153 9986Institute for Pathology, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - José I. Martín-Subero
- grid.5841.80000 0004 1937 0247Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Reiner Siebert
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany ,grid.410712.10000 0004 0473 882XPresent Address: Institute of Human Genetics, University of Ulm and University Medical Center Ulm, Ulm, Germany
| | - Brigitte Schlegelberger
- grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
| | - Ralf Küppers
- grid.5718.b0000 0001 2187 5445Faculty of Medicine, Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Virchowstr. 177, 45122 Essen, Germany
| | - Jan Dürig
- grid.500068.bDepartment of Internal Medicine, University Hospital Essen, St. Josef-Krankenhaus, University Medicine Essen, Essen, Germany
| | - Eva M. Murga Penas
- grid.9764.c0000 0001 2153 9986Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - Enrique Carillo-de Santa Pau
- grid.482878.90000 0004 0500 5302Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, 28049 Madrid, Spain
| | - Anke K. Bergmann
- grid.10423.340000 0000 9529 9877Institute of Human Genetics, Medical School Hannover (MHH), Hannover, Germany
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Tang L, Wei R, Chen R, Fan G, Zhou J, Qi Z, Wang K, Wei Q, Wei X, Xu X. Establishment and validation of a cholesterol metabolism-related prognostic signature for hepatocellular carcinoma. Comput Struct Biotechnol J 2022; 20:4402-4414. [PMID: 36051877 PMCID: PMC9420502 DOI: 10.1016/j.csbj.2022.07.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/16/2022] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) represents the most important type of liver cancer, the 5-year survival rate for advanced HCC is 2%. The heterogeneity of HCC makes previous models fail to achieve satisfactory results. The role of Cholesterol-based metabolic reprogramming in cancer has attracted more and more attention. In this study, we screened cholesterol metabolism-related genes (CMRGs) based on a systematical analysis from TCGA and GEO database. Then, we constructed a prognostic signature based on the screened 5 CMRGs: FDPS, FABP5, ANXA2, ACADL and HMGCS2. The clinical value of the five CMRGs was validated by TCGA database and HPA database. HCC patients were assigned to the high-risk and low-risk groups on the basis of median risk score calculated by the five CMRGs. We evaluated the signature in TCGA database and validated in ICGC database. The results revealed that the prognostic signature had good prognostic performance, even among different clinicopathological subgroups. The function analysis linked CMRGs with KEGG pathway, such as cell adhesion molecules, drug metabolism-cytochrome P450 and other related pathways. In addition, patients in the high-risk group exhibited characteristics of high TP53 mutation, high immune checkpoints expression and high immune cell infiltration. Furthermore, based on the prognostic signature, we identified 25 most significant small molecule drugs as potential drugs for HCC patients. Finally, a nomogram combined risk score and TNM stage was constructed. These results indicated our prognostic signature has an excellent prediction performance. This study is expected to provide a potential diagnostic and therapeutic strategies for HCC.
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Gao J, Huo S, Zhang Y, Zhao Z, Pan H, Liu X. Construction of ovarian metastasis-related immune signature predicting prognosis of gastric cancer patients. Cancer Med 2022; 12:913-929. [PMID: 35621244 PMCID: PMC9844635 DOI: 10.1002/cam4.4857] [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: 12/21/2021] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Ovarian metastasis (OM) results in poor survival of gastric cancer (GC) patients. While immunotherapy has emerged as a promising approach for late-stage GC, validated immune-related prognostic signatures still remain in need. In this study, we constructed an ovarian metastasis- and immune-related prognostic signature (OMIRPS), characterized the molecular and immune features of OMIRPS-categorized subgroups and predicted their potential response to immunotherapy. METHODS Three individual cohorts were used to construct and evaluate OMIRPS: RNA-seq of matched primary GC and OM from Fudan University Shanghai Cancer Center (FUSCC) (discovery cohort, n = 4), The Cancer Genome Atlas (TCGA) (training cohort, n = 544) and GSE84437 (validation cohort, n = 433). Differentially expressed genes (DEGs) identified between primary GC and OM and immune-related genes (IRGs) from the ImmPort and InnateDB databases were used to identify immune-related prognostic hub genes, which were further used to construct OMIRPS by using LASSO regression analysis. Prognosis, molecular characteristics, immune features, and differential immunotherapy efficacy between different OMIRPS subgroups were analyzed. RESULTS Functional analyses of DEGs revealed the significance of immune-related signatures and pathways in the OM. Immune-related prognostic hub genes including TNFRSF18, CARD11, BCL11B, NRP1, BNIP3L, and ATF3 were utilized to construct OMIRPS, which was identified as an independent prognostic factor. Comprehensive analyses unveiled the distinctive molecular and immune characteristics of OMIRPS-high and -low subgroup in regard to enriched pathways, mutation rate, tumor mutation burden, microsatellite instability status, infiltrated immune cell, immune exclusion score, and the prediction of immunotherapy efficacy. Additionally, OMIRPS was associated with Immune Subtypes with borderline significance. CONCLUSIONS RNA-seq of paired primary and ovarian metastatic tumors unveiled the significance of immune-related pathways and tumor immune microenvironment in OM. OMIRPS served as a promising biomarker to predict the prognosis of GC patients and distinguish the molecular features, immune characteristics, and efficacy of immunotherapy between different subgroups.
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Affiliation(s)
- Jianpeng Gao
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shiying Huo
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yu Zhang
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Zhenxiong Zhao
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Hongda Pan
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Xiaowen Liu
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
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9
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Khashkhashi Moghadam S, Bakhshinejad B, Khalafizadeh A, Mahmud Hussen B, Babashah S. Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma. J Cell Mol Med 2021; 26:287-305. [PMID: 34907642 PMCID: PMC8743668 DOI: 10.1111/jcmm.17126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.
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Affiliation(s)
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Sadegh Babashah
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Sha R, Xu Y, Yuan C, Sheng X, Wu Z, Peng J, Wang Y, Lin Y, Zhou L, Xu S, Zhang J, Yin W, Lu J. Predictive and prognostic impact of ferroptosis-related genes ACSL4 and GPX4 on breast cancer treated with neoadjuvant chemotherapy. EBioMedicine 2021; 71:103560. [PMID: 34482070 PMCID: PMC8417304 DOI: 10.1016/j.ebiom.2021.103560] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 08/08/2021] [Accepted: 08/15/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Recent evidence shows that inducing ferroptosis may improve efficacy of tumor therapy. However, ferroptosis-related genes have been little studied in patients with breast cancer especially in the neoadjuvant setting. ACSL4 and GPX4 have been well established as the positive and negative regulator of ferroptosis, respectively. This study aimed to explore the predictive value of ACSL4 and GPX4 for patients with breast cancer administered neoadjuvant chemotherapy. METHODS This study included patients treated with paclitaxel-cisplatin-based neoadjuvant chemotherapy. Immunohistochemistry staining of ACSL4 and GPX4 was carried out on the core needle biopsy specimens. Logistic regression was performed to explore the predictive biomarkers of pathological complete response (pCR). Survival analyses were examined by log-rank test and Cox proportional hazard regression. FINDINGS A total of 199 patients were included for the analyses. Both ACSL4 expression and ACSL4/GPX4 combination status could serve as independent predictive factors for pCR. The interaction for pCR was observed between ACSL4 and clinical tumor stage. Besides, ACSL4 expression, GPX4 expression, and their combination status were independent prognostic factors for disease-free survival. Analyses of the Kaplan-Meier Plotter database suggested that higher ACSL4 expression is related to better overall survival, and higher GPX4 expression is related to better distant metastasis-free survival. Pathway analyses revealed that ACSL4 and GPX4 might function in crucial pathways including apoptosis, autophagy, cell adhesion, lipid metabolism, etc. INTERPRETATION: This study revealed the critical value of ACSL4 and GPX4 serving as novel predictive and prognostic biomarkers for patients with breast cancer receiving neoadjuvant chemotherapy. It might be a novel strategy to induce ferroptosis to promote chemosensitivity. Future studies are required to elucidate the potential mechanisms. FUNDING This work was supported by Shanghai Natural Science Foundation [grant number 19ZR1431100], Clinical Research Plan of Shanghai Hospital Development Center [grant numbers SHDC2020CR3003A, 16CR3065B, and 12016231], Shanghai "Rising Stars of Medical Talent" Youth Development Program for Youth Medical Talents - Specialist Program [grant number 2018-15], Shanghai "Rising Stars of Medical Talent" Youth Development Program for Outstanding Youth Medical Talents [grant number 2018-16], Shanghai Collaborative Innovation Center for Translational Medicine [grant number TM201908], Multidisciplinary Cross Research Foundation of Shanghai Jiao Tong University [grant numbers YG2017QN49, ZH2018QNA42, and YG2019QNA28], Nurturing Fund of Renji Hospital [grant numbers PYMDT-002, PY2018-IIC-01, PY2018-III-15, and PYIII20-09], Science and Technology Commission of Shanghai Municipality [grant numbers 20DZ2201600 and 15JC1402700], and Shanghai Municipal Key Clinical Specialty.
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Affiliation(s)
- Rui Sha
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Yaqian Xu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Chenwei Yuan
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaonan Sheng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Ziping Wu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Jing Peng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Yaohui Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
| | - Yanping Lin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Liheng Zhou
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Shuguang Xu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Jie Zhang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Wenjin Yin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
| | - Jinsong Lu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
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Hu Q, Ma X, Li C, Zhou C, Chen J, Gu X. Downregulation of THRSP Promotes Hepatocellular Carcinoma Progression by Triggering ZEB1 Transcription in an ERK-dependent Manner. J Cancer 2021; 12:4247-4256. [PMID: 34093825 PMCID: PMC8176411 DOI: 10.7150/jca.51657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 05/01/2021] [Indexed: 11/05/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a major leading cause of cancer mortality worldwide. Thyroid hormone responsive (THRSP) gene is primarily known for regulating responses to thyroid hormones, but its expression has been correlated with differential outcomes in some cancers. To date, however, its role in the progression of HCC remains unknown. Methods: The mRNA and protein expression of THRSP was measured in HCC tissues and cell lines via qPCR and western blot assays. Lentiviral transfection was used to establish stable cell lines overexpressing THRSP and shRNA was used to silence THRSP. The effects of THRSP on cell growth were then determined in vivo and in vitro. Cell migration and invasion of HCC cells were investigated using transwell and wound healing assays. Results: In tissue samples from patients, HCC tissues had decreased THRSP expression relative to adjacent healthy tissues. Further, patients with decreased THRSP protein and mRNA expression had worse outcomes. Knockdown of THRSP led to increased cell growth, migration, and invasion of HCC cells, and THRSP overexpression exerted an anti-tumor effect in vivo and in vitro. We found that increased expression of THRSP inhibited hepatocellular carcinogenesis by inhibiting the process of epithelial-to-mesenchymal transition through acting on the ERK/ZEB1 signaling pathway. Conclusion: THRSP may act as a functional tumor suppressor and was frequently reduced in HCC tissue samples. We identified a novel pathway for the THRSP/ERK/ZEB1-regulated suppression of HCC tumorigenesis and invasion. Restoring THRSP expression may represent a promising approach for HCC therapies.
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Affiliation(s)
- Qiong Hu
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, Zhejiang, 316021, China
| | - Xiaolu Ma
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Chuner Li
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, Zhejiang, 316021, China
| | - Chenhao Zhou
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, Zhejiang, 316021, China
| | - Jiayao Chen
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, Zhejiang, 316021, China
| | - Xuechun Gu
- Department of Laboratory Medicine, Zhoushan Hospital of Zhejiang Province, Zhoushan, Zhejiang, 316021, China
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