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Audu CO, Wolf SJ, Joshi AD, Moon JY, Melvin WJ, Sharma SB, Davis FM, Obi AT, Wasikowski R, Tsoi LC, Barrett EC, Mangum KD, Bauer TM, Kunkel SL, Moore BB, Gallagher KA. Histone demethylase JARID1C/KDM5C regulates Th17 cells by increasing IL-6 expression in diabetic plasmacytoid dendritic cells. JCI Insight 2024; 9:e172959. [PMID: 38912581 DOI: 10.1172/jci.insight.172959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Plasmacytoid dendritic cells (pDCs) are first responders to tissue injury, where they prime naive T cells. The role of pDCs in physiologic wound repair has been examined, but little is known about pDCs in diabetic wound tissue and their interactions with naive CD4+ T cells. Diabetic wounds are characterized by increased levels of inflammatory IL-17A cytokine, partly due to increased Th17 CD4+ cells. This increased IL-17A cytokine, in excess, impairs tissue repair. Here, using human tissue and murine wound healing models, we found that diabetic wound pDCs produced excess IL-6 and TGF-β and that these cytokines skewed naive CD4+ T cells toward a Th17 inflammatory phenotype following cutaneous injury. Further, we identified that increased IL-6 cytokine production by diabetic wound pDCs is regulated by a histone demethylase, Jumonji AT-rich interactive domain 1C histone demethylase (JARID1C). Decreased JARID1C increased IL-6 transcription in diabetic pDCs, and this process was regulated upstream by an IFN-I/TYK2/JAK1,3 signaling pathway. When inhibited in nondiabetic wound pDCs, JARID1C skewed naive CD4+ T cells toward a Th17 phenotype and increased IL-17A production. Together, this suggests that diabetic wound pDCs are epigenetically altered to increase IL-6 expression that then affects T cell phenotype. These findings identify a therapeutically manipulable pathway in diabetic wounds.
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Affiliation(s)
- Christopher O Audu
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Sonya J Wolf
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amrita D Joshi
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jadie Y Moon
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - William J Melvin
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sriganesh B Sharma
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Frank M Davis
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrea T Obi
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rachel Wasikowski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily C Barrett
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kevin D Mangum
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tyler M Bauer
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Steven L Kunkel
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Pathology, School of Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Beth B Moore
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katherine A Gallagher
- Section of Vascular Surgery, Department of Surgery, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Bajinka O, Ouedraogo SY, Golubnitschaja O, Li N, Zhan X. Energy metabolism as the hub of advanced non-small cell lung cancer management: a comprehensive view in the framework of predictive, preventive, and personalized medicine. EPMA J 2024; 15:289-319. [PMID: 38841622 PMCID: PMC11147999 DOI: 10.1007/s13167-024-00357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 06/07/2024]
Abstract
Energy metabolism is a hub of governing all processes at cellular and organismal levels such as, on one hand, reparable vs. irreparable cell damage, cell fate (proliferation, survival, apoptosis, malignant transformation etc.), and, on the other hand, carcinogenesis, tumor development, progression and metastazing versus anti-cancer protection and cure. The orchestrator is the mitochondria who produce, store and invest energy, conduct intracellular and systemically relevant signals decisive for internal and environmental stress adaptation, and coordinate corresponding processes at cellular and organismal levels. Consequently, the quality of mitochondrial health and homeostasis is a reliable target for health risk assessment at the stage of reversible damage to the health followed by cost-effective personalized protection against health-to-disease transition as well as for targeted protection against the disease progression (secondary care of cancer patients against growing primary tumors and metastatic disease). The energy reprogramming of non-small cell lung cancer (NSCLC) attracts particular attention as clinically relevant and instrumental for the paradigm change from reactive medical services to predictive, preventive and personalized medicine (3PM). This article provides a detailed overview towards mechanisms and biological pathways involving metabolic reprogramming (MR) with respect to inhibiting the synthesis of biomolecules and blocking common NSCLC metabolic pathways as anti-NSCLC therapeutic strategies. For instance, mitophagy recycles macromolecules to yield mitochondrial substrates for energy homeostasis and nucleotide synthesis. Histone modification and DNA methylation can predict the onset of diseases, and plasma C7 analysis is an efficient medical service potentially resulting in an optimized healthcare economy in corresponding areas. The MEMP scoring provides the guidance for immunotherapy, prognostic assessment, and anti-cancer drug development. Metabolite sensing mechanisms of nutrients and their derivatives are potential MR-related therapy in NSCLC. Moreover, miR-495-3p reprogramming of sphingolipid rheostat by targeting Sphk1, 22/FOXM1 axis regulation, and A2 receptor antagonist are highly promising therapy strategies. TFEB as a biomarker in predicting immune checkpoint blockade and redox-related lncRNA prognostic signature (redox-LPS) are considered reliable predictive approaches. Finally, exemplified in this article metabolic phenotyping is instrumental for innovative population screening, health risk assessment, predictive multi-level diagnostics, targeted prevention, and treatment algorithms tailored to personalized patient profiles-all are essential pillars in the paradigm change from reactive medical services to 3PM approach in overall management of lung cancers. This article highlights the 3PM relevant innovation focused on energy metabolism as the hub to advance NSCLC management benefiting vulnerable subpopulations, affected patients, and healthcare at large. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00357-5.
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Affiliation(s)
- Ousman Bajinka
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, University Hospital Bonn, Venusberg Campus 1, Rheinische Friedrich-Wilhelms-University of Bonn, 53127 Bonn, Germany
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
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Tong D, Tang Y, Zhong P. The emerging roles of histone demethylases in cancers. Cancer Metastasis Rev 2024; 43:795-821. [PMID: 38227150 DOI: 10.1007/s10555-023-10160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Modulation of histone methylation status is regarded as an important mechanism of epigenetic regulation and has substantial clinical potential for the therapy of diseases, including cancer and other disorders. The present study aimed to provide a comprehensive introduction to the enzymology of histone demethylases, as well as their cancerous roles, molecular mechanisms, therapeutic possibilities, and challenges for targeting them, in order to advance drug design for clinical therapy and highlight new insight into the mechanisms of these enzymes in cancer. A series of clinical trials have been performed to explore potential roles of histone demethylases in several cancer types. Numerous targeted inhibitors associated with immunotherapy, chemotherapy, radiotherapy, and targeted therapy have been used to exert anticancer functions. Future studies should evaluate the dynamic transformation of histone demethylases leading to carcinogenesis and explore individual therapy.
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Affiliation(s)
- Dali Tong
- Department of Urological Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| | - Ying Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China.
| | - Peng Zhong
- Department of Pathology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
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Picard LC, Rich FJ, Kenwright DN, Stevens AJ. Epigenetic changes associated with Bacillus Calmette-Guerin (BCG) treatment in bladder cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189123. [PMID: 38806074 DOI: 10.1016/j.bbcan.2024.189123] [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: 12/06/2023] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
Bacillus Calmette-Guérin (BCG) treatment for non-muscle invasive bladder cancer (NMIBC) is an established immunotherapeutic, however, a significant portion of patients do not respond to treatment. Despite extensive research into the therapeutic mechanism of BCG, gaps remain in our understanding. This review specifically focuses on the epigenomic contributions in the immune microenvironment, in the context of BCG treatment for NMIBC. We also summarise the current understanding of NMIBC epigenetic characteristics, and discuss how future targeted strategies for BCG therapy should incorporate epigenomic biomarkers in conjunction with genomic biomarkers.
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Affiliation(s)
- Lucy C Picard
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Fenella J Rich
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Diane N Kenwright
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand
| | - Aaron J Stevens
- University of Otago, Wellington, Department of Pathology and Molecular Medicine, Wellington 6021, New Zealand.
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Cui Z, Li Y, Lin Y, Zheng C, Luo L, Hu D, Chen Y, Xiao Z, Sun Y. Lactylproteome analysis indicates histone H4K12 lactylation as a novel biomarker in triple-negative breast cancer. Front Endocrinol (Lausanne) 2024; 15:1328679. [PMID: 38779451 PMCID: PMC11109423 DOI: 10.3389/fendo.2024.1328679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/28/2024] [Indexed: 05/25/2024] Open
Abstract
Objective The established link between posttranslational modifications of histone and non-histone lysine (K) residues in cell metabolism, and their role in cancer progression, is well-documented. However, the lactylation expression signature in triple-negative breast cancer (TNBC) remains underexplored. Methods We conducted a comprehensive lactylproteome profiling of eight pairs of TNBC samples and their matched adjacent tissues. This was achieved through 4-Dimensional label-free quantitative proteomics combined with lactylation analysis (4D-LFQP-LA). The expression of identified lactylated proteins in TNBC was detected using immunoblotting and immunohistochemistry (IHC) with specific primary antibodies, and their clinicopathological and prognostic significance was evaluated. Results Our analysis identified 58 lactylation sites on 48 proteins, delineating the protein lactylation alteration signature in TNBC. Bioinformatic and functional analyses indicated that these lactylated proteins play crucial roles in regulating key biological processes in TNBC. Notably, lactylation of lysine at position 12 (H4K12lac) in the histone H4 domain was found to be upregulated in TNBC. Further investigations showed a high prevalence of H4K12lac upregulation in TNBC, with positive rates of 93.19% (137/147) and 92.93% (92/99) in TNBC tissue chip and validation cohorts, respectively. H4K12lac expression correlated positively with Ki-67 and inversely with overall survival (OS) in TNBC (HR [hazard ratio] =2.813, 95%CI [credibility interval]: 1.242-6.371, P=0.0164), suggesting its potential as an independent prognostic marker (HR=3.477, 95%CI: 1.324-9.130, P=0.011). Conclusions Lactylation is a significant post-translational modification in TNBC proteins. H4K12lac emerges as a promising biomarker for TNBC, offering insights into the lactylation profiles of TNBC proteins and linking histone modifications to clinical implications in TNBC.
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Affiliation(s)
- Zhaolei Cui
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yanhong Li
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yingying Lin
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Chaoqiang Zheng
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Lingqing Luo
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Dan Hu
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yan Chen
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Zhenzhou Xiao
- Laboratory of Biochemistry and Molecular Biology Research, Department of Laboratory Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yang Sun
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
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Chen D, Cai B, Zhu Y, Ma Y, Yu X, Xiong J, Shen J, Tie W, Zhang Y, Guo F. Targeting histone demethylases JMJD3 and UTX: selenium as a potential therapeutic agent for cervical cancer. Clin Epigenetics 2024; 16:51. [PMID: 38576048 PMCID: PMC10993516 DOI: 10.1186/s13148-024-01665-3] [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: 12/09/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The intriguing connection between selenium and cancer resembles a captivating puzzle that keeps researchers engaged and curious. While selenium has shown promise in reducing cancer risks through supplementation, its interaction with epigenetics in cervical cancer remains a fascinating yet largely unexplored realm. Unraveling the intricacies of selenium's role and its interaction with epigenetic factors could unlock valuable insights in the battle against this complex disease. RESULT Selenium has shown remarkable inhibitory effects on cervical cancer cells in various ways. In in vitro studies, it effectively inhibits the proliferation, migration, and invasion of cervical cancer cells, while promoting apoptosis. Selenium also demonstrates significant inhibitory effects on human cervical cancer-derived organoids. Furthermore, in an in vivo study, the administration of selenium dioxide solution effectively suppresses the growth of cervical cancer tumors in mice. One of the mechanisms behind selenium's inhibitory effects is its ability to inhibit histone demethylases, specifically JMJD3 and UTX. This inhibition is observed both in vitro and in vivo. Notably, when JMJD3 and UTX are inhibited with GSK-J4, similar biological effects are observed in both in vitro and in vivo models, effectively inhibiting organoid models derived from cervical cancer patients. Inhibiting JMJD3 and UTX also induces G2/M phase arrest, promotes cellular apoptosis, and reverses epithelial-mesenchymal transition (EMT). ChIP-qPCR analysis confirms that JMJD3 and UTX inhibition increases the recruitment of a specific histone modification, H3K27me3, to the transcription start sites (TSS) of target genes in cervical cancer cells (HeLa and SiHa cells). Furthermore, the expressions of JMJD3 and UTX are found to be significantly higher in cervical cancer tissues compared to adjacent normal cervical tissues, suggesting their potential as therapeutic targets. CONCLUSIONS Our study highlights the significant inhibitory effects of selenium on the growth, migration, and invasion of cervical cancer cells, promoting apoptosis and displaying promising potential as a therapeutic agent. We identified the histone demethylases JMJD3 and UTX as specific targets of selenium, and their inhibition replicates the observed effects on cancer cell behavior. These findings suggest that JMJD3 and UTX could be valuable targets for selenium-based treatments of cervical cancer.
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Affiliation(s)
- Dezhi Chen
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
- The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Bo Cai
- The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China
- Jiangxi Maternal and Child Health Hospital, Nanchang, 330008, Jiangxi Province, China
| | - Yingying Zhu
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
| | - Yimin Ma
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
| | - Xiaoting Yu
- The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Jieqi Xiong
- Jiangxi Maternal and Child Health Hospital, Nanchang, 330008, Jiangxi Province, China
| | - Jiaying Shen
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
| | - Weiwei Tie
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
| | - Yisheng Zhang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China
| | - Fei Guo
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315100, Zhejiang Province, China.
- The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China.
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Wen X, Hou J, Chu Y, Liao G, Wu G, Fang S, Xiao S, Qiu L, Xiong L. Immunotherapeutic value of NUSAP1 associated with bladder cancer through a comprehensive analysis of 33 human cancer cases. Am J Cancer Res 2024; 14:959-978. [PMID: 38590423 PMCID: PMC10998758 DOI: 10.62347/bgae1505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
To investigate the correlation between nucleolar spindle-associated protein 1 (NUSAP1) and cancer immunotherapy across 33 different types of human cancers. We conducted an analysis of The Cancer Genome Atlas (TCGA) database to retrieve gene expression data and clinical characteristics for 33 different cancer types. The immunotherapy cohorts encompassed GSE67501, GSE78220, and IMvigor210. Relevant information was extracted from the gene expression repository. We assessed the prognostic significance of NUSAP1 by examining various clinical parameters. The single-sample gene-set enrichment analysis (ssGSEA) method was utilized to gauge NUSAP1 activity and to contrast NUSAP1 transcriptome and protein levels. We delved into the correlation between NUSAP1 and various immune processes and components to gain insights into NUSAP1's role. We also discussed coherent pathways associated with NUSAP1 signal transduction and its impact on immunotherapy biomarkers. To authenticate and validate the differential expression patterns of NUSAP1 in bladder tumor tissues versus normal bladder counterparts, we utilized Western blotting (WB), real-time quantitative polymerase chain reaction (RT-qPCR), and immunohistochemistry (IHC) techniques. NUSAP1 exhibits overexpression across a spectrum of malignancies, and its expression levels correlate with overall survival (OS), disease-specific survival, and tumor stage in specific cancer types. Furthermore, NUSAP1 expression is linked to mutations, methylation patterns, and immunotherapy responses in human cancers. Meanwhile, our experiments, involving WB, RT-qPCR, and IHC, consistently demonstrated significantly higher NUSAP1 expression in bladder tumor tissues compared to normal controls. Our study underscores the potential of NUSAP1 as a promising prognostic indicator and immunotherapeutic target for a range of malignant tumors.
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Affiliation(s)
- Xiangyang Wen
- Division of Urology, Department of Surgery, The Second People’s Hospital of Longgang DistrictShenzhen 518112, Guangdong, China
| | - Jian Hou
- Department of Urology, The First Affiliated Hospital of Kunming Medical UniversityKunming 650500, Yunnan, China
| | - Yuanqi Chu
- Department of Pathology, Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Guoqiang Liao
- Division of Urology, Department of Surgery, The Second People’s Hospital of Longgang DistrictShenzhen 518112, Guangdong, China
| | - Guoqing Wu
- Division of Urology, Department of Surgery, The University of Hongkong-Shenzhen HospitalShenzhen 518000, Guangdong, China
| | - Shaohong Fang
- Division of Urology, Department of Surgery, The Second People’s Hospital of Longgang DistrictShenzhen 518112, Guangdong, China
| | - Song Xiao
- Division of Urology, Department of Surgery, The Second People’s Hospital of Longgang DistrictShenzhen 518112, Guangdong, China
| | - Longlong Qiu
- Division of Urology, Department of Surgery, The Second People’s Hospital of Longgang DistrictShenzhen 518112, Guangdong, China
| | - Lin Xiong
- Division of Urology, Department of Surgery, The University of Hongkong-Shenzhen HospitalShenzhen 518000, Guangdong, China
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Zhang W, Yan Z, Peng J, Zhao S, Ran L, Yin H, Zhong D, Yang J, Ye J, Xu S. Magnetic resonance imaging and deoxyribonucleic acid methylation-based radiogenomic models for survival risk stratification of glioblastoma. Med Biol Eng Comput 2024; 62:853-864. [PMID: 38057447 DOI: 10.1007/s11517-023-02971-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023]
Abstract
Glioblastoma multiforme (GBM) is one of the deadliest tumours. This study aimed to construct radiogenomic prognostic models of glioblastoma overall survival (OS) based on magnetic resonance imaging (MRI) Gd-T1WI images and deoxyribonucleic acid (DNA) methylation-seq and to understand the related biological pathways. The ResNet3D-18 model was used to extract radiomic features, and Lasso-Cox regression analysis was utilized to establish the prognostic models. A nomogram was constructed by combining the radiogenomic features and clinicopathological variables. The DeLong test was performed to compare the area under the curve (AUC) of the models. We screened differentially expressed genes (DEGs) with original ribonucleic acid (RNA)-seq in risk stratification and used Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotations for functional enrichment analysis. For the 1-year OS models, the AUCs of the radiogenomic set, methylation set and deep learning set in the training cohort were 0.864, 0.804 and 0.787, and those in the validation cohort were 0.835, 0.768 and 0.651, respectively. The AUCs of the 0.5-, 1- and 2-year nomograms in the training cohort were 0.943, 0.861 and 0.871, and those in the validation cohort were 0.864, 0.885 and 0.805, respectively. A total of 245 DEGs were screened; functional enrichment analysis showed that these DEGs were associated with cell immunity. The survival risk-stratifying radiogenomic models for glioblastoma OS had high predictability and were associated with biological pathways related to cell immunity.
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Affiliation(s)
- Wentao Zhang
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Zikang Yan
- Department of Bioinformatics, the Basic Medical School of Chongqing Medical University, Chongqing, 400016, China
| | - Jian Peng
- The Center for Clinical Molecular Medical Detection, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Shan Zhao
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Longke Ran
- Department of Bioinformatics, the Basic Medical School of Chongqing Medical University, Chongqing, 400016, China
| | - Haoyang Yin
- Department of Neurosurgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Dong Zhong
- Department of Neurosurgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Junjun Yang
- Key Laboratory of Optoelectronic Technologyand, Systems of the Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Junyong Ye
- Key Laboratory of Optoelectronic Technologyand, Systems of the Ministry of Education, Chongqing University, Chongqing, 400044, China.
| | - Shengsheng Xu
- Department of Radiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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Nardozza AM, Guarnera L, Travaglini S, Ottone T, Divona M, De Bellis E, Savi A, Banella C, Noguera NI, Di Fusco D, Monteleone I, Voso MT. Characterization of a novel IDH2-R159H mutation in acute myeloid leukaemia: Effects on cell metabolism and differentiation. Br J Haematol 2024; 204:719-723. [PMID: 38009542 DOI: 10.1111/bjh.19216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Affiliation(s)
- Anna Maria Nardozza
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Luca Guarnera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Mariadomenica Divona
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- UniCamillus-Saint Camillus International University of Health Sciences, Rome, Italy
| | - Eleonora De Bellis
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
- SC Ematologia, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Arianna Savi
- Department of clinical and biological sciences, University of Turin, Turin, Italy
| | - Cristina Banella
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Nelida Ines Noguera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Davide Di Fusco
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
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10
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Xiang K, Kunin M, Larafa S, Busch M, Dünker N, Jendrossek V, Matschke J. α-Ketoglutarate supplementation and NAD+ modulation enhance metabolic rewiring and radiosensitization in SLC25A1 inhibited cancer cells. Cell Death Discov 2024; 10:27. [PMID: 38225236 PMCID: PMC10789775 DOI: 10.1038/s41420-024-01805-x] [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: 07/18/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Metabolic rewiring is the result of the increasing demands and proliferation of cancer cells, leading to changes in the biological activities and responses to treatment of cancer cells. The mitochondrial citrate transport protein SLC25A1 is involved in metabolic reprogramming offering a strategy to induce metabolic bottlenecks relevant to radiosensitization through the accumulation of the oncometabolite D-2-hydroxyglutarate (D-2HG) upon SLC25A1 inhibition (SLC25A1i). Previous studies have revealed the comparative effects of SLC25A1i or cell-permeable D-2HG (octyl-D-2HG) treatments on DNA damage induction and repair, as well as on energy metabolism and cellular function, which are crucial for the long-term survival of irradiated cells. Here, α-ketoglutarate (αKG), the precursor of D-2HG, potentiated the effects observed upon SLC25A1i on DNA damage repair, cell function and long-term survival in vitro and in vivo, rendering NCI-H460 cancer cells more vulnerable to ionizing radiation. However, αKG treatment alone had little effect on these phenotypes. In addition, supplementation with nicotinamide (NAM), a precursor of NAD (including NAD+ and NADH), counteracted the effects of SLC25A1i or the combination of SLC25A1i with αKG, highlighting a potential importance of the NAD+/NADH balance on cellular activities relevant to the survival of irradiated cancer cells upon SLC25A1i. Furthermore, inhibition of histone lysine demethylases (KDMs), as a major factor affected upon SLC25A1i, by JIB04 treatment alone or in combination with αKG supplementation phenocopied the broad effects on mitochondrial and cellular function induced by SLC25A1i. Taken together, αKG supplementation potentiated the effects on cellular processes observed upon SLC25A1i and increased the cellular demand for NAD to rebalance the cellular state and ensure survival after irradiation. Future studies will elucidate the underlying metabolic reprogramming induced by SLC25A1i and provide novel therapeutic strategies for cancer treatment.
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Affiliation(s)
- Kexu Xiang
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
- Department of Gastroenterology, Chongqing University Cancer Hospital, 400030, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, 400030, Chongqing, China
| | - Mikhail Kunin
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Safa Larafa
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Maike Busch
- Center for Translational Neuro- and Behavioral Sciences, Institute of Anatomy II, Department of Neuroanatomy, Medical Faculty, University of Duisburg-Essen, 45147, Essen, Germany
| | - Nicole Dünker
- Center for Translational Neuro- and Behavioral Sciences, Institute of Anatomy II, Department of Neuroanatomy, Medical Faculty, University of Duisburg-Essen, 45147, Essen, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
- German Cancer Consortium (DKTK) partner site Essen a partnership between DKFZ and University Hospital, Essen, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
- German Cancer Consortium (DKTK) partner site Essen a partnership between DKFZ and University Hospital, Essen, Germany.
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11
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Yu F, Li L, Gu Y, Wang S, Zhou L, Cheng X, Jiang H, Huang Y, Zhang Y, Qian W, Li X, Liu Z. Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression. Mol Med 2024; 30:9. [PMID: 38216914 PMCID: PMC10785505 DOI: 10.1186/s10020-023-00775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Lysine demethylase 5C (KDM5C) has been implicated in the development of several human cancers. This study aims to investigate the role of KDM5C in the progression of colorectal cancer (CRC) and explore the associated molecular mechanism. METHODS Bioinformatics tools were employed to predict the target genes of KDM5C in CRC. The expression levels of KDM5C and prefoldin subunit 5 (PFDN5) in CRC cells were determined by RT-qPCR and western blot assays. The interaction between KDM5C, H3K4me3, and PFDN5 was validated by chromatin immunoprecipitation. Expression and prognostic values of KDM5C and PFDN5 in CRC were analyzed in a cohort of 72 patients. The function of KDM5C/PFDN5 in c-Myc signal transduction was analyzed by luciferase assay. Silencing of KDM5C and PFDN5 was induced in CRC cell lines to analyze the cell malignant phenotype in vitro and tumorigenic activity in nude mice. RESULTS KDM5C exhibited high expression, while PFDN5 displayed low expression in CRC cells and clinical CRC samples. High KDM5C levels correlated with poor survival and unfavorable clinical presentation, whereas elevated PFDN5 correlated with improved patient outcomes. KDM5C mediated demethylation of H3K4me3 on the PFDN5 promoter, suppressing its transcription and thereby enhancing the transcriptional activity of c-Myc. KDM5C knockdown in CRC cells suppressed cell proliferation, migration and invasion, epithelial-mesenchymal transition, and tumorigenic activity while increasing autophagy and apoptosis rates. However, the malignant behavior of cells was restored by the further silencing of PFDN5. CONCLUSION This study demonstrates that KDM5C inhibits PFDN5 transcription, thereby activating c-Myc signal transduction and promoting CRC progression.
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Affiliation(s)
- Fulong Yu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Liang Li
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Yimei Gu
- Emergency ICU, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui, People's Republic of China
| | - Song Wang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Lianbang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Xiaohu Cheng
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Heng Jiang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Yang Huang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Yingfeng Zhang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Wenbao Qian
- Department of Molecular Pathology, Hefei Da'an Medical Laboratory Co., Ltd., Hefei, 230012, Anhui, People's Republic of China
| | - Xianghua Li
- Department of Molecular Pathology, Hefei Da'an Medical Laboratory Co., Ltd., Hefei, 230012, Anhui, People's Republic of China.
| | - Zhining Liu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China.
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12
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Yan W, Hou N, Zheng J, Zhai W. Predictive genomic biomarkers of therapeutic effects in renal cell carcinoma. Cell Oncol (Dordr) 2023; 46:1559-1575. [PMID: 37223875 DOI: 10.1007/s13402-023-00827-4] [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] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND In recent years, there have been great improvements in the therapy of renal cell carcinoma. Nevertheless, the therapeutic effect varies significantly from person to person. To discern the effective treatment for different populations, predictive molecular biomarkers in response to target, immunological, and combined therapies are widely studied. CONCLUSION This review summarized those studies from three perspectives (SNPs, mutation, and expression level) and listed the relationship between biomarkers and therapeutic effect, highlighting the great potential of predictive molecular biomarkers in metastatic RCC therapy. However, due to a series of reasons, most of these findings require further validation.
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Affiliation(s)
- Weijie Yan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Naiqiao Hou
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junhua Zheng
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhai
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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13
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Edrei Y, Levy R, Kaye D, Marom A, Radlwimmer B, Hellman A. Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation. Genome Biol 2023; 24:264. [PMID: 38012713 PMCID: PMC10683314 DOI: 10.1186/s13059-023-03094-6] [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: 05/23/2022] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation. RESULTS In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. Under experimental conditions, DNA methylation induces enhancers to alter their enhancing effects or convert into silencers, while silencers are affected inversely. High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). Upon increased methylation of these units, their target-genes either increased or decreased in expression. Gene-enhancing and silencing units constitute cis-regulatory networks of genes. Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. Methylation variation in these sites effectively describe inter-patient expression variation and, compared with DNA sequence-alterations, appears as a major contributor of gene-expression variation among glioblastoma patients. CONCLUSIONS We describe complex cis-regulatory networks, which determine gene expression by summing the effects of positive and negative transcriptional inputs. In these networks, DNA methylation induces both enhancing and silencing effects, depending on the context. The revealed mechanism sheds light on the regulatory role of DNA methylation, explains inter-individual gene-expression variation, and opens the way for monitoring the driving forces behind deferential courses of cancer and other diseases.
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Affiliation(s)
- Yifat Edrei
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Revital Levy
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Daniel Kaye
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Anat Marom
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asaf Hellman
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel.
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14
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Singh S, Joshi V, Upadhyay A. Amyloids and brain cancer: molecular linkages and crossovers. Biosci Rep 2023; 43:BSR20230489. [PMID: 37335084 PMCID: PMC10548166 DOI: 10.1042/bsr20230489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023] Open
Abstract
Amyloids are high-order proteinaceous formations deposited in both intra- and extracellular spaces. These aggregates have tendencies to deregulate cellular physiology in multiple ways; for example, altered metabolism, mitochondrial dysfunctions, immune modulation, etc. When amyloids are formed in brain tissues, the endpoint often is death of neurons. However, interesting but least understood is a close connection of amyloids with another set of conditions in which brain cells proliferate at an extraordinary rate and form tumor inside brain. Glioblastoma is one such condition. Increasing number of evidence indicate a possible link between amyloid formation and depositions in brain tumors. Several proteins associated with cell cycle regulation and apoptotic pathways themselves have shown to possess high tendencies to form amyloids. Tumor suppressor protein p53 is one prominent example that mutate, oligomerize and form amyloids leading to loss- or gain-of-functions and cause increased cell proliferation and malignancies. In this review article, we present available examples, genetic links and common pathways that indicate that possibly the two distantly placed pathways: amyloid formation and developing cancers in the brain have similarities and are mechanistically intertwined together.
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Affiliation(s)
- Shalini Singh
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jheepasani, Jodhpur, Rajasthan 342001, India
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, U.S.A
| | - Vibhuti Joshi
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jheepasani, Jodhpur, Rajasthan 342001, India
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, Uttar Pradesh 201310, India
| | - Arun Upadhyay
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jheepasani, Jodhpur, Rajasthan 342001, India
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, U.S.A
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15
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Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
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Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
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16
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Tai R, Leng J, Li W, Wu Y, Yang J. Construction of the metabolic reprogramming-associated gene signature for clear cell renal cell carcinoma prognosis prediction. BMC Urol 2023; 23:147. [PMID: 37715154 PMCID: PMC10503121 DOI: 10.1186/s12894-023-01317-3] [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: 12/29/2022] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Metabolism reprogramming is a hallmark that associates tumor growth, metastasis, progressive, and poor prognosis. However, the metabolism-related molecular patterns and mechanism in clear cell renal cell carcinoma (ccRCC) remain unclear. Herein, the purpose of this study was to identify metabolism-related molecular pattern and to investigate the characteristics and prognostic values of the metabolism-related clustering. METHODS We comprehensively analyzed the differentially expressed genes (DEGs), and metabolism-related genes (MAGs) in ccRCC based on the TCGA database. Consensus clustering was used to construct a metabolism-related molecular pattern. Then, the biological function, molecular characteristics, Estimate/immune/stomal scores, immune cell infiltration, response to immunotherapy, and chemotherapy were analyzed. We also identified the DEGs between subclusters and constructed a poor signature and risk model based on LASSO regression cox analysis and univariable and multivariable cox regression analyses. Then, a predictive nomogram was constructed and validated by calibration curves. RESULTS A total of 1942 DEGs (1004 upregulated and 838 downregulated) between ccRCC tumor and normal samples were identified, and 254 MRGs were screened out from those DEGs. Then, 526 ccRCC patients were divided into two subclusters. The 7 metabolism-related pathways enriched in cluster 2. And cluster 2 with high Estimate/immune/stomal scores and poor survival. While, cluster 1 with higher immune cell infiltrating, expression of the immune checkpoint, IFN, HLA, immune activation-related genes, response to anti-CTLA4 treatment, and chemotherapy. Moreover, we identified 295 DEGs between two metabolism-related subclusters and constructed a 15-gene signature and 9 risk factors. Then, a risk score was calculated and the patients into high- and low-risk groups in TCGA-KIRC and E-MTAB-1980 datasets. And the prediction viability of the risk score was validated by ROC curves. Finally, the clinicopathological characteristics (age and stage), risk score, and molecular clustering, were identified as independent prognostic variables, and were used to construct a nomogram for 1-, 3-, 5-year overall survival predicting. The calibration curves were used to verify the performance of the predicted ability of the nomogram. CONCLUSION Our finding identified two metabolism-related molecular subclusters for ccRCC, which facilitates the estimation of response to immunotherapy and chemotherapy, and prognosis after treatment.
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Affiliation(s)
- Rongfen Tai
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Jinjun Leng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Wei Li
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Yuerong Wu
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Junfeng Yang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China.
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17
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Feitelson MA, Arzumanyan A, Medhat A, Spector I. Short-chain fatty acids in cancer pathogenesis. Cancer Metastasis Rev 2023; 42:677-698. [PMID: 37432606 PMCID: PMC10584782 DOI: 10.1007/s10555-023-10117-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/05/2023] [Indexed: 07/12/2023]
Abstract
Cancer is a multi-step process that can be viewed as a cellular and immunological shift away from homeostasis in response to selected infectious agents, mutations, diet, and environmental carcinogens. Homeostasis, which contributes importantly to the definition of "health," is maintained, in part by the production of short-chain fatty acids (SCFAs), which are metabolites of specific gut bacteria. Alteration in the composition of gut bacteria, or dysbiosis, is often a major risk factor for some two dozen tumor types. Dysbiosis is often characterized by diminished levels of SCFAs in the stool, and the presence of a "leaky gut," permitting the penetration of microbes and microbial derived molecules (e.g., lipopolysaccharides) through the gut wall, thereby triggering chronic inflammation. SCFAs attenuate inflammation by inhibiting the activation of nuclear factor kappa B, by decreasing the expression of pro-inflammatory cytokines such as tumor necrosis factor alpha, by stimulating the expression of anti-inflammatory cytokines such as interleukin-10 and transforming growth factor beta, and by promoting the differentiation of naïve T cells into T regulatory cells, which down-regulate immune responses by immunomodulation. SCFA function epigenetically by inhibiting selected histone acetyltransferases that alter the expression of multiple genes and the activity of many signaling pathways (e.g., Wnt, Hedgehog, Hippo, and Notch) that contribute to the pathogenesis of cancer. SCFAs block cancer stem cell proliferation, thereby potentially delaying or inhibiting cancer development or relapse by targeting genes and pathways that are mutated in tumors (e.g., epidermal growth factor receptor, hepatocyte growth factor, and MET) and by promoting the expression of tumor suppressors (e.g., by up-regulating PTEN and p53). When administered properly, SCFAs have many advantages compared to probiotic bacteria and fecal transplants. In carcinogenesis, SCFAs are toxic against tumor cells but not to surrounding tissue due to differences in their metabolic fate. Multiple hallmarks of cancer are also targets of SCFAs. These data suggest that SCFAs may re-establish homeostasis without overt toxicity and either delay or prevent the development of various tumor types.
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Affiliation(s)
- Mark A Feitelson
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA.
| | - Alla Arzumanyan
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Arvin Medhat
- Department of Molecular Cell Biology, Islamic Azad University Tehran North Branch, Tehran, 1975933411, Iran
| | - Ira Spector
- SFA Therapeutics, Jenkintown, PA, 19046, USA
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18
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Gruber E, Kats LM. The curious case of IDH mutant acute myeloid leukaemia: biochemistry and therapeutic approaches. Biochem Soc Trans 2023; 51:1675-1686. [PMID: 37526143 PMCID: PMC10586776 DOI: 10.1042/bst20230017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
Of the many genetic alterations that occur in cancer, relatively few have proven to be suitable for the development of targeted therapies. Mutations in isocitrate dehydrogenase (IDH) 1 and -2 increase the capacity of cancer cells to produce a normally scarce metabolite, D-2-hydroxyglutarate (2-HG), by several orders of magnitude. The discovery of the unusual biochemistry of IDH mutations spurred a flurry of activity that revealed 2-HG as an 'oncometabolite' with pleiotropic effects in malignant cells and consequences for anti-tumour immunity. Over the next decade, we learned that 2-HG dysregulates a wide array of molecular pathways, among them a large family of dioxygenases that utilise the closely related metabolite α-ketoglutarate (α-KG) as an essential co-substrate. 2-HG not only contributes to malignant transformation, but some cancer cells become addicted to it and sensitive to inhibitors that block its synthesis. Moreover, high 2-HG levels and loss of wild-type IDH1 or IDH2 activity gives rise to synthetic lethal vulnerabilities. Herein, we review the biology of IDH mutations with a particular focus on acute myeloid leukaemia (AML), an aggressive disease where selective targeting of IDH-mutant cells is showing significant promise.
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Affiliation(s)
- Emily Gruber
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Lev M. Kats
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
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19
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Guan J, Xu X, Qiu G, He C, Lu X, Wang K, Liu X, Li Y, Ling Z, Tang X, Liang Y, Tao X, Cheng B, Yang B. Cellular hierarchy framework based on single-cell/multi-patient sample sequencing reveals metabolic biomarker PYGL as a therapeutic target for HNSCC. J Exp Clin Cancer Res 2023; 42:162. [PMID: 37420300 DOI: 10.1186/s13046-023-02734-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/04/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND A growing body of research has revealed the connection of metabolism reprogramming and tumor progression, yet how metabolism reprogramming affects inter-patient heterogeneity and prognosis in head and neck squamous cell carcinoma (HNSCC) still requires further explorations. METHODS A cellular hierarchy framework based on metabolic properties discrepancy, METArisk, was introduced to re-analyze the cellular composition from bulk transcriptomes of 486 patients through deconvolution utilizing single-cell reference profiles from 25 primary and 8 metastatic HNSCC sample integration of previous studies. Machine learning methods were used to identify the correlations between metabolism-related biomarkers and prognosis. The functions of the genes screened out in tumor progression, metastasis and chemotherapy resistance were validated in vitro by cellular functional experiments and in vivo by xenograft tumor mouse model. RESULTS Incorporating the cellular hierarchy composition and clinical properties, the METArisk phenotype divided multi-patient cohort into two classes, wherein poor prognosis of METArisk-high subgroup was associated with a particular cluster of malignant cells with significant activity of metabolism reprogramming enriched in metastatic single-cell samples. Subsequent analysis targeted for phenotype differences between the METArisk subgroups identified PYGL as a key metabolism-related biomarker that enhances malignancy and chemotherapy resistance by GSH/ROS/p53 pathway, leading to poor prognosis of HNSCC. CONCLUSION PYGL was identified as a metabolism-related oncogenic biomarker that promotes HNSCC progression, metastasis and chemotherapy resistance though GSH/ROS/p53 pathway. Our study revealed the cellular hierarchy composition of HNSCC from the cell metabolism reprogramming perspective and may provide new inspirations and therapeutic targets for HNSCC in the future.
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Affiliation(s)
- Jiezhong Guan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xi Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guo Qiu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chong He
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoyue Lu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kang Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xinyu Liu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Yuanyuan Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Zihang Ling
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xuan Tang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Yujie Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xiaoan Tao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.
| | - Bo Yang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.
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20
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Qu L, Yin T, Zhao Y, Lv W, Liu Z, Chen C, Liu K, Shan S, Zhou R, Li X, Dong H. Histone demethylases in the regulation of immunity and inflammation. Cell Death Discov 2023; 9:188. [PMID: 37353521 DOI: 10.1038/s41420-023-01489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogens or danger signals trigger the immune response. Moderate immune response activation removes pathogens and avoids excessive inflammation and tissue damage. Histone demethylases (KDMs) regulate gene expression and play essential roles in numerous physiological processes by removing methyl groups from lysine residues on target proteins. Abnormal expression of KDMs is closely associated with the pathogenesis of various inflammatory diseases such as liver fibrosis, lung injury, and autoimmune diseases. Despite becoming exciting targets for diagnosing and treating these diseases, the role of these enzymes in the regulation of immune and inflammatory response is still unclear. Here, we review the underlying mechanisms through which KDMs regulate immune-related pathways and inflammatory responses. In addition, we also discuss the future applications of KDMs inhibitors in immune and inflammatory diseases.
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Affiliation(s)
- Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Tong Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yijin Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenting Lv
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ziqi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shigang Shan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaoqing Li
- Biological Targeted Therapy Key Laboratory in Hubei, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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21
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Matar M, Prince G, Hamati I, Baalbaky M, Fares J, Aoude M, Matar C, Kourie HR. Implication of KDM6A in bladder cancer. Pharmacogenomics 2023; 24:509-522. [PMID: 37458596 DOI: 10.2217/pgs-2023-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Background: Bladder cancer is a common urogenital malignancy characterized by frequent genetic alterations. Histone demethylase gene KDM6A is commonly mutated in bladder cancer. Aim: To review the characteristics of KDM6A and its mutation consequences, and to introduce a potential KDM6A-targeted treatment. Methods: We conducted a comprehensive literature search using two electronic databases, MEDLINE and Cochrane Library, to retrieve topic-related articles from July 2013 to July 2022 using keywords 'KDM6A', 'bladder cancer', 'UTX', 'treatment' and 'mutation'. Five reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted and 30 articles were retained. Main Results: A total of 30 articles were retrieved. Experimental and clinical data were collected and grouped by theme. Therapeutic strategies are depicted and organized by tables for a better understanding. Conclusion: This review demonstrates that KDM6A has crucial implications in bladder cancer pathogenesis and treatment.
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Affiliation(s)
- Marianne Matar
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Gilles Prince
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Ibrahim Hamati
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Maria Baalbaky
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Jonas Fares
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Marc Aoude
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
| | - Charbel Matar
- Division of Hematology-Oncology, Internal Medicine Department, George Washington University Hospital, 20037, Washington DC, USA
| | - Hampig Raphael Kourie
- Hematology-Oncology Department, Hotel Dieu De France Hospital, Saint Joseph University of Beirut, Riad El Solh, Lebanon
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22
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Guo H, Lu F, Lu R, Huang M, Li X, Yuan J, Wang F. A novel tumor 4-driver gene signature for the prognosis of hepatocellular carcinoma. Heliyon 2023; 9:e17054. [PMID: 37484410 PMCID: PMC10361245 DOI: 10.1016/j.heliyon.2023.e17054] [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: 01/11/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC), the main type of liver cancer, is the second most lethal tumor worldwide, with a 5-year survival rate of only 18%. Driver genes facilitate cancer cell growth and spread in the tumor microenvironment. Here, a comprehensive driver gene signature for the prognosis of HCC was developed. Methods HCC driver genes were analyzed comprehensively to develop a better prognostic signature. The dataset of HCC patients included mRNA sequencing data and clinical information from the TCGA, the ICGC, and the Guangxi Medical University Cancer Hospital cohorts. First, LASSO was performed to develop a prognostic signature for differentially expressed driver genes in the TCGA cohort. Then, the robustness of the signature was assessed using survival and time-dependent ROC curves. Furthermore, independent predictors were determined using univariate and multivariate Cox regression analyses. Stepwise multi-Cox regression analysis was employed to identify significant variables for the construction of a nomogram that predicts survival rates. Functional analysis by Spearman correlation analysis, enrichment analysis (GO, KEGG, and GSEA), and immunoassay (ssGSEA and xCell) were performed. Result A 4-driver gene signature (CLTC, DNMT3A, GMPS, and NRAS) was successfully constructed and showed excellent predictive efficiency in three cohorts. The nomogram indicated high predictive accuracy for the 1-, 3-, and 5-year prognoses of HCC patients, which included clinical information and risk score. Enrichment analysis revealed that driver genes were involved in regulating oncogenic processes, including the cell cycle and metabolic pathways, which were associated with the progression of HCC. ssGSEA and xCell showed differences in immune infiltration and the immune microenvironment between the two risk groups. Conclusion The 4-driver gene signature is closely associated with the survival prediction of HCC and is expected to provide new insights into targeted therapy for HCC patients.
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Affiliation(s)
- Houtian Guo
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Fei Lu
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Rongqi Lu
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Meiqi Huang
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Xuejing Li
- Department of Physiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Jianhui Yuan
- Department of Physics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Feng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
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23
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Ghazaryan A, Wallace JA, Tang WW, Barba C, Lee SH, Bauer KM, Nelson MC, Kim CN, Stubben C, Voth WP, Rao DS, O’Connell RM. miRNA-1 promotes acute myeloid leukemia cell pathogenesis through metabolic regulation. Front Genet 2023; 14:1192799. [PMID: 37229187 PMCID: PMC10203238 DOI: 10.3389/fgene.2023.1192799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous and deadly disease characterized by uncontrolled expansion of malignant blasts. Altered metabolism and dysregulated microRNA (miRNA) expression profiles are both characteristic of AML. However, there is a paucity of studies exploring how changes in the metabolic state of the leukemic cells regulate miRNA expression leading to altered cellular behavior. Here, we blocked pyruvate entry into mitochondria by deleting the Mitochondria Pyruvate Carrier (MPC1) gene in human AML cell lines, which decreased Oxidative Phosphorylation (OXPHOS). This metabolic shift also led to increased expression of miR-1 in the human AML cell lines tested. AML patient sample datasets showed that higher miR-1 expression correlates with reduced survival. Transcriptional and metabolic profiling of miR-1 overexpressing AML cells revealed that miR-1 increased OXPHOS, along with key metabolites that fuel the TCA cycle such as glutamine and fumaric acid. Inhibition of glutaminolysis decreased OXPHOS in miR-1 overexpressing MV4-11 cells, highlighting that miR-1 promotes OXPHOS through glutaminolysis. Finally, overexpression of miR-1 in AML cells exacerbated disease in a mouse xenograft model. Together, our work expands current knowledge within the field by uncovering novel connections between AML cell metabolism and miRNA expression that facilitates disease progression. Further, our work points to miR-1 as a potential new therapeutic target that may be used to disrupt AML cell metabolism and thus pathogenesis in the clinic.
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Affiliation(s)
- Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Jared A. Wallace
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - William W. Tang
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Cindy Barba
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Soh-Hyun Lee
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Kaylyn M. Bauer
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Morgan C. Nelson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Carissa N. Kim
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Chris Stubben
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Warren P. Voth
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Dinesh S. Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Ryan M. O’Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
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24
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Lovatel VL, Bueno AP, Kós EAAD, Meyer LGC, Ferreira GM, Kalonji MDF, Mello FVD, Milito CB, Costa ESD, Abdelhay E, Redondo MDT, Pombo-de-Oliveira MS, Fernandez TDS. A Novel Constitutional t(3;8)(p26;q21) and ANKRD26 and SRP72 Variants in a Child with Myelodysplastic Neoplasm: Clinical Implications. J Clin Med 2023; 12:jcm12093171. [PMID: 37176611 PMCID: PMC10179081 DOI: 10.3390/jcm12093171] [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: 03/20/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Childhood myelodysplastic neoplasm (cMDS) often raises concerns about an underlying germline predisposition, and its verification is necessary to guide therapeutic choice and allow family counseling. Here, we report a novel constitutional t(3;8)(p26;q21) in a child with MDS, inherited from the father, the ANKRD26 and SRP72 variants from the maternal origin, and the acquisition of molecular alterations during MDS evolution. CASE PRESENTATION A 4-year-old girl showed repeated infections and severe neutropenia. Bone marrow presented hypocellularity with dysplastic features. The patient had a t(3;8)(p26;q21)c identified by G-banding and FISH analysis. The family nucleus investigation identified the paternal origin of the chromosomal translocation. The NGS study identified ANKRD26 and SRP72 variants of maternal origin. CGH-array analysis detected alterations in PRSS3P2 and KANSL genes. Immunohistochemistry showed abnormal p53 expression during the MDS evolution. CONCLUSION This study shows for the first time, cytogenetic and genomic abnormalities inherited from the father and mother, respectively, and their clinical implications. It also shows the importance of investigating patients with constitutional cytogenetic alterations and/or germline variants to provide information to their family nucleus for genetic counseling and understanding of the pathogenesis of childhood MDS.
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Affiliation(s)
- Viviane Lamim Lovatel
- Cytogenetic Laboratory, Cell and Gene Therapy Program, Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, Brazil
| | - Ana Paula Bueno
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Pathology Department, Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil
| | - Elaiza Almeida Antônio de Kós
- Cytogenetic Laboratory, Cell and Gene Therapy Program, Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, Brazil
| | - Laura Guimarães Corrêa Meyer
- Outpatient Department, Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | - Gerson Moura Ferreira
- Stem Cell Laboratory, Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | - Mayara de Fátima Kalonji
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Fabiana Vieira de Mello
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Cristiane Bedran Milito
- Pathology Department, Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil
| | - Elaine Sobral da Costa
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Eliana Abdelhay
- Stem Cell Laboratory, Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | | | | | - Teresa de Souza Fernandez
- Cytogenetic Laboratory, Cell and Gene Therapy Program, Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, Brazil
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Liu P, Luo J, Tan N, Li C, Xu J, Yang X. Establishing a prognostic model of chromatin modulators and identifying potential drug candidates in renal clear cell patients. BMC Bioinformatics 2023; 24:104. [PMID: 36941564 PMCID: PMC10029171 DOI: 10.1186/s12859-023-05229-9] [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: 11/14/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Renal carcinoma is a common malignant tumor of the urinary system. Advanced renal carcinoma has a low 5-year survival rate and a poor prognosis. More and more studies have confirmed that chromatin regulators (CRs) can regulate the occurrence and development of cancer. This article investigates the functional and prognostic value of CRs in renal carcinoma patients. METHODS mRNA expression and clinical information were obtained from The Cancer Genome Atlas database. Univariate Cox regression analysis and LASSO regression analysis were used to select prognostic chromatin-regulated genes and use them to construct a risk model for predicting the prognosis of renal cancer. Differences in prognosis between high-risk and low-risk groups were compared using Kaplan-Meier analysis. In addition, we analyzed the relationship between chromatin regulators and tumor immune infiltration, and explored differences in drug sensitivity between risk groups. RESULTS We constructed a model consisting of 11 CRs to predict the prognosis of renal cancer patients. We not only successfully validated its feasibility, but also found that the 11 CR-based model was an independent prognostic factor. Functional analysis showed that CRs were mainly enriched in cancer development-related signalling pathways. We also found through the TIMER database that CR-based models were also associated with immune cell infiltration and immune checkpoints. At the same time, the genomics of drug sensitivity in cancer database was used to analyze the commonly used drugs of renal clear cell carcinoma patients. It was found that patients in the low-risk group were sensitive to medicines such as axitinib, pazopanib, sorafenib, and gemcitabine. In contrast, those in the high-risk group may be sensitive to sunitinib. CONCLUSION The chromatin regulator-related prognostic model we constructed can be used to assess the prognostic risk of patients with clear cell renal cell carcinoma. The results of this study can bring new ideas for targeted therapy of clear cell renal carcinoma, helping doctors to take corresponding measures in advance for patients with different risks.
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Affiliation(s)
- Puyu Liu
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Jihang Luo
- Department of Infectious Diseases, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Na Tan
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Chengfang Li
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Jieyu Xu
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China
| | - Xiaorong Yang
- Department of Clinical Pathology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi City, 563000, Guizhou Province, China.
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26
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Wang M, Yue S, Yang Z. Downregulation of PSAT1 inhibits cell proliferation and migration in uterine corpus endometrial carcinoma. Sci Rep 2023; 13:4081. [PMID: 36906716 PMCID: PMC10008565 DOI: 10.1038/s41598-023-31325-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/09/2023] [Indexed: 03/13/2023] Open
Abstract
Phosphoserine aminotransferase 1 (PSAT1) has been associated with the occurrence and development of various carcinomas; however, its function in uterine corpus endometrial carcinoma (UCEC) is unknown. We aimed to explore the relationship between PSAT1 and UCEC using The Cancer Genome Atlas database and functional experiments. PSAT1 expression levels in UCEC were employed using the paired sample t-test, Wilcoxon rank-sum test, the Clinical Proteomic Tumor Analysis Consortium database, and the Human Protein Atlas database, while survival curves were constructed using the Kaplan-Meier plotter. We performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to explore the possible functions and related pathways of PSAT1. Furthermore, single-sample gene set enrichment analysis was performed to detect the relationship between PSAT1 and tumor immune infiltration. StarBase and quantitative PCR were used to predict and verify the interactions between miRNAs and PSAT1. The Cell Counting Kit-8, EdU assay, clone formation assay, western blotting and flow cytometry were used to evaluate cell proliferation. Finally, Transwell and Wound healing assays were used to assess cell invasion and migration. Our study found that PSAT1 was significantly overexpressed in UCEC, and this high expression was associated with a worse prognosis. A high level of PSAT1 expression was associated with a late clinical stage and, histological type. In addition, the results of GO and KEGG enrichment analysis showed that PSAT1 was mainly involved in the regulation of cell growth, immune system and cell cycle in UCEC. In addition, PSAT1 expression was positively correlated with Th2 cells and negatively correlated with Th17 cells. Furthermore, we also found that miR-195-5P negatively regulated the expression of PSAT1 in UCEC. Finally, the knockdown of PSAT1 resulted in the inhibition of cell proliferation, migration, and invasion in vitro. Overall, PSAT1 was identified as a potential target for the diagnosis and immunotherapy of UCEC.
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Affiliation(s)
- Min Wang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Song Yue
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Zhu Yang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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Jin J, Xie Y, Zhang JS, Wang JQ, Dai SJ, He WF, Li SY, Ashby CR, Chen ZS, He Q. Sunitinib resistance in renal cell carcinoma: From molecular mechanisms to predictive biomarkers. Drug Resist Updat 2023; 67:100929. [PMID: 36739809 DOI: 10.1016/j.drup.2023.100929] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
Currently, renal cell carcinoma (RCC) is the most prevalent type of kidney cancer. Targeted therapy has replaced radiation therapy and chemotherapy as the main treatment option for RCC due to the lack of significant efficacy with these conventional therapeutic regimens. Sunitinib, a drug used to treat gastrointestinal tumors and renal cell carcinoma, inhibits the tyrosine kinase activity of a number of receptor tyrosine kinases, including vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), c-Kit, rearranged during transfection (RET) and fms-related receptor tyrosine kinase 3 (Flt3). Although sunitinib has been shown to be efficacious in the treatment of patients with advanced RCC, a significant number of patients have primary resistance to sunitinib or acquired drug resistance within the 6-15 months of therapy. Thus, in order to develop more efficacious and long-lasting treatment strategies for patients with advanced RCC, it will be crucial to ascertain how to overcome sunitinib resistance that is produced by various drug resistance mechanisms. In this review, we discuss: 1) molecular mechanisms of sunitinib resistance; 2) strategies to overcome sunitinib resistance and 3) potential predictive biomarkers of sunitinib resistance.
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Affiliation(s)
- Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China
| | - Yuhao Xie
- Institute for Biotechnology, St. John's University, Queens, NY 11439, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Jin-Shi Zhang
- Urology & Nephrology Center, Department of Nephrology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Shi-Jie Dai
- Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, Zhejiang 311258, China
| | - Wen-Fang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China
| | - Shou-Ye Li
- Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, Zhejiang 311258, China
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Zhe-Sheng Chen
- Institute for Biotechnology, St. John's University, Queens, NY 11439, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
| | - Qiang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China.
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Yang Y, Fu X, Liu R, Yan L, Yang Y. Exploring the prognostic value of HK3 and its association with immune infiltration in glioblastoma multiforme. Front Genet 2023; 13:1033572. [PMID: 36712881 PMCID: PMC9877303 DOI: 10.3389/fgene.2022.1033572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Hexokinase 3 (HK3) is one of the key enzymes involved in glucose phosphorylation (the first step in most glucose metabolic pathways). Many studies have demonstrated the vital role of dysregulation of HK3 in several tumors. However, there is a need for in-depth characterization of the role of HK3 in glioblastoma multiforme (GBM). Methods: All data were sourced from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA). Kaplan-Meier analysis and univariate regression were applied for survival analysis. Gene set enrichment analysis (GSEA) was used for enrichment analysis. Tumor Immune Single Cell Hub (TISCH) database was applied for single-cell analysis. Tumor Immune Dysfunction and Exclusion (TIDE) analysis was applied to evaluate the immune response. Results: HK3 expression was upregulated in GBM and correlated with poor prognosis. The high HK3 expression group was primarily enriched in adaptive immune response, chemokine signaling pathway, and cytokine-cytokine receptor interaction. The high HK3 expression group showed significantly greater enrichment of the majority of immune cells and immune-related pathways. HK3 showed significant correlation with most immune cells, especially macrophages (p < .001, R = .81). TISCH analysis showed that HK3 was predominantly expressed in macrophages in most cancers. HK3 showed significant correlation with most immune-related genes, such as PD-1 (p < .001, R = .41), PDL-1 (p < .001, R = .27), and CTLA-4 (p < .001, R = .29). TIDE analysis revealed that the low HK3 expression group has a lower TIDE score and may benefit from immunotherapy. Drug sensitivity analysis showed that patients with high HK3 expression frequently showed drug resistance. Conclusion: HK3 was associated with poor prognosis and may serve as a biomarker of macrophages in GBM. HK3 was also associated with immune response and drug resistance. Our findings may provide novel insights for GBM immunotherapy.
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Affiliation(s)
- Yuling Yang
- Department of Radiation Oncology, Shaanxi Provincial Cancer Hospital, Xi’an Medical University, Xi’an, China
| | - Xing Fu
- Department of Radiation Oncology, Ankang Central Hospital, Ankang, China
| | - Runsha Liu
- Department of Radiation Oncology, Shaanxi Provincial Cancer Hospital, Xi’an Medical University, Xi’an, China
| | - Lijuan Yan
- Department of Radiation Oncology, Shaanxi Provincial Cancer Hospital, Xi’an Medical University, Xi’an, China
| | - Yiping Yang
- Clinical Research Center for Shaanxi Provincial Radiotherapy, Department of Radiation Oncology, Shaanxi Provincial Cancer Hospital, Xi’an, China,*Correspondence: Yiping Yang,
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Liu WJ, Zhao Y, Chen X, Miao ML, Zhang RQ. Epigenetic modifications in esophageal cancer: An evolving biomarker. Front Genet 2023; 13:1087479. [PMID: 36704345 PMCID: PMC9871503 DOI: 10.3389/fgene.2022.1087479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Esophageal cancer is a widespread cancer of the digestive system that has two main subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EA). In the diverse range of cancer therapy schemes, the side effects of conventional treatments remain an urgent challenge to be addressed. Therefore, the pursuit of novel drugs with multiple targets, good efficacy, low side effects, and low cost has become a hot research topic in anticancer therapy. Based on this, epigenetics offers an attractive target for the treatment of esophageal cancer, where major mechanisms such as DNA methylation, histone modifications, non-coding RNA regulation, chromatin remodelling and nucleosome localization offer new opportunities for the prevention and treatment of esophageal cancer. Recently, research on epigenetics has remained at a high level of enthusiasm, focusing mainly on translating the basic research into the clinical setting and transforming epigenetic alterations into targets for cancer screening and detection in the clinic. With the increasing emergence of tumour epigenetic markers and antitumor epigenetic drugs, there are also more possibilities for anti-esophageal cancer treatment. This paper focuses on esophageal cancer and epigenetic modifications, with the aim of unravelling the close link between them to facilitate precise and personalized treatment of esophageal cancer.
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Affiliation(s)
- Wen-Jian Liu
- Department of Thoracic Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuan Zhao
- Department of Thoracic Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xu Chen
- School of Basic Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Man-Li Miao
- School of Basic Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ren-Quan Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China,*Correspondence: Ren-Quan Zhang,
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30
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Zhang K, Zhang C, Wang K, Teng X, Chen M. Identifying diagnostic markers and constructing a prognostic model for small-cell lung cancer based on blood exosome-related genes and machine-learning methods. Front Oncol 2022; 12:1077118. [PMID: 36620585 PMCID: PMC9814973 DOI: 10.3389/fonc.2022.1077118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background Small-cell lung cancer (SCLC) usually presents as an extensive disease with a poor prognosis at the time of diagnosis. Exosomes are rich in biological information and have a powerful impact on tumor progression and metastasis. Therefore, this study aimed to screen for diagnostic markers of blood exosomes in SCLC patients and to build a prognostic model. Methods We identified blood exosome differentially expressed (DE) RNAs in the exoRBase cohort and identified feature RNAs by the LASSO, Random Forest, and SVM-REF three algorithms. Then, we identified DE genes (DEGs) between SCLC tissues and normal lung tissues in the GEO cohort and obtained exosome-associated DEGs (EDEGs) by intersection with exosomal DEmRNAs. Finally, we performed univariate Cox, LASSO, and multivariate Cox regression analyses on EDEGs to construct the model. We then compared the patients' overall survival (OS) between the two risk groups and assessed the independent prognostic value of the model using receiver operating characteristic (ROC) curve analysis. Results We identified 952 DEmRNAs, 210 DElncRNAs, and 190 DEcircRNAs in exosomes and identified 13 feature RNAs with good diagnostic value. Then, we obtained 274 EDEGs and constructed a risk model containing 7 genes (TBX21, ZFHX2, HIST2H2BE, LTBP1, SIAE, HIST1H2AL, and TSPAN9). Low-risk patients had a longer OS time than high-risk patients. The risk model can independently predict the prognosis of SCLC patients with the areas under the ROC curve (AUCs) of 0.820 at 1 year, 0.952 at 3 years, and 0.989 at 5 years. Conclusions We identified 13 valuable diagnostic markers in the exosomes of SCLC patients and constructed a new promising prognostic model for SCLC.
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Shishido K, Reinders A, Asuthkar S. Epigenetic regulation of radioresistance: insights from preclinical and clinical studies. Expert Opin Investig Drugs 2022; 31:1359-1375. [PMID: 36524403 DOI: 10.1080/13543784.2022.2158810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Oftentimes, radiation therapy (RT) is ineffective due to the development of radioresistance (RR). However, studies have shown that targeting epigenetic modifiers to enhance radiosensitivity represents a promising direction of clinical investigation. AREAS COVERED This review discusses the mechanisms by which epigenetic modifiers alter radiosensitivity through dysregulation of MAPK-ERK and AKT-mTOR signaling. Finally, we discuss the clinical directions for targeting epigenetic modifiers and current radiology techniques used in the clinic. METHODOLOGY We searched PubMed and ScienceDirect databases from April 4th, 2022 to October 18th, 2022. We examined 226 papers related to radioresistance, epigenetics, MAPK, and PI3K/AKT/mTOR signaling. 194 papers were selected for this review. Keywords used for this search include, 'radioresistance,' 'radiosensitivity,' 'radiation,' 'radiotherapy,' 'particle radiation,' 'photon radiation,' 'epigenetic modifiers,' 'MAPK,' 'AKT,' 'mTOR,' 'cancer,' and 'PI3K.' We examined 41 papers related to clinical trials on the aforementioned topics. Outcomes of interest were safety, overall survival (OS), dose-limiting toxicities (DLT), progression-free survival (PFS), and maximum tolerated dose (MTD). EXPERT OPINION Current studies focusing on epigenetic mechanisms of RR strongly support the use of targeting epigenetic modifiers as adjuvants to standard cancer therapies. To further the success of such treatments and their clinical benefit , both preclinical and clinical studies are needed to broaden the scope of known radioresistant mechanisms.
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Affiliation(s)
- Katherine Shishido
- Department of Cancer Biology and Pharmacology and Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL, United States of America
| | - Alexis Reinders
- Department of Cancer Biology and Pharmacology and Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL, United States of America
| | - Swapna Asuthkar
- Department of Cancer Biology and Pharmacology and Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL, United States of America
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Zaman R, Islam RA, Chowdhury EH. Evolving therapeutic proteins to precisely kill cancer cells. J Control Release 2022; 351:779-804. [DOI: 10.1016/j.jconrel.2022.09.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/31/2022]
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022; 378:68-78. [PMID: 36201590 PMCID: PMC9926876 DOI: 10.1126/science.abj2890] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase (IDH)-mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1R132H-driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.
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Affiliation(s)
- Connor Yanchus
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristen L. Drucker
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas M. Kollmeyer
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
| | - Minggao Liang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Judy Pawling
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Silvana B. De Lorenzo
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asma Ali
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul A. Decker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Matt L. Kosel
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Arijit Panda
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lingyan Jiang
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jared W. L. Browning
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Chris Lowden
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Michael Geuenich
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J. Javier Hernandez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica T. Gosio
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Sampath Kumar Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jacob Berman
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Brittany Carson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lily Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Daniel J. Murphy
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, Scotland, UK
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, Scotland, UK
| | - Liguo Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - James W. Dennis
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Philipp G. Maass
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kieran Campbell
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniel H. Lachance
- Departments of Neurology and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Tak Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Taylor
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gelareh Zadeh
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peter Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Cristiane M. Ida
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Robert B. Jenkins
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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Zhang J, Lin H, Hou L, Xiao H, Gong X, Guo X, Cao X, Liu Z. Exploration of the breast ductal carcinoma in situ signature and its prognostic implications. Cancer Med 2022; 12:3758-3772. [PMID: 35880695 PMCID: PMC9939111 DOI: 10.1002/cam4.5071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 07/03/2022] [Indexed: 11/06/2022] Open
Abstract
Following the implementation of breast screening programs, the occurrence of ductal carcinoma in situ (DCIS) as an early type of neoplasia has increased. Although the prognosis is promising, 20%-50% of DCIS patients will progress to invasive ductal carcinoma (IDC) if not treated. It is essential to look for promising biomarkers for predicting DCIS prognosis. The Gene Expression Omnibus (GEO) database was used to explore the expression of genes that differed between DCIS and normal tissue in this investigation. Enrichment analysis was performed to characterize the biological role and intrinsic process pathway. The Cancer Genome Atlas Breast Cancer Dataset was used to categorize the hub genes, and the results were confirmed using the Cytoscape plugin CytoHubba and MCODE. The prognostic ability of the core gene signature was determined through time-dependent receiver operating characteristic (ROC), Kaplan-Meier survival curve, Oncomine databases, and UALCAN databases. In addition, the prognostic value of core genes was verified in proliferation assays. We identified 217 common differentially expressed genes (DEGs) in the present study, with 101 upregulated and 138 downregulated genes. The top genes were obtained from the PPI network (protein-protein interaction). A unique six-gene signature (containing GAPDH, CDH2, BIRC5, NEK2, IDH2, and MELK) was developed for DCIS prognostic prediction. Centered on the Cancer Genome Atlas (TCGA) cohort, the ROC curve showed strong results in prognosis prediction. The six core gene signatures is often overexpressed in DCIS, with a weak prognosis. Furthermore, when breast cancer cells are transfected with small interfering RNAs, downregulation of core gene expression substantially inhibits cell proliferation, revealing a high potential for employing core genes in DCIS prognosis. In conclusion, the current investigation verified the six core genes signatures for prospective DCIS biomarkers, which may aid clinical decision-making for individual care.
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Affiliation(s)
- Jiao Zhang
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
| | - Hui Lin
- The First Department of Breast CancerTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of EducationTianjinChina,Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical UniversityTaizhouChina
| | - Lei Hou
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
| | - Hui Xiao
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
| | - Xilong Gong
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
| | - Xuhui Guo
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
| | - Xuchen Cao
- The First Department of Breast CancerTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of EducationTianjinChina
| | - Zhenzhen Liu
- Department of Breast Disease, Henan Breast Cancer CenterAffiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouChina
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Sun Q, Wang H, Xiao B, Xue D, Wang G. Development and Validation of a 6-Gene Hypoxia-Related Prognostic Signature For Cholangiocarcinoma. Front Oncol 2022; 12:954366. [PMID: 35924146 PMCID: PMC9339701 DOI: 10.3389/fonc.2022.954366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022] Open
Abstract
Cholangiocarcinoma (CHOL) is highly malignant and has a poor prognosis. This study is committed to creating a new prognostic model based on hypoxia related genes. Here, we established a novel tumor hypoxia-related prognostic model consisting of 6 hypoxia-related genes by univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) algorithm to predict CHOL prognosis and then the risk score for each patient was calculated. The results showed that the patients with high-risk scores had poor prognosis compared with those with low-risk scores, which was verified as an independent predictor by multivariate analysis. The hypoxia-related prognostic model was validated in both TCGA and GEO cohorts and exhibited excellent performance in predicting overall survival in CHOL. The PPI results suggested that hypoxia-related genes involved in the model may play a central role in regulating the hypoxic state. In addition, the presence of IDH1 mutations in the high-risk group was high, and GSEA results showed that some metabolic pathways were upregulated, but immune response processes were generally downregulated. These factors may be potential reasons for the high-risk group with worse prognosis. The analysis of different immune regulation-related processes in the high- and low-risk groups revealed that the expression of genes related to immune checkpoints would show differences between these two groups. We further verified the expression of the oncogene PPFIA4 in the model, and found that compared with normal samples, CHOL patients were generally highly expressed, and the patients with high-expression of PPFIA4 had a poor prognosis. In summary, the present study may provide a valid prognostic model for bile duct cancer to inform better clinical management of patients.
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Affiliation(s)
- Qi Sun
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huxia Wang
- Mammary Department, Shaanxi Provincial Cancer Hospital, Xi’an, China
| | - Baoan Xiao
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Dong Xue
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Guanghui Wang
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Guanghui Wang,
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Pavlenko E, Ruengeler T, Engel P, Poepsel S. Functions and Interactions of Mammalian KDM5 Demethylases. Front Genet 2022; 13:906662. [PMID: 35899196 PMCID: PMC9309374 DOI: 10.3389/fgene.2022.906662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
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Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
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Glutamine Is Required for M1-like Polarization of Macrophages in Response to Mycobacterium tuberculosis Infection. mBio 2022; 13:e0127422. [PMID: 35762591 PMCID: PMC9426538 DOI: 10.1128/mbio.01274-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to Mycobacterium tuberculosis infection, macrophages mount proinflammatory and antimicrobial responses similar to those observed in M1 macrophages activated by lipopolysaccharide (LPS) and interferon gamma (IFN-γ). A metabolic reprogramming to hypoxia-inducible-factor 1 (HIF-1)-mediated uptake of glucose and its metabolism by glycolysis is required for M1-like polarization, but little is known about other metabolic programs driving the M1-like polarization during infection. We report that glutamine serves as a carbon and nitrogen source for the metabolic reprogramming to M1-like macrophages. Widely targeted metabolite screening identified an association of glutamine and/or glutamate with highly affected metabolic pathways of M1-like macrophages. Moreover, stable isotope-assisted metabolomics of U13C glutamine and U13C glucose revealed that glutamine, rather than glucose, is catabolized in both the oxidative and reductive tricarboxylic acid (TCA) cycles of M1-like macrophages, thereby generating signaling molecules that include succinate, biosynthetic precursors such as aspartate, and itaconate. U15N glutamine-tracing metabolomics further revealed participation of glutamine nitrogen in synthesis of intermediates of purine and pyrimidine metabolism plus amino acids, including aspartate. These findings were corroborated by diminished M1 polarization from chemical inhibition of glutaminase (GLS), the key enzyme in the glutaminolysis pathway, and by genetic deletion of GLS in infected macrophages. Thus, the catabolism of glutamine is an integral component of metabolic reprogramming in activating macrophages and it coordinates with elevated cytosolic glycolysis to satisfy the cellular demand for bioenergetic and biosynthetic precursors of M1-like macrophages. Knowledge of these new immunometabolic features of M1-like macrophages should advance the development of host-directed therapies for tuberculosis.
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Fan M, Shi H, Yao H, Wang W, Zhang Y, Jiang C, Lin R. Glutamate regulates gliosis of BMSCs to promote ENS regeneration through α-KG and H3K9/H3K27 demethylation. Stem Cell Res Ther 2022; 13:255. [PMID: 35715822 PMCID: PMC9205030 DOI: 10.1186/s13287-022-02936-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background There is a lack of effective therapies for enteric nervous system (ENS) injury. Our previous study showed that transplanted bone marrow-derived mesenchymal stem cells (BMSCs) play a “glia-like cells” role in initiating ENS regeneration in denervated mice. Cellular energy metabolism is an important factor in maintaining the biological characteristics of stem cells. However, how cellular energy metabolism regulates the fate of BMSCs in the ENS-injured microenvironment is unclear. Methods The biological characteristics, energy metabolism, and histone methylation levels of BMSCs following ENS injury were determined. Then, glutamate dehydrogenase 1 (Glud1) which catalyzes the oxidative deamination of glutamate to α-KG was overexpressed (OE) in BMSCs. Further, OE-Glud1 BMSCs were targeted–transplanted into the ENS injury site of denervated mice to determine their effects on ENS regeneration. Results In vitro, in the ENS-injured high-glutamate microenvironment, the ratio of α-ketoglutarate (α-KG) to succinate (P < 0.05), the histone demethylation level (P < 0.05), the protein expression of glial cell markers (P < 0.05), and the gene expression of Glud1 (P < 0.05) were significantly increased. And the binding of H3K9me3 to the GFAP, S100B, and GDNF promoter was enhanced (P < 0.05). Moreover, α-KG treatment increased the monomethylation and decreased the trimethylation on H3K9 (P < 0.01) and H3K27 (P < 0.05) in BMSCs and significantly upregulated the protein expression of glial cell markers (P < 0.01), which was reversed by the α-KG competitive inhibitor D-2-hydroxyglutarate (P < 0.05). Besides, overexpression of Glud1 in BMSCs exhibited increases in monomethylation and decreases in trimethylation on H3K9 (P < 0.05) and H3K27 (P < 0.05), and upregulated protein expression of glial cell markers (P < 0.01). In vivo, BMSCs overexpressing Glud1 had a strong promotion effect on ENS regeneration in denervated mice through H3K9/H3K27 demethylation (P < 0.05), and upregulating the expression of glial cell protein (P < 0.05). Conclusions BMSCs overexpressing Glud1 promote the expression of glial cell markers and ENS remodeling in denervated mice through regulating intracellular α-KG and H3K9/H3K27 demethylation. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02936-7.
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Affiliation(s)
- Mengke Fan
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Huiying Shi
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hailing Yao
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weijun Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yurui Zhang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chen Jiang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Liu C, Liu D, Wang F, Xie J, Liu Y, Wang H, Rong J, Xie J, Wang J, Zeng R, Xie Y. The Interferon Gamma-Related Long Noncoding RNA Signature Predicts Prognosis and Indicates Immune Microenvironment Infiltration in Colon Adenocarcinoma. Front Oncol 2022; 12:876660. [PMID: 35747790 PMCID: PMC9211770 DOI: 10.3389/fonc.2022.876660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 12/17/2022] Open
Abstract
Colon adenocarcinoma (COAD) is one of the most common clinically malignant tumours of the digestive system, with high incidence and mortality and poor prognosis. Interferon-gamma (IFN-γ) and long noncoding RNAs (lncRNAs) have prognostic values and were closely associated with immune microenvironment in COAD. Thus, identifying IFN-γ-related lncRNAs may be valuable in predicting the survival of patients with COAD. In this study, we identified IFN-γ-related lncRNAs and divided COAD patients from the Cancer Genome Atlas (TCGA) database into training and validation sets. Pearson’s correlation analysis and least absolute shrinkage and selection operator (LASSO) Cox regression were performed to select IFN-γ-related lncRNA-associated prognoses. Thirteen lncRNAs (AC025165.8, AC091633.3, FENDRR, LINC00882, LINC01828, LINC01829, MYOSLID, RP11-154H23.4, RP11-20J15.3, RP11-324L17.1, RP11-342A23.2, RP11-805I24.3, SERTAD4-AS1) were identified to construct an IFN-γ-related lncRNA prognostic signature in TCGA training (n =213) and validation (n =213) cohorts. COAD patient risk scores were calculated and classified into high- and low-risk groups based on the median value of the risk scores in each dataset. We compared the overall survival (OS) of patients stratified by age, gender, and stage. The OS in the high-risk group was significantly shorter than that in the low-risk group. In addition, the clinical nomogram incorporating the prognostic signature and clinical features showed a high concordance index of 0.78 and accurately predicted 1-, 3-, and 5-year survival times among COAD patients in the high- and low-risk groups. Based on the risk model, the high- and low-risk groups exhibited distinct differences in the immune system by gene set enrichment analysis (GSEA) functional annotation, and differentially expressed genes (DEGs) between the high- and low-risk groups were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We investigated the expression of multiple immune checkpoint genes in the high- and low-risk groups and plotted Kaplan-Meier survival curves, indicating that immune checkpoint genes, such as LAG3 and PD. L1, STING and TIM 3, were also expressed differently between the two risk groups. Subsequently, there were dramatic differences in mutated genes, SNV (single nucleotide variants) classes, variant types and variant allele frequencies between low- and high-risk patients with COAD. Patients stratified by risk scores had different sensitivities to common chemotherapeutic agents. Finally, we used quantitative real-time polymerase chain reaction (qRT-PCR) assays to demonstrate that three lncRNAs were significantly differentially expressed in COAD tissues and adjacent normal tissues. Considered together, a thirteen-lncRNA prognostic signature has great potential to be a prognostic biomarker and could play an essential role in the immune microenvironment of COAD.
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Affiliation(s)
- Cong Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Dingwei Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Fangfei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jun Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Yang Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Huan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jianfang Rong
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jinliang Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jinyun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Rong Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Yong Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
- *Correspondence: Yong Xie,
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The effects of Epigallocatechin-3-gallate and Dabrafenib combination on apoptosis and the genes involved in epigenetic events in anaplastic thyroid cancer cells. Med Oncol 2022; 39:98. [DOI: 10.1007/s12032-022-01688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/17/2022] [Indexed: 11/27/2022]
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Dai J, Reyimu A, Sun A, Duoji Z, Zhou W, Liang S, Hu S, Dai W, Xu X. Establishment of prognostic risk model and drug sensitivity based on prognostic related genes of esophageal cancer. Sci Rep 2022; 12:8008. [PMID: 35568702 PMCID: PMC9107481 DOI: 10.1038/s41598-022-11760-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
At present, the treatment of esophageal cancer (EC) is mainly surgical and drug treatment. However, due to drug resistance, these therapies can not effectively improve the prognosis of patients with the EC. Therefore, a multigene prognostic risk scoring system was constructed by bioinformatics analysis method to provide a theoretical basis for the prognosis and treatment decision of EC. The gene expression profiles and clinical data of esophageal cancer patients were gathered from the Cancer Genome Atlas TCGA database, and the differentially expressed genes (DEGs) were screened by R software. Genes with prognostic value were screened by Kaplan Meier analysis, followed by functional enrichment analysis. A cox regression model was used to construct the prognostic risk score model of DEGs. ROC curve and survival curve were utilized to evaluate the performance of the model. Univariate and multivariate Cox regression analysis was used to evaluate whether the model has an independent prognostic value. Network tool mirdip was used to find miRNAs that may regulate risk genes, and Cytoscape software was used to construct gene miRNA regulatory network. GSCA platform is used to analyze the relationship between gene expression and drug sensitivity. 41 DEGs related to prognosis were pre-liminarily screened by survival analysis. A prognostic risk scoring model composed of 8 DEGs (APOA2, COX6A2, CLCNKB, BHLHA15, HIST1H1E, FABP3, UBE2C and ERO1B) was built by Cox regression analysis. In this model, the prognosis of the high-risk score group was poor (P < 0.001). The ROC curve showed that (AUC = 0.862) the model had a good performance in predicting prognosis. In Cox regression analysis, the comprehensive risk score can be employed as an independent prognostic factor of the EC. HIST1H1E, UBE2C and ERO1B interacted with differentially expressed miRNAs. High expression of HIST1H1E was resistant to trametinib, selumetinib, RDEA119, docetaxel and 17-AAG, High expression of UBE2C was resistant to masitinib, and Low expression of ERO1B made the EC more sensitive to FK866. We constructed an EC risk score model composed of 8 DEGs and gene resistance analysis, which can provide reference for prognosis prediction, diagnosis and treatment of the EC patients.
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Affiliation(s)
- Jingjing Dai
- Department of Hematology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Abdusemer Reyimu
- Department of Hematology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, Jiangsu, People's Republic of China.,Medical College, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China
| | - Ao Sun
- Class 11, grade 2018, Clinical Medicine, Nanjing Medical University, Nanjing, 223300, Jiangsu, People's Republic of China
| | - Zaxi Duoji
- Research Center of High Altitude Medicine, Naqu, Tibet, China, People's Hospital of Naqu Affiliated to Dalian Medical University, Tibet, 852000, People's Republic of China
| | - Wubi Zhou
- Department of Pathology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, Jiangsu, People's Republic of China.
| | - Song Liang
- Department of Medical Laboratory, Second branch, The Affiliated Huaian No, People's Hospital of Nanjing Medical University, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Suxia Hu
- Department of Medical Laboratory, Huainan First People's Hospital, The First Affiliated Hospital of Anhui University of Science and Technology, Huainan, Anhui, People's Republic of China.
| | - Weijie Dai
- Department of Endoscopy Center, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, Jiangsu, People's Republic of China.
| | - Xiaoguang Xu
- Research Center of High Altitude Medicine, Naqu, Tibet, China, People's Hospital of Naqu Affiliated to Dalian Medical University, Tibet, 852000, People's Republic of China.
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Gougousis S, Petanidis S, Poutoglidis A, Tsetsos N, Vrochidis P, Skoumpas I, Argyriou N, Katopodi T, Domvri K. Epigenetic editing and tumor‑dependent immunosuppressive signaling in head and neck malignancies (Review). Oncol Lett 2022; 23:196. [PMID: 35572491 PMCID: PMC9100602 DOI: 10.3892/ol.2022.13317] [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: 01/02/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancer (HNC) comprises a heterogeneous variety of malignant tumors, characterized by a relatively high tumor mutation burden. Previous data have revealed that immune system dysfunction appears to serve a key role in the development and progression of HNC and established immunosuppression is vital for evading the host immune response. Despite progress in chemotherapy and radiotherapy, the survival rate of patients with HNC is still low. Therefore, the present review discusses the development of novel immunotherapy approaches based on the various immune cell signaling routes that trigger drug resistance and immunosuppression. Additionally, the present review discusses the epigenetic alterations, including DNA methylation, histone modifications, chromatin remodeling and non-coding RNAs that drive and support HNC progression. Furthermore, the role of cancer-associated fibroblasts, tumor macrophages and myeloid cells in tumor-related immunosuppression are considered. Specifically, the molecular immune-related mechanisms in the tumor microenvironment, which lead to decreased drug sensitivity and tumor relapse, and strategies for reversing drug resistance and targeting immunosuppressive tumor networks are discussed. Deciphering these molecular mechanisms is essential for preclinical and clinical investigations in order to enhance therapeutic efficacy. Furthermore, an improved understanding of these immune cell signaling pathways that drive immune surveillance, immune-driven inflammation and tumor-related immunosuppression is necessary for future personalized HNC-based therapeutic approaches.
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Affiliation(s)
- Spyridon Gougousis
- Ear Nose Throat Department, General Hospital of Thessaloniki ‘G. Papanikolaou’, Thessaloniki GR‑57010, Greece
| | - Savvas Petanidis
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University, Moscow 119992, Russian Federation
| | - Alexandros Poutoglidis
- Ear Nose Throat Department, General Hospital of Thessaloniki ‘G. Papanikolaou’, Thessaloniki GR‑57010, Greece
| | - Nikolaos Tsetsos
- Ear Nose Throat Department, General Hospital of Thessaloniki ‘G. Papanikolaou’, Thessaloniki GR‑57010, Greece
| | - Paraskevas Vrochidis
- Ear Nose Throat Department, General Hospital of Goumenissa, Kilkis GR‑61100, Greece
| | - Ioannis Skoumpas
- Ear Nose Throat Department, General Hospital of Katerini, Katerini GR‑60100, Greece
| | - Nektarios Argyriou
- Ear Nose Throat Department, General Hospital of Thessaloniki ‘G. Gennimatas’, Thessaloniki GR‑54635, Greece
| | - Theodora Katopodi
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki GR‑54124, Greece
| | - Kalliopi Domvri
- Pulmonary Department, General Hospital of Thessaloniki ‘G. Papanikolaou’, Aristotle University of Thessaloniki, Thessaloniki GR‑57010, Greece
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High Risk-Human Papillomavirus in HNSCC: Present and Future Challenges for Epigenetic Therapies. Int J Mol Sci 2022; 23:ijms23073483. [PMID: 35408843 PMCID: PMC8998945 DOI: 10.3390/ijms23073483] [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: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is a highly heterogeneous group of tumors characterized by an incidence of 650,000 new cases and 350,000 deaths per year worldwide and a male to female ratio of 3:1. The main risk factors are alcohol and tobacco consumption and Human Papillomavirus (HPV) infections. HNSCC cases are divided into two subgroups, the HPV-negative (HPV−) and the HPV-positive (HPV+) which have different clinicopathological and molecular profiles. However, patients are still treated with the same therapeutic regimens. It is thus of utmost importance to characterize the molecular mechanisms underlying these differences to find new biomarkers and novel therapeutic targets towards personalized therapies. Epigenetic alterations are a hallmark of cancer and can be exploited as both promising biomarkers and potential new targets. E6 and E7 HPV oncoviral proteins besides targeting p53 and pRb, impair the expression and the activity of several epigenetic regulators. While alterations in DNA methylation patterns have been well described in HPV+ and HPV− HNSCC, accurate histone post-translational modifications (hPTMs) characterization is still missing. Herein, we aim to provide an updated overview on the impact of HPV on the hPTMs landscape in HNSCC. Moreover, we will also discuss the sex and gender bias in HNSCC and how the epigenetic machinery could be involved in this process, and the importance of taking into account sex and/or gender also in this field.
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The Emerging Significance of Histone Lysine Demethylases as Prognostic Markers and Therapeutic Targets in Head and Neck Cancers. Cells 2022; 11:cells11061023. [PMID: 35326475 PMCID: PMC8946939 DOI: 10.3390/cells11061023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic aberrations, associated with altered DNA methylation profiles and global changes in the level of histone modifications, are commonly detected in head and neck squamous cell carcinomas (HNSCC). Recently, histone lysine demethylases have been implicated in the pathogenesis of HNSCC and emerged as potential molecular targets. Histone lysine demethylases (KDMs) catalyze the removal of methyl groups from lysine residues in histones. By affecting the methylation of H3K4, H3K9, H3K27, or H3K36, these enzymes take part in transcriptional regulation, which may result in changes in the level of expression of tumor suppressor genes and protooncogenes. KDMs are involved in many biological processes, including cell cycle control, senescence, DNA damage response, and heterochromatin formation. They are also important regulators of pluripotency. The overexpression of most KDMs has been observed in HNSCC, and their inhibition affects cell proliferation, apoptosis, cell motility, invasiveness, and stemness. Of all KDMs, KDM1, KDM4, KDM5, and KDM6 proteins are currently regarded as the most promising prognostic and therapeutic targets in head and neck cancers. The aim of this review is to present up-to-date knowledge on the significance of histone lysine demethylases in head and neck carcinogenesis and to discuss the possibility of using them as prognostic markers and pharmacological targets in patients’ treatment.
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Besaratinia A, Caceres A, Tommasi S. DNA Hydroxymethylation in Smoking-Associated Cancers. Int J Mol Sci 2022; 23:2657. [PMID: 35269796 PMCID: PMC8910185 DOI: 10.3390/ijms23052657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
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Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem 2022; 403:731-747. [PMID: 35119801 DOI: 10.1515/hsz-2021-0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]
Abstract
The DNA-binding AT-rich interactive domain (ARID) exists in a wide range of proteins throughout eukaryotic kingdoms. ARID domain-containing proteins are involved in manifold biological processes, such as transcriptional regulation, cell cycle control and chromatin remodeling. Their individual domain composition allows for a sub-classification within higher mammals. ARID is categorized as binder of double-stranded AT-rich DNA, while recent work has suggested ARIDs as capable of binding other DNA motifs and also recognizing RNA. Despite a broad variability on the primary sequence level, ARIDs show a highly conserved fold, which consists of six α-helices and two loop regions. Interestingly, this minimal core domain is often found extended by helices at the N- and/or C-terminus with potential roles in target specificity and, subsequently function. While high-resolution structural information from various types of ARIDs has accumulated over two decades now, there is limited access to ARID-DNA complex structures. We thus find ourselves left at the beginning of understanding ARID domain target specificities and the role of accompanying domains. Here, we systematically summarize ARID domain conservation and compare the various types with a focus on their structural differences and DNA-binding preferences, including the context of multiple other motifs within ARID domain containing proteins.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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Qian X, Bao ZM, Yao D, Shi Y. Lysine demethylase 5C epigenetically reduces transcription of ITIH1 that results in augmented progression of liver hepatocellular carcinoma. Kaohsiung J Med Sci 2022; 38:437-446. [PMID: 35080113 DOI: 10.1002/kjm2.12501] [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: 07/12/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
Lysine demethylase 5C (KDM5C) is a member of the KDM family of demethylases and has been reported as a cancer driver. This study aimed to probe the function of KDM5C in the development of liver hepatocellular carcinoma (LIHC) and the molecules of action. According to data from publicly accessible bioinformatic databases, KDM5C is highly expressed in LIHC and associated with poor patient prognosis. High expression of KDM5C was detected in acquired LIHC cell lines. Downregulation of KDM5C weakened proliferation, migration, invasiveness, and resistance to death of the LIHC cells in vitro, and it reduced growth of the xenograft tumors in nude mice. Inter-alpha-trypsin inhibitor heavy chain 1 (ITIH1) was predicted as a downstream gene negatively regulated by KDM5C. KDM5C-regulated H3K4me1 modification at the promoter region of ITIH1, inducing its transcriptional inactivation. Further downregulation of ITIH1 in cancer cells blocked the functions of KDM5C silencing and restored the malignant behaviors of LIHC cells. The activity of the PI3K/AKT signaling was decreased following KDM5C downregulation but recovered upon ITIH1 silencing. In conclusion, this study suggested that KDM5C epigenetically reduces ITIH1 and activates the PI3K/AKT signaling pathway to promote LIHC progression.
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Affiliation(s)
- Xu Qian
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China.,Department of Thyroid and Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, P.R. China
| | - Zhong-Ming Bao
- Department of Hepatobiliary Surgery, Huaiyin People's Hospital, Huaiyin, Jiangsu, P.R. China
| | - Dan Yao
- Department of Gastrointestinal Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, P.R. China
| | - Yang Shi
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
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Wang Y, Ye H, Yang Y, Li J, Cen A, Zhao L. microRNA-181a promotes the oncogene S100A2 and enhances papillary thyroid carcinoma growth by mediating the expression of histone demethylase KDM5C. J Endocrinol Invest 2022; 45:17-28. [PMID: 34143366 DOI: 10.1007/s40618-021-01606-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND PURPOSE Papillary thyroid carcinoma (PTC) is an endocrine malignancy. Increasing evidence highlights microRNAs (miRNAs) as important participants in PTC. Here, we investigated the role of miR-181a in PTC. METHODS A microarray-based analysis was performed to identify the differential expression of miR-181a in PTC, which was validated with RT-qPCR. Protein expression of the proliferation-related factor Ki-67 and apoptosis- and migration-related factors in PTC was assessed with immunoblot analysis. A dual-luciferase reporter gene assay was adopted to verify the relationship between miR-181a and lysine demethylase 5C (KDM5C). Chromatin immunoprecipitation (ChIP) was used to detect the level of the H3K4me3 modification on S100 calcium-binding protein A2 (S100A2). Cell viability, apoptosis, and invasion and migration abilities were evaluated by Cell Counting Kit-8 (CCK-8), flow cytometry, and transwell assays, respectively. The in vitro results were verified in in vivo nude mouse models. RESULTS miR-181a was highly expressed in PTC tissues and cell lines. Silencing miR-181a repressed the proliferation and migration of PTC cells. KDM5C was identified as the target gene of miR-181a and represses S100A2 expression through histone demethylation to diminish the migration and proliferation of PTC cells. miR-181a depletion suppressed tumor growth. CONCLUSION Collectively, these results suggest that highly expressed miR-181a promotes the proliferation of PTC cells by increasing the expression of the oncogene S100A2. This study contributes to the advancement of miR-181a-targeted therapeutics.
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Affiliation(s)
- Y Wang
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China.
| | - H Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Hepatopancreatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Y Yang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - J Li
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China
| | - A Cen
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China
| | - L Zhao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
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KDM6A missense variants hamper H3 histone demethylation in lung squamous cell carcinoma. Comput Struct Biotechnol J 2022; 20:3151-3160. [PMID: 35782738 PMCID: PMC9232545 DOI: 10.1016/j.csbj.2022.06.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/22/2022] Open
Abstract
KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease; it is also a known cancer driver gene, with multiple somatic mutations found in a few cancer types. In this study, we looked at eleven missense variants in lung squamous cell carcinoma, one of the most common lung cancer subtypes, to see how they affect the KDM6A catalytic mechanisms. We found that they influence the interaction with histone H3 and the exposure of the trimethylated Lys27, which is critical for wild-type physiological function to varying degrees, by altering the conformational transition.
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