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Oshi M, Chida K, Roy AM, Mann GK, An N, Yan L, Endo I, Takabe K. Higher inflammatory response in hepatocellular carcinoma is associated with immune cell infiltration and a better outcome. Hepatol Int 2024:10.1007/s12072-024-10678-2. [PMID: 38898190 DOI: 10.1007/s12072-024-10678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/01/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND AND AIMS Hepatocellular carcinoma (HCC) often develops from chronic liver inflammation. Inflammation within a tumor can either promote cancer progression or activate an immune response against it. This study aims to determine the clinical significance of enhanced inflammation in HCC. METHODS Data from 655 HCC patients across four cohorts (TCGA, GSE6764, GSE76427, GSE89377) were examined. Inflammatory response was quantified using a scoring system derived from the gene set variation analysis of the "INFLAMMATORY_RESPONSE" gene set. RESULTS A stepwise increase in inflammatory response was noted from normal liver to cirrhosis, with consistently lower levels in HCC across both GSE6764 and GSE89377 cohorts (both p < 0.001). Similar trends were observed in interferon response, pathways such as IL6/JAK/STAT3 and complement signaling, coagulation cascade, and allograft rejection (all p < 0.02). HCCs with high inflammatory response were associated with increased immune cell infiltrations (p < 0.01) and cytolytic activity (p < 0.001). Interestingly, these HCCs had reduced mutation rates, no relationship with cell proliferation, and displayed both immune responses and pro-cancerous signals including epithelial-mesenchymal transition, KRAS, and hypoxia. Further, a high inflammatory score correlated with improved disease-free survival in TCGA (p = 0.034) and overall survival in GSE76427 (p = 0.008). CONCLUSION HCC with higher levels of inflammatory response demonstrated increased immune cell infiltration, enhanced immune-related and other pro-cancerous-related signaling, and showed a trend toward a better patient prognosis.
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Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Arya Mariam Roy
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Gabriella Kim Mann
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Nan An
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan.
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan.
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1194, Japan.
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8520, Japan.
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan.
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, 14263, USA.
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Gimeno-Valiente F, López-Rodas G, Castillo J, Franco L. The Many Roads from Alternative Splicing to Cancer: Molecular Mechanisms Involving Driver Genes. Cancers (Basel) 2024; 16:2123. [PMID: 38893242 PMCID: PMC11171328 DOI: 10.3390/cancers16112123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer driver genes are either oncogenes or tumour suppressor genes that are classically activated or inactivated, respectively, by driver mutations. Alternative splicing-which produces various mature mRNAs and, eventually, protein variants from a single gene-may also result in driving neoplastic transformation because of the different and often opposed functions of the variants of driver genes. The present review analyses the different alternative splicing events that result in driving neoplastic transformation, with an emphasis on their molecular mechanisms. To do this, we collected a list of 568 gene drivers of cancer and revised the literature to select those involved in the alternative splicing of other genes as well as those in which its pre-mRNA is subject to alternative splicing, with the result, in both cases, of producing an oncogenic isoform. Thirty-one genes fall into the first category, which includes splicing factors and components of the spliceosome and splicing regulators. In the second category, namely that comprising driver genes in which alternative splicing produces the oncogenic isoform, 168 genes were found. Then, we grouped them according to the molecular mechanisms responsible for alternative splicing yielding oncogenic isoforms, namely, mutations in cis splicing-determining elements, other causes involving non-mutated cis elements, changes in splicing factors, and epigenetic and chromatin-related changes. The data given in the present review substantiate the idea that aberrant splicing may regulate the activation of proto-oncogenes or inactivation of tumour suppressor genes and details on the mechanisms involved are given for more than 40 driver genes.
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Affiliation(s)
- Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London WC1E 6DD, UK;
| | - Gerardo López-Rodas
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
| | - Josefa Castillo
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Luis Franco
- Department of Oncology, Institute of Health Research INCLIVA, 46010 Valencia, Spain; (G.L.-R.); (J.C.)
- Department of Biochemistry and Molecular Biology, Universitat de València, 46010 Valencia, Spain
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Guo F, Li Y, Yu W, Fu Y, Zhang J, Cao H. Recent Progress of Small Interfering RNA Delivery on the Market and Clinical Stage. Mol Pharm 2024; 21:2081-2096. [PMID: 38630656 DOI: 10.1021/acs.molpharmaceut.3c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Small interfering RNAs (siRNAs) are promising therapeutic strategies, and five siRNA drugs have been approved by the Food and Drug Administration (FDA) and the European Commission (EC). This marks a significant milestone in the development of siRNA for clinical applications. The approved siRNA agents can effectively deliver siRNAs to the liver and treat liver-related diseases. Currently, researchers have developed diverse delivery platforms for transporting siRNAs to different tissues such as the brain, lung, muscle, and others, and a large number of siRNA drugs are undergoing clinical trials. Here, these delivery technologies and the latest advancements in clinical applications are summarized, and this Review provides a concise overview of the strategies employed for siRNA delivery to both hepatic and extrahepatic tissues.
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Affiliation(s)
- Fan Guo
- School of Pharmacy, Binzhou Medical University, Shandong 264003, China
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
| | - Yan Li
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Wenjun Yu
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Yuanlei Fu
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Jing Zhang
- School of Pharmacy, Binzhou Medical University, Shandong 264003, China
| | - Haiqiang Cao
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Shandong 264000, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Shafieizadeh Z, Shafieizadeh Z, Davoudi M, Afrisham R, Miao X. Role of Fibrinogen-like Protein 1 in Tumor Recurrence Following Hepatectomy. J Clin Transl Hepatol 2024; 12:406-415. [PMID: 38638375 PMCID: PMC11022061 DOI: 10.14218/jcth.2023.00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/29/2023] [Accepted: 01/25/2024] [Indexed: 04/20/2024] Open
Abstract
Partial hepatectomy is a first-line treatment for hepatocellular carcinoma. Within 2 weeks following partial hepatectomy, specific molecular pathways are activated to promote liver regeneration. Nevertheless, residual microtumors may also exploit these pathways to reappear and metastasize. Therapeutically targeting molecules that are differentially regulated between normal cells and malignancies, such as fibrinogen-like protein 1 (FGL1), appears to be an effective approach. The potential functions of FGL1 in both regenerative and malignant cells are discussed within the ambit of this review. While FGL1 is normally elevated in regenerative hepatocytes, it is normally downregulated in malignant cells. Hepatectomy does indeed upregulate FGL1 by increasing the release of transcription factors that promote FGL1, including HNF-1α and STAT3, and inflammatory effectors, such as TGF-β and IL6. This, in turn, stimulates certain proliferative pathways, including EGFR/Src/ERK. Hepatectomy alters the phase transition of highly differentiated hepatocytes from G0 to G1, thereby transforming susceptible cells into cancerous ones. Activation of the PI3K/Akt/mTOR pathway by FGL1 allele loss on chromosome 8, a tumor suppressor area, may also cause hepatocellular carcinoma. Interestingly, FGL1 is specifically expressed in the liver via HNF-1α histone acetylase activity, which triggers lipid metabolic reprogramming in malignancies. FGL1 might also be involved in other carcinogenesis processes such as hypoxia, epithelial-mesenchymal transition, immunosuppression, and sorafenib-mediated drug resistance. This study highlights a research gap in these disciplines and the necessity for additional research on FGL1 function in the described processes.
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Affiliation(s)
- Zahra Shafieizadeh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Zohreh Shafieizadeh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Davoudi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Afrisham
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Xiaolei Miao
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
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Mohamed FEZA, Dewidar B, Lin T, Ebert MP, Dooley S, Meindl‐Beinker NM, Hammad S. TGFβR1 inhibition drives hepatocellular carcinoma proliferation through induction of toll-like-receptor signalling. Int J Exp Pathol 2024; 105:64-74. [PMID: 38328944 PMCID: PMC10951419 DOI: 10.1111/iep.12501] [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: 08/24/2023] [Revised: 12/18/2023] [Accepted: 01/06/2024] [Indexed: 02/09/2024] Open
Abstract
Transforming growth factor (TGF)-β and toll-like receptors (TLRs) have been shown to independently modulate the proliferation of hepatocellular carcinoma (HCC). Since a direct cross-talk between these two signalling pathways in HCC has not been clearly described before, we aimed here to explore the possibility of such interaction. A human HCC tissue array (n = 20 vs. four control samples), human HCC samples (n = 10) and steatohepatitis-driven murine HCC samples (control, NASH and HCC; n = 6/group) were immunostained for TGFβR1, pSMAD2, TRAF6, IRAK1 and PCNA. The results were confirmed by immunoblotting. Effects of constant activation of the SMAD pathway by constitutive expression of ALK5 or knockdown of mediators of TLR signalling, IRAK1 and MyD88, on HCC proliferation, were investigated in the HCC cell line (HUH-7) after treatment with TGFβ1 cytokine or TGFβR1 kinase inhibitor (LY2157299) using PCNA and MTS assay. TGFβR1 expression is decreased in human and murine HCC and associated with downregulated pSMAD2, but increased IRAK1, TRAF6 and PCNA staining. TGFβR1 kinase inhibition abolished the cytostatic effects of TGFβ1 and led to the induction of IRAK1, pIRAK1 and elevated mRNA levels of TLR-9. Overexpression of ALK5 and knockdown of MyD88 or IRAK1 augmented the cytostatic effects of TGFβ1 on HUH-7. In another epithelial HCC cell line, that is, HepG2, TGFβR1 kinase inhibitor similarly elevated cellular proliferation. There is a balance between the canonical SMAD-driven tumour-suppressing arm and the non-canonical tumour-promoting arm of TGFβ signalling. Disruption of this balance, by inhibition of the canonical pathway, induces HCC proliferation through TLR signalling.
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Affiliation(s)
- Fatma El Zahraa Ammar Mohamed
- Department of Pathology, Faculty of MedicineMinia UniversityMiniaEgypt
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Bedair Dewidar
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Department of Pharmacology and Toxicology, Faculty of PharmacyTanta UniversityTantaEgypt
- Institute for Clinical Diabetology, German Diabetes CenterLeibniz Center for Diabetes Research at Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
| | - Tao Lin
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Matthias P. Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Mannheim Institute for Innate Immunoscience (MI3), University Medical Center Mannheim, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, University Medical Center Mannheim, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Steven Dooley
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Nadja M. Meindl‐Beinker
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Seddik Hammad
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
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Harb OA, Elfeky MA, Alabiad MA, Hemeda R, Allam AS, El Hawary AT, Elbaz M, Sharaf AL, Gertallah LM, Abdelaziz AM, Shalaby AM, Alorini M, Yahia AIO, Negm M. PYCR1, BANF1, and STARD8 Expression in Gastric Carcinoma: A Clinicopathologic, Prognostic, and Immunohistochemical Study. Appl Immunohistochem Mol Morphol 2024; 32:102-110. [PMID: 37982568 DOI: 10.1097/pai.0000000000001173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND It will be important to understand the molecular pathways of gastric cancer (GC) occurrence and progression, thus detecting predictive and prognostic biomarkers of GC. Pyrroline-5-carboxylate reductase 1 (PYCR1) was upregulated in many cancers, suggesting its possible roles in carcinogenesis and tumor metastases. Barrier-of-autointegration factor 1 (BANF1) is a protein family that plays essential roles in maintaining the integrity of an intact cellular genome. Rho-GTPs are molecular switches that control many signal transduction pathways in normal cells, including 3 subgroups from 1 to 3 (DLC1-3). DLC-3, known as StAR-related lipid transfer domain protein 8 (STARD8), and its role in cancers were not sufficiently studied. The study aimed to investigate the significance of PYCR1, BANF1, and STARD8 protein expression in GC tissues and normal gastric mucosa retrieved from patients with GC to detect prognostic roles of expression. PATIENTS AND METHODS Specimens were collected from 100 patients with gastric carcinoma. After the application of the inclusion criteria of the study, we prepared 100 paraffin blocks from samples of the 100 included patients; each block included samples from gastric carcinoma and adjacent non-neoplastic gastric mucosa. We assessed the expression of PYCR1, BANF1, and STARD8 using immunohistochemistry in all studied samples. We followed patients for the detection of disease progression and survival rates. We correlate PYCR1, BANF1, and STARD8 expression with clinical, pathologic, and prognostic parameters. RESULTS Overexpression of PYCR1 and BANF1 and decreased expression of STARD8 was found in gastric carcinoma tissues than adjacent non-neoplastic gastric mucosa ( P <0.001), and was positively associated with high grade ( P =0.006), depth of tumor invasion, presence of lymph nodes metastases and advanced stage ( P =0.001), high incidence of GC progression, recurrence, unfavorable disease-free survival ( P =0.003) and unfavorable overall survival rates ( P <0.001). Thus, it was revealed that; in univariate and multivariate analyses, levels of PYCR1, BANF1, and STARD8 are associated with the overall survival rate of GC patients. CONCLUSIONS We showed that overexpression of PYCR1 and BANF1 and decreased expression of STARD8 in GC tissues was associated with poor prognosis and GC progression.
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Affiliation(s)
| | | | | | | | | | | | - Mohammed Elbaz
- Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo
| | - Ahmed L Sharaf
- Tropical Medicine, Faculty of Medicine, Zagazig University, Zagazig
| | | | | | - Amany Mohamed Shalaby
- Department of Histology and Cell Biology, Faculty of Medicine, Tanta University, Tanta
| | - Mohammed Alorini
- Department of Basic Medical Sciences, Unaizah College of Medicine and Medical Sciences, Qassim University, Unaizah
| | - Amar Ibrahim Omer Yahia
- Department of Pathology, College of Medicine, University of Bisha, Bisha, Kingdom of Saudi Arabia
- Department of Pathology, Faculty of Medicine and Health Sciences, University of Kordofan, Elobeid, Sudan
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Oshi M, Chida K, Roy AM, Mann GK, An N, Yan L, Endo I, Takabe K. Higher Inflammatory Response in Hepatocellular Carcinoma is Associated with Immune Cell Infiltration and a Better Outcome. RESEARCH SQUARE 2024:rs.3.rs-3768964. [PMID: 38260290 PMCID: PMC10802714 DOI: 10.21203/rs.3.rs-3768964/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background & Aims Hepatocellular carcinoma (HCC) often develops from chronic liver inflammation. Inflammation within a tumor can either promote cancer progression or activate an immune response against it. This study aims to determine the clinical significance of enhanced inflammation in HCC. Methods Data from 655 HCC patients across four cohorts (TCGA, GSE6764, GSE76427, GSE89377) were examined. Inflammatory response was quantified using a scoring system derived from the gene set variation analysis of the "INFLAMMATORY_RESPONSE" gene set. Results A stepwise increase in inflammatory response was noted from normal liver to cirrhosis, with consistently lower levels in HCC across both GSE6764 and GSE89377 cohorts (both p<0.001). Similar trends were observed in interferon response, pathways such as IL6/JAK/STAT3 and complement signaling, coagulation cascade, and allograft rejection (all p<0.02). HCCs with high inflammatory response were associated with increased immune cell infiltrations (p<0.01) and cytolytic activity (p<0.001). Interestingly, these HCCs had reduced mutation rates, no relationship with cell proliferation, and displayed both immune responses and pro-cancerous signals including epithelial-mesenchymal transition, KRAS, and hypoxia. Further, a high inflammatory score correlated with improved disease-free survival in TCGA (p=0.034) and overall survival in GSE76427 (p=0.008). Conclusion HCC with higher levels of inflammatory response demonstrated increased immune cell infiltration, enhanced immune-related and other pro-cancerous-related signaling, and better patient prognosis.
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Affiliation(s)
| | | | | | | | - Nan An
- Roswell Park Comprehensive Cancer Center
| | - Li Yan
- Roswell Park Comprehensive Cancer Center
| | - Itaru Endo
- Yokohama City University: Yokohama Shiritsu Daigaku
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Wang K, Shi JH, Gao J, Sun Y, Wang Z, Shi X, Guo W, Jin Y, Zhang S. Arachidonic acid metabolism CYP450 pathway is deregulated in hepatocellular carcinoma and associated with microvascular invasion. Cell Biol Int 2024; 48:31-45. [PMID: 37655528 DOI: 10.1002/cbin.12086] [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: 04/06/2023] [Revised: 07/08/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
Arachidonic acid metabolism plays a crucial role in the development and progression of inflammatory and metabolic liver diseases. However, its role in hepatocellular carcinoma (HCC) remains unclear. In this study, we investigated the expression of key genes involved in the arachidonic acid metabolism pathway in HCC using a combination of bioinformatics, proteomics and immunohistochemistry analyses. Through a comprehensive analysis of publicly available datasets, clinical HCC tissues, and tissue microarrays, we compared the expression of hepatic arachidonic acid metabolic genes. We observed significant downregulation of cytochrome P450 (CYP450) pathway genes at both the messenger RNA and protein levels in HCC tissues compared to normal liver tissues. Furthermore, we observed a strong correlation between the deregulation of the arachidonic acid metabolism CYP450 pathway and the pathological features and prognosis of HCC. Specifically, the expression of CYP2C8/9/18/19 was significantly correlated with pathological grade (r = -.484, p < .0001), vascular invasion (r = -.402, p < .0001), aspartate transaminase (r = -.246, p = .025), gamma-glutamyl transpeptidase (r = -.252, p = .022), alkaline phosphatase (r = -.342, p = .002), alpha-fetoprotein (r = -.311, p = .004) and carbohydrate antigen 19-9 (r = -.227, p = .047). Moreover, we discovered a significant association between CYP450 pathway activity and vascular invasion in HCC. Collectively, these data indicate that arachidonic acid CYP450 metabolic pathway deregulation is implicated in HCC progression and may be a potential predictive factor for early recurrence in patients with HCC.
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Affiliation(s)
- Kai Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Ji-Hua Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Yaohui Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Zhihui Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Xiaoyi Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Yang Jin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
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Son JA, Weon JH, Baek GO, Ahn HR, Choi JY, Yoon MG, Cho HJ, Cheong JY, Eun JW, Kim SS. Circulating small extracellular vesicle-derived splicing factor 3b subunit 4 as a non-invasive diagnostic biomarker of early hepatocellular carcinoma. J Exp Clin Cancer Res 2023; 42:288. [PMID: 37899451 PMCID: PMC10614366 DOI: 10.1186/s13046-023-02867-y] [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: 05/25/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) accounts for a majority of primary liver cancer cases and related deaths. The purpose of this study was to assess the diagnostic value of splicing factor 3b subunit 4 (SF3B4) as a novel non-invasive biomarker for HCC and determine the association between SF3B4 expression and immune cell infiltration. METHODS An enzyme-linked immunosorbent assay (ELISA) was used to detect SF3B4 levels in plasma samples obtained from healthy controls (HCs) and patients with chronic hepatitis, liver cirrhosis, and HCC. The expression levels of autoantibodies that detect SF3B4 in the plasma samples of each group of patients were measured. Small extracellular vesicles (EVs) were isolated from patient sera, and the expression levels of EV-SF3B4 were measured using quantitative reverse transcription PCR. RESULTS ELISA results confirmed that the expression levels of SF3B4 proteins and autoantibodies in the plasma of patients with HCC were higher than those in HCs. However, their diagnostic performance was not better than that of alpha-fetoprotein (AFP). The mRNA expression of SF3B4 in serum EV increased but not in the buffy coat or serum of patients with HCC. Serum EV-SF3B4 displayed better diagnostic power than AFP for all stages of HCC (AUC = 0.968 vs. 0.816), including early-stage HCC (AUC = 0.960 vs. 0.842), and this was consistent in the external cohort. Single-cell RNA sequencing indicated that SF3B4 expression was correlated with myeloid-derived suppressor cells. The Tumor Immune Estimation Resource database reconfirmed the correlation between SF3B4 expression and immune cell infiltration in HCC. CONCLUSIONS SF3B4 may be associated with tumor immune infiltration in HCC, and EV-SF3B4 shows potential as a novel non-invasive diagnostic biomarker of HCC.
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Affiliation(s)
- Ju A Son
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Ji Hyang Weon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Ji Yi Choi
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Moon Gyeong Yoon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea.
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea.
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10
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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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11
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Eun JW, Cheong JY, Jeong JY, Kim HS. A New Understanding of Long Non-Coding RNA in Hepatocellular Carcinoma-From m 6A Modification to Blood Biomarkers. Cells 2023; 12:2272. [PMID: 37759495 PMCID: PMC10528438 DOI: 10.3390/cells12182272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
With recent advancements in biological research, long non-coding RNAs (lncRNAs) with lengths exceeding 200 nucleotides have emerged as pivotal regulators of gene expression and cellular phenotypic modulation. Despite initial skepticism due to their low sequence conservation and expression levels, their significance in various biological processes has become increasingly apparent. We provided an overview of lncRNAs and discussed their defining features and modes of operation. We then explored their crucial function in the hepatocarcinogenesis process, elucidating their complex involvement in hepatocellular carcinoma (HCC). The influential role of lncRNAs within the HCC tumor microenvironment is emphasized, illustrating their potential as key modulators of disease dynamics. We also investigated the significant influence of N6-methyladenosine (m6A) modification on lncRNA function in HCC, enhancing our understanding of both their roles and their upstream regulators. Additionally, the potential of lncRNAs as promising biomarkers was discussed in liver cancer diagnosis, suggesting a novel avenue for future research and clinical application. Finally, our work underscored the dual potential of lncRNAs as both contributors to HCC pathogenesis and innovative tools for its diagnosis. Existing challenges and prospective trajectories in lncRNA research are also discussed, emphasizing their potential in advancing liver cancer research.
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Affiliation(s)
- Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; (J.W.E.); (J.Y.C.)
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; (J.W.E.); (J.Y.C.)
| | - Jee-Yeong Jeong
- Department of Biochemistry, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea;
- Institute for Medical Science, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea
| | - Hyung Seok Kim
- Department of Biochemistry, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea;
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12
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Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C. Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations. J Med Genet 2023; 60:910-917. [PMID: 36707240 PMCID: PMC10447385 DOI: 10.1136/jmg-2022-108920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND De novo mutations (DNMs) are linked with many severe early-onset disorders ranging from rare congenital malformation to intellectual disability. Conventionally, DNMs are considered to have an estimated recurrence rate of 1%. Recently, studies have revealed a higher prevalence of parental mosaicism, leading to a greater recurrence risk, resulting in a second child harbouring the same DNM as a previous child. METHODS In this study, we included 10 families with DNMs leading to adverse pregnancy outcomes. DNA was extracted from tissue samples, including parental peripheral blood, parental saliva and paternal sperm. High-throughput sequencing was used to screen for parental mosaicism with a depth of more than 5000× on average and a variant allele fraction (VAF) detection limit of 0.5%. RESULTS The presence of mosaicism was detected in sperms in two families, with VAFs of 2.8% and 2.5%, respectively. Both families have a history of multiple adverse pregnancies and DNMs shared by siblings. Preimplantation genetic testing (PGT) and prenatal diagnosis were performed in one family, thereby preventing the reoccurrence of DNMs. CONCLUSION This study is the first to report the successful implementation of PGT for monogenic/single gene defects in the parental mosaicism family. Our study suggests that mosaic detection of paternal sperm is warranted in families with recurrent DNMs leading to adverse pregnancy outcomes, and PGT can effectively block the transmission of the pathogenic mutation.
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Affiliation(s)
- Naixin Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Weihui Shi
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xianling Cao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Li Jin
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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13
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Manabile MA, Hull R, Khanyile R, Molefi T, Damane BP, Mongan NP, Bates DO, Dlamini Z. Alternative Splicing Events and Their Clinical Significance in Colorectal Cancer: Targeted Therapeutic Opportunities. Cancers (Basel) 2023; 15:3999. [PMID: 37568815 PMCID: PMC10417810 DOI: 10.3390/cancers15153999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) ranks as one of the top causes of cancer mortality worldwide and its incidence is on the rise, particularly in low-middle-income countries (LMICs). There are several factors that contribute to the development and progression of CRC. Alternative splicing (AS) was found to be one of the molecular mechanisms underlying the development and progression of CRC. With the advent of genome/transcriptome sequencing and large patient databases, the broad role of aberrant AS in cancer development and progression has become clear. AS affects cancer initiation, proliferation, invasion, and migration. These splicing changes activate oncogenes or deactivate tumor suppressor genes by producing altered amounts of normally functional or new proteins with different, even opposing, functions. Thus, identifying and characterizing CRC-specific alternative splicing events and variants might help in designing new therapeutic splicing disrupter drugs. CRC-specific splicing events can be used as diagnostic and prognostic biomarkers. In this review, alternatively spliced events and their role in CRC development will be discussed. The paper also reviews recent research on alternatively spliced events that might be exploited as prognostic, diagnostic, and targeted therapeutic indicators. Of particular interest is the targeting of protein arginine methyltransferase (PMRT) isoforms for the development of new treatments and diagnostic tools. The potential challenges and limitations in translating these discoveries into clinical practice will also be addressed.
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Affiliation(s)
- Mosebo Armstrong Manabile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
| | - Richard Khanyile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Thulo Molefi
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa;
| | - Nigel Patrick Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2QL, UK;
| | - David Owen Bates
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Centre for Cancer Sciences, Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
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14
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Shen C, Cao Y, Qi GQ, Huang J, Liu ZP. Discovering pathway biomarkers of hepatocellular carcinoma occurrence and development by dynamic network entropy analysis. Gene 2023; 873:147467. [PMID: 37164125 DOI: 10.1016/j.gene.2023.147467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
OBJECTIVE Gene expression profiling techniques measure the transcription of thousands of genes in a parallel manner. With more and more hepatocellular carcinoma (HCC) transcriptomic data becoming available, the high-throughput data provides an unprecedented opportunity to discover HCC diagnostic biomarkers. In this work, we propose a bioinformatics method based on dynamic network entropy analysis, called DNEA, to identify potential pathway biomarkers for HCC occurrence and development by integrating transcriptome and interactome. METHODS We firstly collect the pathways documented in different knowledge-bases and then impose the genome-wide human transcriptomic data of multistage cancerous tissues during the development and progression of HCC. After linking the gene sets of pathways into individual connected networks, we map the corresponding gene expression information onto these pathways. The dynamic network entropy of individual pathways is calculated to evaluate its activities and dysfunctionalities during the disease occurrence and development. We use the overall significant difference in the entropic dynamics during the time course to prioritize distinctive pathways during disease progression. Then machine learning classification methods are employed to screen out pathway biomarkers with the classification ability to distinguish different-stage samples of HCC progression. RESULTS Pathway biomarkers discovered based on DNEA demonstrate good classification performance in measuring HCC progression. The classification accuracy is as follows: DNA replication pathway (mean AUC= 0.82, 20 genes) from KEGG, FMLP pathway (mean AUC=0.84, 14 genes) from BioCarta, and downstream signaling of activated FGFR pathway (mean AUC =0.80, 15 genes) from Reactome. At the same time, previous studies have shown that these genes and pathways screened are closely related to the occurrence and development of HCC in terms of oncogenesis dysfunctions. CONCLUSIONS Our method for cancer biomarker discovery based on dynamic network entropy analysis is effective and efficient in identifying pathway biomarkers related to the progression of complex diseases.
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Affiliation(s)
- Chen Shen
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China; Department of Data and Information, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou, Zhejiang 310052, China
| | - Yi Cao
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China; Center for Biomedical Engineering, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Guo-Qiang Qi
- Department of Data and Information, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou, Zhejiang 310052, China
| | - Jian Huang
- Department of Data and Information, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou, Zhejiang 310052, China
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China.
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15
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Du TY, Gao YX, Zheng YS. Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis. Sci Rep 2023; 13:1876. [PMID: 36725885 PMCID: PMC9892033 DOI: 10.1038/s41598-022-26794-8] [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: 08/08/2022] [Accepted: 12/20/2022] [Indexed: 02/03/2023] Open
Abstract
Cirrhosis is the most common subclass of liver disease worldwide and correlated to immune infiltration. However, the immune-related molecular mechanism underlying cirrhosis remains obscure. Two gene expression profiles GSE89377 and GSE139602 were investigated to identify differentially expressed genes (DEGs) related to cirrhosis. Enrichment analysis for DEGs was conducted. Next, the immune infiltration of DEGs was evaluated using CIBERSORT algorithm. The hub DEGs with tight connectivity were identified using the String and Cytoscape databases, and the expression difference of these hub genes between normal liver and cirrhosis samples was determined. Moreover, in order to evaluate the discriminatory ability of hub genes and obtained the area under the receiver operating characteristic curve values in the GSE89377 and GSE139602 datasets. Finally, the association between hub DEGs and immune cell infiltration was explored by Spearman method. Among the 299 DEGs attained, 136 were up-regulated and 163 were down-regulated. Then the enrichment function analysis of DEGs and CIBERSORT algorithm showed significant enrichment in immune and inflammatory responses. And four hub DEGs (ACTB, TAGLN, VIM, SOX9) were identified, which also showed a diagnostic value in the GSE89377 and GSE 139,602 datasets. Finally, the immune infiltration analysis indicated that, these hub DEGs were highly related to immune cells. This study revealed key DEGs involved in inflammatory immune responses of cirrhosis, which could be used as biomarkers for diagnosis or therapeutic targets of cirrhosis.
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Affiliation(s)
- Tong-Yue Du
- Department of Critical Care Medicine, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, No.-1-1, Zhongfu Road, Nanjing, 210003, China
| | - Ya-Xian Gao
- Department of Critical Care Medicine, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, No.-1-1, Zhongfu Road, Nanjing, 210003, China
| | - Yi-Shan Zheng
- Department of Critical Care Medicine, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, No.-1-1, Zhongfu Road, Nanjing, 210003, China.
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16
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ADAR1-dependent miR-3144-3p editing simultaneously induces MSI2 expression and suppresses SLC38A4 expression in liver cancer. Exp Mol Med 2023; 55:95-107. [PMID: 36599932 PMCID: PMC9898302 DOI: 10.1038/s12276-022-00916-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 01/06/2023] Open
Abstract
Aberrant adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminase acting on double-stranded RNA (ADAR), has been implicated in various cancers, but the mechanisms by which microRNA (miRNA) editing contributes to cancer development are largely unknown. Our multistage hepatocellular carcinogenesis transcriptome data analyses, together with publicly available data, indicated that ADAR1 was the most profoundly dysregulated gene among RNA-editing enzyme family members in liver cancer. Targeted inactivation of ADAR1 inhibited the in vitro tumorigenesis of liver cancer cells. An integrative computational analyses of RNA-edited hotspots and the known editing frequency of miRNAs suggested that the miRNA miR-3144-3p was edited by ADAR1 during liver cancer progression. Specifically, ADAR1 promoted A-to-I editing of canonical miR-3144-3p to replace the adenosine at Position 3 in the seed region with a guanine (ED_miR-3144-3p(3_A < G)) in liver cancer cells. We then demonstrated that Musashi RNA-binding protein 2 (MSI2) was a specific target of miR-3144-3p and that MSI2 overexpression was due to excessive ADAR1-dependent over-editing of canonical miR-3144-3p in liver cancer. In addition, target prediction analyses and validation experiments identified solute carrier family 38 member 4 (SLC38A4) as a specific gene target of ED_miR-3144-3p(3_A < G). The ectopic expression of both ADAR1 and the ED_miR-3144-3p(3_A < G) mimic enhanced mitotic activities, and ADAR1 suppressed SLC38A4 expression in liver cancer cells. Treatments with mouse-specific ADAR1-, MSI2-siRNA-, or SLC38A4-expressing plasmids suppressed tumorigenesis and tumor growth in a mouse model of spontaneous liver cancer. Our findings suggest that the aberrant regulation of ADAR1 augments oncogenic MSI2 effects by excessively editing canonical miR-3144-3p and that the resultant ED_miR-3144-3p(3_A < G) simultaneously suppresses tumor suppressor SLC38A4 expression, contributing to hepatocellular carcinogenesis.
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17
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Jiang Y, Zhang JX, Liu R. Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing. PLoS Comput Biol 2022; 18:e1010744. [PMID: 36534703 PMCID: PMC9810203 DOI: 10.1371/journal.pcbi.1010744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/03/2023] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
The synergy between human immunodeficiency virus (HIV) and Mycobacterium tuberculosis (MTB) could accelerate the deterioration of immunological functions. Previous studies have explored the pathogenic mechanisms of HIV mono-infection (HMI), MTB mono-infection (MMI) and MTB/HIV co-infection (MHCI), but their similarities and specificities remain to be profoundly investigated. We thus designed a computational framework named IDEN to identify gene pairs related to these states, which were then compared from different perspectives. MMI-related genes showed the highest enrichment level on a greater number of chromosomes. Genes shared by more states tended to be more evolutionarily conserved, posttranslationally modified and topologically important. At the expression level, HMI-specific gene pairs yielded higher correlations, while the overlapping pairs involved in MHCI had significantly lower correlations. The correlation changes of common gene pairs showed that MHCI shared more similarities with MMI. Moreover, MMI- and MHCI-related genes were enriched in more identical pathways and biological processes, further illustrating that MTB may play a dominant role in co-infection. Hub genes specific to each state could promote pathogen infections, while those shared by two states could enhance immune responses. Finally, we improved the network proximity measure for drug repurposing by considering the importance of gene pairs, and approximately ten drug candidates were identified for each disease state.
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Affiliation(s)
- Yao Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jia-Xuan Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail:
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18
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Zhang Q, Gao Y, Zhang Y, Jing M, Wang D, Wang Y, Khattak S, Qi H, Cai C, Zhang J, Ngowi EE, Khan NH, Li T, Ji A, Jiang Q, Ji X, Li Y, Wu D. Cystathionine γ-lyase mediates cell proliferation, migration, and invasion of nasopharyngeal carcinoma. Oncogene 2022; 41:5238-5252. [PMID: 36310322 DOI: 10.1038/s41388-022-02512-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is an epithelia-derived malignancy with a distinctive geographic distribution. Cystathionine γ-lyase (CSE) is involved in cancer development and progression. Nevertheless, the role of CSE in the growth of NPC is unknown. In this study, we found that CSE levels in human NPC cells were higher than those in normal nasopharyngeal cells. CSE overexpression enhanced the proliferative, migrative, and invasive abilities of NPC cells and CSE downregulation exerted reverse effects. Overexpression of CSE decreased the expressions of cytochrome C, cleaved caspase (cas)-3, cleaved cas-9, and cleaved poly-ADP-ribose polymerase, whereas CSE knockdown exhibited reverse effects. CSE overexpression decreased reactive oxygen species (ROS) levels and the expressions of phospho (p)-extracellular signal-regulated protein kinase 1/2, p-c-Jun N-terminal kinase, and p-p38, but promoted the expressions of p-phosphatidylinositol 3-kinase (PI3K), p-AKT, and p-mammalian target of rapamycin (mTOR), whereas CSE knockdown showed oppose effects. In addition, CSE overexpression promoted NPC xenograft tumor growth and CSE knockdown decreased tumor growth by modulating proliferation, angiogenesis, cell cycle, and apoptosis. Furthermore, DL-propargylglycine (an inhibitor of CSE) dose-dependently inhibited NPC cell growth via ROS-mediated mitogen-activated protein kinase (MAPK) and PI3K/AKT/mTOR pathways without significant toxicity. In conclusion, CSE could regulate the growth of NPC cells through ROS-mediated MAPK and PI3K/AKT/mTOR cascades. CSE might be a novel tumor marker for the diagnosis and prognosis of NPC. Novel donors/drugs that inhibit the expression/activity of CSE can be developed in the treatment of NPC.
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Affiliation(s)
- Qianqian Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Yingran Gao
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Yanxia Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Mirong Jing
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Di Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Yizhen Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China.,School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Huiwen Qi
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Chunbo Cai
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Jing Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Ebenezeri Erasto Ngowi
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, 475004, China.,Department of Biological Sciences, Faculty of Science, Dar es Salaam University College of Education, Dar es Salaam, 2329, Tanzania
| | - Nazeer Hussain Khan
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China.,School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Tao Li
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Ailing Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Qiying Jiang
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China
| | - Xinying Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China. .,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China. .,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, 475004, China.
| | - Yanzhang Li
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China. .,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China.
| | - Dongdong Wu
- School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China. .,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, Henan, 475004, China. .,School of Stomatology, Henan University, Kaifeng, Henan, 475004, China.
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19
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Duan SF, Zhang MM, Zhang X, Liu W, Zhang SH, Yang B, Dong Q, Han JG, Yu HL, Li T, Ji XY, Wu DD, Zhang XJ. HA-ADT suppresses esophageal squamous cell carcinoma progression via apoptosis promotion and autophagy inhibition. Exp Cell Res 2022; 420:113341. [PMID: 36075445 DOI: 10.1016/j.yexcr.2022.113341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a major cause of cancer-related deaths. We have previously connected a non-sulfated glycosaminoglycan, hyaluronic acid (HA), with a common hydrogen sulfide (H2S) donor, 5-(4-hydroxyphenyl)-3H-1,2-dithiol-3-thione (ADT-OH), to reconstruct a novel conjugate, HA-ADT. In this study, we determined the effect of HA-ADT on the growth of ESCC. Our data suggested that HA-ADT exerted more potent effects than sodium hydrosulfide (NaHS, a fast H2S-releasing donor) and morpholin-4-ium (4-methoxyphenyl)-morpholin-4-ylsulfanylidenesulfido-λ5-phosphane (GYY4137, a slow H2S-releasing donor) on inhibiting the viability, proliferation, migration, and invasion of human ESCC cells. HA-ADT increased apoptosis by suppressing the protein expressions of phospho (p)-Ser473-protein kinase B (PKB/AKT), p-Tyr199/Tyr458-phosphatidylinositol 3-kinase (PI3K), and p-Ser2448-mammalian target of rapamycin (mTOR), but suppressed autophagy through the inhibition of the protein levels of p-Ser552-β-catenin, p-Ser9-glycogen synthase kinase-3β (GSK-3β), and Wnt3a in human ESCC cells. In addition, HA-ADT was more effective in terms of the growth inhibition of human ESCC xenograft tumor than NaHS and GYY4137. In conclusion, HA-ADT can suppress ESCC progression via apoptosis promotion and autophagy inhibition. HA-ADT might be efficacious for the treatment of cancer.
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Affiliation(s)
- Shao-Feng Duan
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Meng-Meng Zhang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Xin Zhang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Wei Liu
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Shi-Hui Zhang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Bo Yang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Qian Dong
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Ju-Guo Han
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Hai-Lan Yu
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Tao Li
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China.
| | - Dong-Dong Wu
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, 475004, China; School of Stomatology, Henan University, Kaifeng, Henan, 475004, China.
| | - Xiao-Ju Zhang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan, 450003, China.
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20
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Kim H, Lee J, Jung SY, Yun HH, Ko JH, Lee JH. SF3B4 Depletion Retards the Growth of A549 Non-Small Cell Lung Cancer Cells via UBE4B-Mediated Regulation of p53/p21 and p27 Expression. Mol Cells 2022; 45:718-728. [PMID: 35996826 PMCID: PMC9589371 DOI: 10.14348/molcells.2022.0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/27/2022] Open
Abstract
Splicing factor B subunit 4 (SF3B4), a component of the U2-pre-mRNA spliceosomal complex, contributes to tumorigenesis in several types of tumors. However, the oncogenic potential of SF3B4 in lung cancer has not yet been determined. The in vivo expression profiles of SF3B4 in non-small cell lung cancer (NSCLC) from publicly available data revealed a significant increase in SF3B4 expression in tumor tissues compared to that in normal tissues. The impact of SF3B4 deletion on the growth of NSCLC cells was determined using a siRNA strategy in A549 lung adenocarcinoma cells. SF3B4 silencing resulted in marked retardation of the A549 cell proliferation, accompanied by the accumulation of cells at the G0/G1 phase and increased expression of p27, p21, and p53. Double knockdown of SF3B4 and p53 resulted in the restoration of p21 expression and partial recovery of cell proliferation, indicating that the p53/p21 axis is involved, at least in part, in the SF3B4-mediated regulation of A549 cell proliferation. We also provided ubiquitination factor E4B (UBE4B) is essential for p53 accumulation after SF3B4 depletion based on followings. First, co-immunoprecipitation showed that SF3B4 interacts with UBE4B. Furthermore, UBE4B levels were decreased by SF3B4 depletion. UBE4B depletion, in turn, reproduced the outcome of SF3B4 depletion, including reduction of polyubiquitinated p53 levels, subsequent induction of p53/p21 and p27, and proliferation retardation. Collectively, our findings indicate the important role of SF3B4 in the regulation of A549 cell proliferation through the UBE4B/p53/p21 axis and p27, implicating the therapeutic strategies for NSCLC targeting SF3B4 and UBE4B.
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Affiliation(s)
- Hyungmin Kim
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine & Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeehan Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Soon-Young Jung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye Hyeon Yun
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine & Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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21
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Wei M, Yan X, Xin X, Chen H, Hou L, Zhang J. Hepatocyte-Specific Smad4 Deficiency Alleviates Liver Fibrosis via the p38/p65 Pathway. Int J Mol Sci 2022; 23:ijms231911696. [PMID: 36232998 PMCID: PMC9570188 DOI: 10.3390/ijms231911696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/17/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Liver fibrosis is a wound-healing response caused by the abnormal accumulation of extracellular matrix, which is produced by activated hepatic stellate cells (HSCs). Most studies have focused on the activated HSCs themselves in liver fibrosis, and whether hepatocytes can modulate the process of fibrosis is still unclear. Sma mothers against decapentaplegic homologue 4 (Smad4) is a key intracellular transcription mediator of transforming growth factor-β (TGF-β) during the development and progression of liver fibrosis. However, the role of hepatocyte Smad4 in the development of fibrosis is poorly elucidated. Here, to explore the functional role of hepatocyte Smad4 and the molecular mechanism in liver fibrosis, a CCl4-induced liver fibrosis model was established in mice with hepatocyte-specific Smad4 deletion (Smad4Δhep). We found that hepatocyte-specific Smad4 deficiency reduced liver inflammation and fibrosis, alleviated epithelial-mesenchymal transition, and inhibited hepatocyte proliferation and migration. Molecularly, Smad4 deletion in hepatocytes suppressed the expression of inhibitor of differentiation 1 (ID1) and the secretion of connective tissue growth factor (CTGF) of hepatocytes, which subsequently activated the p38 and p65 signaling pathways of HSCs in an epidermal growth factor receptor-dependent manner. Taken together, our results clearly demonstrate that the Smad4 expression in hepatocytes plays an important role in promoting liver fibrosis and could therefore be a promising target for future anti-fibrotic therapy.
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Affiliation(s)
- Miaomiao Wei
- The College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Xinlong Yan
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xin Xin
- The College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Haiqiang Chen
- The College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Lingling Hou
- The College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jinhua Zhang
- The College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
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22
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Chen Y, Ye B, Wang C, Nie Y, Qin J, Shen Z. PLOD3 contributes to HER-2 therapy resistance in gastric cancer through FoxO3/Survivin pathway. Cell Death Dis 2022; 8:321. [PMID: 35835735 PMCID: PMC9283410 DOI: 10.1038/s41420-022-01103-4] [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: 10/24/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/05/2022]
Abstract
Human epidermal growth factor receptor 2 (HER-2), a famous therapeutic target for breast cancer, is also associated with an increased risk of recurrence and poor outcomes of other malignancies, including gastric cancer. Yet the mechanism of HER-2 therapy resistance remains controversial due to the heterogeneity of gastric adenocarcinoma. We know, Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 (PLOD3), a key gene coding enzymes that catalyze the lysyl hydroxylation of extracellular matrix collagen, plays an important contributor to HER-2 targeting agent Trastuzumab resistance in gastric cancer. Herein, we analyzed clinical samples of gastric cancer patients and gastric cancer cell lines and identified PLOD3, unveiled that depletion of PLOD3 leads to decreased cell proliferation, tumor growth and Trastuzumab sensitivity in these Trastuzumab resistant GC cell lines. Clinically, increased PLOD3 expression correlates with decreased Trastuzumab therapy responsiveness in GC patients. Mechanistically, we show that PLOD3 represses tumor suppressor FoxO3 expression, therefore upregulating Survivin protein expression that contributes to Trastuzumab resistance in GC. Therefore, our study identifies a new signaling axis PLOD3-FoxO3- Survivin pathway that may be therapeutically targeted in HER-2 positive gastric cancer.
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Affiliation(s)
- Yueda Chen
- Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, 361015, China
| | - Botian Ye
- Department of General Surgery, Gastric Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chunyan Wang
- Department of Obstetrics and Gynecology, Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yanyan Nie
- Shanghai Lab, Animal Research Center, Shanghai, 201203, China
| | - Jing Qin
- Department of General Surgery, Gastric Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhenbin Shen
- Department of General Surgery, Gastric Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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23
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Cystathionine β-Synthase Regulates the Proliferation, Migration, and Invasion of Thyroid Carcinoma Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8678363. [PMID: 35795862 PMCID: PMC9252770 DOI: 10.1155/2022/8678363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/17/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022]
Abstract
Thyroid cancer is considered to be one of the most common endocrine tumors worldwide. Cystathionine β-synthase (CBS) plays a crucial role in the occurrence of several types of malignancies. And yet, the mechanism of action of CBS in the growth of thyroid carcinoma cells is still unrevealed. We found that CBS level in thyroid carcinoma tissue was higher than that in adjacent normal tissue. The overexpression of CBS enhanced the proliferation, migration, and invasion of thyroid cancer cells, while the downregulation of CBS exerted reverse effects. CBS overexpression reduced the levels of cleaved caspase-3 and cleaved poly ADP-ribose polymerase in thyroid cancer cells, whereas CBS knockdown showed reverse trends. CBS overexpression decreased reactive oxygen species (ROS) levels but increased the levels of Wnt3a and phosphorylations of phosphatidylinositol 3-kinase (PI3K), protein kinase B (PKB/AKT), mammalian target of rapamycin (mTOR), β-catenin, and glycogen synthase kinase-3 beta, while CBS knockdown exerted opposite effects. In addition, CBS overexpression promoted the growth of xenografted thyroid carcinoma, whereas CBS knockdown decreased the tumor growth by modulating angiogenesis, cell cycle, and apoptosis. Furthermore, aminooxyacetic acid (an inhibitor of CBS) dose-dependently inhibited thyroid carcinoma cell growth. CBS can regulate the proliferation, migration, and invasion of human thyroid cancer cells via ROS-mediated PI3K/AKT/mTOR and Wnt/β-catenin pathways. CBS can be a potential biomarker for diagnosing or prognosing thyroid carcinoma. Novel donors that inhibit the expression of CBS can be developed in the treatment of thyroid carcinoma.
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24
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Tang H, Wang XQ. Cytochrome P450 family members CYP2E1, CYP3A4, and CYP1A2 are related to prognosis of HCC and can be used as molecular markers for its diagnosis. Shijie Huaren Xiaohua Zazhi 2022; 30:402-410. [DOI: 10.11569/wcjd.v30.i9.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant tumor of the digestive system, and its exact pathogenesis is unclear. Most studies believe that dysregulation of the spatiotemporal expression of multiple genes is closely related to the occurrence of HCC.
AIM To identify the differentially expressed genes in HCC, analyze their value as molecular markers for the diagnosis of HCC, and explore the relationship between differentially expressed key genes and prognosis of HCC patients.
METHODS The differentially expressed gene profiles in HCC patients and non-HCC liver tissues were selected from GEO database, and the differentially expressed genes were screened. The selected differential genes were clustered, and Kyoto encyclopedia of genes and genomes (KEGG) and protein-protein interaction (PPI) analyses were performed. At the same time, hub genes were identified from the differentially expressed genes. According to the identified HUB gene expression, the HCC patients were divided into high and low expression groups, and the overall survival (OS) and progression-free survival (PFS) were compared between the two groups. Hub genes were then evaluated for their value in HCC diagnosis.
RESULTS In GSE62232, GSE67764, GSE89377, and GSE112790 data sets, differentially expressed genes in HCC and normal liver tissues were 370, 1386, 76, and 418, respectively, and a total of 37 common differentially expressed genes were found in the four data sets. These 37 differentially expressed genes are mainly enriched in recognition of apoptotic cells, transition metal ion binding, and chemical carcinogenesis. The clustering heat map of seven differentially expressed genes showed obvious clustering between tumor tissues and normal tissues. PPI topological network was plotted for the 37 differentially expressed genes, and there were 42 protein nodes and 145 action relationships in the network, with an average action degree of 6.9 and regional clustering index of 0.586, indicating significant enrichment (P < 0.05). CYP3A4 and CYP1A2 were the first three hub genes among the 37 differential genes. The areas under the ROC curves for HCC diagnosis based on CYP2E1, CYP3A4, and CYP1A2 alone were 0.83 (95% confidence interval [CI]: 0.74-0.93), 0.93 (95%CI: 0.88-0.97), and 0.96 (95%CI: 0.924-0.98), respectively. OS (hazard ratio [HR] = 0.57, 95%CI: 0.39-0.84; HR = 0.57, 95%CI: 0.40-0.81) and PFS (HR = 0.63, 95%CI: 0.46-0.88; HR = 0.61, 95%CI: 0.45-0.83) in the high CYP2E1 and CYP3A4 expression groups were significantly higher than those in their respective low expression groups (P < 0.05), while there was no statistical difference in OS or PFS in the CYP1A2 high and low expression groups (P > 0.05).
CONCLUSION CYP2E1, CYP3A4, and CYP1A2 may be associated with the occurrence of HCC and can be applied as molecular markers for the prognosis and diagnosis of HCC.
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Affiliation(s)
- Hui Tang
- Zhejiang University of Chinese Medicine, Lishui 323000, Zhejiang Province. China,Department of Interventional Surgery, Lishui People's Hospital, Lishui 323000, Zhejiang Province. China
| | - Xiao-Qiu Wang
- Department of Oncology, Lishui People's Hospital, Lishui 323000, Zhejiang Province. China
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25
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Serum Proteins, HMMR, NXPH4, PITX1 and THBS4; A Panel of Biomarkers for Early Diagnosis of Hepatocellular Carcinoma. J Clin Med 2022; 11:jcm11082128. [PMID: 35456219 PMCID: PMC9027255 DOI: 10.3390/jcm11082128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/21/2023] Open
Abstract
The high morbidity rate of hepatocellular carcinoma (HCC) is mainly linked to late diagnosis. Early diagnosis of this leading cause of mortality is therefore extremely important. We designed a gene selection strategy to identify potential secretory proteins by predicting signal peptide cleavage sites in amino acid sequences derived from transcriptome data of human multistage HCC comprising chronic hepatitis, liver cirrhosis and early and overt HCCs. The gene selection process was validated by the detection of molecules in the serum of HCC patients. From the computational approaches, 10 gene elements were suggested as potent candidate secretory markers for detecting HCC patients. ELISA testing of serum showed that hyaluronan mediated motility receptor (HMMR), neurexophilin 4 (NXPH4), paired like homeodomain 1 (PITX1) and thrombospondin 4 (THBS4) are early-stage HCC diagnostic markers with superior predictive capability in a large cohort of HCC patients. In the assessment of differential diagnostic accuracy, receiver operating characteristic curve analyses showed that HMMR and THBS4 were superior to α-fetoprotein (AFP) in diagnosing HCC, as evidenced by the high area under the curve, sensitivity, specificity, accuracy and other values. In addition, comparative analysis of all four markers and AFP combinations demonstrated that HMMR-PITX1-AFP and HMMR-NXPH4-PITX1 trios were the optimal combinations for reaching 100% accuracy in HCC diagnosis. Serum proteins HMMR, NXPH4, PITX1 and THBS4 can complement measurement of AFP in diagnosing HCC and improve identification of patients with AFP-negative HCC as well as discriminate HCC from non-malignant chronic liver disease.
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26
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PLOD3 regulates the expression of YAP1 to affect the progression of non-small cell lung cancer via the PKCδ/CDK1/LIMD1 signaling pathway. J Transl Med 2022; 102:440-451. [PMID: 35039611 DOI: 10.1038/s41374-021-00674-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022] Open
Abstract
Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD3) is a crucial oncogene in human lung cancer, whereas protein kinase C δ (PKCδ) acts as a tumor suppressor. In this study, we aimed to explore the regulation by PLOD3 on the expression of YAP1 to affect the progression of non-small cell lung cancer (NSCLC) via the PKCδ/CDK1/LIMD1 signaling pathway. We found that PLOD3, CDK1, and YAP1 were highly expressed, while LIMD1 was poorly expressed in NSCLC tissues. Mechanistic investigation demonstrated that silencing PLOD3 promoted the cleavage of PKCδ in a caspase-dependent manner to generate a catalytically active fragment cleaved PKCδ, enhanced phosphorylation levels of CDK1, and LIMD1 but suppressed nuclear translocation of YAP1. Furthermore, functional experimental results suggested that loss of PLOD3 led to increased phosphorylation levels of CDK1 and LIMD1 and downregulated YAP1, thereby suppressing the proliferation, colony formation, cell cycle entry, and resistance to apoptosis of NSCLC cells in vitro and inhibiting tumor growth in vivo. Taken together, these results show that PLOD3 silencing activates the PKCδ/CDK1/LIMD1 signaling pathway to prevent the progression of NSCLC, thus providing novel insight into molecular targets for treating NSCLC.
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27
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Ge S, Zhang Q, Yang X. GPAA1 promotes the proliferation, invasion and migration of hepatocellular carcinoma cells by binding to RNA‑binding protein SF3B4. Oncol Lett 2022; 23:160. [PMID: 35399327 PMCID: PMC8987926 DOI: 10.3892/ol.2022.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Song Ge
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Qiang Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Xiaoyong Yang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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28
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Koh HH, Choi S, Park CK, Ha SY. Down-regulation of TRPV6 Is Associated With Adverse Prognosis in Hepatocellular Carcinoma Treated With Curative Resection. Cancer Genomics Proteomics 2022; 19:259-269. [PMID: 35181592 DOI: 10.21873/cgp.20318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/AIM Transient receptor potential vanilloid 6 (TRPV6), an endothelial Ca2+-selective entry channel, is expressed in various cancer types, and a selective TRPV6 inhibitor is currently being investigated in a clinical trial. However, TRPV6 expression in hepatocellular carcinoma (HCC) has not been reported. MATERIALS AND METHODS We evaluated TRPV6 expression in 219 cases of HCC and analyzed its association with clinicopathological parameters and prognostic significance. TRPV6 mRNA expression was compared between HCC and non-tumor liver tissues using various public datasets, and its prognostic effect was examined in The Cancer Genome Atlas (TCGA) cohort. RESULTS Low TRPV6 expression was found in 37.4% of patients, which was significantly associated with adverse histologic features, and patients with low TRPV6 expression had shorter recurrence-free and disease-free survival. TRPV6 mRNA expression was consistently lower in HCC compared to non-tumor liver samples in public datasets, at the whole tissue level as well as single-cell level. Patients with low TRPV6 expression in the TCGA cohort had shorter progression-free survival. CONCLUSION TRPV6 expression is down-regulated in HCCs and associated with a poor prognosis. TRPV6 may be a prognostic biomarker in HCC.
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Affiliation(s)
- Hyun Hee Koh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sangjoon Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-Keun Park
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Anatomic Pathology Reference Lab, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea;
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Novel Gene Signatures as Prognostic Biomarkers for Predicting the Recurrence of Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14040865. [PMID: 35205612 PMCID: PMC8870597 DOI: 10.3390/cancers14040865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary A high percentage of patients who undergo surgical resection for hepatocellular carcinoma (HCC) experience recurrence. Therefore, identification of accurate molecular markers for predicting recurrence of HCC is important. We analyzed recurrence and non-recurrence HCC tissues using two public omics datasets comprising microarray and RNA-sequencing and found novel gene signatures associated with recurrent HCC. These molecules might be used to not only predict for recurrence of HCC but also act as potential prognostic indicators for patients with HCC. Abstract Hepatocellular carcinoma (HCC) has a high rate of cancer recurrence (up to 70%) in patients who undergo surgical resection. We investigated prognostic gene signatures for predicting HCC recurrence using in silico gene expression analysis. Recurrence-associated gene candidates were chosen by a comparative analysis of gene expression profiles from two independent whole-transcriptome datasets in patients with HCC who underwent surgical resection. Five promising candidate genes, CETN2, HMGA1, MPZL1, RACGAP1, and SNRPB were identified, and the expression of these genes was evaluated using quantitative reverse transcription PCR in the validation set (n = 57). The genes CETN2, HMGA1, RACGAP1, and SNRPB, but not MPZL1, were upregulated in patients with recurrent HCC. In addition, the combination of HMGA1 and MPZL1 demonstrated the best area under the curve (0.807, 95% confidence interval [CI] = 0.681–0.899) for predicting HCC recurrence. In terms of clinicopathological correlation, CETN2, MPZL1, RACGAP1, and SNRPB were upregulated in patients with microvascular invasion, and the expression of MPZL1 and SNRPB was increased in proportion to the Edmonson tumor differentiation grade. Additionally, overexpression of CETN2, HMGA1, and RACGAP1 correlated with poor overall survival (OS) and disease-free survival (DFS) in the validation set. Finally, Cox regression analysis showed that the expression of serum alpha-fetoprotein and RACGAP1 significantly affected OS, whereas platelet count, microvascular invasion, and HMGA1 expression significantly affected DFS. In conclusion, HMGA1 and RACGAP1 may be potential prognostic biomarkers for predicting the recurrence of HCC after surgical resection.
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Correia Soeiro MDN, Vergoten G, Bailly C. Molecular docking of brazilin and its analogs to barrier‐to‐autointegration factor 1 (BAF1). Ann N Y Acad Sci 2022; 1511:154-163. [DOI: 10.1111/nyas.14742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Affiliation(s)
| | - Gérard Vergoten
- University of Lille, Inserm, INFINITE ‐ U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL) Faculté de Pharmacie Lille France
| | - Christian Bailly
- OncoWitan Scientific Consulting Office Lille (Wasquehal), 59290 France
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Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking. Comput Struct Biotechnol J 2022; 20:206-217. [PMID: 35024093 PMCID: PMC8715301 DOI: 10.1016/j.csbj.2021.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/13/2021] [Accepted: 12/04/2021] [Indexed: 12/23/2022] Open
Abstract
This paper describes an ensemble method with supervised module detection and further module prioritization for reliable network-based biomarker discovery. We design a module detection and ranking method called mRank to discover reliable network modules as cancer diagnostic biomarkers, with two procedures: (1) an iterative supervised module detection guided by phenotypic states in a specific network, (2) a block-based module ranking locally and globally via network topological centrality. We validate its effectiveness and efficiency by identifying hepatocellular carcinoma (HCC) network modules on a comprehensive gene regulatory network with specifying gene interactions by HCC RNA-seq data from the Cancer Genome Atlas (TCGA). These top-ranked modules by mRank get a mean AUC of 0.995 on TCGA HCC dataset with 371 tumor samples and 50 controls by cross-validation SVM. Based on the prior knowledge of cancer dysfunctions enriched in top-ranked modules, 69 genes are identified as HCC candidate biomarkers. They are further validated in independent cohorts with a classifier trained on TCGA HCC dataset. A mean AUC of 0.846 is achieved in distinguishing 976 disease samples from 827 controls. Moreover, some known HCC signatures such as AFP and SPP1 are also included in our identified biomarkers. mRank enables us to find more reliable network modules for cancer diagnosis. For a proof-of-concept study, we validate it in identifying HCC network biomarkers and it is generalizable to other cancers or complex disease. The overall results have demonstrated that mRank can find effective network biomarkers for cancer diagnosis which result in less false positives.
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Bailly C, Vergoten G. Interaction of obtusilactone B and related butanolide lactones with the barrier-to-autointegration factor 1 (BAF1). A computational study. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100059. [PMID: 34909681 PMCID: PMC8663951 DOI: 10.1016/j.crphar.2021.100059] [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: 08/16/2021] [Revised: 09/08/2021] [Accepted: 09/20/2021] [Indexed: 11/06/2022] Open
Abstract
The barrier-to-autointegration factor 1 (BAF1) protein is a DNA-binding protein implicated in nuclear envelop repair and reformation after mitosis. This nuclear protein is frequently overexpressed in cancer cells and plays a role in the occurrence and development of different tumors. It is a potential therapeutic target for gastric cancer, breast cancer and other malignancies. For this reason, BAF1 inhibitors are searched. The butanolide lactone obtusilactone B (Ob-B) has been found to inhibit VRK1-dependent phosphorylation of BAF1, upon direct binding to the nuclear protein. Taking advantage of the known crystallographic structure of BAF1, we have elaborated molecular models of Ob-B bound to BAF1 to delimit the binding site and binding configuration. The long endoolefinic alkyl side chain of Ob-B extends into a small groove on the protein surface, and the adjacent exomethylene-γ-lactone moiety occupies a pocket comprising to the Ser-4 phosphorylation site of BAF1. Twenty butanolide lactones structurally close to ObB were screened for BAF1 binding. Several natural products with BAF1-binding capacity potentially superior to Ob-B were identified, including mahubanolide, kotomolide B, epilitsenolide D2, and a few other known anticancer plant natural products. Our study provides new ideas to guide the discovery and design of BAF1 inhibitors. Obtusilactone B (Ob-B) is an anticancer inhibitor of VRK1-mediated BAF1 phosphorylation. Molecular models of Ob-B bound to BAF1 have been constructed and the binding site determined. Screening of 20 butanolide lactones led to the identification of new potential BAF1 binders. Mahubanolide, kotomolide B and epilitsenolide D2 emerge as potential BAF1 inhibitors.
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Affiliation(s)
| | - Gérard Vergoten
- University of Lille, Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, 3 rue du Professeur Laguesse, BP-83, F-59006, Lille, France
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Shi J, Bao M, Wang W, Wu X, Li Y, Zhao C, Liu W. Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer. Front Immunol 2021; 12:722807. [PMID: 34646265 PMCID: PMC8503557 DOI: 10.3389/fimmu.2021.722807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 (PLOD3) is related to a variety of human diseases. However, its function in Colorectal cancer (CRC) remains uncertain. PLOD3 expression was analyzed using The Cancer Genome Atlas (TCGA) pan-cancer data. DAVID was used for enrichment analysis of PLOD3-related genes. The correlation between PLOD3 expression and immune cell infiltration was evaluated. Four expression profile datasets (GSE17536, GSE39582, GSE74602, and GSE113513) from Gene Expression Omnibus, and two proteomic datasets were used as validation cohorts for assessing the diagnostic and prognostic value of PLOD3 in CRC. What's more, we performed immunohistochemistry (IHC) staining for PLOD3 in 160 paired CRC specimens and corresponding adjacent non-tumor tissues. PLOD3 was highly expressed in many tumors including CRC. PLOD3 was upregulated in advanced stage CRCs, and high PLOD3 expression was associated with poor survival. High PLOD3 expression was associated with low levels of B cells, CD4+ T cells, M1 macrophages, CD8+ T cells, and multiple immunerelated characteristics. In addition, the high PLOD3 expression group had a higher TIDE score and a lower tumor mutation burden and microsatellite instability, indicating that patients with high PLOD3 expression may be resistant to immunotherapy. Additional datasets and IHC analysis were used to validate the diagnostic and prognostic value of PLOD3 at the mRNA and protein levels in CRC. Patients with non-response to immunotherapy showed increased PLOD3 expression in an immunotherapy treated dataset. PLOD3 is a potential biomarker for CRC diagnosis and prognosis prediction. CRCs with high PLOD3 expression may be resistant to immune checkpoint therapy.
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Affiliation(s)
- Junhong Shi
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Meiyu Bao
- Department of Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Weifeng Wang
- Department of Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Xuan Wu
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yueying Li
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changdong Zhao
- Department of Gastroenterology, Second People's Hospital of Lianyungang City, Lianyungang, China
| | - Weiwei Liu
- Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
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Zhang Y, Pan M, Li CY, Li JY, Ge W, Xu L, Xiao Y. Exploration of the typical features of tubulovillous adenoma using in-depth quantitative proteomics analysis. Bioengineered 2021; 12:6831-6843. [PMID: 34585630 PMCID: PMC8806592 DOI: 10.1080/21655979.2021.1971036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This present study aimed to explore the typical protein features of tubulovillous adenoma (TVA) using proteomic and bioinformatic analyses. Tandem mass tag (TMT)-based quantitative proteomic analyses were conducted on normal mucosa, tubular adenoma, TVA and adenocarcinoma tissues. We identified 5,665 proteins categorized into seven clusters based on Pearson’s correlation analysis. The bioinfomatic analysis showed mitochondrial and metabolism-related events were typical characteristics of TVA and mitochondrial-, ribosome- and matrisome-related biological processes may contribute to carcinogenesis. PLOD3 was identified as a key protein associated with the malignant potential of TVA and promoted the viability of adenoma organoids. The Cancer Genome Atlas (TCGA) analysis revealed PLOD3 as a risk factor for disease-free and overall survival. Furthermore, the PLOD3 expression correlated negatively with the abundance of B cells, CD8 + T cells, CD4 + T cells, neutrophils, macrophages and myeloid dendritic cells. In conclusion, enhanced metabolic and mitochondrial reprogramming are typical features of TVA, and PLOD3 might be related to the “immune desert” phenotype and contribute to TVA tumorigenesis and colorectal cancer development.
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Affiliation(s)
- Yin Zhang
- Department of General Surgery, Division of Colorectal Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Pan
- State Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Chun-Yuan Li
- State Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jing-Ying Li
- State Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Wei Ge
- State Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lai Xu
- Department of General Surgery, Division of Colorectal Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Xiao
- Department of General Surgery, Division of Colorectal Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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PLOD3 Is Associated with Immune Cell Infiltration and Genomic Instability in Colon Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4714526. [PMID: 34239923 PMCID: PMC8235962 DOI: 10.1155/2021/4714526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) are a family of enzymes. However, the clinical and functional roles of PLOD3 in colon adenocarcinoma (COAD) have not been investigated. The present study found that PLOD3 was highly upregulated in COAD, which may be resulted from its aberrant DNA methylation. The upregulation of both PLOD3 mRNA and protein was confirmed in our tissue samples. Moreover, high PLOD3 was identified to be associated with unfavorable prognosis in COAD. As genome instability is a hallmark of cancer, PLOD3 was expressed higher in COAD samples with high chromosomal instability (CIN-high) than those with low CIN (CIN-low) and higher in those with low MSI than high MSI, indicating that PLOD3 expression was associated with tumor genomic instability. Furthermore, immune cells showed significantly different infiltrating levels between the high and low PLOD3 expression groups, and the immune score was negatively correlated with PLOD3 expression and higher in samples with low PLOD3 expression, suggesting that high PLOD3 expression was associated with reduced immune cell infiltrating levels in COAD. To further uncover the underlying mechanism of PLOD3 in PLOD3, we compared the COAD samples of high PLOD3 expression with those of low PLOD3 expression and found that high expression of PLOD3 was associated with reduced expression of immune regulators and enhanced activities of two tumor-promoting pathways, including gluconeogenesis and TGF-beta signaling in epithelial-mesenchymal transition (EMT), suggesting that high expression of PLOD3 causes poor prognosis in COAD by weakening the immune cell infiltration and enhancing activities of tumor-promoting pathways. In summary, the present study highlights the importance of PLOD3 and provides the evidence about the functional role of PLOD3 in COAD.
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36
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Gao S, Wang Z. Comprehensive Analysis of Regulatory Network for LINC00472 in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:3533608. [PMID: 34221297 PMCID: PMC8211516 DOI: 10.1155/2021/3533608] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Renal cell carcinoma (RCC) accounts for about 2% to 3% of adult malignancies, and clear cell renal cell carcinoma (ccRCC) is the most common and aggressive type of kidney cancer. It accounts for 75% of all kidney tumors. Although new targeted drugs continue to appear, they are still not suitable for all patients. Therefore, an in-depth study of the molecular mechanism of the development of ccRCC and exploration of new targets for the treatment of ccRCC will help to achieve precise treatment for ccRCC. With the development of molecular research, the study of long noncoding RNA (LncRNA) has given us a new understanding of tumors. Although LncRNA does not encode proteins, it directly interacts with proteins in various signaling pathways and affects cell functions. Therefore, it is of great significance to study the mechanism of LncRNA in ccRCC. The expression level of Linc00472 in ccRCC tissues is significantly lower than adjacent normal tissues, and its low expression is closely related to Furman's high grade. The low expression of Linc00472 is associated with poor prognosis in patients with ccRCC. The results of protein interaction and functional enrichment analysis indicate that genes upregulated in renal clear cell carcinoma may play a major role. Analysis of target gene prediction results showed that Linc00472 may be used as ceRNA in the miR-24-3p-HLA-DPB1 pathway, miR-24-3p-CXCL9 pathway, miR-221-3p-C3aR1-VEGFR2 pathway, miR-17-5p-HLA-DQA1/HLA-DQB1 pathway, and miR-17-5p-C3aR1/C5aR1-VEGFR2 pathway which play important functions. In addition, the regulatory relationship between miR-24-3p and TNFR2 (TNFRSF1B), CD36, and COL4A1 should also be noted. The value of Linc00472 in the diagnosis and treatment of ccRCC is worthy of further study.
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Affiliation(s)
- Shuoze Gao
- Institute of Gansu Nephro-Urological Clinical Center, Department of Urology, Institute of Urology, Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhiping Wang
- Institute of Gansu Nephro-Urological Clinical Center, Department of Urology, Institute of Urology, Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
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Guo T, Gu C, Li B, Xu C. PLODs are overexpressed in ovarian cancer and are associated with gap junctions via connexin 43. J Transl Med 2021; 101:564-569. [PMID: 33483598 DOI: 10.1038/s41374-021-00533-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) play important roles in cancer progression, but their role in ovarian cancer remains elusive. In silico analysis of expression of PLODs in ovarian cancer was performed with reproduction of The Cancer Genome Atlas dataset. PLOD-enriched pathways and related gene(s) were validated by immunohistochemistry (IHC) in 80 ovarian cancer tissue blocks and in vivo xenograft murine models. PLODs (PLOD-1, -2, and -3) were overexpressed in ovarian cancer tissue. Overexpression of individual PLODs showed mutual exclusivity. Each of the three PLODs was differentially expressed between normal and cancer tissue of the ovary. PLOD1 was not prognostic, whereas lower PLOD2 and higher PLOD3 expression were associated with worsened prognosis, respectively. Cases with PLOD overexpression showed enrichment in gap junctions. GJA1 (connexin 43) was significantly overexpressed in cases with PLOD overexpression. IHC in tissue showed the strongest positive correlation between PLOD3 and connexin 43 expression, followed by PLOD2. As per Harmonizome, we selected SKOV3 and CAOV3 cell lines based on constitutive high PLOD1 and PLOD2/PLOD3 expression, respectively for in vitro and in vivo modeling. Only knockdown of PLOD3 was significantly associated with decreased GJA1 expression level in both cell lines. IHC in murine xenograft tumors also showed significantly lower connexin 43 in PLOD3-KD SKOV3 tumors. We conclude that PLODs are generally overexpressed in ovarian cancer and each PLOD may be functionally non-redundant. Association between PLOD3 and gap junctions warrants further investigation.
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Affiliation(s)
- Ting Guo
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Rd, Shanghai, 200011, PR China
| | - Chao Gu
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Rd, Shanghai, 200011, PR China
| | - Bin Li
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Rd, Shanghai, 200011, PR China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Rd, Shanghai, 200011, PR China.
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Epigallocatechin-3-Gallate Alleviates High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease via Inhibition of Apoptosis and Promotion of Autophagy through the ROS/MAPK Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5599997. [PMID: 33953830 PMCID: PMC8068552 DOI: 10.1155/2021/5599997] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 12/18/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) represents one of the most common chronic liver diseases in the world. It has been reported that epigallocatechin-3-gallate (EGCG) plays important biological and pharmacological roles in mammalian cells. Nevertheless, the mechanism underlying the beneficial effect of EGCG on the progression of NAFLD has not been fully elucidated. In the present study, the mechanisms of action of EGCG on the growth, apoptosis, and autophagy were examined using oleic acid- (OA-) treated liver cells and the high-fat diet- (HFD-) induced NAFLD mouse model. Administration of EGCG promoted the growth of OA-treated liver cells. EGCG could reduce mitochondrial-dependent apoptosis and increase autophagy possibly via the reactive oxygen species- (ROS-) mediated mitogen-activated protein kinase (MAPK) pathway in OA-treated liver cells. In line with in vitro findings, our in vivo study verified that treatment with EGCG attenuated HFD-induced NAFLD through reduction of apoptosis and promotion of autophagy. EGCG can alleviate HFD-induced NAFLD possibly by decreasing apoptosis and increasing autophagy via the ROS/MAPK pathway. EGCG may be a promising agent for the treatment of NAFLD.
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Abstract
The extracellular matrix is a fundamental, core component of all tissues and organs, and is essential for the existence of multicellular organisms. From the earliest stages of organism development until death, it regulates and fine-tunes every cellular process in the body. In cancer, the extracellular matrix is altered at the biochemical, biomechanical, architectural and topographical levels, and recent years have seen an exponential increase in the study and recognition of the importance of the matrix in solid tumours. Coupled with the advancement of new technologies to study various elements of the matrix and cell-matrix interactions, we are also beginning to see the deployment of matrix-centric, stromal targeting cancer therapies. This Review touches on many of the facets of matrix biology in solid cancers, including breast, pancreatic and lung cancer, with the aim of highlighting some of the emerging interactions of the matrix and influences that the matrix has on tumour onset, progression and metastatic dissemination, before summarizing the ongoing work in the field aimed at developing therapies to co-target the matrix in cancer and cancer metastasis.
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Affiliation(s)
- Thomas R Cox
- The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.
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Ding J, Li C, Cheng Y, Du Z, Wang Q, Tang Z, Song C, Xia Q, Bai W, Lin L, Liu W, Xu L, Li E, Wu B. Alterations of RNA splicing patterns in esophagus squamous cell carcinoma. Cell Biosci 2021; 11:36. [PMID: 33563334 PMCID: PMC7871539 DOI: 10.1186/s13578-021-00546-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 01/29/2021] [Indexed: 02/05/2023] Open
Abstract
Alternative splicing (AS) is an important biological process for regulating the expression of various isoforms from a single gene and thus to promote proteome diversity. In this study, RNA-seq data from 15 pairs of matched esophageal squamous cell carcinoma (ESCC) and normal tissue samples as well as two cell lines were analyzed. AS events with significant differences were identified between ESCC and matched normal tissues, which were re-annotated to find protein coding genes or non-coding RNAs. A total of 45,439 AS events were found. Of these, 6019 (13.25%) significant differentially AS events were identified. Exon skipping (SE) events occupied the largest proportion of abnormal splicing events. Fifteen differential splicing events with the same trends of ΔΨ values in ESCC tissues, as well in the two cell lines were found. Four pathways and 20 biological processes related to pro-metastasis cell junction and migration were significantly enriched for the differentially spliced genes. The upregulated splicing factor SF3B4, which regulates 92 gene splicing events, could be a potential prognostic factor of ESCC. Differentially spliced genes, including HNRNPC, VCL, ZNF207, KIAA1217, TPM1 and CALD1 are shown with a sashimi plot. These results suggest that cell junction- and migration-related biological processes are influenced by AS abnormalities, and aberrant splicing events can be affected by splicing factor expression changes. The involved splicing factor SF3B4 was found to be a survival-related gene in ESCC and is presumed to regulate AS in multiple cancers. In summary, we identified significant differentially expressed AS events which may be related to the development of ESCC.
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Affiliation(s)
- Jiyu Ding
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Chunquan Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Yinwei Cheng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Zepeng Du
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, 515041, China
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Zhidong Tang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Chao Song
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Qiaoxi Xia
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Wenjing Bai
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Ling Lin
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Wei Liu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, China
| | - Enmin Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
| | - Bingli Wu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
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Zhao Y, Zhang X, Yao J. Comprehensive analysis of PLOD family members in low-grade gliomas using bioinformatics methods. PLoS One 2021; 16:e0246097. [PMID: 33503035 PMCID: PMC7840023 DOI: 10.1371/journal.pone.0246097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/13/2021] [Indexed: 12/20/2022] Open
Abstract
Low-grade gliomas (LGGs) is a primary invasive brain tumor that grows slowly but is incurable and eventually develops into high malignant glioma. Novel biomarkers for the tumorigenesis and lifetime of LGG are critically demanded to be investigated. In this study, the expression levels of procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) were analyzed by ONCOMINE, HPA and GEPIA. The GEPIA online platform was applied to evaluate the interrelation between PLODs and survival index in LGG. Furthermore, functions of PLODs and co-expression genes were inspected by the DAVID. Moreover, we used TIMER, cBioportal, GeneMINIA and NetworkAnalyst analysis to reveal the mechanism of PLODs in LGG. We found that expression levels of each PLOD family members were up-regulated in patients with LGG. Higher expression of PLODs was closely related to shorter disease-free survival (DFS) and overall survival (OS). The findings showed that LGG cases with or without alterations were significantly correlated with the OS and DFS. The mechanism of PLODs in LGG may be involved in response to hypoxia, oxidoreductase activity, Lysine degradation and immune cell infiltration. In general, this research has investigated the values of PLODs in LGG, which could serve as biomarkers for diagnosis, prognosis and potential therapeutic targets of LGG patients.
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Affiliation(s)
- Yonghui Zhao
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
- * E-mail:
| | - Xiang Zhang
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
| | - Junchao Yao
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
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Integrated bioinformatic analysis of RNA binding proteins in hepatocellular carcinoma. Aging (Albany NY) 2020; 13:2480-2505. [PMID: 33411682 PMCID: PMC7880356 DOI: 10.18632/aging.202281] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
RNA binding proteins (RBPs) are aberrantly expressed in a tissue-specific manner across many tumors. These proteins, which play a vital role in post-transcriptional gene regulation, are involved in RNA splicing, maturation, transport, stability, degradation, and translation. We set out to establish an accurate risk score model based on RBPs to estimate prognosis in hepatocellular carcinoma (HCC). RNA-sequencing data, proteomic data and corresponding clinical information were acquired from the Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database respectively. We identified 406 differentially expressed RBPs between HCC tumor and normal tissues at the transcriptional and protein level. Overall, 11 RBPs (BRIX1, DYNC1H1, GTPBP4, PRKDC, RAN, RBM19, SF3B4, SMG5, SPATS2, TAF9, and THOC5) were selected to establish a risk score model. We divided HCC patients into low-risk and high-risk groups based on the median of risk score values. The survival analysis indicated that patients in the high-risk group had poorer overall survival compared to patients in the low-risk group. Our study demonstrated that 11 RBPs were associated with the overall survival of HCC patients. These RBPs may represent potential drug targets and can help optimize future clinical treatment.
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Wu D, Zhong P, Wang Y, Zhang Q, Li J, Liu Z, Ji A, Li Y. Hydrogen Sulfide Attenuates High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease by Inhibiting Apoptosis and Promoting Autophagy via Reactive Oxygen Species/Phosphatidylinositol 3-Kinase/AKT/Mammalian Target of Rapamycin Signaling Pathway. Front Pharmacol 2020; 11:585860. [PMID: 33390956 PMCID: PMC7774297 DOI: 10.3389/fphar.2020.585860] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver disease worldwide. Hydrogen sulfide (H2S) is involved in a wide range of physiological and pathological processes. Nevertheless, the mechanism of action of H2S in NAFLD development has not been fully clarified. Here, the reduced level of H2S was observed in liver cells treated with oleic acid (OA). Administration of H2S increased the proliferation of OA-treated cells. The results showed that H2S decreased apoptosis and promoted autophagy through reactive oxygen species (ROS)-mediated phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) cascade in OA-treated cells. In addition, administration of H2S relieved high-fat diet (HFD)-induced NAFLD via inhibition of apoptosis and promotion of autophagy. These findings suggest that H2S could ameliorate HFD-induced NAFLD by regulating apoptosis and autophagy through ROS/PI3K/AKT/mTOR signaling pathway. Novel H2S-releasing donors may have therapeutic potential for the treatment of NAFLD.
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Affiliation(s)
- Dongdong Wu
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,School of Stomatology, Henan University, Kaifeng, China
| | - Peiyu Zhong
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Yizhen Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Qianqian Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Jianmei Li
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Zhengguo Liu
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Ailing Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Yanzhang Li
- School of Basic Medical Sciences, Henan University, Kaifeng, China.,Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
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Recent Discoveries on the Involvement of Krüppel-Like Factor 4 in the Most Common Cancer Types. Int J Mol Sci 2020; 21:ijms21228843. [PMID: 33266506 PMCID: PMC7700188 DOI: 10.3390/ijms21228843] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Krüppel-like factor 4 (KLF4) is a transcription factor highly conserved in evolution. It is particularly well known for its role in inducing pluripotent stem cells. In addition, KLF4 plays many roles in cancer. The results of most studies suggest that KLF4 is a tumor suppressor. However, the functioning of KLF4 is regulated at many levels. These include regulation of transcription, alternative splicing, miRNA, post-translational modifications, subcellular localization, protein stability and interactions with other molecules. Simple experiments aimed at assaying transcript levels or protein levels fail to address this complexity and thus may deliver misleading results. Tumor subtypes are also important; for example, in prostate cancer KLF4 is highly expressed in indolent tumors where it impedes tumor progression, while it is absent from aggressive prostate tumors. KLF4 is important in regulating response to many known drugs, and it also plays a role in tumor microenvironment. More and more information is available about upstream regulators, downstream targets and signaling pathways associated with the involvement of KLF4 in cancer. Furthermore, KLF4 performs critical function in the overall regulation of tissue homeostasis, cellular integrity, and progression towards malignancy. Here we summarize and analyze the latest findings concerning this fascinating transcription factor.
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Xiao S, Tang H, Bai Y, Zou R, Ren Z, Wu X, Shi Z, Lan S, Liu W, Wu T, Zhang C, Wang L. Swertiamarin suppresses proliferation, migration, and invasion of hepatocellular carcinoma cells <em>via</em> negative regulation of FRAT1. Eur J Histochem 2020; 64. [PMID: 33131270 PMCID: PMC7586251 DOI: 10.4081/ejh.2020.3169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023] Open
Abstract
Studies have shown that swertiamarin (STM) has multiple biological activities, but its anti-tumour effects and molecular mechanisms are still unclear. The present research aimed to validate the STM's impacts on the proliferation, migration, and invasion of hepatocellular carcinoma (HCC) cells, and to study its potential mechanism. Two HCC cell lines were treated with STM. Tumour growth was observed by the mouse tumour xenografts model. HCC cell lines stably expressing T-cell lymphomas 1 (FRAT1) were generated by lentivirusmediated overexpression. Cell viability, proliferation, migration, and invasion were observed using Cell Counting Kit-8 (CCK8), the xCELLigence Real-Time Cell Analyzer system (RTCA), and transwell analysis, respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting were used to observe the expression of FRAT1 and proteins related to the Wnt/β-catenin signalling pathway. Tumour growth was inhibited by STM in vivo. STM suppressed the proliferation, migration, and invasion of HCC cells. STM negatively regulated FRAT1 expression, whereas overexpressed FRAT1 blocked the anti-tumour function of STM. The results revealed that STM suppressed the FRAT1/Wnt/β-catenin signalling pathway. The findings of this study provide new insights into investigation of therapeutic strategies against HCC.
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Affiliation(s)
- Shufeng Xiao
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming; Department of General Surgery, Puer People's Hospital, Puer.
| | - Haoren Tang
- Department of Gastroenterological Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming.
| | - Yao Bai
- School of Medicine, Yunnan University, Kunming.
| | - Renchao Zou
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming 2Department of General Surgery, Puer People's Hospital, Puer.
| | - Zongfang Ren
- Department of Critical Care Medicine, the Second Affiliated Hospital of Kunming Medical University, Kunming.
| | - Xuesong Wu
- Department of Gastroenterological Surgery, the Second Affiliated Hospital of Kunming Medical University.
| | - Zhitian Shi
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming.
| | - Song Lan
- Department of Pathology, Puer People's Hospital, Puer.
| | - Wei Liu
- Department of Hepatobiliary Surgery, The People's Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong.
| | - Tiangen Wu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming.
| | - Cheng Zhang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming.
| | - Lin Wang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, Kunming.
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Yang B, Zhao Y, Wang L, Zhao Y, Wei L, Chen D, Chen Z. Identification of PLOD Family Genes as Novel Prognostic Biomarkers for Hepatocellular Carcinoma. Front Oncol 2020; 10:1695. [PMID: 33014843 PMCID: PMC7509443 DOI: 10.3389/fonc.2020.01695] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/30/2020] [Indexed: 12/23/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignancies with rising incidence and persistently high mortality. Previous researches have demonstrated that some PLOD family members are associated with tumor progression and metastasis in most human cancers. However, the prognostic and biological roles of PLODs in HCC remain largely unknown. Methods ONCOMINE, HPA, UALCAN, GEPIA, cBioPortal, GeneMANIA, NetworkAnalyst, Metascape, DAVID 6.8, and TIMER were used to determine the prognostic values and biological function of PLOD family members in HCC. Results The mRNA and protein expression patterns of PLOD family members were noticeably upregulated in HCC compared to normal tissue. The high expression levels of PLOD1 and PLOD2 genes were significantly correlated with higher tumor grades in HCC patients. In addition, the high expression levels of PLOD1–3 were remarkably associated with poor overall survival in HCC patients, while high PLOD1 and PLOD3 expression were markedly associated with worse disease-free survival. In the co-expression gene analysis, 20 genes were primarily associated with the differentially expressed PLOD family members in HCC cases. Through functional enrichment analysis, the biological functions of PLODs in HCC were mainly involved in collagen fibril organization, lysine degradation, collagen biosynthesis, and modifying enzymes. Furthermore, the expression levels of PLOD1–3 were positively correlated with the activities of tumor-infiltrating immune cells, including macrophages, neutrophils, CD4+ T cells, and dendritic cells. Besides, the expression levels of PLOD2 and PLOD3 were positively correlated with the infiltrating levels of B cells. Conclusion The findings of this study could provide novel insights into the identification of prognostic biomarkers for HCC patients.
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Affiliation(s)
- Bo Yang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Public Health, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yonghui Zhao
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, China
| | - Lan Wang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhao
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Public Health, Chinese Academy of Medical Sciences, Wuhan, China
| | - Lai Wei
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Public Health, Chinese Academy of Medical Sciences, Wuhan, China
| | - Dong Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Public Health, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhishui Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Public Health, Chinese Academy of Medical Sciences, Wuhan, China
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Lv J, He Y, Li L, Wang Z. Alternative Splicing Events and Splicing Factors Are Prognostic in Adrenocortical Carcinoma. Front Genet 2020; 11:918. [PMID: 33101358 PMCID: PMC7494975 DOI: 10.3389/fgene.2020.00918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/23/2020] [Indexed: 01/22/2023] Open
Abstract
Alternative splicing is involved in the pathogenesis of human diseases, including cancer. Here, we investigated the potential application of alternative splicing events (ASEs) and splicing factors (SFs) in the prognosis of adrenocortical carcinoma (ACC). Transcriptome data from 79 ACC cases were downloaded from The Cancer Genome Atlas database, and percent spliced-in values of seven splicing types were downloaded from The Cancer Genome Atlas SpliceSeq database. By the univariate Cox regression analysis, 1,839 survival-related ASEs were identified. Prognostic indices based on seven types of survival-related ASEs were calculated by multivariate Cox regression analysis. Survival curves and receiver operating characteristic curves were used to assess the diagnostic value of the prognostic model. Independent prognosis analysis identified several ASEs (e.g., THNSL2| 54469| ME) that could be used as biomarkers to predict the prognosis of patients with ACC accurately. By analyzing the co-expression correlation between SFs and ASEs, 188 highly correlated interactions were established. From the protein interaction network, we finally screened six hub SFs, including YBX1, SART1, PRCC, SNRPG, SNRPE, and SF3B4, whose expression levels were significantly related to the overall survival and prognosis of ACC. Our findings provide a reliable model for predicting the prognosis of ACC patients based on aberrant alternative splicing patterns.
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Affiliation(s)
- Jian Lv
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan He
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lili Li
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhihua Wang
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
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48
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Liang TT, Shao Q, Deng ZC, Wang T, Kang QZ. Systemic Expression Analysis Reveals Prognostic Significance of WIPI3 in Hepatocellular Carcinoma. Front Genet 2020; 11:847. [PMID: 32973867 PMCID: PMC7468542 DOI: 10.3389/fgene.2020.00847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/13/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction WD repeat domain phosphoinositide-interacting protein 3 (WIPI3) is a member of the WIPI protein family, autophagy marker, that is associated with the malignant progression of various human cancers, but its role in hepatocellular carcinoma (HCC) is still unclear. Materials and Methods Firstly, we collected the mRNA expression of WIPI3 in HCC through the platform of Oncomine, as well as the DNA copy number variations (CNVs), and verified it on human HCC cell line and the GEO database. Then, the subgroups and prognosis of HCC were performed by the UALCAN web tool. The mutation of WIPI3 was analyzed by cBioPortal. The coexpression of WIPI3 in HCC was identified from the LinkedOmics database, and function enrichment analysis was done using the LinkFinder module in LinkedOmics. Coexpression gene network was constructed through the STRING database, and the MCODE plug-in of which was used to build the gene modules; both of them were visualized by the Cytoscape software. Finally, the top modular genes in the same patient cohort were constructed through data mining in The Cancer Genome Atlas (TCGA) liver hepatocellular carcinoma (LIHC) by using the UCSC Xena browser. Results The results indicated that WIPI3 was frequently overexpressed in HCC, which could lead to a poor prognosis through the Kaplan-Meier (KM) analysis. Moreover, there existed mutations of WIPI3 in HCC, and the prognosis of WIPI3-altered group was significantly poor based on KM plotter data. Coexpression analysis showed that the coexpression gene of WIPI3 was associated with cell cycle and spliceosome. Further analysis suggested that WIPI3 and eukaryotic translation initiation factor 4A3 (EIF4A3) coordinately regulated the cancer cell cycle by spliceosome as a result of the strong positive correlation between them. Conclusion In summary, WIPI3 is constantly overexpressed in HCC tissues, resulting in a poor prognosis; therefore, we can identify it as an effective target for the treatment of HCC.
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Affiliation(s)
- Tao-Tao Liang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qi Shao
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhi-Chao Deng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ting Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiao-Zhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Hu Z, Dong L, Li S, Li Z, Qiao Y, Li Y, Ding J, Chen Z, Wu Y, Wang Z, Huang S, Gao Q, Zhao Y, He X. Splicing Regulator p54 nrb /Non-POU Domain-Containing Octamer-Binding Protein Enhances Carcinogenesis Through Oncogenic Isoform Switch of MYC Box-Dependent Interacting Protein 1 in Hepatocellular Carcinoma. Hepatology 2020; 72:548-568. [PMID: 31815296 DOI: 10.1002/hep.31062] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS Alternative splicing (AS) is a key step that increases the diversity and complexity of the cancer transcriptome. Recent evidence has highlighted that AS has an increasingly crucial role in cancer. Nonetheless, the mechanisms underlying AS and its dysregulation in hepatocellular carcinoma (HCC) remain elusive. Here, we report that the expression of RNA-binding protein p54nrb /non-POU domain-containing octamer-binding protein (NONO) is frequently increased in patients with HCC and is associated with poor outcomes. APPROACH AND RESULTS Knockdown of NONO significantly abolished liver cancer cell proliferation, migration, and tumor formation. RNA-sequencing revealed that NONO regulates MYC box-dependent interacting protein 1 (or bridging integrator 1 [BIN1]; also known as amphiphysin 2 3P9) exon 12a splicing. In the normal liver, BIN1 generates a short isoform (BIN1-S) that acts as a tumor suppressor by inhibiting the binding of c-Myc to target gene promoters. In HCC, NONO is highly up-regulated and produces a long isoform (BIN1-L, which contains exon 12a) instead of BIN1-S. High levels of BIN1-L promote carcinogenesis by binding with the protein polo-like kinase 1 to enhance its stability through the prevention of ubiquitin/proteasome-dependent cullin 3 degradation. Further analysis revealed that NONO promotes BIN1 exon 12a inclusion through interaction with DExH-box helicase 9 (DHX9) and splicing factor proline and glutamine-rich (SFPQ). Notably, frequent coexpression of DHX9-NONO-SFPQ is observed in patients with HCC. CONCLUSIONS Taken together, our findings identify the DHX9-NONO-SFPQ complex as a key regulator manipulating the oncogenic splicing switch of BIN1 and as a candidate therapeutic target in liver cancer.
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Affiliation(s)
- Zhixiang Hu
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liangqing Dong
- Key Laboratory of Carcinogenesis and Cancer Invasion, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Ministry of Education, Fudan University, Shanghai, China
| | - Shengli Li
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhe Li
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yejun Qiao
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuchen Li
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie Ding
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yangjun Wu
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen Wang
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiang Gao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Ministry of Education, Fudan University, Shanghai, China
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Centers, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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50
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Cho HJ, Baek GO, Seo CW, Ahn HR, Sung S, Son JA, Kim SS, Cho SW, Jang JW, Nam SW, Cheong JY, Eun JW. Exosomal microRNA-4661-5p-based serum panel as a potential diagnostic biomarker for early-stage hepatocellular carcinoma. Cancer Med 2020; 9:5459-5472. [PMID: 32537885 PMCID: PMC7402848 DOI: 10.1002/cam4.3230] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Currently, a reliable serum biomarker for hepatocellular carcinoma (HCC) has not been established, particularly for early-stage HCC (single tumor < 2 cm). We aimed to investigate diagnostic serum exosomal microRNA (exo-miR) panel for early-stage HCC. Driver oncogenic miR (onco-miR) candidates were selected by integrative analysis of miR expression profiles from three different RNA sequencing datasets of human HCC. Expressions of selected onco-miRs in serum exosome were measured using quantitative real-time PCR. Diagnostic performances of serum exo-miRs for HCC were evaluated in the test cohort (N = 24) and validation cohort (N = 144). Serum exo-miR panels were developed using a logistic regression model, and their diagnostic performance was evaluated. Six promising driver onco-miRs, including miR-25-3p, miR-140-3p, miR-423-3p, miR-1269a, miR-4661-5p, and miR-4746-5p, were identified by integrative analysis of three different RNA sequencing datasets. Among the six candidates, four serum exo-miRs (miR-25-3p, miR-1269a, miR-4661-5p, and miR-4746-5p) showed promising performance in the test cohort with area under the receiving operator curve (AUROC) >0.8. In our validation study, serum exo-miR-4661-5p could diagnose HCC in all stages (AUROC = 0.917), even in early stage (AUROC = 0.923), with a greater accuracy than other candidate serum exo-miRs and serum AFP. The panel composed of exo-miR-4661-5p and exo-miR-4746-5p was identified as the most accurate biomarker for early-stage HCC (AUROC = 0.947, 95% confidence interval = 0.889-0.980, sensitivity = 81.8%, and specificity = 91.7%). In conclusion, exo-miR-4661-5p-based serum panel is a promising diagnostic marker for early-stage HCC.
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Affiliation(s)
- Hyo Jung Cho
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Geum Ok Baek
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Chul Won Seo
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
- Department of Biomedical SciencesAjou University Graduate School of MedicineSuwonSouth Korea
| | - Hye Ri Ahn
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
- Department of Biomedical SciencesAjou University Graduate School of MedicineSuwonSouth Korea
| | - Suna Sung
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
- Department of Biomedical SciencesAjou University Graduate School of MedicineSuwonSouth Korea
| | - Ju A Son
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Soon Sun Kim
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Sung Won Cho
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Jeong Won Jang
- Department of Internal MedicineCollege of MedicineThe Catholic University of KoreaSeoulKorea
- Liver Cirrhosis Clinical Research CenterSeoulKorea
| | - Suk Woo Nam
- Department of PathologyCollege of MedicineThe Catholic University of KoreaSeoulRepublic of Korea
- Functional RNomics Research CenterThe Catholic University of KoreaSeoulRepublic of Korea
- Department of Biomedicine & Health SciencesGraduate School of MedicineThe Catholic University of KoreaSeoulRepublic of Korea
| | - Jae Youn Cheong
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
| | - Jung Woo Eun
- Department of GastroenterologyAjou University School of MedicineSuwonSouth Korea
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