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Kim Y, Min S, Kim S, Lee SY, Park YJ, Heo Y, Park SS, Park TJ, Lee JH, Kang HC, Ji JH, Cho H. PARP1-TRIM44-MRN loop dictates the response to PARP inhibitors. Nucleic Acids Res 2024:gkae756. [PMID: 39217466 DOI: 10.1093/nar/gkae756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 07/12/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
PARP inhibitors (PARPi) show selective efficacy in tumors with homologous recombination repair (HRR)-defects but the activation mechanism of HRR pathway in PARPi-treated cells remains enigmatic. To unveil it, we searched for the mediator bridging PARP1 to ATM pathways by screening 211 human ubiquitin-related proteins. We discovered TRIM44 as a crucial mediator that recruits the MRN complex to damaged chromatin, independent of PARP1 activity. TRIM44 binds PARP1 and regulates the ubiquitination-PARylation balance of PARP1, which facilitates timely recruitment of the MRN complex for DSB repair. Upon exposure to PARPi, TRIM44 shifts its binding from PARP1 to the MRN complex via its ZnF UBP domain. Knockdown of TRIM44 in cells significantly enhances the sensitivity to olaparib and overcomes the resistance to olaparib induced by 53BP1 deficiency. These observations emphasize the central role of TRIM44 in tethering PARP1 to the ATM-mediated repair pathway. Suppression of TRIM44 may enhance PARPi effectiveness and broaden their use even to HR-proficient tumors.
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Affiliation(s)
- Yonghyeon Kim
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
- Department of Biochemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Soyeon Kim
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Seo Yun Lee
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Yeon-Ji Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Yungyeong Heo
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Soon Sang Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Tae Jun Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jae-Ho Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jae-Hoon Ji
- Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, TX 78229-3000, USA
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Republic of Korea
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He L, Chen H, Ruan B, He L, Luo M, Fu Y, Zou R. UBQLN4 promotes the proliferation and invasion of non-small cell lung cancer cell by regulating PI3K/AKT pathway. J Cancer Res Clin Oncol 2024; 150:335. [PMID: 38969831 PMCID: PMC11226510 DOI: 10.1007/s00432-024-05862-8] [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: 05/06/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Ubiquilin-4 (UBQLN4), a member of the ubiquilin family, has received limited attention in cancer research to date. Here, we investigated for the first time the functional role and mechanism of UBQLN4 in non-small cell lung cancer (NSCLC). METHODS The Cancer Genome Atlas (TCGA) database was employed to validate UBQLN4 as a differentially expressed gene. Expression differences of UBQLN4 in NSCLC cells and tissues were assessed using immunohistochemistry (IHC) experiment and western blotting (WB) experiment. Kaplan-Meier analysis was conducted to examine the association between UBQLN4 expression and NSCLC prognosis. Functional analyses of UBQLN4 were performed through cell counting kit-8 (CCK-8), colony formation, and transwell invasion assays. The impact of UBQLN4 on tumor-associated signaling pathways was assessed using the path scan intracellular signaling array. In vivo tumorigenesis experiments were conducted to further investigate the influence of UBQLN4 on tumor formation. RESULTS UBQLN4 exhibited up-regulation in both NSCLC tissues and cells. Additionally, over-expression of UBQLN4 was associated with an unfavorable prognosis in NSCLC patients. Functional loss analyses demonstrated that inhibiting UBQLN4 could suppress the proliferation and invasion of NSCLC cells in both in vitro and in vivo settings. Conversely, functional gain experiments yielded opposite results. Path scan intracellular signaling array results suggested that the role of UBQLN4 is associated with the PI3K/AKT pathway, a correlation substantiated by in vitro and in vivo tumorigenesis experiments. CONCLUSION We validated that UBQLN4 promotes proliferation and invasion of NSCLC cells by activating the PI3K/AKT pathway, thereby facilitating the progression of NSCLC. These findings underscore the potential of targeting UBQLN4 as a therapeutic strategy for NSCLC.
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Affiliation(s)
- Li He
- Department of Oncology, The People's Hospital of Xinyu City, Xinyu, Jiangxi, 338099, People's Republic of China
| | - Heng Chen
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical Collge, Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Bin Ruan
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical Collge, Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Li He
- Department of Pathology, Jingdezhen First People's Hospital, Jingdezhen, Jiangxi, 333000, People's Republic of China
| | - Ming Luo
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical Collge, Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yulun Fu
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical Collge, Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Rui Zou
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical Collge, Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi, 330006, People's Republic of China.
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Wang Y, Liu X, Zuo X, Wang C, Zhang Z, Zhang H, Zeng T, Chen S, Liu M, Chen H, Song Q, Li Q, Yang C, Le Y, Xing J, Zhang H, An J, Jia W, Kang L, Zhang H, Xie H, Ye J, Wu T, He F, Zhang X, Li Y, Zhou G. NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors. CELL GENOMICS 2024; 4:100550. [PMID: 38697125 PMCID: PMC11099347 DOI: 10.1016/j.xgen.2024.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, including NRDE2, RANBP17, RTEL1, and STEAP3. Using NRDE2 (index rs199890497 [p.N377I], p = 1.19 × 10-9) as an exemplary candidate, we demonstrated that it promotes homologous recombination (HR) repair and suppresses HCC. Mechanistically, NRDE2 binds to the subunits of casein kinase 2 (CK2) and facilitates the assembly and activity of the CK2 holoenzyme. This NRDE2-mediated enhancement of CK2 activity increases the phosphorylation of MDC1 and then facilitates the HR repair. These functions are eliminated almost completely by the NRDE2-p.N377I variant, which sensitizes the HCC cells to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with chemotherapy. Collectively, our findings highlight the relevance of the rare variants to genetic susceptibility to HCC, which would be helpful for the precise treatment of this malignancy.
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Affiliation(s)
- Yahui Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Xinyi Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Xianbo Zuo
- Department of Dermatology, Department of Pharmacy, China-Japan Friendship Hospital, Beijing, P.R. China
| | - Cuiling Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Zheng Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Haitao Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Tao Zeng
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Shunqi Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Mengyu Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Hongxia Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Qingfeng Song
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning City, Guangxi Province, P.R. China
| | - Qi Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Department of Neurosciences, School of Medicine, University of South China, Hengyang City, Hunan Province, P.R. China
| | - Chenning Yang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Yi Le
- Department of Hepatobiliary Surgery, the 5th Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Experimental Teaching Center of Basic Medicine, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Hongxin Zhang
- Department of Pain Treatment, Tangdu Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Weihua Jia
- State Key Laboratory of Oncology in Southern China, Guangzhou City, Guangdong Province, P.R. China; Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang City, Shaanxi Province, P.R. China
| | - Hongxing Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Hui Xie
- Department of Interventional Oncology, the Fifth Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jiazhou Ye
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Tianzhun Wu
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China.
| | - Xuejun Zhang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, Anhui Province, P.R. China.
| | - Yuanfeng Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.
| | - Gangqiao Zhou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, P.R. China.
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Duan BT, Zhao XK, Cui YY, Liu DZ, Wang L, Zhou L, Zhang XY. Construction and validation of somatic mutation-derived long non-coding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma. World J Gastrointest Surg 2024; 16:842-859. [PMID: 38577085 PMCID: PMC10989333 DOI: 10.4240/wjgs.v16.i3.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) have been found to be a potential prognostic factor for cancers, including hepatocellular carcinoma (HCC). Some LncRNAs have been confirmed as potential indicators to quantify genomic instability (GI). Nevertheless, GI-LncRNAs remain largely unexplored. This study established a GI-derived LncRNA signature (GILncSig) that can predict the prognosis of HCC patients. AIM To establish a GILncSig that can predict the prognosis of HCC patients. METHODS Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles. The GI-LncRNAs were then analyzed for functional enrichment. The GILncSig was established in the training set by Cox regression analysis, and its predictive ability was verified in the testing set and TCGA set. In addition, we explored the effects of the GILncSig and TP53 on prognosis. RESULTS A total of 88 GI-LncRNAs were found, and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI. The GILncSig was constructed by 5 LncRNAs (miR210HG, AC016735.1, AC116351.1, AC010643.1, LUCAT1). In the training set, the prognosis of high-risk patients was significantly worse than that of low-risk patients, and similar results were verified in the testing set and TCGA set. Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor. Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve (0.773) was higher than the two LncRNA signatures published recently. Furthermore, the GILncSig may have a better predictive performance than TP53 mutation status alone. CONCLUSION We established a GILncSig that can predict the prognosis of HCC patients, which will help to guide prognostic evaluation and treatment decisions.
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Affiliation(s)
- Bo-Tao Duan
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Xue-Kai Zhao
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Yang-Yang Cui
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - De-Zheng Liu
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Lin Wang
- Department of Ophthalmology, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Lei Zhou
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Xing-Yuan Zhang
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
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5
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Bidany-Mizrahi T, Shweiki A, Maroun K, Abu-Tair L, Mali B, Aqeilan RI. Unveiling the relationship between WWOX and BRCA1 in mammary tumorigenicity and in DNA repair pathway selection. Cell Death Discov 2024; 10:145. [PMID: 38499540 PMCID: PMC10948869 DOI: 10.1038/s41420-024-01878-8] [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: 11/29/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Breast cancer is the leading cause of cancer-related deaths in women worldwide, with the basal-like or triple-negative breast cancer (TNBC) subtype being particularly aggressive and challenging to treat. Understanding the molecular mechanisms driving the development and progression of TNBC is essential. We previously showed that WW domain-containing oxidoreductase (WWOX) is commonly inactivated in TNBC and is implicated in the DNA damage response (DDR) through ATM and ATR activation. In this study, we investigated the interplay between WWOX and BRCA1, both frequently inactivated in TNBC, on mammary tumor development and on DNA double-strand break (DSB) repair choice. We generated and characterized a transgenic mouse model (K14-Cre;Brca1fl/fl;Wwoxfl/fl) and observed that mice lacking both WWOX and BRCA1 developed basal-like mammary tumors and exhibited a decrease in 53BP1 foci and an increase in RAD51 foci, suggesting impaired DSB repair. We examined human TNBC cell lines harboring wild-type and mutant BRCA1 and found that WWOX expression promoted NHEJ repair in cells with wild-type BRCA1. Our findings suggest that WWOX and BRCA1 play an important role in DSB repair pathway choice in mammary epithelial cells, underscoring their functional interaction and significance in breast carcinogenesis.
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Affiliation(s)
- Tirza Bidany-Mizrahi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aya Shweiki
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kian Maroun
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lina Abu-Tair
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bella Mali
- Department of Pathology, Hadassah University Hospital, Jerusalem, Israel
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus.
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6
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Jiang Q, Chen H, Zhou S, Zhu T, Liu W, Wu H, Zhang Y, Liu F, Sun Y. Ubiquilin-4 induces immune escape in gastric cancer by activating the notch signaling pathway. Cell Oncol (Dordr) 2024; 47:303-319. [PMID: 37702916 DOI: 10.1007/s13402-023-00869-8] [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] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
PURPOSE We aimed to investigate the role of ubiquilin-4 in predicting the immunotherapy response in gastric cancer. METHODS Retrospective RNA-sequencing and immunohistochemical analysis were performed for patients with gastric cancer who received programmed death-1 blockade therapy after recurrence. Multiplex immunohistochemistry identified immune cell types in gastric cancer tissues. We used immunocompetent 615 mice and immunodeficient nude mice to perform tumorigenic experiments. RESULTS Ubiquilin-4 expression was significantly higher in responders (p < 0.05, false discovery rate > 2.5) and showed slight superiority over programmed death ligand 1 in predicting programmed death-1 inhibitor therapy response (area under the curve: 87.08 vs. 72.50). Ubiquilin-4-high patients exhibited increased CD4+ and CD8+ T cells, T follicular helper cells, monocytes, and macrophages. Ubiquilin-4-overexpressed mouse forestomach carcinoma cells showed significantly enhanced growth in immunocompetent mice but not in immunodeficient mice. Upregulation or downregulation of ubiquilin-4 synergistically affected programmed death ligand 1 at the protein and messenger RNA levels. Functional enrichment analysis revealed significant enrichment of the Notch, JAK-STAT, and WNT signaling pathways in ubiquilin-4-high gastric cancers. Ubiquilin-4 promoted Numb degaration, activating the Notch signaling pathway and upregulating programmed death ligand 1. CONCLUSIONS Ubiquilin-4 may contribute to immune escape in gastric cancer by upregulating programmed death ligand 1 expression in tumor cells through Notch signaling activation. Thus, ubiquilin-4 could serve as a predictive marker for programmed death ligand 1 inhibitor therapy response in gastric cancer.
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Affiliation(s)
- Quan Jiang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Retroperitoneal Tumor and Soft Tissue Sarcoma Surgery, Fudan University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shixin Zhou
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Retroperitoneal Tumor and Soft Tissue Sarcoma Surgery, Fudan University, Shanghai, China
| | - Wenshuai Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Wu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Retroperitoneal Tumor and Soft Tissue Sarcoma Surgery, Fudan University, Shanghai, China.
| | - Fenglin Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yihong Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
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7
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Chen Y, Wu J, Zhai L, Zhang T, Yin H, Gao H, Zhao F, Wang Z, Yang X, Jin M, Huang B, Ding X, Li R, Yang J, He Y, Wang Q, Wang W, Kloeber JA, Li Y, Hao B, Zhang Y, Wang J, Tan M, Li K, Wang P, Lou Z, Yuan J. Metabolic regulation of homologous recombination repair by MRE11 lactylation. Cell 2024; 187:294-311.e21. [PMID: 38128537 DOI: 10.1016/j.cell.2023.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 08/09/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
Lactylation is a lactate-induced post-translational modification best known for its roles in epigenetic regulation. Herein, we demonstrate that MRE11, a crucial homologous recombination (HR) protein, is lactylated at K673 by the CBP acetyltransferase in response to DNA damage and dependent on ATM phosphorylation of the latter. MRE11 lactylation promotes its binding to DNA, facilitating DNA end resection and HR. Inhibition of CBP or LDH downregulated MRE11 lactylation, impaired HR, and enhanced chemosensitivity of tumor cells in patient-derived xenograft and organoid models. A cell-penetrating peptide that specifically blocks MRE11 lactylation inhibited HR and sensitized cancer cells to cisplatin and PARPi. These findings unveil lactylation as a key regulator of HR, providing fresh insights into the ways in which cellular metabolism is linked to DSB repair. They also imply that the Warburg effect can confer chemoresistance through enhancing HR and suggest a potential therapeutic strategy of targeting MRE11 lactylation to mitigate the effects.
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Affiliation(s)
- Yuping Chen
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jinhuan Wu
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hui Yin
- Department of Thoracic Surgery, The First Affiliated Hospital of Shaoyang University, Shaoyang 422001, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhe Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaoning Yang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mingpeng Jin
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Bingsong Huang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xin Ding
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Rui Li
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jie Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yiming He
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Qianwen Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Yunxuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Zhang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Shanghai 200072, China
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China.
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8
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Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fábián Z, Gambus A, Mailand N, Duxin JP, Nielsen ML. Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nat Commun 2023; 14:8293. [PMID: 38097601 PMCID: PMC10721886 DOI: 10.1038/s41467-023-43873-0] [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: 05/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFβ-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFβ-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.
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Affiliation(s)
- Camilla S Colding-Christensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Javier Arroyo-Gomez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Connor Arkinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- California Institute for Quantitative Biosciences and Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Niels Mailand
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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9
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Haj M, Levon A, Frey Y, Hourvitz N, Campisi J, Tzfati Y, Elkon R, Ziv Y, Shiloh Y. Accelerated replicative senescence of ataxia-telangiectasia skin fibroblasts is retained at physiologic oxygen levels, with unique and common transcriptional patterns. Aging Cell 2023; 22:e13869. [PMID: 37254625 PMCID: PMC10410012 DOI: 10.1111/acel.13869] [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: 11/28/2022] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The genetic disorder, ataxia-telangiectasia (A-T), is caused by loss of the homeostatic protein kinase, ATM, and combines genome instability, tissue degeneration, cancer predisposition, and premature aging. Primary fibroblasts from A-T patients exhibit premature senescence when grown at ambient oxygen concentration (21%). Here, we show that reducing oxygen concentration to a physiological level range (3%) dramatically extends the proliferative lifespan of human A-T skin fibroblasts. However, they still undergo senescence earlier than control cells grown under the same conditions and exhibit high genome instability. Comparative RNA-seq analysis of A-T and control fibroblasts cultured at 3% oxygen followed by cluster analysis of differentially expressed genes and functional enrichment analysis, revealed distinct transcriptional dynamics in A-T fibroblasts senescing in physiological oxygen concentration. While some transcriptional patterns were similar to those observed during replicative senescence of control cells, others were unique to the senescing A-T cells. We observed in them a robust activation of interferon-stimulated genes, with undetected expression the interferon genes themselves. This finding suggests an activation of a non-canonical cGAS-STING-mediated pathway, which presumably responds to cytosolic DNA emanating from extranuclear micronuclei detected in these cells. Senescing A-T fibroblasts also exhibited a marked, intriguely complex alteration in the expression of genes associated with extracellular matrix (ECM) remodeling. Notably, many of the induced ECM genes encode senescence-associated secretory phenotype (SASP) factors known for their paracrine pro-fibrotic effects. Our data provide a molecular dimension to the segmental premature aging observed in A-T patients and its associated symptoms, which develop as the patients advance in age.
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Affiliation(s)
- Majd Haj
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Amit Levon
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yann Frey
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Noa Hourvitz
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Yehuda Tzfati
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Ran Elkon
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yael Ziv
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yosef Shiloh
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
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10
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Shi Z, Chen B, Han X, Gu W, Liang S, Wu L. Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types. Sci Rep 2023; 13:8899. [PMID: 37264024 DOI: 10.1038/s41598-023-35092-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/12/2023] [Indexed: 06/03/2023] Open
Abstract
Homologous recombination deficiency (HRD) causes faulty double-strand break repair and is a prevalent cause of tumorigenesis. However, the incidence of HRD and its clinical significance in pan-cancer patients remain unknown. Using computational analysis of Single-nucleotide polymorphism array data from 10,619 cancer patients, we demonstrate that HRD frequently occurs across multiple cancer types. Analysis of the pan-cancer cohort revealed that HRD is not only a biomarker for ovarian cancer and triple-negative breast cancer, but also has clinical prognostic value in numerous cancer types, including adrenocortical cancer and thymoma. We discovered that homologous recombination-related genes have a high mutation or deletion frequency. Pathway analysis shows HRD is positively correlated with the DNA damage response and the immune-related signaling pathways. Single cell RNA sequencing of tumor-infiltrating lymphocytes reveals a significantly higher proportion of exhausted T cells in HRD patients, indicating pre-existing immunity. Finally, HRD could be utilized to predict pan-cancer patients' responses to Programmed cell death protein 1 immunotherapy. In summary, our work establishes a comprehensive map of HRD in pan-cancer. The findings have significant implications for expanding the scope of Poly ADP-ribose polymerase inhibitor therapy and, possibly, immunotherapy.
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Affiliation(s)
- Zhiwen Shi
- Department of Translational Medicine Center, Chigene (Beijing) Translational Medical Research Center Co., Beijing, 100176, China
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200032, China
| | - Bolin Chen
- Department of Thoracic Medical Oncology,Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, China
| | - Xiao Han
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200032, China
| | - Weiyue Gu
- Department of Translational Medicine Center, Chigene (Beijing) Translational Medical Research Center Co., Beijing, 100176, China
| | - Shuzhi Liang
- Department of Thoracic Medical Oncology,Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, China
| | - Lin Wu
- Department of Thoracic Medical Oncology,Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, China.
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11
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Inchingolo MA, Diman A, Adamczewski M, Humphreys T, Jaquier-Gubler P, Curran JA. TP53BP1, a dual-coding gene, uses promoter switching and translational reinitiation to express a smORF protein. iScience 2023; 26:106757. [PMID: 37216125 PMCID: PMC10193022 DOI: 10.1016/j.isci.2023.106757] [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: 06/20/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
The complexity of the metazoan proteome is significantly increased by the expression of small proteins (<100 aa) derived from smORFs within lncRNAs, uORFs, 3' UTRs and, reading frames overlapping the CDS. These smORF encoded proteins (SEPs) have diverse roles, ranging from the regulation of cellular physiological to essential developmental functions. We report the characterization of a new member of this protein family, SEP53BP1, derived from a small internal ORF that overlaps the CDS encoding 53BP1. Its expression is coupled to the utilization of an alternative, cell-type specific promoter coupled to translational reinitiation events mediated by a uORF in the alternative 5' TL of the mRNA. This uORF-mediated reinitiation at an internal ORF is also observed in zebrafish. Interactome studies indicate that the human SEP53BP1 associates with components of the protein turnover pathway including the proteasome, and the TRiC/CCT chaperonin complex, suggesting that it may play a role in cellular proteostasis.
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Affiliation(s)
- Marta A. Inchingolo
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aurélie Diman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maxime Adamczewski
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculté de Médecine et Pharmacie, Université Grenoble Alpes, Grenoble, France
| | - Tom Humphreys
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Pascale Jaquier-Gubler
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joseph A. Curran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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12
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The Impact of YRNAs on HNSCC and HPV Infection. Biomedicines 2023; 11:biomedicines11030681. [PMID: 36979661 PMCID: PMC10045647 DOI: 10.3390/biomedicines11030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.
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13
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Belmonte-Fernández A, Herrero-Ruíz J, Galindo-Moreno M, Limón-Mortés MC, Mora-Santos M, Sáez C, Japón MÁ, Tortolero M, Romero F. Cisplatin-induced cell death increases the degradation of the MRE11-RAD50-NBS1 complex through the autophagy/lysosomal pathway. Cell Death Differ 2023; 30:488-499. [PMID: 36477079 PMCID: PMC9950126 DOI: 10.1038/s41418-022-01100-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Cisplatin and other platinum-based anticancer agents are among the most widely used chemotherapy drugs in the treatment of different types of cancer. However, it is common to find patients who respond well to treatment at first but later relapse due to the appearance of resistance to cisplatin. Among the mechanisms responsible for this phenomenon is the increase in DNA damage repair. Here, we elucidate the effect of cisplatin on the MRN (MRE11-RAD50-NBS1) DNA damage sensor complex. We found that the tumor suppressor FBXW7 is a key factor in controlling the turnover of the MRN complex by inducing its degradation through lysosomes. Inhibition of lysosomal enzymes allowed the detection of the association of FBXW7-dependent ubiquitylated MRN with LC3 and the autophagy adaptor p62/SQSTM1 and the localization of MRN in lysosomes. Furthermore, cisplatin-induced cell death increased MRN degradation, suggesting that this complex is one of the targets that favor cell death. These findings open the possibility of using the induction of the degradation of the MRN complex after genotoxic damage as a potential therapeutic strategy to eliminate tumor cells.
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Affiliation(s)
| | - Joaquín Herrero-Ruíz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain
| | - María Galindo-Moreno
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain
| | - M Cristina Limón-Mortés
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain
| | - Mar Mora-Santos
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain
| | - Carmen Sáez
- Instituto de Biomedicina de Sevilla (IBiS) and Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, Sevilla, E-41013, Spain
| | - Miguel Á Japón
- Instituto de Biomedicina de Sevilla (IBiS) and Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, Sevilla, E-41013, Spain
| | - Maria Tortolero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain
| | - Francisco Romero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, E-41012, Spain.
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14
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Liu W, Zheng M, Zhang R, Jiang Q, Du G, Wu Y, Yang C, Li F, Li W, Wang L, Wu J, Shi L, Li W, Zhang K, Zhou Z, Liu R, Gao Y, Huang X, Fan S, Zhi X, Jiang D, Chen C. RNF126-Mediated MRE11 Ubiquitination Activates the DNA Damage Response and Confers Resistance of Triple-Negative Breast Cancer to Radiotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203884. [PMID: 36563124 PMCID: PMC9929257 DOI: 10.1002/advs.202203884] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/05/2022] [Indexed: 05/27/2023]
Abstract
Triple-negative breast cancer (TNBC) has higher molecular heterogeneity and metastatic potential and the poorest prognosis. Because of limited therapeutics against TNBC, irradiation (IR) therapy is still a common treatment option for patients with lymph nodes or brain metastasis. Thus, it is urgent to develop strategies to enhance the sensitivity of TNBC tumors to low-dose IR. Here, the authors report that E3 ubiquitin ligase Ring finger protein 126 (RNF126) is important for IR-induced ATR-CHK1 pathway activation to enhance DNA damage repair (DDR). Mechanistically, RNF126 physically associates with the MRE11-RAD50-NBS1 (MRN) complex and ubiquitinates MRE11 at K339 and K480 to increase its DNA exonuclease activity, subsequent RPA binding, and ATR phosphorylation, promoting sustained DDR in a homologous recombination repair-prone manner. Accordingly, depletion of RNF126 leads to increased genomic instability and radiation sensitivity in both TNBC cells and mice. Furthermore, it is found that RNF126 expression is induced by IR activating the HER2-AKT-NF-κB pathway and targeting RNF126 expression with dihydroartemisinin significantly improves the sensitivity of TNBC tumors in the brain to IR treatment in vivo. Together, these results reveal that RNF126-mediated MRE11 ubiquitination is a critical regulator of the DDR, which provides a promising target for improving the sensitivity of TNBC to radiotherapy.
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Affiliation(s)
- Wenjing Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Min Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Rou Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
| | - Qiuyun Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Guangshi Du
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Yingying Wu
- Department of the PathologyFirst Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Chuanyu Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Fubing Li
- Academy of Biomedical EngineeringKunming Medical UniversityKunming650500China
| | - Wei Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Luzhen Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- School of Life ScienceUniversity of Science & Technology of ChinaHefei230027China
| | - Jiao Wu
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Lei Shi
- Department of Biochemistry and Molecular BiologyTianjin Medical UniversityTianjin300070China
| | - Wenhui Li
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Kai Zhang
- Department of Biochemistry and Molecular BiologyTianjin Medical UniversityTianjin300070China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Translational Cancer Research CenterPeking University First HospitalBeijing100034China
| | - Yingzheng Gao
- Department of the Central LaboratorySecond Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Xinwei Huang
- Department of the Central LaboratorySecond Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Songqing Fan
- Department of Pathologythe Second Xiangya HospitalCentral South UniversityChangsha410000China
| | - Xu Zhi
- Center for Reproductive MedicineDepartment of Obstetrics and GynecologyPeking University Third HospitalBeijing100191China
| | - Dewei Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
- Academy of Biomedical EngineeringKunming Medical UniversityKunming650500China
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15
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Genomic Amplification of UBQLN4 Is a Prognostic and Treatment Resistance Factor. Cells 2022; 11:cells11203311. [PMID: 36291176 PMCID: PMC9600423 DOI: 10.3390/cells11203311] [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: 09/16/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Ubiquilin-4 (UBQLN4) is a proteasomal shuttle factor that directly binds to ubiquitylated proteins and delivers its cargo to the 26S proteasome for degradation. We previously showed that upregulated UBQLN4 determines the DNA damage response (DDR) through the degradation of MRE11A. However, the regulatory mechanism at DNA level, transcriptionally and post-transcriptional levels that control UBQLN4 mRNA levels remains unknown. In this study, we screened 32 solid tumor types and validated our findings by immunohistochemistry analysis. UBQLN4 is upregulated at both mRNA and protein levels and the most significant values were observed in liver, breast, ovarian, lung, and esophageal cancers. Patients with high UBQLN4 mRNA levels had significantly poor prognoses in 20 of 32 cancer types. DNA amplification was identified as the main mechanism promoting UBQLN4 upregulation in multiple cancers, even in the early phases of tumor development. Using CRISPR screen datasets, UBQLN4 was identified as a common essential gene for tumor cell viability in 81.1% (860/1,060) of the solid tumor derived cell lines. Ovarian cancer cell lines with high UBQLN4 mRNA levels were platinum-based chemotherapy resistant, while they were more sensitive to poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPi). Our findings highlight the utilities of UBQLN4 as a significant pan-cancer theranostic factor and a precision oncology biomarker for DDR-related drug resistance.
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16
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Lin BC, Higgins NR, Phung TH, Monteiro MJ. UBQLN proteins in health and disease with a focus on UBQLN2 in ALS/FTD. FEBS J 2022; 289:6132-6153. [PMID: 34273246 PMCID: PMC8761781 DOI: 10.1111/febs.16129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023]
Abstract
Ubiquilin (UBQLN) proteins are a dynamic and versatile family of proteins found in all eukaryotes that function in the regulation of proteostasis. Besides their canonical function as shuttle factors in delivering misfolded proteins to the proteasome and autophagy systems for degradation, there is emerging evidence that UBQLN proteins play broader roles in proteostasis. New information suggests the proteins function as chaperones in protein folding, protecting proteins prior to membrane insertion, and as guardians for mitochondrial protein import. In this review, we describe the evidence for these different roles, highlighting how different domains of the proteins impart these functions. We also describe how changes in the structure and phase separation properties of UBQLNs may regulate their activity and function. Finally, we discuss the pathogenic mechanisms by which mutations in UBQLN2 cause amyotrophic lateral sclerosis and frontotemporal dementia. We describe the animal model systems made for different UBQLN2 mutations and how lessons learnt from these systems provide fundamental insight into the molecular mechanisms by which UBQLN2 mutations drive disease pathogenesis through disturbances in proteostasis.
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Affiliation(s)
- Brian C. Lin
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicole R. Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Trong H. Phung
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mervyn J. Monteiro
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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17
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Lv Z, Wang Q, Liu X, Du Z, Liang W, Liu T, Zheng Y, Ma B, Xue D. Genetic instability-related lncRNAs predict prognosis and influence the immune microenvironment in breast cancer. Front Genet 2022; 13:926984. [PMID: 36118853 PMCID: PMC9478756 DOI: 10.3389/fgene.2022.926984] [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: 04/23/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
Genome instability is a hallmark of cancer, and the function of lncRNAs in regulating genomic stability has been gradually characterized. However, the prognostic value of lncRNAs related to genetic instability has not been found in breast cancer. Here we constructed a genetic instability-related lncRNA model including U62317.4, SEMA3B-AS1, MAPT-AS1, AC115837.2, LINC01269, AL645608.7, and GACAT2. This model can evaluate the risk and predict the survival outcomes of patients. Further analysis showed that the differentially expressed genes between the high- and low-risk groups were enriched in immunity and cornified envelope formation pathways. In addition, M2 macrophages infiltrated more obviously in the high-risk group. In summary, lncRNAs related to genetic instability may influence the development of breast cancer through immune infiltration and keratinization. This study provides a wider insight into breast cancer development and treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - Biao Ma
- *Correspondence: Biao Ma, ; Dongbo Xue,
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18
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Zhang T, Yang H, Zhou Z, Bai Y, Wang J, Wang W. Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin. Nat Commun 2022; 13:5133. [PMID: 36050397 PMCID: PMC9436968 DOI: 10.1038/s41467-022-32920-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
DNA end resection is delicately regulated through various types of post-translational modifications to initiate homologous recombination, but the involvement of SUMOylation in this process remains incompletely understood. Here, we show that MRE11 requires SUMOylation to shield it from ubiquitin-mediated degradation when resecting damaged chromatin. Upon DSB induction, PIAS1 promotes MRE11 SUMOylation on chromatin to initiate DNA end resection. Then, MRE11 is deSUMOylated by SENP3 mainly after it has moved away from DSB sites. SENP3 deficiency results in MRE11 degradation failure and accumulation on chromatin, causing genome instability. We further show that cancer-related MRE11 mutants with impaired SUMOylation exhibit compromised DNA repair ability. Thus, we demonstrate that MRE11 SUMOylation in coordination with ubiquitylation is dynamically controlled by PIAS1 and SENP3 to facilitate DNA end resection and maintain genome stability. DNA end resection initiating DNA repair by homologous recombination needs to be delicately regulated. This study shows the interplay between SUMOylation and ubiquitylation maintains MRE11 homeostasis on chromatin, thus facilitating genome stability.
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Affiliation(s)
- Tao Zhang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Han Yang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zenan Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yongtai Bai
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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19
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Zeng X, Zhao F, Cui G, Zhang Y, Deshpande RA, Chen Y, Deng M, Kloeber JA, Shi Y, Zhou Q, Zhang C, Hou J, Kim W, Tu X, Yan Y, Xu Z, Chen L, Gao H, Guo G, Liu J, Zhu Q, Cao Y, Huang J, Wu Z, Zhu S, Yin P, Luo K, Mer G, Paull TT, Yuan J, Tao K, Lou Z. METTL16 antagonizes MRE11-mediated DNA end resection and confers synthetic lethality to PARP inhibition in pancreatic ductal adenocarcinoma. NATURE CANCER 2022; 3:1088-1104. [PMID: 36138131 DOI: 10.1038/s43018-022-00429-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. Characterization of genetic alterations will improve our understanding and therapies for this disease. Here, we report that PDAC with elevated expression of METTL16, one of the 'writers' of RNA N6-methyladenosine modification, may benefit from poly-(ADP-ribose)-polymerase inhibitor (PARPi) treatment. Mechanistically, METTL16 interacts with MRE11 through RNA and this interaction inhibits MRE11's exonuclease activity in a methyltransferase-independent manner, thereby repressing DNA end resection. Upon DNA damage, ATM phosphorylates METTL16 resulting in a conformational change and autoinhibition of its RNA binding. This dissociates the METTL16-RNA-MRE11 complex and releases inhibition of MRE11. Concordantly, PDAC cells with high METTL16 expression show increased sensitivity to PARPi, especially when combined with gemcitabine. Thus, our findings reveal a role for METTL16 in homologous recombination repair and suggest that a combination of PARPi with gemcitabine could be an effective treatment strategy for PDAC with elevated METTL16 expression.
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Affiliation(s)
- Xiangyu Zeng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Yuping Chen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | - Yu Shi
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jing Hou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Wootae Kim
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yuanliang Yan
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lifeng Chen
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Center for Reproductive Medicine, Department of Gynecology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaqi Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yueyu Cao
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China.
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
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20
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A Genomic Instability-Related Long Noncoding RNA Signature for Predicting Hepatocellular Carcinoma Prognosis. JOURNAL OF ONCOLOGY 2022; 2022:3090523. [PMID: 36072979 PMCID: PMC9444385 DOI: 10.1155/2022/3090523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/02/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Background. Long noncoding RNAs (lncRNAs) are found to be novel biomarkers for hepatocellular carcinoma (HCC) and play an important role in tumor progression. We established a genomic instability-related long noncoding RNA signature (GIlncSig) as an independent prognosis factor and also investigated its impact on prognosis significance. Method. Somatic mutation profiles, clinical characteristics, and RNA sequencing data were obtained from The Cancer Genome Atlas (TCGA) database. Lasso regression was used to construct GIlncSig. KEGG was used to identify the possible biological pathways. ESTIMATE and CIBERSORT algorithms were used to calculate the immune microenvironment scores and proportion of immune cells in HCC patients. The expression of LINC00501 was conducted by qRT-PCR. Cell proliferation was measured by EdU, CCK-8, and colony formation assay, and cell migration and invasion ability were measured by wound healing and transwell assay. Results. 135 genomic instability-related lncRNAs were identified, and GIlncSig was constructed using 13 independent lncRNAs with significant prognosis values. Based on the GIlncSig, high-risk group had worse clinical outcomes than low-risk group, while high-risk group also had higher UBQLN4, KRAS, ARID1A, and PIK3CA expression. Moreover, the efficiency of GIlncSig combining single-gene mutation was higher than single-gene mutation alone such as TP53. The results of CIBERSORT and ESTIMATE showed that GS group and GU group had significantly different immune infiltration. In addition, LINC00501 was identified as a potential biomarker in HCC with strong relationship with clinical characteristics. In vitro assays validated that LINC00501 promoted proliferation and migration of HCC cell lines. Conclusion. Our results showed that GIlncSig serves as a potential independent prognosis factor to predict HCC patients’ prognosis for exploring potential mechanism and therapy strategy. Besides, LINC00501 plays an important role in the progression of HCC, which may be a potential therapy target.
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21
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Jing L, Du Y, Fu D. Characterization of tumor immune microenvironment and cancer therapy for head and neck squamous cell carcinoma through identification of a genomic instability-related lncRNA prognostic signature. Front Genet 2022; 13:979575. [PMID: 36105083 PMCID: PMC9465021 DOI: 10.3389/fgene.2022.979575] [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: 06/27/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) represents one of the most prevalent and malignant tumors of epithelial origins with unfavorable outcomes. Increasing evidence has shown that dysregulated long non-coding RNAs (lncRNAs) correlate with tumorigenesis and genomic instability (GI), while the roles of GI-related lncRNAs in the tumor immune microenvironment (TIME) and predicting cancer therapy are still yet to be clarified. In this study, transcriptome and somatic mutation profiles with clinical parameters were obtained from the TCGA database. Patients were classified into GI-like and genomic stable (GS)-like groups according to the top 25% and bottom 25% cumulative counts of somatic mutations. Differentially expressed lncRNAs (DElncRNAs) between GI- and GS-like groups were identified as GI-related lncRNAs. These lncRNA-related coding genes were enriched in cancer-related KEGG pathways. Patients totaling 499 with clinical information were randomly divided into the training and validation sets. A total of 18 DElncRNAs screened by univariate Cox regression analysis were associated with overall survival (OS) in the training set. A GI-related lncRNA signature that comprised 10 DElncRNAs was generated through least absolute shrinkage and selection operator (Lasso)-Cox regression analysis. Patients in the high-risk group have significantly decreased OS vs. patients in the low-risk group, which was verified in internal validation and entire HNSCC sets. Integrated HNSCC sets from GEO confirmed the notable survival stratification of the signature. The time-dependent receiver operating characteristic curve demonstrated that the signature was reliable. In addition, the signature retained a strong performance of OS prediction for patients with various clinicopathological features. Cell composition analysis showed high anti-tumor immunity in the low-risk group which was evidenced by increased infiltrating CD8+ T cells and natural killer cells and reduced cancer-associated fibroblasts, which was convinced by immune signatures analysis via ssGSEA algorithm. T helper/IFNγ signaling, co-stimulatory, and co-inhibitory signatures showed increased expression in the low-risk group. Low-risk patients were predicted to be beneficial to immunotherapy, which was confirmed by patients with progressive disease who had high risk scores vs. complete remission patients. Furthermore, the drugs that might be sensitive to HNSCC were identified. In summary, the novel prognostic GILncRNA signature provided a promising approach for characterizing the TIME and predicting therapeutic strategies for HNSCC patients.
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Affiliation(s)
- Lijun Jing
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Denggang Fu,
| | - Yabing Du
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Denggang Fu,
| | - Denggang Fu
- School of Medicine, Indiana University, Indianapolis, IN, United States
- *Correspondence: Denggang Fu,
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22
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Song Q, Hu Y, Yin A, Wang H, Yin Q. DNA Holliday Junction: History, Regulation and Bioactivity. Int J Mol Sci 2022; 23:9730. [PMID: 36077130 PMCID: PMC9456528 DOI: 10.3390/ijms23179730] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
DNA Holliday junction (HJ) is a four-way stranded DNA intermediate that formed in replication fork regression, homology-dependent repair and mitosis, performing a significant role in genomic stability. Failure to remove HJ can induce an acceptable replication fork stalling and DNA damage in normal cells, leading to a serious chromosomal aberration and even cell death in HJ nuclease-deficient tumor cells. Thus, HJ is becoming an attractive target in cancer therapy. However, the development of HJ-targeting ligand faces great challenges because of flexile cavities on the center of HJs. This review introduces the discovery history of HJ, elucidates the formation and dissociation procedures of HJ in corresponding bio-events, emphasizes the importance of prompt HJ-removing in genome stability, and summarizes recent advances in HJ-based ligand discovery. Our review indicate that target HJ is a promising approach in oncotherapy.
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Affiliation(s)
- Qinqin Song
- State/Key Laboratory of Microbial Technology, Shandong University, 72 Jimo Binhai Road, Qingdao 266237, China
| | - Yuemiao Hu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Anqi Yin
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Qikun Yin
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
- Bohai Rim Advanced Research Institute for Drug Discovery, 198 Binhai East Road, Yantai 264005, China
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23
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Yang H, Messina-Pacheco J, Corredor ALG, Gregorieff A, Liu JL, Nehme A, Najafabadi HS, Riazalhosseini Y, Gao B, Gao ZH. An integrated model of acinar to ductal metaplasia-related N7-methyladenosine regulators predicts prognosis and immunotherapy in pancreatic carcinoma based on digital spatial profiling. Front Immunol 2022; 13:961457. [PMID: 35979350 PMCID: PMC9377277 DOI: 10.3389/fimmu.2022.961457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022] Open
Abstract
Acinar-to-ductal metaplasia (ADM) is a recently recognized, yet less well-studied, precursor lesion of pancreatic ductal adenocarcinoma (PDAC) developed in the setting of chronic pancreatitis. Through digital spatial mRNA profiling, we compared ADM and adjacent PDAC tissues from patient samples to unveil the bridging genes during the malignant transformation of pancreatitis. By comparing the bridging genes with the 7-methylguanosine (m7G)-seq dataset, we screened 19 m7G methylation genes for a subsequent large sample analysis. We constructed the “m7G score” model based on the RNA-seq data for pancreatic cancer in The Cancer Genome Atlas (TCGA) database and The Gene Expression Omnibus (GEO) database. Tumors with a high m7G score were characterized by increased immune cell infiltration, increased genomic instability, higher response rate to combined immune checkpoint inhibitors (ICIs), and overall poor survival. These findings indicate that the m7G score is associated with tumor invasiveness, immune cell infiltration, ICI treatment response, and overall patients’ survival. We also identified FN1 and ITGB1 as core genes in the m7Gscore model, which affect immune cell infiltration and genomic instability not only in pancreatic cancer but also in pan-cancer. FN1 and ITGB1 can inhibit immune T cell activition by upregulation of macrophages and neutrophils, thereby leading to immune escape of pancreatic cancer cells and reducing the response rate of ICI treatment.
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Affiliation(s)
- Hao Yang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Julia Messina-Pacheco
- Department of Pathology, McGill University and the Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Andrea Liliam Gomez Corredor
- Department of Pathology, McGill University and the Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Alex Gregorieff
- Department of Pathology, McGill University and the Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Jun-li Liu
- MeDic Program, The Research Institute of McGill University Health Centre, & Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Ali Nehme
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Hamed S. Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Bo Gao
- Department of General Surgery, Peking University People’s Hospital, Beijing, China
- *Correspondence: Zu-hua Gao, ; Bo Gao,
| | - Zu-hua Gao
- Department of Pathology and Laboratory Medicine, British Columbia (BC) Cancer Research Center, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Zu-hua Gao, ; Bo Gao,
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24
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [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: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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25
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Ding Q, Hou Z, Zhao Z, Chen Y, Zhao L, Xiang Y. Identification of the prognostic signature based on genomic instability-related alternative splicing in colorectal cancer and its regulatory network. Front Bioeng Biotechnol 2022; 10:841034. [PMID: 35923577 PMCID: PMC9340224 DOI: 10.3389/fbioe.2022.841034] [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: 12/21/2021] [Accepted: 06/27/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a heterogeneous disease with many somatic mutations defining its genomic instability. Alternative Splicing (AS) events, are essential for maintaining genomic instability. However, the role of genomic instability-related AS events in CRC has not been investigated. Methods: From The Cancer Genome Atlas (TCGA) program, we obtained the splicing profiles, the single nucleotide polymorphism, transcriptomics, and clinical information of CRC. Combining somatic mutation and AS events data, a genomic instability-related AS signature was constructed for CRC. Mutations analyses, clinical stratification analyses, and multivariate Cox regression analyses evaluated this signature in training set. Subsequently, we validated the sensitivity and specificity of this prognostic signature using a test set and the entire TCGA dataset. We constructed a nomogram for the prognosis prediction of CRC patients. Differentially infiltrating immune cells were screened by using CIBERSORT. Inmmunophenoscore (IPS) analysis was used to evaluate the response of immunotherapy. The AS events-related splicing factors (SF) were analyzed by Pearson’s correlation. The effects of SF regulating the prognostic AS events in proliferation and migration were validated in Caco2 cells. Results: A prognostic signature consisting of seven AS events (PDHA1-88633-ES, KIAA1522-1632-AP, TATDN1-85088-ES, PRMT1-51042-ES, VEZT-23786-ES, AIG1-77972-AT, and PHF11-25891-AP) was constructed. Patients in the high-risk score group showed a higher somatic mutation. The genomic instability risk score was an independent variable associated with overall survival (OS), with a hazard ratio of a risk score of 1.537. The area under the curve of receiver operator characteristic curve of the genomic instability risk score in predicting the OS of CRC patients was 0.733. Furthermore, a nomogram was established and could be used clinically to stratify patients to predict prognosis. Patients defined as high-risk by this signature showed a lower proportion of eosinophils than the low-risk group. Patients with low risk were more sensitive to anti-CTLA4 immunotherapy. Additionally, HSPA1A and FAM50B were two SF regulating the OS-related AS. Downregulation of HSPA1A and FAM50B inhibited the proliferation and migration of Caco2 cells. Conclusion: We constructed an ideal prognostic signature reflecting the genomic instability and OS of CRC patients. HSPA1A and FAM50B were verified as two important SF regulating the OS-related AS.
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Affiliation(s)
- Qiuying Ding
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zhengping Hou
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zhibo Zhao
- The Department of Hepatobiliary Surgery of the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yao Chen
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
| | - Lei Zhao
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
| | - Yue Xiang
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
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26
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Shoji Y, Yokoe T, Kobayashi Y, Murakami T, Bostick PJ, Shiloh Y, Hoon DSB, Bustos MA. UBQLN4 promotes STING proteasomal degradation during cisplatin-induced DNA damage in triple-negative breast cancer. Clin Transl Med 2022; 12:e985. [PMID: 35839317 PMCID: PMC9286529 DOI: 10.1002/ctm2.985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/11/2022] [Accepted: 07/03/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- Yoshiaki Shoji
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
| | - Takamichi Yokoe
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
| | - Yuta Kobayashi
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
| | - Tomohiro Murakami
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
| | - Peter J Bostick
- Mayo Clinic Care Network, Baton Rouge General Medical Center, Baton Rouge, Louisiana, USA
| | - Yosef Shiloh
- David and Inez Myers Laboratory for Cancer Genetics, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, California, USA
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27
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Feng YQ, Zhao AH, Wang JJ, Tian Y, Yan ZH, Dri M, Shen W, De Felici M, Li L. Oxidative stress as a plausible mechanism for zearalenone to induce genome toxicity. Gene 2022; 829:146511. [PMID: 35447234 DOI: 10.1016/j.gene.2022.146511] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 02/27/2022] [Accepted: 04/14/2022] [Indexed: 02/07/2023]
Abstract
Zearalenone (ZEN), a common non-steroidal estrogenic mycotoxin of the Fusarium genus, is one of the most frequent and powerful contaminant of grains and cereal products representing a serious threat for people and livestock health. In fact, ZEN causes cytotoxicity and genotoxicity in a variety of cell types at least in part through binding to estrogen receptors (ERs). The main pathways through which ZEN induces such effects remain, however, elusive. In particular, how the mycotoxin causes DNA damage, dysregulates DNA repair mechanisms, changes epigenome of targeted cells and, not least, affects chromatin conformation and non-coding RNA (ncRNA), is unclear. In the present paper, following extensive review of the literature about such ZEN effects and our own experience in studying the effects of this compound on reproductive processes, we propose that increased production of reactive oxygen species (ROS) and consequently oxidative stress (OS) are central in ZEN genotoxicity. Besides to shed light on the action mechanisms of the mycotoxin, this notion might help to develop effective strategies to counteract its deleterious biological effects.
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Affiliation(s)
- Yan-Qin Feng
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
| | - Ai-Hong Zhao
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Jun-Jie Wang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu Tian
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
| | - Zi-Hui Yan
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
| | - Maria Dri
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Wei Shen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
| | - Massimo De Felici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy.
| | - Lan Li
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China.
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28
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Deng Y, Wang Y, Li L, Miao EA, Liu P. Post-Translational Modifications of Proteins in Cytosolic Nucleic Acid Sensing Signaling Pathways. Front Immunol 2022; 13:898724. [PMID: 35795661 PMCID: PMC9250978 DOI: 10.3389/fimmu.2022.898724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
The innate immune response is the first-line host defense against pathogens. Cytosolic nucleic acids, including both DNA and RNA, represent a special type of danger signal to initiate an innate immune response. Activation of cytosolic nucleic acid sensors is tightly controlled in order to achieve the high sensitivity needed to combat infection while simultaneously preventing false activation that leads to pathologic inflammatory diseases. In this review, we focus on post-translational modifications of key cytosolic nucleic acid sensors that can reversibly or irreversibly control these sensor functions. We will describe phosphorylation, ubiquitination, SUMOylation, neddylation, acetylation, methylation, succinylation, glutamylation, amidation, palmitoylation, and oxidation modifications events (including modified residues, modifying enzymes, and modification function). Together, these post-translational regulatory modifications on key cytosolic DNA/RNA sensing pathway members reveal a complicated yet elegantly controlled multilayer regulator network to govern innate immune activation.
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Affiliation(s)
- Yu Deng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ying Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lupeng Li
- Department of Immunology and Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Edward A. Miao
- Department of Immunology and Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Pengda Liu,
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29
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Ratz L, Brambillasca C, Bartke L, Huetzen MA, Goergens J, Leidecker O, Jachimowicz RD, van de Ven M, Proost N, Siteur B, de Korte-Grimmerink R, Bouwman P, Pulver EM, de Bruijn R, Isensee J, Hucho T, Pandey G, van Lohuizen M, Mallmann P, Reinhardt HC, Jonkers J, Puppe J. Combined inhibition of EZH2 and ATM is synthetic lethal in BRCA1-deficient breast cancer. Breast Cancer Res 2022; 24:41. [PMID: 35715861 PMCID: PMC9206299 DOI: 10.1186/s13058-022-01534-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Background The majority of BRCA1-mutant breast cancers are characterized by a triple-negative phenotype and a basal-like molecular subtype, associated with aggressive clinical behavior. Current treatment options are limited, highlighting the need for the development of novel targeted therapies for this tumor subtype. Methods Our group previously showed that EZH2 is functionally relevant in BRCA1-deficient breast tumors and blocking EZH2 enzymatic activity could be a potent treatment strategy. To validate the role of EZH2 as a therapeutic target and to identify new synergistic drug combinations, we performed a high-throughput drug combination screen in various cell lines derived from BRCA1-deficient and -proficient mouse mammary tumors.
Results We identified the combined inhibition of EZH2 and the proximal DNA damage response kinase ATM as a novel synthetic lethality-based therapy for the treatment of BRCA1-deficient breast tumors. We show that the combined treatment with the EZH2 inhibitor GSK126 and the ATM inhibitor AZD1390 led to reduced colony formation, increased genotoxic stress, and apoptosis-mediated cell death in BRCA1-deficient mammary tumor cells in vitro. These findings were corroborated by in vivo experiments showing that simultaneous inhibition of EZH2 and ATM significantly increased anti-tumor activity in mice bearing BRCA1-deficient mammary tumors.
Conclusion Taken together, we identified a synthetic lethal interaction between EZH2 and ATM and propose this synergistic interaction as a novel molecular combination for the treatment of BRCA1-mutant breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01534-y.
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Affiliation(s)
- Leonie Ratz
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany.
| | - Chiara Brambillasca
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Leandra Bartke
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Maxim A Huetzen
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jonas Goergens
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Orsolya Leidecker
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ron D Jachimowicz
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marieke van de Ven
- Oncode Institute, Amsterdam, The Netherlands.,Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Peter Bouwman
- Oncode Institute, Amsterdam, The Netherlands.,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Emilia M Pulver
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jörg Isensee
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, University Hospital Cologne, Faculty of Medicine, University Cologne, Cologne, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, University Hospital Cologne, Faculty of Medicine, University Cologne, Cologne, Germany
| | - Gaurav Pandey
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Genetics, Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Genetics, Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Mallmann
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, German Cancer Consortium (DKTK Partner Site Essen), Essen, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julian Puppe
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany.
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30
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Schjeide BMM, Schenke M, Seeger B, Püschel GP. Validation of a Novel Double Control Quantitative Copy Number PCR Method to Quantify Off-Target Transgene Integration after CRISPR-Induced DNA Modification. Methods Protoc 2022; 5:mps5030043. [PMID: 35736544 PMCID: PMC9229199 DOI: 10.3390/mps5030043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
In order to improve a recently established cell-based assay to assess the potency of botulinum neurotoxin, neuroblastoma-derived SiMa cells and induced pluripotent stem-cells (iPSC) were modified to incorporate the coding sequence of a reporter luciferase into a genetic safe harbor utilizing CRISPR/Cas9. A novel method, the double-control quantitative copy number PCR (dc-qcnPCR), was developed to detect off-target integrations of donor DNA. The donor DNA insertion success rate and targeted insertion success rate were analyzed in clones of each cell type. The dc-qcnPCR reliably quantified the copy number in both cell lines. The probability of incorrect donor DNA integration was significantly increased in SiMa cells in comparison to the iPSCs. This can possibly be explained by the lower bundled relative gene expression of a number of double-strand repair genes (BRCA1, DNA2, EXO1, MCPH1, MRE11, and RAD51) in SiMa clones than in iPSC clones. The dc-qcnPCR offers an efficient and cost-effective method to detect off-target CRISPR/Cas9-induced donor DNA integrations.
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Affiliation(s)
- Brit-Maren Michaud Schjeide
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany;
- Department of Nutritional Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, 95326 Kulmbach, Germany
- Correspondence:
| | - Maren Schenke
- Research Group Food Toxicology and Alternative/Complementary Methods to Animal Experiments, Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (M.S.); (B.S.)
| | - Bettina Seeger
- Research Group Food Toxicology and Alternative/Complementary Methods to Animal Experiments, Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (M.S.); (B.S.)
| | - Gerhard Paul Püschel
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany;
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31
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Wang X, Zhang H, Ye J, Gao M, Jiang Q, Zhao T, Wang S, Mao W, Wang K, Wang Q, Chen X, Hou X, Han D. Genome Instability-Associated Long Non-Coding RNAs Reveal Biomarkers for Glioma Immunotherapy and Prognosis. Front Genet 2022; 13:850888. [PMID: 35571034 PMCID: PMC9094631 DOI: 10.3389/fgene.2022.850888] [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: 01/08/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Genome instability is a hallmark of tumors and is involved in proliferation, invasion, migration, and treatment resistance of many tumors. However, the relationship of genome instability with gliomas remains unclear. Here, we constructed genome instability-derived long non-coding RNA (lncRNA)-based gene signatures (GILncSig) using genome instability-related lncRNAs derived from somatic mutations. Multiple platforms were used to confirm that the GILncSig were closely related to patient prognosis and clinical characteristics. We found that GILncSig, the glioma microenvironment, and glioma cell DNA methylation-based stemness index (mDNAsi) interacted with each other to form a complex regulatory network. In summary, this study confirmed that GILncSig was an independent prognostic indicator for patients, distinguished high-risk and low-risk groups, and affected immune-cell infiltration and tumor-cell stemness indicators (mDNAsi) in the tumor microenvironment, resulting in tumor heterogeneity and immunotherapy resistance. GILncSig are expected to provide new molecular targets for the clinical treatment of patients with gliomas.
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Affiliation(s)
- Xinzhuang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Zhang
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, China
| | - Junyi Ye
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ming Gao
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qiuyi Jiang
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tingting Zhao
- Biochip Laboratory, Yantai Yu-Huang-Ding Hospital, Qingdao University, Yantai, China
| | - Shengtao Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenbin Mao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kaili Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin Chen
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xu Hou
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dayong Han
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
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32
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Li J, Wei S, Zhang Y, Lu S, Zhang X, Wang Q, Yan J, Yang S, Chen L, Liu Y, Huang Z. Comprehensive Analyses of Mutation-Derived Long-Chain Noncoding RNA Signatures of Genome Instability in Kidney Renal Papillary Cell Carcinoma. Front Genet 2022; 13:874673. [PMID: 35547247 PMCID: PMC9082950 DOI: 10.3389/fgene.2022.874673] [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: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The role of long-chain noncoding RNA (lncRNA) in genomic instability has been demonstrated to be increasingly importance. Therefore, in this study, lncRNAs associated with genomic instability were identified and kidney renal papillary cell carcinoma (KIRP)-associated predictive features were analysed to classify high-risk patients and improve individualised treatment. Methods: The training (n = 142) and test (n = 144) sets were created using raw RNA-seq and patient’s clinical data of KIRP obtained from The Cancer Genome Atlas (TCGA).There are 27 long-chain noncoding RNAs (lncRNAs) that are connected with genomic instability, these lncRNAs were identified using the ‘limma’ R package based on the numbers of somatic mutations and lncRNA expression profiles acquired from KIRP TCGA cohort. Furthermore, Cox regression analysis was carried out to develop a genome instability-derived lncRNA-based gene signature (GILncSig), whose prognostic value was confirmed in the test cohort as well as across the entire KIRP TCGA dataset. Results: A GILncSig derived from three lncRNAs (BOLA3-AS1, AC004870, and LINC00839), which were related with poor KIRP survival, was identified, which was split up into high- and low-risk groups. Additionally, the GILncSig was found to be an independent prognostic predictive index in KIRP using univariate and multivariate Cox analysis. Furthermore, the prognostic significance and characteristics of GilncSig were confirmed in the training test and TCGA sets. GilncSig also showed better predictive performance than other prognostic lncRNA features. Conclusion: The function of lncRNAs in genomic instability and the genetic diversity of KIRP were elucidated in this work. Moreover, three lncRNAs were screened for prediction of the outcome of KIRP survival and novel insights into identifying cancer biomarkers related to genomic instability were discussed.
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Affiliation(s)
- Jian Li
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Shimei Wei
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yan Zhang
- Department of Pediatrics, Shanxi Children's Hospital, Taiyuan, China
| | - Shuangshuang Lu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiaoxu Zhang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qiong Wang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiawei Yan
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Sanju Yang
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Liying Chen
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Yunguang Liu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhijing Huang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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33
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MRNIP condensates promote DNA double-strand break sensing and end resection. Nat Commun 2022; 13:2638. [PMID: 35551189 PMCID: PMC9098523 DOI: 10.1038/s41467-022-30303-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/25/2022] [Indexed: 01/07/2023] Open
Abstract
The rapid recognition of DNA double-strand breaks (DSBs) by the MRE11/RAD50/NBS1 (MRN) complex is critical for the initiation of DNA damage response and DSB end resection. Here, we show that MRN complex interacting protein (MRNIP) forms liquid-like condensates to promote homologous recombination-mediated DSB repair. The intrinsically disordered region is essential for MRNIP condensate formation. Mechanically, the MRN complex is compartmentalized and concentrated into MRNIP condensates in the nucleus. After DSB formation, MRNIP condensates move to the damaged DNA rapidly to accelerate the binding of DSB by the concentrated MRN complex, therefore inducing the autophosphorylation of ATM and subsequent activation of DNA damage response signaling. Meanwhile, MRNIP condensates-enhanced MRN complex loading further promotes DSB end resection. In addition, data from xenograft models and clinical samples confirm a correlation between MRNIP and radioresistance. Together, these results reveal an important role of MRNIP phase separation in DSB response and the MRN complex-mediated DSB end resection. The MRN complex is a critical sensor and processor of DNA double-strand breaks (DSBs). Here, the authors show that MRNIP forms liquid-like condensates to accelerate the MRN-mediated sensing and end resection of DSB, thereby promoting DSB repair.
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34
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Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Nat Commun 2022; 13:2436. [PMID: 35508466 PMCID: PMC9068765 DOI: 10.1038/s41467-022-29960-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/09/2022] [Indexed: 12/13/2022] Open
Abstract
Proteogenomic analyses of hepatocellular carcinomas (HCC) have focused on early-stage, HBV-associated HCCs. Here we present an integrated proteogenomic analysis of HCCs across clinical stages and etiologies. Pathways related to cell cycle, transcriptional and translational control, signaling transduction, and metabolism are dysregulated and differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. We describe candidate copy number-driven driver genes involved in epithelial-to-mesenchymal transition, the Wnt-β-catenin, AKT/mTOR and Notch pathways, cell cycle and DNA damage regulation. The targetable aurora kinase A and CDKs are upregulated. CTNNB1 and TP53 mutations are associated with altered protein phosphorylation related to actin filament organization and lipid metabolism, respectively. Integrative proteogenomic clusters show that HCC constitutes heterogeneous subgroups with distinct regulation of biological processes, metabolic reprogramming and kinase activation. Our study provides a comprehensive overview of the proteomic and phophoproteomic landscapes of HCCs, revealing the major pathways altered in the (phospho)proteome. Proteogenomic analyses of hepatocellular carcinomas (HCC) have focused on early-stage, HBV-associated tumours and lacked information about the phosphoproteome. Here, the authors present a comprehensive HCC proteogenomics and phosphoproteomics study in patient samples from multiple etiologies and stages.
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35
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Zhu L, Kuang X, Zhang G, Liang L, Liu D, Hu B, Xie Z, Li H, Liu H, Ye M, Chen X, Liu J. Albendazole induces immunotherapy response by facilitating ubiquitin-mediated PD-L1 degradation. J Immunother Cancer 2022; 10:jitc-2021-003819. [PMID: 35577504 PMCID: PMC9115032 DOI: 10.1136/jitc-2021-003819] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have been increasingly used in patients with various cancers and have shown efficient therapeutic outcomes. However, fewer than 40% of cases across multiple cancer types show a response to ICIs. Therefore, developing more efficient combinational approaches with ICIs and revealing the underlying mechanisms are important goals for achieving rapid clinical transformation and application. Methods The effects on antitumor immunity activity of albendazole (ABZ) and the synergistic effects of ABZ with CD73 blockade were investigated in the melanoma B16F10 and the Lewis lung cancer tumor-bearing immune-competent mice models. The mechanism of ABZ reducing PD-L1 protein level through suppressing UBQLN4 was identified and validated through immunoprecipitation-mass spectrometry and molecular methods. Bioinformatics and anti-PD-1 therapy melanoma patients samples analysis were used to assess the level of UBQLN4/PD-L1 in the therapeutic efficacy of anti-PD-1 therapy. Results ABZ induces CD8+ T cell activity and subsequent immunotherapy response associated with suppression of PD-L1 protein level. Mechanistically, we revealed that ABZ promotes ubiquitin-mediated degradation of PD-L1 via suppressing UBQLN4, which was bound to PD-L1 and stabilized PD-L1 protein. Preclinically, genetic deletion or target inhibition of CD73 showed synergistic effects with ABZ treatment in the immune-competent mice models. Significantly, UBQLN4 and PD-L1 levels were higher in the tumor region of responders versus non-responders and correlated with better progression-free survival and overall survival in anti-PD-1 therapy melanoma patients. Conclusions Our findings revealed a previously unappreciated role of ABZ in antitumor immunity by inducing ubiquitin-mediated PD-L1 protein degradation, identified predictors for assessing the therapeutic efficacy of anti-PD-1 therapy, and provided novel therapeutic possibility by combination treatment of ABZ and CD73 blockade in cancers.
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Affiliation(s)
- Lin Zhu
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinwei Kuang
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guanxiong Zhang
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Research and Development, Beijing GAP Biotechnology Co., Ltd, Beijing, China
| | - Long Liang
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dandan Liu
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Hu
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zuozhong Xie
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Li
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China .,Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China.,Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan, China
| | - Hong Liu
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China .,Research Center of Molecular Metabolomics, Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, Hunan, China
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Zhu J, Huang Q, Peng X, Luo C, Liu S, Liu Z, Wu X, Luo H. Identification of LncRNA Prognostic Signature Associated With Genomic Instability in Pancreatic Adenocarcinoma. Front Oncol 2022; 12:799475. [PMID: 35433487 PMCID: PMC9012103 DOI: 10.3389/fonc.2022.799475] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Genomic instability (GI) is a critical feature of cancer which plays a key role in the occurrence and development of pancreatic adenocarcinoma (PAAD). Long non-coding RNA (LncRNA) is an emerging prognostic biomarker because it is involved in regulating GI. Recently, researchers used such GI-related LncRNAs (GILncRNAs) to establish a prognostic signature for patients with cancer and helped in predicting the overall prognosis of the patients. However, it is evident that patients with PAAD still lack such prognostic signature constructed with GILncRNA. Methods The present study screened GILncRNAs from 83 patients with PAAD. Prognosis-related GILncRNAs were identified by univariate Cox regression analysis. The correlation coefficients of these GILncRNAs were obtained by multivariate Cox regression analysis and used to construct a signature. The signature in the present study was then assessed through survival analysis, mutation correlation analysis, independent prognostic analysis, and clinical stratification analysis in the training set and validated in the testing as well as all TCGA set. The current study performed external clinical relevance validation of the signature and validated the effect of AC108134.2 in GILncSig on PAAD using in vitro experiments. Finally, the function of GILncRNA signature (GILncSig) dependent on Gene Ontology enrichment analysis was explored and chemotherapeutic drug sensitivity analysis was also performed. Results Results of the present study found that a total of 409 GILncRNAs were identified, 5 of which constituted the prognostic risk signature in this study, namely, AC095057.3, AC108134.2, AC124798.1, AL606834.1, and AC104695.4. It was found that the signature of the present study was better than others in predicting the overall survival and applied to patients with PAAD of all ages, genders, and tumor grades. Further, it was noted that the signature of the current study in the GSE102238, was correlated with tumor length, and tumor stage of patients with PAAD. In vitro, functional experiments were used in the present study to validate that AC108134.2 is associated with PAAD genomic instability and progression. Notably, results of the pRRophetic analysis in the current study showed that the high-risk group possessed reverse characteristics and was sensitive to chemotherapy. Conclusions In conclusion, it was evident that the GILncSig used in the present study has good prognostic performance. Therefore, the signature may become a potential sensitive biological indicator of PAAD chemotherapy, which may help in clinical decision-making and management of patients with cancer.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Qian Huang
- Department of General Practice, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Chen Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xun Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongliang Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Liu J, Cui G, Ye J, Wang Y, Wang C, Bai J. Comprehensive Analysis of the Prognostic Signature of Mutation-Derived Genome Instability-Related lncRNAs for Patients With Endometrial Cancer. Front Cell Dev Biol 2022; 10:753957. [PMID: 35433686 PMCID: PMC9012522 DOI: 10.3389/fcell.2022.753957] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Emerging evidence shows that genome instability-related long non-coding RNAs (lncRNAs) contribute to tumor–cell proliferation, differentiation, and metastasis. However, the biological functions and molecular mechanisms of genome instability-related lncRNAs in endometrial cancer (EC) are underexplored.Methods: EC RNA sequencing and corresponding clinical data obtained from The Cancer Genome Atlas (TCGA) database were used to screen prognostic lncRNAs associated with genomic instability via univariate and multivariate Cox regression analysis. The genomic instability-related lncRNA signature (GILncSig) was developed to assess the prognostic risk of high- and low-risk groups. The prediction performance was analyzed using receiver operating characteristic (ROC) curves. The immune status and mutational loading of different risk groups were compared. The Genomics of Drug Sensitivity in Cancer (GDSC) and the CellMiner database were used to elucidate the relationship between the correlation of prognostic lncRNAs and drug sensitivity. Finally, we used quantitative real-time PCR (qRT-PCR) to detect the expression levels of genomic instability-related lncRNAs in clinical samples.Results: GILncSig was built using five lncRNAs (AC007389.3, PIK3CD-AS2, LINC01224, AC129507.4, and GLIS3-AS1) associated with genomic instability, and their expression levels were verified using qRT-PCR. Further analysis revealed that risk score was negatively correlated with prognosis, and the ROC curve demonstrated the higher accuracy of GILncSig. Patients with a lower risk score had higher immune cell infiltration, a higher immune score, lower tumor purity, higher immunophenoscores (IPSs), lower mismatch repair protein expression, higher microsatellite instability (MSI), and a higher tumor mutation burden (TMB). Furthermore, the level of expression of prognostic lncRNAs was significantly related to the sensitivity of cancer cells to anti-tumor drugs.Conclusion: A novel signature composed of five prognostic lncRNAs associated with genome instability can be used to predict prognosis, influence immune status, and chemotherapeutic drug sensitivity in EC.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Ye
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yutong Wang
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Can Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianling Bai
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, Nanjing, China
- *Correspondence: Jianling Bai,
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Wang LN, Huang KJ, Wang L, Cheng HY. Overexpression of Ubiquilin4 is associated with poor prognosis in patients with cervical cancer. World J Clin Cases 2022; 10:2783-2791. [PMID: 35434088 PMCID: PMC8968826 DOI: 10.12998/wjcc.v10.i9.2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ubiquilins (UBQLNs) are important factors for cell proteostasis maintenance. UBQLNs are involved in the modulation of the cell cycle, as well as in apoptosis, membrane receptors regulation, DNA repair, epithelial-mesenchymal transition, and miRNA activities. They also affect the selection of double-strand break repair pathways. Abnormal UBQLNs expression can lead to many diseases, including cancer. Studies have found that the expression of Ubiquilin4 (UBQLN4) is associated with the development of several tumor types. However, the association between UBQLN4 and cervical cancer has not been examined yet.
AIM To investigate the expression of UBQLN4 in cervical cancer and to evaluate its correlation with disease prognosis.
METHODS Immunohistochemistry was performed to examine the expression of UBQLN4 in 117 cervical cancer tissues and 32 matching pericervical tissues. Paired t-test (two-tailed) was used to compare the differences between groups. We collected patients’ clinical characteristics, including age, histological grade, pathologic type, lymph node metastasis, and FIGO stage (2018) and compared them by chi-square test. All patients were followed for 5.5 to 6.8 years. Kaplan-Meier method and log-rank test were used to compare the differences in the overall survival (OS) and progression-free survival (PFS) among the different groups.
RESULTS Overexpression of UBQLN4 was observed in 70.9% (83/117) of all cervical cancer tissues and in 15.6% (5/32) of the paired parauterine tissues. The expression of UBQLN4 was associated with lymph node metastasis, poor differentiation, and advanced stage, but the difference was not significant. Kaplan-Meier and log-rank test results suggested the high expression of UBQLN4 was associated with short OS and PFS. Regardless of UBQLN4 expression, the patient age and FIGO stage were also associated with disease prognosis. The statistically significant variables obtained from univariate the Kaplan-Meier analysis were subjected to Cox multivariate survival regression analysis, which showed that, in addition to the FIGO stage and age, UBQLN4 was also an independent prognostic marker for OS and PFS (P = 0.011 and P = 0.024, respectively).
CONCLUSION The overexpression of UBQLN4 was associated with poor prognosis in cervical cancer. Our study proposed a novel prognostic factor and improved the existing understanding of the pathogenesis of cervical cancer.
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Affiliation(s)
- Li-Na Wang
- Department of Gynaecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Ke-Jin Huang
- Department of Gynaecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Le Wang
- Department of Gynaecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Hai-Yan Cheng
- Department of Gynaecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
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Mohan HM, Trzeciakiewicz H, Pithadia A, Crowley EV, Pacitto R, Safren N, Trotter B, Zhang C, Zhou X, Zhang Y, Basrur V, Paulson HL, Sharkey LM. RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cell Mol Life Sci 2022; 79:176. [PMID: 35247097 PMCID: PMC9376861 DOI: 10.1007/s00018-022-04170-z] [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: 04/19/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The brain-expressed ubiquilins (UBQLNs) 1, 2 and 4 are a family of ubiquitin adaptor proteins that participate broadly in protein quality control (PQC) pathways, including the ubiquitin proteasome system (UPS). One family member, UBQLN2, has been implicated in numerous neurodegenerative diseases including ALS/FTD. UBQLN2 typically resides in the cytoplasm but in disease can translocate to the nucleus, as in Huntington's disease where it promotes the clearance of mutant Huntingtin. How UBQLN2 translocates to the nucleus and clears aberrant nuclear proteins, however, is not well understood. In a mass spectrometry screen to discover UBQLN2 interactors, we identified a family of small (13 kDa), highly homologous uncharacterized proteins, RTL8, and confirmed the interaction between UBQLN2 and RTL8 both in vitro using recombinant proteins and in vivo using mouse brain tissue. Under endogenous and overexpressed conditions, RTL8 localizes to nucleoli. When co-expressed with UBQLN2, RTL8 promotes nuclear translocation of UBQLN2. RTL8 also facilitates UBQLN2's nuclear translocation during heat shock. UBQLN2 and RTL8 colocalize within ubiquitin-enriched subnuclear structures containing PQC components. The robust effect of RTL8 on the nuclear translocation and subnuclear localization of UBQLN2 does not extend to the other brain-expressed ubiquilins, UBQLN1 and UBQLN4. Moreover, compared to UBQLN1 and UBQLN4, UBQLN2 preferentially stabilizes RTL8 levels in human cell lines and in mouse brain, supporting functional heterogeneity among UBQLNs. As a novel UBQLN2 interactor that recruits UBQLN2 to specific nuclear compartments, RTL8 may regulate UBQLN2 function in nuclear protein quality control.
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Affiliation(s)
- Harihar Milaganur Mohan
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | | | - Amit Pithadia
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Emily V Crowley
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Regina Pacitto
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Bryce Trotter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
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Yan Y, Ren L, Liu Y, Liu L. Development and Validation of Genome Instability-Associated lncRNAs to Predict Prognosis and Immunotherapy of Patients With Hepatocellular Carcinoma. Front Genet 2022; 12:763281. [PMID: 35154241 PMCID: PMC8832282 DOI: 10.3389/fgene.2021.763281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
The pathophysiology of hepatocellular carcinoma (HCC) is prevalently related to genomic instability. However, research on the association of extensive genome instability lncRNA (GILnc) with the prognosis and immunotherapy of HCC remains scarce. We placed the top 25% of somatic mutations into the genetically unstable group and placed the bottom 25% of somatic mutations into the genetically stable group, and then to identify different expression of GILnc between the two groups. Then, LASSO was used to identify the most powerful prognostic GILnc, and a risk score for each patient was calculated according to the formula. Based on a computational frame, 245 different GILncs in HCC were identified. An eight GILnc model was successfully established to predict overall survival in HCC patients based on LASSO, then we divided HCC patients into high-risk and low-risk groups, and a significantly shorter overall survival in the high-risk group was observed compared to those in the low-risk group, and this was validated in GSE76427 and Tongji cohorts. GSEA revealed that the high-risk group was more likely to be enriched in cancer-specific pathways. Besides, the GILnc signature has greater prognostic significance than TP53 mutation status alone, and it is capable of identifying intermediate subtype groups existing with partial TP53 functionality in TP53 wild-type patients. Importantly, the high-risk group was associated with the therapeutic efficacy of PD-L1 blockade, suggesting that the development of potential drugs targeting these GILnc could aid the clinical benefits of immunotherapy. Finally, the GILnc signature model is better than the prediction performance of two recently published lncRNA signatures. In summary, we applied bioinformatics approaches to suggest that an eight GILnc model could serve as prognostic biomarkers to provide a novel direction to explore the pathogenesis of HCC.
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Affiliation(s)
- Yifeng Yan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Forensic Medicine, Wannan Medical College, Wuhu, China
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Liang Liu, ,
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Yi C, Zhang X, Chen X, Huang B, Song J, Ma M, Yuan X, Zhang C. A novel 8-genome instability-associated lncRNAs signature predicting prognosis and drug sensitivity in gastric cancer. Int J Immunopathol Pharmacol 2022; 36:1-15. [PMID: 35696730 PMCID: PMC9203952 DOI: 10.1177/03946320221103195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genome instability lncRNA (GILnc) is prevalently related with gastric cancer (GC) pathophysiology. However, the study on the relationship GILnc and prognosis and drug sensitivity of GC remains scarce. METHOD We extracted expression data of 375 GC patients from TCGA cohort and 205 GC patients from GSE26942 cohort. Then, lncRNA was separated from expression data, and systematically characterized the 8 marker lncRNAs using the LASSO method. Next, we constructed a GILnc model (GILnc score) to quantify the GILnc index of each GC patient. Finally, we analyzed the relationship between GILnc score and clinical traits including survival outcomes, TP53, and drug sensitivity of GC. RESULTS Based on a computational frame, 205 GILncs in GC has been identified. Then, a 8 GILncs was successfully established to predict overall survival in GC patients based on LASSO analysis, divided GC samples into high GILnc score and low GILnc score groups with significantly different outcome and was validated in multiple independent patient cohorts. Furthermore, GILnc model is better than the prediction performance of two recently published lncRNA signatures, and the high GILnc score group was more sensitive to mitomycin. Besides, the GILnc score has greater prognostic significance than TP53 mutation status alone and is capable of identifying intermediate subtype group existing with partial TP53 functionality in TP53 wild-type patients. Finally, GILnc signature as verified in GSE26942. CONCLUSION We applied bioinformatics approaches to suggest that a 8 GILnc signature could serve as prognostic biomarkers, and provide a novel direction to explore the pathogenesis of GC.
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Affiliation(s)
- Changhong Yi
- Department of Interventional, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xiulan Zhang
- Department of Nuclear Medicine, The First People’s Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xia Chen
- Department of Oncology, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, China
| | - Birun Huang
- Department of Vascular Surgery, The First People’s Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Jing Song
- Department of Nursing, Hubei College of Chinese Medicine, Jingzhou, People's Republic of China
| | - Minghui Ma
- Department of Gastrointestinal Surgery, Maoming People’s Hospital, Maoming, China
| | - Xiaolu Yuan
- Department of Gastrointestinal Surgery, Maoming People’s Hospital, Maoming, China
| | - Chaohao Zhang
- Department of Gastrointestinal Surgery, Maoming People’s Hospital, Maoming, China
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UBQLN4 is activated by C/EBPβ and exerts oncogenic effects on colorectal cancer via the Wnt/β-catenin signaling pathway. Cell Death Dis 2021; 7:398. [PMID: 34930912 PMCID: PMC8688525 DOI: 10.1038/s41420-021-00795-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/24/2021] [Accepted: 12/10/2021] [Indexed: 01/17/2023]
Abstract
Ubiquilin 4 (UBQLN4) is an important member of the ubiquitin-like protein family. An increasing number of studies have shown that UBQLN4 is an important regulator of tumorigenesis. Nevertheless, the biological function and detailed mechanisms of UBQLN4 in colorectal cancer (CRC) development and progression remain unclear. Here, we identified UBQLN4 upregulation in CRC tissues and it is positively associated with CRC size, TNM stage, and lymphatic metastasis. Patients with high UBQLN4 expression had a poor prognosis. Functionally, overexpression of UBQLN4 significantly promoted CRC cell proliferation, migration, and invasion, while UBQLN4 silencing elicited the opposite effect. This result was consistent with the conclusion that UBQLN4 expression correlated positively with the CRC size and lymphatic metastasis. In vivo, UBQLN4 silencing also inhibited tumor growth. Mechanistically, using gene set enrichment analysis (GSEA) and western blot experiments, we identified that UBQLN4 activated the Wnt/β-catenin signaling pathway to upregulate β-catenin and c-Myc expression, thereby promoting CRC proliferation, migration and invasion. A rescue experiment further verified this conclusion. Dual luciferase reporter, real-time quantitative PCR (RT-qPCR), western blot and chromatin immunoprecipitation (ChIP) assays indicated that the transcription factor CCAAT/enhancer-binding protein beta (C/EBPβ) directly bound to the UBQLN4 core promoter region and activated its transcription, upregulating β-catenin and c-Myc expression to promote CRC progression. Thus, our findings suggest that UBQLN4 is a key oncogene in CRC and may be a promising target for the diagnosis and treatment of patients with CRC.
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Kilgas S, Kiltie AE, Ramadan K. Immunofluorescence microscopy-based detection of ssDNA foci by BrdU in mammalian cells. STAR Protoc 2021; 2:100978. [PMID: 34888531 PMCID: PMC8634038 DOI: 10.1016/j.xpro.2021.100978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA end resection converts broken ends of double-stranded DNA (dsDNA) to 3'-single-stranded DNA (3'-ssDNA). The extent of resection regulates DNA double-strand break (DSB) repair pathway choice and thereby genomic stability. Here, we characterize an optimized immunofluorescence (IF) microscopy-based protocol for measuring ssDNA in mammalian cells by labeling genomic DNA with 5-bromo-2'-deoxyuridine (BrdU). BrdU foci can be detected under non-denaturing conditions by anti-BrdU antibody, providing an accurate and reliable readout of DNA end resection in most mammalian cell lines. For complete details on the use and execution of this protocol, please refer to Kilgas et al. (2021).
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Affiliation(s)
- Susan Kilgas
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Anne E. Kiltie
- Rowett Institute, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Kristijan Ramadan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
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Wu J, Ren X, Wang N, Zhou R, Chen M, Cai Y, Lin S, Zhang H, Xie X, Dang C, Zhang S, Zhou Z. A Mutation-Related Long Noncoding RNA Signature of Genome Instability Predicts Immune Infiltration and Hepatocellular Carcinoma Prognosis. Front Genet 2021; 12:779554. [PMID: 34880908 PMCID: PMC8645863 DOI: 10.3389/fgene.2021.779554] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have been discovered to play a regulatory role in genomic instability (GI), which participates in the carcinogenesis of various cancers, including hepatocellular carcinoma (HCC). We endeavored to establish a GI-derived lncRNA signature (GILncSig) as a potential biomarker and explore its impact on immune infiltration and prognostic significance. Methods: Combining expression and somatic mutation profiles from The Cancer Genome Atlas database, we identified GI-related lncRNAs and conducted functional analyses on co-expressed genes. Based on Cox regression analysis, a GILncSig was established in the training cohort (n = 187), and an independent testing patient cohort (n = 183) was used to validate its predictive ability. Kaplan-Meier method and receiver operating characteristic curves were adopted to evaluate the performance. The correlation between GI and immune infiltration status was investigated based on the CIBERSORT algorithm and single sample gene set enrichment analysis. In addition, a comprehensive nomogram integrating the GILncSig and clinicopathological variables was constructed to efficiently assess HCC patient prognosis in clinical applications. Results: A total of 88 GI-related lncRNAs were screened out and the functional analyses indicated diversified effects on HCC progression. The GILncSig was established using four independent lncRNAs (AC116351.1, ZFPM2-AS1, AC145343.1, and MIR210HG) with significant prognostic value (p < 0.05). Following evaluation with the GILncSig, low-risk patients had significantly better clinical outcomes than high-risk patients in the training cohort (p < 0.001), which was subsequently validated in the independent testing cohort. High-risk group exhibited more immunocyte infiltration including B cells memory, macrophages M0 and neutrophils and higher expression of HLA gene set and immune checkpoint genes. Compared to existing HCC signatures, the GILncSig showed better prognosis predictive performance [area under the curve (AUC) = 0.709]. Furthermore, an integrated nomogram was constructed and validated to efficiently and reliably evaluate HCC patient prognosis (3-years survival AUC = 0.710 and 5-years survival AUC = 0.707). Conclusion: The GILncSig measuring GI and impacting immune infiltration serves as a potential biomarker and independent predictor of HCC patient prognosis. Our results highlight further investigation of GI and HCC molecular mechanisms.
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Affiliation(s)
- Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengsha Chen
- Department of Anesthesia, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yifan Cai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Xie
- Department of Nuclear Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Guo CR, Mao Y, Jiang F, Juan CX, Zhou GP, Li N. Computational detection of a genome instability-derived lncRNA signature for predicting the clinical outcome of lung adenocarcinoma. Cancer Med 2021; 11:864-879. [PMID: 34866362 PMCID: PMC8817082 DOI: 10.1002/cam4.4471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Evidence has been emerging of the importance of long non-coding RNAs (lncRNAs) in genome instability. However, no study has established how to classify such lncRNAs linked to genomic instability, and whether that connection poses a therapeutic significance. Here, we established a computational frame derived from mutator hypothesis by combining profiles of lncRNA expression and those of somatic mutations in a tumor genome, and identified 185 candidate lncRNAs associated with genomic instability in lung adenocarcinoma (LUAD). Through further studies, we established a six lncRNA-based signature, which assigned patients to the high- and low-risk groups with different prognosis. Further validation of this signature was performed in a number of separate cohorts of LUAD patients. In addition, the signature was found closely linked to genomic mutation rates in patients, indicating it could be a useful way to quantify genomic instability. In summary, this research offered a novel method by through which more studies may explore the function of lncRNAs and presented a possible new way for detecting biomarkers associated with genomic instability in cancers.
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Affiliation(s)
- Chen-Rui Guo
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Mao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Neonatology,, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chen-Xia Juan
- Department of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Li
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Identification of Mutator-Derived lncRNA Signatures of Genomic Instability for Promoting the Clinical Outcome in Hepatocellular Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1205029. [PMID: 34840594 PMCID: PMC8613502 DOI: 10.1155/2021/1205029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/13/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence proves that long noncoding RNA (lncRNA) plays a crucial role in maintaining genomic instability. However, it is significantly absent from exploring genomic instability-associated lncRNAs and discovering their clinical significance. Objective To identify crucial mutator-derived lncRNAs and construct a predictive model for prognosis and genomic instability in hepatocellular carcinoma. Methods First, we constructed a mutator hypothesis-derived calculative framework through uniting the lncRNA expression level and somatic mutation number to screen for genomic instability-associated lncRNA in hepatocellular carcinoma. We then selected mutator-derived lncRNA from the genome instability-associated lncRNA by univariate Cox analysis and Lasso regression analysis. Next, we created a prognosis model with the mutator-derived lncRNA signature. Furthermore, we verified the vital role of the model in the prognosis and genomic instability of hepatocellular carcinoma patients. Finally, we examined the potential relationship between the model and the mutation status of TP53. Results In this study, we screened 88 genome instability-associated lncRNAs and built a prognosis model with four mutator-derived lncRNAs. Moreover, the model was an independent predictor of prognosis and an accurate indicator of genomic instability in hepatocellular carcinoma. Finally, the model could catch the TP53 mutation status, and the model was a more effective indicator than the mutation status of TP53 for hepatocellular carcinoma patients. Conclusion This research adopted a reliable method to analyze the role of lncRNA in genomic instability. Besides, the prognostic model with four mutator-derived lncRNAs is an excellent new indicator of prognosis and genomic instability in hepatocellular carcinoma. In addition, this finding may help clinicians develop therapeutic systems.
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Abstract
DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genome integrity and cell viability. Typically, cells repair DSBs by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The relative use of these two pathways depends on many factors, including cell cycle stage and the nature of the DNA ends. A critical determinant of repair pathway selection is the initiation of 5'→3' nucleolytic degradation of DNA ends, a process referred to as DNA end resection. End resection is essential to create single-stranded DNA overhangs, which serve as the substrate for the Rad51 recombinase to initiate HR and are refractory to NHEJ repair. Here, we review recent insights into the mechanisms of end resection, how it is regulated, and the pathological consequences of its dysregulation.
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Affiliation(s)
- Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; .,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; .,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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Tu G, Peng W, Cai Q, Zhao Z, Peng X, He B, Zhang P, Shi S, Wang X. A Novel Model Based on Genomic Instability-Associated Long Non-Coding RNAs for Predicting Prognosis and Response to Immunotherapy in Patients With Lung Adenocarcinoma. Front Genet 2021; 12:720013. [PMID: 34777461 PMCID: PMC8585772 DOI: 10.3389/fgene.2021.720013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/04/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Emerging scientific evidence has shown that long non-coding RNAs (lncRNAs) exert critical roles in genomic instability (GI), which is considered a hallmark of cancer. To date, the prognostic value of GI-associated lncRNAs (GI-lncRNAs) remains largely unexplored in lung adenocarcinoma (LUAC). The aims of this study were to identify GI-lncRNAs associated with the survival of LUAC patients, and to develop a novel GI-lncRNA-based prognostic model (GI-lncRNA model) for LUAC. Methods: Clinicopathological data of LUAC patients, and their expression profiles of lncRNAs and somatic mutations were obtained from The Cancer Genome Atlas database. Pearson correlation analysis was conducted to identify the co-expressed mRNAs of GI-lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted to determine the main biological function and molecular pathways of the differentially expressed GI-lncRNAs. Univariate and multivariate Cox proportional hazard regression analyses were performed to identify GI-lncRNAs significantly related to overall survival (OS) for construction of the GI-lncRNA model. Kaplan–Meier survival analysis and receiver operating characteristic curve analysis were performed to evaluate the predictive accuracy. The performance of the newly developed GI-lncRNA model was compared with the recently published lncRNA-based prognostic index models. Results: A total of 19 GI-lncRNAs were found to be significantly associated with OS, of which 9 were identified by multivariate analysis to construct the GI-lncRNA model. Notably, the GI-lncRNA model showed a prognostic value independent of key clinical characteristics. Further performance evaluation indicated that the area under the curve (AUC) of the GI-lncRNA model was 0.771, which was greater than that of the TP53 mutation status and three existing lncRNA-based models in predicting the prognosis of patients with LUAC. In addition, the GI-lncRNA model was highly correlated with programed death ligand 1 (PD-L1) expression and tumor mutational burden in immunotherapy for LUAC. Conclusion: The GI-lncRNA model was established and its performance was found to be superior to existing lncRNA-based models. As such, the GI-lncRNA model holds promise as a more accurate prognostic tool for the prediction of prognosis and response to immunotherapy in patients with LUAC.
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Affiliation(s)
- Guangxu Tu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Weilin Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuai Shi
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, China
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Liu Y, Cheng L, Huang W, Cheng X, Peng W, Shi D. Genome Instability-Related miRNAs Predict Survival, Immune Landscape, and Immunotherapy Responses in Gastric Cancer. J Immunol Res 2021; 2021:2048833. [PMID: 34761007 PMCID: PMC8575650 DOI: 10.1155/2021/2048833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Increasing evidence suggests that microRNAs (miRNAs) are involved in genome instability (GI) and drive the occurrence of tumors. However, the role of GI-related miRNAs in gastric cancer (GC) remains largely unknown. Herein, we developed a novel GI-related miRNA signature (GIMiSig) and further investigated its role in prognosis, the immune landscape, and immunotherapy responses in GC patients. METHODS An analysis of somatic mutation data on 434 gastric cancer cases from The Cancer Genome Atlas (TCGA) database was performed, thereby generating genome stability (GS) and GI groups. By detecting differentially expressed miRNAs between the GS and GI groups that were associated with overall survival, 8 miRNAs were identified and used to construct the GIMiSig. RESULTS The GIMiSig showed high accuracy in detecting GC patients. Using GIMiSig to stratify the patients into the high- and low-risk subgroups to predict survival outperformed the use of regular clinical features such as age, gender, or disease stage. Patients with low risk had a more favorable survival time than those with high risk. More importantly, the high-risk patients were associated with decreased UBQLN4 expression, higher accumulation of immune cells, lower Titin (TTN) mutation frequency, worse immunotherapy efficacy, and cancer-associated pathways. Conversely, the low-risk patients were characterized by UBQLN4 overexpression, lower fraction of immune cells, higher TTN mutation frequency, better response to immunotherapy, and GI-related pathways. CONCLUSION In summary, we constructed a novel GIMiSig that could stratify GC patients into distinct risk groups that have different survival outcomes and immunotherapy efficacy. The results may provide new clues for improving GC outcomes.
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Affiliation(s)
- Yaqiong Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Regenerative Medicine Institute (REMEDI), CURAM, National University of Ireland Galway, H91TK33, Galway, Ireland
| | - Lin Cheng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Wei Huang
- Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xin Cheng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Dazun Shi
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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50
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Song ZB, Yu Y, Zhang GP, Li SQ. Genomic Instability of Mutation-Derived Gene Prognostic Signatures for Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:728574. [PMID: 34676211 PMCID: PMC8523793 DOI: 10.3389/fcell.2021.728574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major cancer-related deaths worldwide. Genomic instability is correlated with the prognosis of cancers. A biomarker associated with genomic instability might be effective to predict the prognosis of HCC. In the present study, data of HCC patients from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases were used. A total of 370 HCC patients from the TCGA database were randomly classified into a training set and a test set. A prognostic signature of the training set based on nine overall survival (OS)–related genomic instability–derived genes (SLCO2A1, RPS6KA2, EPHB6, SLC2A5, PDZD4, CST2, MARVELD1, MAGEA6, and SEMA6A) was constructed, which was validated in the test and TCGA and ICGC sets. This prognostic signature showed more accurate prediction for prognosis of HCC compared with tumor grade, pathological stage, and four published signatures. Cox multivariate analysis revealed that the risk score could be an independent prognostic factor of HCC. A nomogram that combines pathological stage and risk score performed well compared with an ideal model. Ultimately, paired differential expression profiles of genes in the prognostic signature were validated at mRNA and protein level using HCC and paratumor tissues obtained from our institute. Taken together, we constructed and validated a genomic instability–derived gene prognostic signature, which can help to predict the OS of HCC and help us to explore the potential therapeutic targets of HCC.
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Affiliation(s)
- Ze-Bing Song
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yang Yu
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guo-Pei Zhang
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shao-Qiang Li
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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