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Liu Y, Yang J, Li X, Chen S, Zhu C, Shi Y, Dang S, Zhang W, Li W. Pan-cancer analysis reveals the characteristics and roles of tooth agenesis mutant genes. Medicine (Baltimore) 2023; 102:e36001. [PMID: 38115305 PMCID: PMC10727548 DOI: 10.1097/md.0000000000036001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 12/21/2023] Open
Abstract
Tooth development is regulated by numerous genes and signaling pathways. Some studies suggest that mutations in these genes may be associated with several cancer types. However, the tooth agenesis mutated genes role in the prognosis and their clinical therapeutic potentials in pan-cancer have not been elaborately explored. Moreover, the intrinsic correlation between tooth agenesis and cancers also needs to be further verified. We preliminarily analyzed expression levels and prognostic values of causative genes of tooth agenesis, and explored the correlation between the expression of tooth agenesis mutated genes and TME, Stemness score, clinical characteristic, immune subtype, and drug sensitivity in pan-cancer, which based on updated public databases and integrated some bioinformatics analysis methods. In addition, we conducted the enrichment analysis of tooth agenesis mutant genes from KOBAS database. We observed that TA mutant genes had significant gene expression differences in multiple cancer types compared with normal tissues. The expression of causative genes of TA is associated with the prognosis in several cancers from different databases. For example, AXIN2 and MSX1 were correlated to the overall survival (OS) of uterine corpus endometrial carcinoma. PAX9 and TP63 were related to OS of lung squamous cell carcinoma. And TP63 was associated with OS in breast invasive carcinoma and pancreatic adenocarcinoma. Furthermore, the expression of TA mutant genes also has a significant correlation with stromal and immune scores, and RNA stemness score and DNA stemness score in pan-cancer. Besides, we observed that all causative genes of TA were significantly correlated with immune subtypes. Moreover, KEGG pathway analysis showed that causative genes of TA were associated with the development and progression of breast cancer, basal cell carcinoma, gastric cancer, and hepatocellular carcinoma. Finally, AXIN2 expression has a significantly positive or negative correlation with drug sensitivity. Our study indicates the great potential of TA mutant genes as biomarkers for prognosis and provides valuable strategies for further investigation of TA mutant genes as potential therapeutic targets in cancers. Our study can further verify that there may be an intrinsic correlation between tooth agenesis and the occurrence of multiple cancers.
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Affiliation(s)
- Yating Liu
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jie Yang
- Department of Pediatric Dentistry, Peking University School of Stomatology, Beijing, China
| | - Xinyu Li
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Shanshan Chen
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Changyu Zhu
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yijun Shi
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Shoutao Dang
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Weitao Zhang
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Colaco JC, Chandrasekaran AP, Karapurkar JK, Birappa G, Rajkumar S, Gowda DAA, Suresh B, Lee J, Singh V, Hong SH, Kim KS, Ramakrishna S. βTrCP1 promotes SLC35F2 protein ubiquitination and inhibits cancer progression in HeLa cells. Biochem Biophys Res Commun 2023; 682:27-38. [PMID: 37801987 DOI: 10.1016/j.bbrc.2023.09.095] [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: 07/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
The solute carrier family 35 F2 (SLC35F2) belongs to membrane-bound carrier proteins that are associated with multiple cancers. The main factor that determines cancer progression is the expression level of SLC35F2. Thus, identifying the E3 ligase that controls SLC35F2 protein abundance in cancer cells is critical. Here, we identified βTrCP1 interacting with and reducing the SLC35F2 protein level. βTrCP1 signals SLC35F2 protein ubiquitination and reduces SLC35F2 protein half-life. The mRNA expression pattern between βTrCP1 and SLC35F2 across a panel of cancer cell lines showed a negative correlation. Additionally, the depletion of βTrCP1 accumulated SLC35F2 protein and promoted SLC35F2-mediated cell growth, migration, invasion, and colony formation ability in HeLa cells. Overall, we demonstrate that βTrCP1 acts as a tumor suppressor by controlling SLC35F2 protein abundance in cancer cells. The depletion of βTrCP1 promotes SLC35F2-mediated carcinogenesis. Thus, we envision that βTrCP1 may be a potential target for cancer therapeutics.
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Affiliation(s)
- Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | | | | | - Girish Birappa
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Sripriya Rajkumar
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - D A Ayush Gowda
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Junwon Lee
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Eonjuro 211, Gangnam-Gu, Seoul, 06273, South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, 382715, Gujarat, India
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea.
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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Karapurkar JK, Kim MS, Colaco JC, Suresh B, Sarodaya N, Kim DH, Park CH, Hong SH, Kim KS, Ramakrishna S. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. J Exp Clin Cancer Res 2023; 42:121. [PMID: 37170124 PMCID: PMC10176696 DOI: 10.1186/s13046-023-02694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The repressor element-1 silencing transcription factor (REST), a master transcriptional repressor, is essential for maintenance, self-renewal, and differentiation in neuroblastoma. An elevated expression of REST is associated with impaired neuronal differentiation, which results in aggressive neuroblastoma formation. E3 ligases are known to regulate REST protein abundance through the 26 S proteasomal degradation pathway in neuroblastoma. However, deubiquitinating enzymes (DUBs), which counteract the function of E3 ligase-mediated REST protein degradation and their impact on neuroblastoma tumorigenesis have remained unexplored. METHODS We employed a CRISPR/Cas9 system to perform a genome-wide knockout of ubiquitin-specific proteases (USPs) and used western blot analysis to screen for DUBs that regulate REST protein abundance. The interaction between USP3 and REST was confirmed by immunoprecipitation and Duolink in situ proximity assays. The deubiquitinating effect of USP3 on REST protein degradation, half-life, and neuronal differentiation was validated by immunoprecipitation, in vitro deubiquitination, protein-turnover, and immunostaining assays. The correlation between USP3 and REST expression was assessed using patient neuroblastoma datasets. The USP3 gene knockout in neuroblastoma cells was performed using CRISPR/Cas9, and the clinical relevance of USP3 regulating REST-mediated neuroblastoma tumorigenesis was confirmed by in vitro and in vivo oncogenic experiments. RESULTS We identified a deubiquitinase USP3 that interacts with, stabilizes, and increases the half-life of REST protein by counteracting its ubiquitination in neuroblastoma. An in silico analysis showed a correlation between USP3 and REST in multiple neuroblastoma cell lines and identified USP3 as a prognostic marker for overall survival in neuroblastoma patients. Silencing of USP3 led to a decreased self-renewal capacity and promoted retinoic acid-induced differentiation in neuroblastoma. A loss of USP3 led to attenuation of REST-mediated neuroblastoma tumorigenesis in a mouse xenograft model. CONCLUSION The findings of this study indicate that USP3 is a critical factor that blocks neuronal differentiation, which can lead to neuroblastoma. We envision that targeting USP3 in neuroblastoma tumors might provide an effective therapeutic differentiation strategy for improved survival rates of neuroblastoma patients.
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Affiliation(s)
| | - Min-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Dong-Ho Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Chang-Hwan Park
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
- College of Medicine, Hanyang University, Seoul, 04763, South Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea.
- College of Medicine, Hanyang University, Seoul, 04763, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea.
- College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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Zhang X, Gong S, Li H, Jiang J, Jia Y, Zhang R, Liu H, Wang A, Jin Y, Lin P. USP18 promotes endometrial receptivity via the JAK/STAT1 and the ISGylation pathway. Theriogenology 2023; 202:110-118. [PMID: 36934584 DOI: 10.1016/j.theriogenology.2023.03.011] [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: 10/08/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Interferon-tau (IFNT), a pregnancy recognition signal in ruminants, promotes the establishment of endometrial receptivity by inducing the expression of interferon-stimulated genes (ISGs) via the Janus kinase/signal transducer and activator of transcription (JAK/STATs) signaling pathway. However, the precise mechanisms remain largely unknown. Ubiquitin-specific protease 18 (USP18) acts specifically on the ISGylation modification system to exert deubiquitination and participates in the regulation of the type I IFN signaling pathway. The purpose of this study was to determine the role and mechanism of USP18 on endometrial receptivity in goat. USP18 was mainly localized in the uterine luminal and glandular epithelium, and its expression levels were significantly increased from days 5-18 of early pregnancy. Progesterone (P4), estradiol (E2), and IFNT significantly stimulated USP18 expression in goat endometrial epithelial cells (gEECs) cultured in vitro. Meanwhile, the markers of endometrial receptivity HOXA11, ITGB1, ITGB3, and ITGB5 were significantly upregulated after USP18 overexpression in gEECs. However, USP18 interference significantly inhibited the expression of HOXA10, ITGB1, ITGB3, and ITGB5 in gEECs. In addition, both the phosphorylation levels of STAT1 and the expression of ISGylation-modified proteins were significantly increased after USP18 silencing in gEECs. Furthermore, pretreatment with the STAT1 inhibitor Fludara markedly restored the effect of USP18 interference in gEECs. In summary, USP18 may play an important role in promoting goat endometrial receptivity by regulating the JAK/STAT1 pathway and ISGylation.
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Affiliation(s)
- Xinyan Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Suhua Gong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haijing Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiaqi Jiang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanni Jia
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruixue Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haokun Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Pengfei Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Xu K, Chu Y, Liu Q, Fan W, He H, Huang F. NEDD4 E3 Ligases: Functions and Mechanisms in Bone and Tooth. Int J Mol Sci 2022; 23:ijms23179937. [PMID: 36077334 PMCID: PMC9455957 DOI: 10.3390/ijms23179937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
Protein ubiquitination is a precisely controlled enzymatic cascade reaction belonging to the post-translational modification of proteins. In this process, E3 ligases catalyze the binding of ubiquitin (Ub) to protein substrates and define specificity. The neuronally expressed developmentally down-regulated 4 (NEDD4) subfamily, belonging to the homology to E6APC terminus (HECT) class of E3 ligases, has recently emerged as an essential determinant of multiple cellular processes in different tissues, including bone and tooth. Here, we place special emphasis on the regulatory role of the NEDD4 subfamily in the molecular and cell biology of osteogenesis. We elucidate in detail the specific roles, downstream substrates, and upstream regulatory mechanisms of the NEDD4 subfamily. Further, we provide an overview of the involvement of E3 ligases and deubiquitinases in the development, repair, and regeneration of another mineralized tissue—tooth.
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Affiliation(s)
- Ke Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510008, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
| | - Yanhao Chu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510008, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
| | - Qin Liu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510008, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
| | - Wenguo Fan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510008, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
| | - Hongwen He
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
- Correspondence: (H.H.); (F.H.)
| | - Fang Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510008, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510008, China
- Correspondence: (H.H.); (F.H.)
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