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Xia X, Pi W, Chen M, Wang W, Cai D, Wang X, Lan Y, Yang H. Emerging roles of PHLPP phosphatases in lung cancer. Front Oncol 2023; 13:1216131. [PMID: 37576883 PMCID: PMC10414793 DOI: 10.3389/fonc.2023.1216131] [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: 05/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Pleckstrin homologous domain leucine-rich repeating protein phosphatases (PHLPPs) were originally identified as protein kinase B (Akt) kinase hydrophobic motif specific phosphatases to maintain the cellular homeostasis. With the continuous expansion of PHLPPs research, imbalanced-PHLPPs were mainly found as a tumor suppressor gene of a variety of solid tumors. In this review, we simply described the history and structures of PHLPPs and summarized the recent achievements in emerging roles of PHLPPs in lung cancer by 1) the signaling pathways affected by PHLPPs including Phosphoinositide 3-kinase (PI3K)/AKT, RAS/RAF/mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) and Protein kinase C (PKC) signaling cascades. 2) function of PHLPPs regulatory factor USP46 and miR-190/miR-215, 3) the potential roles of PHLPPs in disease prognosis, Epidermal growth factor receptors (EGFR)- tyrosine kinase inhibitor (TKI) resistance and DNA damage, 4) and the possible function of PHLPPs in radiotherapy, ferroptosis and inflammation response. Therefore, PHLPPs can be considered as either biomarker or prognostic marker for lung cancer treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - Haihua Yang
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Department of Radiation Oncology, Taizhou Hospital Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
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2
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Wen M, Xu H, Peng H, Sheng Y, Yang W, Yan J. MiR-27a-3p targets USP46 to inhibit the cell proliferation of hepatocellular carcinoma. Chem Biol Drug Des 2022; 100:280-289. [PMID: 35637630 DOI: 10.1111/cbdd.14063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/05/2022] [Accepted: 05/08/2022] [Indexed: 12/24/2022]
Abstract
Micro-RNAs are involved in the occurrence and development of hepatocellular carcinoma (HCC) as potential therapeutic targets for HCC. In this study, we found that miR-27a-3p was highly expressed in HCC, which was associated with lower survival rates of HCC patients. In vivo and in vitro functional experiments confirmed that over-expression or knock-down miR-27a-3p could significantly affect the proliferation ability of HCCLM3 and Huh-7, two HCC cell lines. Ubiquitin-specific protease 46 (USP46) was confirmed as the key target gene of miR-27a-3p in HCC via RNA-seq, quantitative polymerase chain reaction, Western blotting, and luciferase report. When knocking down USP46, the proliferation activity of HCC cells was significantly enhanced, while it was significantly inhibited after over-expressing USP4. Above results suggest that the abnormally over-expressed miR-27a-3p in liver promotes the proliferation of cancer cells and accelerates the development of HCC by targeting inhibition the expression of USP46. Targeting miR-27a-3p may be an effective strategy for prevention and treatment of HCC.
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Affiliation(s)
- Minghua Wen
- Department of Cardiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongyan Xu
- Department of Pathology, The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Hong Peng
- Department of Colorectal Surgery, The 908th Hospital of Chinese People's Liberation Army Joint, Nanchang, China
| | - Yanling Sheng
- Department of Ultrasound, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Wenlong Yang
- Department of Infectious Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinlong Yan
- Department of general surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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3
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Xu L, Zhang B, Li W. Downregulated expression levels of USP46 promote the resistance of ovarian cancer to cisplatin and are regulated by PUM2. Mol Med Rep 2021; 23:263. [PMID: 33576437 PMCID: PMC7893694 DOI: 10.3892/mmr.2021.11902] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer (OC) is a major contributor to cancer‑related mortality in women. Despite numerous drugs being available for the treatment and improving the prognosis of OC, resistance to clinical chemotherapy remains a major obstacle for the treatment of advanced OC. Therefore, determining how to reverse the chemoresistance of OC has become a research hotspot in recent years. The present study aimed to reveal the potential mechanism of OC chemoresistance. Reverse transcription‑quantitative PCR and western blot analysis were performed to detect the expression levels of Ubiquitin‑specific peptidase 46 (USP46) and Pumilio 2 (PUM2) in OC. Cell viability and apoptosis were evaluated by Cell Counting Kit‑8 assay and flow cytometry, respectively. The association between USP46 and PUM2 was assessed by RNA immunoprecipitation. The results of the present study revealed that the expression levels of USP46 which is associated with tumor progression, was downregulated, while PUM2 expression levels were upregulated in cisplatin (DDP)‑resistant OC cells and patient tissues. The downregulation of USP46 expression levels in SKOV3 cells significantly inhibited cell apoptosis and increased cell viability. In SKOV3/DDP cells, the upregulation of USP46 expression levels notably suppressed cell viability and increased cell apoptosis. The results of the RNA immunoprecipitation chip assay demonstrated that PUM2 bound to USP46 and regulated its expression. Furthermore, following the knockdown of USP46 expression, the mRNA and protein expression levels of the cell apoptosis‑related protein, Bcl‑2, were upregulated, whereas the expression levels of caspase‑3, caspase‑9 and Bax were significantly downregulated. In addition, phosphorylated AKT expression levels were notably upregulated. Following the overexpression of USP46 in SKOV3/DDP cells, the opposite trends were observed. In SKOV3 cells, the knockdown of PUM2 could reverse the DDP resistance induced by small interfering RNA‑USP46 as the expression levels of Bcl‑2 were downregulated whereas those of caspase‑3, caspase‑9 and Bax were upregulated compared with the small interfering‑USP46 group. Similarly, in SKOV3/DDP cells, the overexpression of PUM2 could reverse DDP sensitivity induced by the overexpression of USP46. In conclusion, the findings of the present study suggested that the downregulation of USP46 expression levels may promote DDP resistance in OC, which may be regulated by PUM2. Therefore, targeting PUM2/USP46 may be an effective way to reverse DDP resistance in OC.
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Affiliation(s)
- Lei Xu
- Department of Gynecology, People's Hospital of Qingdao West Coast New Area, Qingdao, Shandong 266400, P.R. China
| | - Bin Zhang
- Department of Surgery, People's Hospital of Qingdao West Coast New Area, Qingdao, Shandong 266400, P.R. China
| | - Wenlan Li
- Department of Outpatient Department, People's Hospital of Qingdao West Coast New Area, Qingdao, Shandong 266400, P.R. China
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4
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Behavioral phenotyping of mice lacking the deubiquitinase USP2. PLoS One 2021; 16:e0241403. [PMID: 33621249 PMCID: PMC7901773 DOI: 10.1371/journal.pone.0241403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/08/2021] [Indexed: 11/19/2022] Open
Abstract
Ubiquitin specific peptidase 2 (USP2) is a deubiquitinating enzyme expressed almost ubiquitously in the body, including in multiple brain regions. We previously showed that mice lacking USP2 present altered locomotor activity rhythms and response of the clock to light. However, the possible implication of USP2 in regulating other behaviors has yet to be tested. To address this, we ran a battery of behavioral tests on Usp2 KO mice. Firstly, we confirmed our prior findings of increased daily activity and reduced activity fragmentation in Usp2 KO mice. Further, mice lacking USP2 showed impaired motor coordination and equilibrium, a decrease in anxiety-like behavior, a deficit in working memory and in sensorimotor gating. On the other hand, no effects of Usp2 gene deletion were found on spatial memory. Hence, our data uncover the implication of USP2 in different behaviors and expands the range of the known functions of this deubiquitinase.
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5
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USP46 Inhibits Cell Proliferation in Lung Cancer through PHLPP1/AKT Pathway. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2509529. [PMID: 33029497 PMCID: PMC7532402 DOI: 10.1155/2020/2509529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/03/2020] [Accepted: 09/10/2020] [Indexed: 11/26/2022]
Abstract
Previous studies have shown that ubiquitin-specific protease 46 (USP46) is a tumor suppressor in colon cancer and renal cell carcinoma. However, its specific role in other cancers is still poorly understood. This study is aimed at investigating the role of USP46 in lung cancer tumorigenesis and identifying its underlying mechanisms. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting (WB) were used to measure the expression levels of USP46 and PHLPP1 in lung cancer tissue and adjacent normal tissue from patients with lung cancer. We examined the ability of USP46 to regulate cell proliferation in lung cancer cells via cell proliferation assay, radiation assay, genetic overexpression and knockdown, and chemical inhibition of relevant genes. We investigated the underlying mechanisms in multiple lung cancer cell line models by coimmunoprecipitation and ubiquitination assays. In this study, we identified a strong downregulation of the expressions of USP46 and PHLPP1 in lung cancer tissues relative to normal adjacent tissues. USP46 was further shown to inhibit lung cancer cell proliferation under conditions of normal growth and during radiation-induced DNA damage by antagonizing the ubiquitination of PHLPP1 resulting in the inhibition of AKT signaling. Exposure to radiation and AKT inhibition significantly reversed the effect of USP46 siRNA on lung cancer cell proliferation. USP46 is downregulated in lung cancer and suppresses the proliferation of lung cancer cells by inhibiting the PHLPP1/AKT pathway. AKT inhibition slows the proliferation of lung cancer cells that have been downregulated by USP46 and exposed to radiation. This suggests a potential therapeutic avenue for USP46-downregulated lung cancer through a combination of radiation and AKT inhibitor treatment.
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Tian M, Zhu R, Ding F, Liu Z. Ubiquitin-specific peptidase 46 promotes tumor metastasis through stabilizing ENO1 in human esophageal squamous cell carcinoma. Exp Cell Res 2020; 395:112188. [PMID: 32707136 DOI: 10.1016/j.yexcr.2020.112188] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/06/2020] [Accepted: 07/19/2020] [Indexed: 01/06/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) has high aggressiveness and poor prognosis, and is the major histological subtype of esophageal cancer in East Asia and East Africa. In this study, we found that USP46, a deubiquitinating enzyme, is overexpressed in clinical ESCC samples, especially in patients with positive lymph node metastasis. Moreover, USP46 enhances the migration and invasion of ESCC cells by mediating the EMT process in vitro, and promotes lymph nodes and lung metastasis of ESCC in vivo. In addition, we found that USP46 is a bona fide deubiquitinating enzyme to stabilize the protein level of ENO1 through deubiquitination. ENO1 protein level was also positively correlated with USP46 in the ESCC samples. In summary, these findings reveal the functional role of USP46 as a deubiquitinating enzyme on ESCC metastasis, providing us a potential therapeutic target for the treatment of ESCC.
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Affiliation(s)
- Maoqing Tian
- Guizhou University School of Medicine, Guizhou, 550025, PR China
| | - Rui Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Fang Ding
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China.
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Abstract
Essential tremor (ET) is a neurological movement disorder characterised by bilateral limb kinetic/postural tremor, with or without tremor in other body parts including head, voice and lower limbs. Since no causative genes for ET have been identified, it is likely that the disorder occurs as a result of complex genetic factors interacting with various cellular and environmental factors that can result in abnormal function of circuitry involving the cerebello-thalamo-cortical pathway. Genetic analyses have uncovered at least 14 loci and 11 genes that are related to ET, as well as various risk or protective genetic factors. Limitations in ET genetic analyses include inconsistent disease definition, small sample size, varied ethnic backgrounds and many other factors that may contribute to paucity of relevant genetic data in ET. Genetic analyses, coupled with functional and animal studies, have led to better insights into possible pathogenic mechanisms underlying ET. These genetic studies may guide the future development of genetic testing and counselling, and specific, pathogenesis-targeted, therapeutic strategies.
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8
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Gui D, Peng W, Jiang W, Huang G, Liu G, Ye Z, Wang Y, Xu Z, Fu J, Luo S, Zhao Y. Ubiquitin-specific peptidase 46 (USP46) suppresses renal cell carcinoma tumorigenesis through AKT pathway inactivation. Biochem Biophys Res Commun 2019; 519:689-696. [PMID: 31542232 DOI: 10.1016/j.bbrc.2019.09.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 12/18/2022]
Abstract
USP46, a member of the ubiquitin-specific protease family, plays essential roles in cancer cell proliferation and metastasis and is used as a candidate target for cancer therapeutics. However, the effects of USP46 on renal cell carcinoma (RCC) and its underlying molecular mechanism remain unknown. In this study, the predictive and prognostic relevance of USP46 in RCC, patient-derived primary tissues, and normal liver tissues obtained from the TCGA dataset were analyzed for the USP46 mRNA levels or prognostic relevance. Gain-of-function or loss-of-function assays were used to evaluate the vital roles of USP46 in tumor cell proliferation and cell migration. As a result, the USP46 expression level in RCC is highly decreased compared to normal tissues, and the Kaplan-Meier curve showed that USP46 high expression patients had good prognoses. Functionally, the forced expression of USP46 significantly restrained tumor cell proliferation, colony formation, and cell migration. The shRNA mediated USP46 knockdown cells exhibited the opposite results. We further showed that ectopically expressed USP46 obviously inhibited the AKT signaling pathway in cancer cells, while USP46 depletion caused a dramatic increase in AKT activity reflected by phosphorylation in the serine and threonine residues of AKT or downstream p70S6K1. Importantly, MK2206, a specific AKT inhibitor, completely counteracted the effects on cell proliferation, cell migration, and AKT activity in the USP46 depletion cells. We thus revealed a novel mechanism of USP46 regulation in RCC, and our data indicate that USP46 is a tumor suppressor in RCC via AKT signaling pathway inactivation.
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Affiliation(s)
- Dingwen Gui
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China.
| | - Wei Peng
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Weidong Jiang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Geng Huang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Gang Liu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Zhihua Ye
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Yang Wang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Zuwei Xu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Jinlun Fu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Shuai Luo
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
| | - Yunfei Zhao
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, Hubei, 435000, PR China; Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei, 435000, PR China
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9
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McClurg UL, Azizyan M, Dransfield DT, Namdev N, Chit NCTH, Nakjang S, Robson CN. The novel anti-androgen candidate galeterone targets deubiquitinating enzymes, USP12 and USP46, to control prostate cancer growth and survival. Oncotarget 2018; 9:24992-25007. [PMID: 29861848 PMCID: PMC5982776 DOI: 10.18632/oncotarget.25167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/10/2018] [Indexed: 12/26/2022] Open
Abstract
Metastatic castration resistant prostate cancer is one of the main causes of male cancer associated deaths worldwide. Development of resistance is inevitable in patients treated with anti-androgen therapies. This highlights a need for novel therapeutic strategies that would be aimed upstream of the androgen receptor (AR). Here we report that the novel small molecule anti-androgen, galeterone targets USP12 and USP46, two highly homologous deubiquitinating enzymes that control the AR-AKT-MDM2-P53 signalling pathway. Consequently, galeterone is effective in multiple models of prostate cancer including both castrate resistant and AR-negative prostate cancer. However, we have observed that USP12 and USP46 selectively regulate full length AR protein but not the AR variants. This is the first report of deubiquitinating enzyme targeting as a strategy in prostate cancer treatment which we show to be effective in multiple, currently incurable models of this disease.
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Affiliation(s)
- Urszula L McClurg
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Mahsa Azizyan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Daniel T Dransfield
- Tokai Pharmaceuticals, 255 State Street, Boston, MA 02109, USA.,Current address: Siamab Therapeutics, Suite 100, Newton, MA 02458, USA
| | - Nivedita Namdev
- Tokai Pharmaceuticals, 255 State Street, Boston, MA 02109, USA
| | - Nay C T H Chit
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Craig N Robson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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10
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Hodul M, Dahlberg CL, Juo P. Function of the Deubiquitinating Enzyme USP46 in the Nervous System and Its Regulation by WD40-Repeat Proteins. Front Synaptic Neurosci 2017; 9:16. [PMID: 29302259 PMCID: PMC5735123 DOI: 10.3389/fnsyn.2017.00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/29/2017] [Indexed: 11/13/2022] Open
Abstract
Posttranslational modification of proteins by ubiquitin regulates synapse development and synaptic transmission. Much progress has been made investigating the role of ubiquitin ligases at the synapse, however very little is known about the deubiquitinating enzymes (DUBs) which remove ubiquitin from target proteins. Although there are far fewer DUBs than ubiquitin ligases encoded by the human genome, it is becoming clear that DUBs have very specific physiological functions, suggesting that DUB activity is tightly regulated in vivo. Many DUBs function as part of larger protein complexes, and multiple regulatory mechanisms exist to control the expression, localization and catalytic activity of DUBs. In this review article, we focus on the role of the DUB USP46 in the nervous system, and illustrate potential mechanisms of regulating DUBs by describing how USP46 is regulated by two WD40-repeat (WDR) proteins, WDR48/UAF1 and WDR20, based on recent structural studies and genetic analyses in vivo.
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Affiliation(s)
- Molly Hodul
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Tufts University, Boston, MA, United States.,Graduate Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Tufts University, Boston, MA, United States
| | - Caroline L Dahlberg
- Biology Department, Western Washington University, Bellingham, WA, United States
| | - Peter Juo
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Tufts University, Boston, MA, United States
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11
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Liu X, Hernandez N, Kisselev S, Floratos A, Sawle A, Ionita-Laza I, Ottman R, Louis ED, Clark LN. Identification of candidate genes for familial early-onset essential tremor. Eur J Hum Genet 2016; 24:1009-15. [PMID: 26508575 PMCID: PMC5070884 DOI: 10.1038/ejhg.2015.228] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
Essential tremor (ET) is one of the most common causes of tremor in humans. Despite its high heritability and prevalence, few susceptibility genes for ET have been identified. To identify ET genes, whole-exome sequencing was performed in 37 early-onset ET families with an autosomal-dominant inheritance pattern. We identified candidate genes for follow-up functional studies in five ET families. In two independent families, we identified variants predicted to affect function in the nitric oxide (NO) synthase 3 gene (NOS3) that cosegregated with disease. NOS3 is highly expressed in the central nervous system (including cerebellum), neurons and endothelial cells, and is one of three enzymes that converts l-arginine to the neurotransmitter NO. In one family, a heterozygous variant, c.46G>A (p.(Gly16Ser)), in NOS3, was identified in three affected ET cases and was absent in an unaffected family member; and in a second family, a heterozygous variant, c.164C>T (p.(Pro55Leu)), was identified in three affected ET cases (dizygotic twins and their mother). Both variants result in amino-acid substitutions of highly conserved amino-acid residues that are predicted to be deleterious and damaging by in silico analysis. In three independent families, variants predicted to affect function were also identified in other genes, including KCNS2 (KV9.2), HAPLN4 (BRAL2) and USP46. These genes are highly expressed in the cerebellum and Purkinje cells, and influence function of the gamma-amino butyric acid (GABA)-ergic system. This is in concordance with recent evidence that the pathophysiological process in ET involves cerebellar dysfunction and possibly cerebellar degeneration with a reduction in Purkinje cells, and a decrease in GABA-ergic tone.
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Affiliation(s)
- Xinmin Liu
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Nora Hernandez
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Sergey Kisselev
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Aris Floratos
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Ashley Sawle
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Ruth Ottman
- G.H Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Division of Epidemiology, New York State Psychiatric Institute, New York, NY, USA
| | - Elan D Louis
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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12
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Genome-wide methylome analyses reveal novel epigenetic regulation patterns in schizophrenia and bipolar disorder. BIOMED RESEARCH INTERNATIONAL 2015; 2015:201587. [PMID: 25734057 PMCID: PMC4334857 DOI: 10.1155/2015/201587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 12/26/2022]
Abstract
Schizophrenia (SZ) and bipolar disorder (BP) are complex genetic disorders. Their appearance is also likely informed by as yet only partially described epigenetic contributions. Using a sequencing-based method for genome-wide analysis, we quantitatively compared the blood DNA methylation landscapes in SZ and BP subjects to control, both in an understudied population, Hispanics along the US-Mexico border. Remarkably, we identified thousands of differentially methylated regions for SZ and BP preferentially located in promoters 3′-UTRs and 5′-UTRs of genes. Distinct patterns of aberrant methylation of promoter sequences were located surrounding transcription start sites. In these instances, aberrant methylation occurred in CpG islands (CGIs) as well as in flanking regions as well as in CGI sparse promoters. Pathway analysis of genes displaying these distinct aberrant promoter methylation patterns showed enhancement of epigenetic changes in numerous genes previously related to psychiatric disorders and neurodevelopment. Integration of gene expression data further suggests that in SZ aberrant promoter methylation is significantly associated with altered gene transcription. In particular, we found significant associations between (1) promoter CGIs hypermethylation with gene repression and (2) CGI 3′-shore hypomethylation with increased gene expression. Finally, we constructed a specific methylation analysis platform that facilitates viewing and comparing aberrant genome methylation in human neuropsychiatric disorders.
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13
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Zhao Z, Li Y, Chen H, Lu J, Thompson PM, Chen J, Wang Z, Xu J, Xu C, Li X. PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders. BMC Med Genomics 2014; 7:71. [PMID: 25551368 PMCID: PMC4308070 DOI: 10.1186/s12920-014-0071-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/11/2014] [Indexed: 02/06/2023] Open
Abstract
Background Psychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BP) are projected to lead the global disease burden within the next decade. Several lines of evidence suggest that epigenetic- or genetic-mediated dysfunction is frequently present in these disorders. To date, the inheritance patterns have been complicated by the problem of integrating epigenomic and transcriptomic factors that have yet to be elucidated. Therefore, there is a need to build a comprehensive database for storing epigenomic and transcriptomic data relating to psychiatric disorders. Description We have developed the PD_NGSAtlas, which focuses on the efficient storage of epigenomic and transcriptomic data based on next-generation sequencing and on the quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The current release of the PD_NGSAtlas contains 43 DNA methylation profiles and 37 transcription profiles detected by MeDIP-Seq and RNA-Seq, respectively, in two distinct brain regions and peripheral blood of SZ, BP and non-psychiatric controls. In addition to these data that were generated in-house, we have included, and will continue to include, published DNA methylation and gene expression data from other research groups, with a focus on psychiatric disorders. A flexible query engine has been developed for the acquisition of methylation profiles and transcription profiles for special genes or genomic regions of interest of the selected samples. Furthermore, the PD_NGSAtlas offers online tools for identifying aberrantly methylated and expressed events involved in psychiatric disorders. A genome browser has been developed to provide integrative and detailed views of multidimensional data in a given genomic context, which can help researchers understand molecular mechanisms from epigenetic and transcriptional perspectives. Moreover, users can download the methylation and transcription data for further analyses. Conclusions The PD_NGSAtlas aims to provide storage of epigenomic and transcriptomic data as well as quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The PD_NGSAtlas will be a valuable data resource and will enable researchers to investigate the pathophysiology and aetiology of disease in detail. The database is available at http://bioinfo.hrbmu.edu.cn/pd_ngsatlas/. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0071-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zheng Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Hong Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Peter M Thompson
- Southwest Brain Bank, Department of Psychiatry, UTHSCSA, San Antonio, TX, USA.
| | - Juan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Zishan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Chun Xu
- Department of Pediatrics, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, El Paso, TX, USA.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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14
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Zhang W, Tian QB, Li QK, Wang JM, Wang CN, Liu T, Liu DW, Wang MW. Lysine 92 amino acid residue of USP46, a gene associated with 'behavioral despair' in mice, influences the deubiquitinating enzyme activity. PLoS One 2011; 6:e26297. [PMID: 22043315 PMCID: PMC3197135 DOI: 10.1371/journal.pone.0026297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by their activity of cleaving ubiquitin from specific protein substrates. Ubiquitin-Specific Protease 46 (USP46) has recently been identified as a quantitative trait gene responsible for immobility in the tail suspension test and forced swimming test in mice. Mice with a lysine codon (Lys 92) deletion in USP46 exhibited loss of ‘behavioral despair’ under inescapable stresses in addition to abnormalities in circadian behavioral rhythms and the GABAergic system. However, whether this deletion affects enzyme activity is unknown. Here we show that USP46 has deubiquitinating enzyme activity detected by USP cleavage assay using GST-Ub52 as a model substrate. Interestingly, compared to wild type, the Lys 92 deletion mutant resulted in a decreased deubiquitinating enzyme activity of 27.04%. We also determined the relative expression levels of Usp46 in rat tissues using real-time RT-PCR. Usp46 mRNA was expressed in various tissues examined including brain, with the highest expression in spleen. In addition, like rat USP46, both human and mouse USP46 are active toward to the model substrate, indicating the USP cleavage assay is a simple method for testing the deubiquitinating enzyme activity of USP46. These results suggest that the Lys 92 deletion of USP46 could influence enzyme activity and thereby provide a molecular clue how the enzyme regulating the pathogenesis of mental illnesses.
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Affiliation(s)
- Wei Zhang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Qing-Bao Tian
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
- * E-mail:
| | - Qing-Kai Li
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Jian-Min Wang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Chao-Nan Wang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Tian Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Dian-Wu Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Ming-Wei Wang
- The First Hospital of Hebei Medical University, Brain Aging and Cognitive Neuroscience Laboratory of Hebei Province, Shijiazhuang, China
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15
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Fukuo Y, Kishi T, Kushima I, Yoshimura R, Okochi T, Kitajima T, Matsunaga S, Kawashima K, Umene-Nakano W, Naitoh H, Inada T, Nakamura J, Ozaki N, Iwata N. Possible association between ubiquitin-specific peptidase 46 gene and major depressive disorders in the Japanese population. J Affect Disord 2011; 133:150-7. [PMID: 21663972 DOI: 10.1016/j.jad.2011.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 12/29/2010] [Accepted: 04/21/2011] [Indexed: 11/26/2022]
Abstract
BACKGROUND Several investigations have reported that abnormalities in circadian rhythms might be related to the pathophysiology of major depressive disorder (MDD) and the therapeutic response to selective serotonin reuptake inhibitors (SSRIs). Recently, ubiquitin-specific peptidase 46 (USP46), a new molecule related to the circadian clock system, has been described. We conducted a case control study between seven tagging SNPs (rs10517263, rs17675844, rs6554557, rs12646800, rs2244291, rs10034164, rs346005) in the USP46 gene, MDD, and the SSRI therapeutic response in MDD in the Japanese population. METHOD We recruited 432 MDD patients (202 males and 230 females) and 792 healthy controls (319 males and 473 females). Two hundred sixty-one of 432 MDD patients were treated with SSRIs (fluvoxamine, sertraline or paroxetine). RESULT We detected an association between the USP46 gene and MDD in a haplotype analysis (rs2244291-rs10034164-rs346005 and rs12646800-rs2244291-rs10034164-rs346005). However, we did not find any association between the USP46 gene and SSRI response or remission in MDD in the Japanese population. LIMITATIONS A replication study using larger samples may be required for conclusive results, since our sample size was small. CONCLUSIONS Our results suggest that the USP46 gene might play a role in the pathophysiology of MDD in the Japanese population.
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Affiliation(s)
- Yasuhisa Fukuo
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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