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Ke S, Lu S, Xu Y, Bai M, Yu H, Yin B, Wang C, Feng Z, Li Z, Huang J, Li X, Qian B, Hua Y, Fu Y, Sun B, Wu Y, Ma Y. RGS19 activates the MYH9/β-catenin/c-Myc positive feedback loop in hepatocellular carcinoma. Exp Mol Med 2024; 56:1412-1425. [PMID: 38825640 DOI: 10.1038/s12276-024-01244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/07/2024] [Accepted: 03/10/2024] [Indexed: 06/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common fatal cancers worldwide, and the identification of novel treatment targets and prognostic biomarkers is urgently needed because of its unsatisfactory prognosis. Regulator of G-protein signaling 19 (RGS19) is a multifunctional protein that regulates the progression of various cancers. However, the specific function of RGS19 in HCC remains unclear. The expression of RGS19 was determined in clinical HCC samples. Functional and molecular biology experiments involving RGS19 were performed to explore the potential mechanisms of RGS19 in HCC. The results showed that the expression of RGS19 is upregulated in HCC tissues and is significantly associated with poor prognosis in HCC patients. RGS19 promotes the proliferation and metastasis of HCC cells in vitro and in vivo. Mechanistically, RGS19, via its RGS domain, stabilizes the MYH9 protein by directly inhibiting the interaction of MYH9 with STUB1, which has been identified as an E3 ligase of MYH9. Moreover, RGS19 activates β-catenin/c-Myc signaling via MYH9, and RGS19 is also a transcriptional target gene of c-Myc. A positive feedback loop formed by RGS19, MYH9, and the β-catenin/c-Myc axis was found in HCC. In conclusion, our research revealed that competition between RGS19 and STUB1 is a critical mechanism of MYH9 regulation and that the RGS19/MYH9/β-catenin/c-Myc feedback loop may represent a promising strategy for HCC therapy.
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Affiliation(s)
- Shanjia Ke
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shounan Lu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanan Xu
- Department of Hepatopancreatobiliary Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Miaoyu Bai
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongjun Yu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Yin
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chaoqun Wang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Zhigang Feng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- The First Department of General Surgery, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Zihao Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingjing Huang
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Thyroid Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinglong Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Baolin Qian
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongliang Hua
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Fu
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bei Sun
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Yaohua Wu
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
- Department of Thyroid Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Yong Ma
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Göbel C, Schoof M, Holdhof D, Spohn M, Schüller U. SMARCA4 Loss and Mutated β-Catenin Induce Proliferative Lesions in the Murine Embryonic Cerebellum. J Neurosci 2024; 44:e1605232024. [PMID: 38383496 PMCID: PMC11007475 DOI: 10.1523/jneurosci.1605-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Almost all medulloblastomas (MB) of the Wingless/Int-1 (WNT) type are characterized by hotspot mutations in CTNNB1, and mouse models have convincingly demonstrated the tumor-initiating role of these mutations. Additional alterations in SMARCA4 are detected in ∼20% of WNT MB, but their functional role is mostly unknown. We, therefore, amended previously described brain lipid binding protein (Blbp)-cre::Ctnnb1(ex3)fl/wt mice by the introduction of floxed Smarca4 alleles. Unexpectedly, mutated and thereby stabilized β-catenin on its own induced severe developmental phenotypes in male and female Blbp-cre::Ctnnb1(ex3)fl/wt mice in our hands, including a thinned cerebral cortex, hydrocephalus, missing cerebellar layering, and cell accumulations in the brainstem and cerebellum. An additional loss of SMARCA4 even resulted in prenatal death for most mice. Respective Blbp-cre::Ctnnb1(ex3)fl/wt::Smarca4fl/rec mutants (male and female) developed large proliferative lesions in the cerebellum evolving from E13.5 to E16.5. Histological and molecular analysis of these lesions by DNA methylation profiling and single-cell RNA sequencing suggested an origin in early undifferentiated SOX2-positive cerebellar progenitors. Furthermore, upregulated WNT signaling, altered actin/cytoskeleton organization, and reduced neuronal differentiation were evident in mutant cells. In vitro, cells harboring alterations in both Ctnnb1 and Smarca4 were negatively selected and did not show tumorigenic potential after transplantation in adult female recipient mice. However, in cerebellar explant cultures, mutant cells displayed significantly increased proliferation, suggesting an important role of the embryonic microenvironment in the development of lesions. Altogether, these results represent an important first step toward the unraveling of tumorigenic mechanisms induced by aberrant WNT signaling and SMARCA4 deficiency.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
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Song J, Li M, Chen C, Zhou J, Wang L, Yan Y, She J, Tong L, Song Y. Regulator of G protein signaling protein 6 alleviates acute lung injury by inhibiting inflammation and promoting cell self-renewal in mice. Cell Mol Biol Lett 2023; 28:102. [PMID: 38066447 PMCID: PMC10709870 DOI: 10.1186/s11658-023-00488-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a disease with high mortality and morbidity. Regulator of G protein signaling protein 6 (RGS6), identified as a tumor suppressor gene, has received increasing attention owing to its close relationship with oxidative stress and inflammation. However, the association between ARDS and RGS6 has not been reported. METHODS Congruously regulated G protein-coupled receptor (GPCR)-related genes and differentially expressed genes (DEGs) in an acute lung injury (ALI) model were identified, and functional enrichment analysis was conducted. In an in vivo study, the effects of RGS6 knockout were studied in a mouse model of ALI induced by lipopolysaccharide (LPS). HE staining, ELISA, and immunohistochemistry were used to evaluate pathological changes and the degree of inflammation. In vitro, qRT‒PCR, immunofluorescence staining, and western blotting were used to determine the dynamic changes in RGS6 expression in cells. The RGS6 overexpression plasmid was constructed for transfection. qRT‒PCR was used to assess proinflammatory factors transcription. Western blotting and flow cytometry were used to evaluate apoptosis and reactive oxygen species (ROS) production. Organoid culture was used to assess the stemness and self-renewal capacity of alveolar epithelial type II cells (AEC2s). RESULTS A total of 110 congruously regulated genes (61 congruously upregulated and 49 congruously downregulated genes) were identified among GPCR-related genes and DEGs in the ALI model. RGS6 was downregulated in vivo and in vitro in the ALI model. RGS6 was expressed in the cytoplasm and accumulated in the nucleus after LPS stimulation. Compared with the control group, we found higher mortality, more pronounced body weight changes, more serious pulmonary edema and pathological damage, and more neutrophil infiltration in the RGS6 knockout group upon LPS stimulation in vivo. Moreover, AEC2s loss was significantly increased upon RGS6 knockout. Organoid culture assays showed slower alveolar organoid formation, fewer alveolar organoids, and impaired development of new structures after passaging upon RGS6 knockout. In addition, RGS6 overexpression decreased ROS production as well as proinflammatory factor transcription in macrophages and decreased apoptosis in epithelial cells. CONCLUSIONS RGS6 plays a protective role in ALI not only in early inflammatory responses but also in endogenous lung stem cell regeneration.
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Affiliation(s)
- Juan Song
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Pulmonary Medicine, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, 361000, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Miao Li
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Cuicui Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Jian Zhou
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Linlin Wang
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Yu Yan
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Respiratory Research Institute, Shanghai, 200032, China
| | - Jun She
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Shanghai Respiratory Research Institute, Shanghai, 200032, China.
| | - Lin Tong
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Department of Pulmonary Medicine, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, 361000, China.
- Shanghai Respiratory Research Institute, Shanghai, 200032, China.
| | - Yuanlin Song
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Department of Pulmonary Medicine, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, 361000, China.
- Shanghai Respiratory Research Institute, Shanghai, 200032, China.
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Shin MG, Pico AR. Using published pathway figures in enrichment analysis and machine learning. BMC Genomics 2023; 24:713. [PMID: 38007419 PMCID: PMC10676589 DOI: 10.1186/s12864-023-09816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. Here, we highlight the utility of PFOCR in disease research in comparison with popular pathway databases through an assessment of disease coverage and analytical applications. In addition to common pathway analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
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Affiliation(s)
- Min-Gyoung Shin
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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Yang C, Zhang X, Yang X, Lian F, Sun Z, Huang Y, Shen W. Function and regulation of RGS family members in solid tumours: a comprehensive review. Cell Commun Signal 2023; 21:316. [PMID: 37924113 PMCID: PMC10623796 DOI: 10.1186/s12964-023-01334-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) play a key role in regulating the homeostasis of the internal environment and are closely associated with tumour progression as major mediators of cellular signalling. As a diverse and multifunctional group of proteins, the G protein signalling regulator (RGS) family was proven to be involved in the cellular transduction of GPCRs. Growing evidence has revealed dysregulation of RGS proteins as a common phenomenon and highlighted the key roles of these proteins in human cancers. Furthermore, their differential expression may be a potential biomarker for tumour diagnosis, treatment and prognosis. Most importantly, there are few systematic reviews on the functional/mechanistic characteristics and clinical application of RGS family members at present. In this review, we focus on the G-protein signalling regulator (RGS) family, which includes more than 20 family members. We analysed the classification, basic structure, and major functions of the RGS family members. Moreover, we summarize the expression changes of each RGS family member in various human cancers and their important roles in regulating cancer cell proliferation, stem cell maintenance, tumorigenesis and cancer metastasis. On this basis, we outline the molecular signalling pathways in which some RGS family members are involved in tumour progression. Finally, their potential application in the precise diagnosis, prognosis and treatment of different types of cancers and the main possible problems for clinical application at present are discussed. Our review provides a comprehensive understanding of the role and potential mechanisms of RGS in regulating tumour progression. Video Abstract.
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Affiliation(s)
- Chenglong Yang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Xiaoyuan Zhang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Xiaowen Yang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Fuming Lian
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Zongrun Sun
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Yongming Huang
- Department of General Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, 272067, China.
| | - Wenzhi Shen
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, 272067, China.
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Huang H, Luo J, Qi Y, Wu Y, Qi J, Yan X, Xu G, He F, Zheng Y. Comprehensive analysis of circRNA expression profile and circRNA-miRNA-mRNA network susceptibility to very early-onset schizophrenia. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2023; 9:70. [PMID: 37816766 PMCID: PMC10564922 DOI: 10.1038/s41537-023-00399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023]
Abstract
To explore the potential role of circular RNAs (circRNAs) in children developing very early-onset schizophrenia (VEOS). Total RNA was extracted from the plasma samples of 10 VEOS patients and eight healthy controls. Expression profiles of circRNAs, micro RNAs (miRNAs), and messenger RNAs (mRNAs) were analyzed using RNA-seq. The interaction networks between miRNAs and targets were predicted using the miRanda tool. A differentially expressed circRNA-miRNA-mRNA (ceRNA) network was further constructed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the target mRNAs in the ceRNA network were performed to predict the potential functions of their host genes. The patient group and the control group were also compared on the regulatory patterns of circRNAs on mRNAs. 1934 circRNAs were identified from the samples and reported for the first time in schizophrenia. The circRNA expression levels were lower in the VEOS group than in the healthy control group, and 1889 circRNAs were expressed only in the control group. Differential expression analysis (i.e., log2fold change > 1.5, p 0.05) identified 235 circRNAs (1 up-regulated, 234 down-regulated), 11 miRNAs (7 up-regulated, 4 down-regulated), and 2,308 mRNAs (1906 up-regulated, 402 down-regulated) respectively. In VEOS, a ceRNA network with 10 down-regulated circRNA targets, 6 up-regulated miRNAs, and 47 down-regulated mRNAs was constructed. The target genes were involved in the membrane, the signal transduction, and the cytoskeleton and transport pathways. Finally, different expression correlation patterns of circRNA and mRNA in the network were observed between the patient group and the control group. The current research is the first to reveal the differentially expressed circRNAs in the plasma of VEOS patients. A circRNA-miRNA-mRNA network was also conducted in this study. It may be implied that the circRNAs in this network are potential diagnostic biomarkers for VEOS and they play an important role in the onset and development of VEOS symptoms.
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Affiliation(s)
- Huanhuan Huang
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Jie Luo
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Yanjie Qi
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Yuanzhen Wu
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Junhui Qi
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Xiuping Yan
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Gaoyang Xu
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China
| | - Fan He
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China.
| | - Yi Zheng
- National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing Institute for Brain Disorders Capital Medical University, Beijing, People's Republic of China.
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Shin MG, Pico A. Using Published Pathway Figures in Enrichment Analysis and Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548037. [PMID: 37461614 PMCID: PMC10350053 DOI: 10.1101/2023.07.06.548037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. PFOCR content is extracted from published pathway figures currently emerging at a rate of 1000 new pathways each month. Here, we compare the pathway information contained in PFOCR against popular pathway databases with respect to overall and disease-specific coverage. In addition to common pathways analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
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Li L, Xu Q, Tang C. RGS proteins and their roles in cancer: friend or foe? Cancer Cell Int 2023; 23:81. [PMID: 37118788 PMCID: PMC10148553 DOI: 10.1186/s12935-023-02932-8] [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: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023] Open
Abstract
As negative modulators of G-protein-coupled receptors (GPCRs) signaling, regulators of G protein signaling (RGS) proteins facilitate various downstream cellular signalings through regulating kinds of heterotrimeric G proteins by stimulating the guanosine triphosphatase (GTPase) activity of G-protein α (Gα) subunits. The expression of RGS proteins is dynamically and precisely mediated by several different mechanisms including epigenetic regulation, transcriptional regulation -and post-translational regulation. Emerging evidence has shown that RGS proteins act as important mediators in controlling essential cellular processes including cell proliferation, survival -and death via regulating downstream cellular signaling activities, indicating that RGS proteins are fundamentally involved in sustaining normal physiological functions and dysregulation of RGS proteins (such as aberrant expression of RGS proteins) is closely associated with pathologies of many diseases such as cancer. In this review, we summarize the molecular mechanisms governing the expression of RGS proteins, and further discuss the relationship of RGS proteins and cancer.
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Affiliation(s)
- Lin Li
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Rd., Hangzhou, 310052, People's Republic of China
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Qiang Xu
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Rd., Hangzhou, 310052, People's Republic of China
| | - Chao Tang
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Rd., Hangzhou, 310052, People's Republic of China.
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Yang S, Sun B, Li W, Yang H, Li N, Zhang X. Fatty acid metabolism is related to the immune microenvironment changes of gastric cancer and RGS2 is a new tumor biomarker. Front Immunol 2022; 13:1065927. [PMID: 36591293 PMCID: PMC9797045 DOI: 10.3389/fimmu.2022.1065927] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Background Alterations in lipid metabolism promote tumor progression. However, the role of lipid metabolism in the occurrence and development of gastric cancer have not been fully clarified. Method Here, genes that are related to fatty acid metabolism and differentially-expressed between normal and gastric cancer tissues were identified in the TCGA-STAD cohort. The intersection of identified differentially-expressed genes with Geneset was determined to obtain 78 fatty acid metabolism-related genes. The ConsensusClusterPlus R package was used to perform differentially-expressed genes, which yielded divided two gastric cancer subtypes termed cluster 1 and cluster 2. Results Patients in cluster 2 was found to display poorer prognosis than patients in cluster 1. Using machine learning method to select 8 differentially expressed genes among subtypes to construct fatty acid prognostic risk score model (FARS), which was found to display good prognostic efficacy. We also identified that certain anticancer drugs, such as bortezomib, elesclomol, GW843682X, and nilotinib, showed significant sensitivity in the high FARS score group. RGS2 was selected as the core gene upon an analysis of the gastric cancer single-cell, and Western blotting and immunofluorescence staining results revealed high level of expression of this gene in gastric cancer cells. The results of immunohistochemical staining showed that a large amount of RGS2 was deposited in the stroma in gastric cancer. A pan-cancer analysis also revealed a significant association of RGS2 with TMB, TIDE, and CD8+ T-cell infiltration in other cancer types as well. RGS2 may thus be studied further as a new target for immunotherapy in future studies on gastric cancer. Conclusion In summary, the FARS model developed here enhances our understanding of lipid metabolism in the TME in gastric cancer, and provides a theoretical basis for predicting tumor prognosis and clinical treatment.
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Affiliation(s)
- Shifeng Yang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin, China
| | - Boshi Sun
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenjing Li
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hao Yang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Nana Li
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyu Zhang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Liu D, Zinski A, Mishra A, Noh H, Park GH, Qin Y, Olorife O, Park JM, Abani CP, Park JS, Fung J, Sawaqed F, Coyle JT, Stahl E, Bendl J, Fullard JF, Roussos P, Zhang X, Stanton PK, Yin C, Huang W, Kim HY, Won H, Cho JH, Chung S. Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development. Mol Psychiatry 2022; 27:4218-4233. [PMID: 35701597 DOI: 10.1038/s41380-022-01654-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 02/07/2023]
Abstract
Remarkable advances have been made in schizophrenia (SCZ) GWAS, but gleaning biological insight from these loci is challenging. Genetic influences on gene expression (e.g., eQTLs) are cell type-specific, but most studies that attempt to clarify GWAS loci's influence on gene expression have employed tissues with mixed cell compositions that can obscure cell-specific effects. Furthermore, enriched SCZ heritability in the fetal brain underscores the need to study the impact of SCZ risk loci in specific developing neurons. MGE-derived cortical interneurons (cINs) are consistently affected in SCZ brains and show enriched SCZ heritability in human fetal brains. We identified SCZ GWAS risk genes that are dysregulated in iPSC-derived homogeneous populations of developing SCZ cINs. These SCZ GWAS loci differential expression (DE) genes converge on the PKC pathway. Their disruption results in PKC hyperactivity in developing cINs, leading to arborization deficits. We show that the fine-mapped GWAS locus in the ATP2A2 gene of the PKC pathway harbors enhancer marks by ATACseq and ChIPseq, and regulates ATP2A2 expression. We also generated developing glutamatergic neurons (GNs), another population with enriched SCZ heritability, and confirmed their functionality after transplantation into the mouse brain. Then, we identified SCZ GWAS risk genes that are dysregulated in developing SCZ GNs. GN-specific SCZ GWAS loci DE genes converge on the ion transporter pathway, distinct from those for cINs. Disruption of the pathway gene CACNA1D resulted in deficits of Ca2+ currents in developing GNs, suggesting compromised neuronal function by GWAS loci pathway deficits during development. This study allows us to identify cell type-specific and developmental stage-specific mechanisms of SCZ risk gene function, and may aid in identifying mechanism-based novel therapeutic targets.
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Affiliation(s)
- Dongxin Liu
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA.
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China.
| | - Amy Zinski
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Akanksha Mishra
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Haneul Noh
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, 02478, USA
| | - Gun-Hoo Park
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Yiren Qin
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Oshoname Olorife
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - James M Park
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Chiderah P Abani
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Joy S Park
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Janice Fung
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Farah Sawaqed
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Joseph T Coyle
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, 02478, USA
| | - Eli Stahl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Xiaolei Zhang
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Patric K Stanton
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Changhong Yin
- Department of Pathology, New York Medical College, Valhalla, NY, 10595, USA
| | - Weihua Huang
- Department of Pathology, New York Medical College, Valhalla, NY, 10595, USA
| | - Hae-Young Kim
- Department of Public Health, New York Medical College, Valhalla, NY, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jun-Hyeong Cho
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
| | - Sangmi Chung
- Department of Cell biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA.
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, 02478, USA.
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11
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Insights into the Promising Prospect of G Protein and GPCR-Mediated Signaling in Neuropathophysiology and Its Therapeutic Regulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8425640. [PMID: 36187336 PMCID: PMC9519337 DOI: 10.1155/2022/8425640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022]
Abstract
G protein-coupled receptors (GPCRs) are intricately involved in the conversion of extracellular feedback to intracellular responses. These specialized receptors possess a crucial role in neurological and psychiatric disorders. Most nonsensory GPCRs are active in almost 90% of complex brain functions. At the time of receptor phosphorylation, a GPCR pathway is essentially activated through a G protein signaling mechanism via a G protein-coupled receptor kinase (GRK). Dopamine, an important neurotransmitter, is primarily involved in the pathophysiology of several CNS disorders; for instance, bipolar disorder, schizophrenia, Parkinson's disease, and ADHD. Since dopamine, acetylcholine, and glutamate are potent neuropharmacological targets, dopamine itself has potential therapeutic effects in several CNS disorders. GPCRs essentially regulate brain functions by modulating downstream signaling pathways. GPR6, GPR52, and GPR8 are termed orphan GPCRs because they colocalize with dopamine D1 and D2 receptors in neurons of the basal ganglia, either alone or with both receptors. Among the orphan GPCRs, the GPR52 is recognized for being an effective psychiatric receptor. Various antipsychotics like aripiprazole and quetiapine mainly target GPCRs to exert their actions. One of the most important parts of signal transduction is the regulation of G protein signaling (RGS). These substances inhibit the activation of the G protein that initiates GPCR signaling. Developing a combination of RGS inhibitors with GPCR agonists may prove to have promising therapeutic potential. Indeed, several recent studies have suggested that GPCRs represent potentially valuable therapeutic targets for various psychiatric disorders. Molecular biology and genetically modified animal model studies recommend that these enriched GPCRs may also act as potential therapeutic psychoreceptors. Neurotransmitter and neuropeptide GPCR malfunction in the frontal cortex and limbic-related regions, including the hippocampus, hypothalamus, and brainstem, is likely responsible for the complex clinical picture that includes cognitive, perceptual, emotional, and motor symptoms. G protein and GPCR-mediated signaling play a critical role in developing new treatment options for mental health issues, and this study is aimed at offering a thorough picture of that involvement. For patients who are resistant to current therapies, the development of new drugs that target GPCR signaling cascades remains an interesting possibility. These discoveries might serve as a fresh foundation for the creation of creative methods for pharmacologically useful modulation of GPCR function.
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12
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Wu QW, Kapfhammer JP. The Emerging Key Role of the mGluR1-PKCγ Signaling Pathway in the Pathogenesis of Spinocerebellar Ataxias: A Neurodevelopmental Viewpoint. Int J Mol Sci 2022; 23:ijms23169169. [PMID: 36012439 PMCID: PMC9409119 DOI: 10.3390/ijms23169169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/19/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a heterogeneous group of autosomal dominantly inherited progressive disorders with degeneration and dysfunction of the cerebellum. Although different subtypes of SCAs are classified according to the disease-associated causative genes, the clinical syndrome of the ataxia is shared, pointing towards a possible convergent pathogenic pathway among SCAs. In this review, we summarize the role of SCA-associated gene function during cerebellar Purkinje cell development and discuss the relationship between SCA pathogenesis and neurodevelopment. We will summarize recent studies on molecules involved in SCA pathogenesis and will focus on the mGluR1-PKCγ signaling pathway evaluating the possibility that this might be a common pathway which contributes to these diseases.
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13
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Li Z, Wang D, Liao H, Zhang S, Guo W, Chen L, Lu L, Huang T, Cai YD. Exploring the Genomic Patterns in Human and Mouse Cerebellums Via Single-Cell Sequencing and Machine Learning Method. Front Genet 2022; 13:857851. [PMID: 35309141 PMCID: PMC8930846 DOI: 10.3389/fgene.2022.857851] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022] Open
Abstract
In mammals, the cerebellum plays an important role in movement control. Cellular research reveals that the cerebellum involves a variety of sub-cell types, including Golgi, granule, interneuron, and unipolar brush cells. The functional characteristics of cerebellar cells exhibit considerable differences among diverse mammalian species, reflecting a potential development and evolution of nervous system. In this study, we aimed to recognize the transcriptional differences between human and mouse cerebellum in four cerebellar sub-cell types by using single-cell sequencing data and machine learning methods. A total of 321,387 single-cell sequencing data were used. The 321,387 cells included 4 cell types, i.e., Golgi (5,048, 1.57%), granule (250,307, 77.88%), interneuron (60,526, 18.83%), and unipolar brush (5,506, 1.72%) cells. Our results showed that by using gene expression profiles as features, the optimal classification model could achieve very high even perfect performance for Golgi, granule, interneuron, and unipolar brush cells, respectively, suggesting a remarkable difference between the genomic profiles of human and mouse. Furthermore, a group of related genes and rules contributing to the classification was identified, which might provide helpful information for deepening the understanding of cerebellar cell heterogeneity and evolution.
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Affiliation(s)
- ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - HuiPing Liao
- Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
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14
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Novel Molecular Targets of Antidepressants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020533. [PMID: 35056845 PMCID: PMC8778443 DOI: 10.3390/molecules27020533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/12/2022]
Abstract
Antidepressants target a variety of proteins in the central nervous system (CNS), the most important belonging to the family of G-protein coupled receptors and the family of neurotransmitter transporters. The increasing number of crystallographic structures of these proteins have significantly contributed to the knowledge of their mechanism of action, as well as to the design of new drugs. Several computational approaches such as molecular docking, molecular dynamics, and virtual screening are useful for elucidating the mechanism of drug action and are important for drug design. This review is a survey of molecular targets for antidepressants in the CNS and computer based strategies to discover novel compounds with antidepressant activity.
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15
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Petyuk VA, Yu L, Olson HM, Yu F, Clair G, Qian WJ, Shulman JM, Bennett DA. Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss. J Proteome Res 2021; 20:2266-2282. [PMID: 33900085 PMCID: PMC9190253 DOI: 10.1021/acs.jproteome.0c00747] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteinaceous aggregates containing α-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson's disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights into proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss, and controls with no neuronal loss. Using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach, we characterized the proteome both in terms of protein abundances and peptide modifications. Statistical testing for differential abundance of the most abundant 2963 proteins, followed by pathway enrichment and Bayesian learning of the causal network structure, was performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g., TDP-43 and FUS), have a strong inverse correlation with Lewy bodies and may reflect an alternative mechanism of nigral neurodegeneration.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Heather M Olson
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Joshua M Shulman
- Departments of Neurology, Molecular & Human Genetics, and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
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16
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Effect of selection bias on two sample summary data based Mendelian randomization. Sci Rep 2021; 11:7585. [PMID: 33828182 PMCID: PMC8027662 DOI: 10.1038/s41598-021-87219-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/18/2021] [Indexed: 01/13/2023] Open
Abstract
Mendelian randomization (MR) is becoming more and more popular for inferring causal relationship between an exposure and a trait. Typically, instrument SNPs are selected from an exposure GWAS based on their summary statistics and the same summary statistics on the selected SNPs are used for subsequent analyses. However, this practice suffers from selection bias and can invalidate MR methods, as showcased via two popular methods: the summary data-based MR (SMR) method and the two-sample MR Steiger method. The SMR method is conservative while the MR Steiger method can be either conservative or liberal. A simple and yet more powerful alternative to SMR is proposed.
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17
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Reiner BC, Doyle GA, Weller AE, Levinson RN, Rao AM, Davila Perea E, Namoglu E, Pigeon A, Arauco-Shapiro G, Weickert CS, Turecki G, Crist RC, Berrettini WH. Inherited L1 Retrotransposon Insertions Associated With Risk for Schizophrenia and Bipolar Disorder. SCHIZOPHRENIA BULLETIN OPEN 2021; 2:sgab031. [PMID: 34901866 PMCID: PMC8650070 DOI: 10.1093/schizbullopen/sgab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of the genetic heritability of schizophrenia and bipolar disorder examining single nucleotide polymorphisms (SNPs) and copy number variations have failed to explain a large portion of the genetic liability, resulting in substantial missing heritability. Long interspersed element 1 (L1) retrotransposons are a type of inherited polymorphic variant that may be associated with risk for schizophrenia and bipolar disorder. We performed REBELseq, a genome wide assay for L1 sequences, on DNA from male and female persons with schizophrenia and controls (n = 63 each) to identify inherited L1 insertions and validated priority insertions. L1 insertions of interest were genotyped in DNA from a replication cohort of persons with schizophrenia, bipolar disorder, and controls (n = 2268 each) to examine differences in carrier frequencies. We identified an inherited L1 insertion in ARHGAP24 and a quadallelic SNP (rs74169643) inside an L1 insertion in SNTG2 that are associated with risk for developing schizophrenia and bipolar disorder (all odds ratios ~1.2). Pathway analysis identified 15 gene ontologies that were differentially affected by L1 burden, including multiple ontologies related to glutamatergic signaling and immune function, which have been previously associated with schizophrenia. These findings provide further evidence supporting the role of inherited repetitive genetic elements in the heritability of psychiatric disorders.
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Affiliation(s)
- Benjamin C Reiner
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn A Doyle
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Weller
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel N Levinson
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya M Rao
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emilie Davila Perea
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Esin Namoglu
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alicia Pigeon
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriella Arauco-Shapiro
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyndi Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia & School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Richard C Crist
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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18
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Abstract
Heterotrimeric G proteins are the core upstream elements that transduce and amplify the cellular signals from G protein-coupled receptors (GPCRs) to intracellular effectors. GPCRs are the largest family of membrane proteins encoded in the human genome and are the targets of about one-third of prescription medicines. However, to date, no single therapeutic agent exerts its effects via perturbing heterotrimeric G protein function, despite a plethora of evidence linking G protein malfunction to human disease. Several recent studies have brought to light that the Gq family-specific inhibitor FR900359 (FR) is unexpectedly efficacious in silencing the signaling of Gq oncoproteins, mutant Gq variants that mostly exist in the active state. These data not only raise the hope that researchers working in drug discovery may be able to potentially strike Gq oncoproteins from the list of undruggable targets, but also raise questions as to how FR achieves its therapeutic effect. Here, we place emphasis on these recent studies and explain why they expand our pharmacological armamentarium for targeting Gq protein oncogenes as well as broaden our mechanistic understanding of Gq protein oncogene function. We also highlight how this novel insight impacts the significance and utility of using G(q) proteins as targets in drug discovery efforts.
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Affiliation(s)
- Evi Kostenis
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany.
| | - Eva Marie Pfeil
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Suvi Annala
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
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19
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Senese NB, Kandasamy R, Kochan KE, Traynor JR. Regulator of G-Protein Signaling (RGS) Protein Modulation of Opioid Receptor Signaling as a Potential Target for Pain Management. Front Mol Neurosci 2020; 13:5. [PMID: 32038168 PMCID: PMC6992652 DOI: 10.3389/fnmol.2020.00005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/09/2020] [Indexed: 12/23/2022] Open
Abstract
Opioid drugs are the gold standard for the management of pain, but their use is severely limited by dangerous and unpleasant side effects. All clinically available opioid analgesics bind to and activate the mu-opioid receptor (MOR), a heterotrimeric G-protein-coupled receptor, to produce analgesia. The activity of these receptors is modulated by a family of intracellular RGS proteins or regulators of G-protein signaling proteins, characterized by the presence of a conserved RGS Homology (RH) domain. These proteins act as negative regulators of G-protein signaling by serving as GTPase accelerating proteins or GAPS to switch off signaling by both the Gα and βγ subunits of heterotrimeric G-proteins. Consequently, knockdown or knockout of RGS protein activity enhances signaling downstream of MOR. In this review we discuss current knowledge of how this activity, across the different families of RGS proteins, modulates MOR activity, as well as activity of other members of the opioid receptor family, and so pain and analgesia in animal models, with particular emphasis on RGS4 and RGS9 families. We discuss inhibition of RGS proteins with small molecule inhibitors that bind to sensitive cysteine moieties in the RH domain and the potential for targeting this family of intracellular proteins as adjuncts to provide an opioid sparing effect or as standalone analgesics by promoting the activity of endogenous opioid peptides. Overall, we conclude that RGS proteins may be a novel drug target to provide analgesia with reduced opioid-like side effects, but that much basic work is needed to define the roles for specific RGS proteins, particularly in chronic pain, as well as a need to develop newer inhibitors.
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Affiliation(s)
- Nicolas B Senese
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Psychiatry, Chicago, IL, United States
| | - Ram Kandasamy
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Psychology, California State University, East Bay, Hayward, CA, United States
| | - Kelsey E Kochan
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John R Traynor
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
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20
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Huang Z, Shu J, Jiang W, Jiang M, Lu Y, Dai H, Xu N, Yuan H, Cai J. Regulator of G Protein Signaling 6 Facilities Cardiac Hypertrophy by Activating Apoptosis Signal-Regulating Kinase 1-P38/c-JUN N-Terminal Kinase 1/2 Signaling. J Am Heart Assoc 2019; 7:e009179. [PMID: 30371330 PMCID: PMC6404897 DOI: 10.1161/jaha.118.009179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background Regulator of G protein signaling 6 (RGS6) is an important member of the RGS family and produces pleiotropic regulatory effects on cardiac pathophysiology. However, the role of RGS6 protein in cardiomyocytes during angiotensin II– and pressure overload–induced cardiac hypertrophy remain unknown. Methods and Results Here, we used a genetic approach to study the regulatory role of RGS6 in cardiomyocytes during pathological cardiac hypertrophy. RGS6 expression was significantly increased in failing human hearts and in hypertrophic murine hearts. The extent of aortic banding–induced cardiac hypertrophy, dysfunction, and fibrosis in cardiac‐specific RGS6 knockout mice was alleviated, whereas the hearts of transgenic mice with cardiac‐specific RGS6 overexpression exhibited exacerbated responses to pressure overload. Consistent with these findings, RGS6 also facilitated an angiotensin II–induced hypertrophic response in isolated cardiomyocytes. According to the mechanistic studies, RGS6 mediated cardiac hypertrophy by directly interacting with apoptosis signal–regulating kinase 1, which further activates the P38‐c‐JUN N‐terminal kinase 1/2 signaling pathway. Conclusions Based on our findings, RGS6 aggravates cardiac hypertrophy, and the RGS6‐apoptosis signal–regulating kinase 1 pathway represents a potential therapeutic target to attenuate pressure overload–driven cardiac remodeling.
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Affiliation(s)
- Zhijun Huang
- 2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
| | - Jingxian Shu
- 2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
| | - Weihong Jiang
- 1 Department of Cardiology The Third Xiangya Hospital Central South University Changsha China
| | - Mengqing Jiang
- 1 Department of Cardiology The Third Xiangya Hospital Central South University Changsha China
| | - Yao Lu
- 2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
| | - Haijiang Dai
- 1 Department of Cardiology The Third Xiangya Hospital Central South University Changsha China
| | - Nana Xu
- 2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
| | - Hong Yuan
- 2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
| | - Jingjing Cai
- 1 Department of Cardiology The Third Xiangya Hospital Central South University Changsha China.,2 The Center of Clinical Pharmacology The Third Xiangya Hospital Central South University Changsha China
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21
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O'Brien JB, Wilkinson JC, Roman DL. Regulator of G-protein signaling (RGS) proteins as drug targets: Progress and future potentials. J Biol Chem 2019; 294:18571-18585. [PMID: 31636120 DOI: 10.1074/jbc.rev119.007060] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) play critical roles in regulating processes such as cellular homeostasis, responses to stimuli, and cell signaling. Accordingly, GPCRs have long served as extraordinarily successful drug targets. It is therefore not surprising that the discovery in the mid-1990s of a family of proteins that regulate processes downstream of GPCRs generated great excitement in the field. This finding enhanced the understanding of these critical signaling pathways and provided potentially new targets for pharmacological intervention. These regulators of G-protein signaling (RGS) proteins were viewed by many as nodes downstream of GPCRs that could be targeted with small molecules to tune signaling processes. In this review, we provide a brief overview of the discovery of RGS proteins and of the gradual and continuing discovery of their roles in disease states, focusing particularly on cancer and neurological disorders. We also discuss high-throughput screening efforts that have led to the discovery first of peptide-based and then of small-molecule inhibitors targeting a subset of the RGS proteins. We explore the unique mechanisms of RGS inhibition these chemical tools have revealed and highlight the most up-to-date studies using these tools in animal experiments. Finally, we discuss the future opportunities in the field, as there are clearly more avenues left to be explored and potentials to be realized.
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Affiliation(s)
- Joseph B O'Brien
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242
| | - Joshua C Wilkinson
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242
| | - David L Roman
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242; Iowa Neuroscience Institute, Iowa City, Iowa 52242; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242.
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22
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Israeli R, Asli A, Avital-Shacham M, Kosloff M. RGS6 and RGS7 Discriminate between the Highly Similar Gα i and Gα o Proteins Using a Two-Tiered Specificity Strategy. J Mol Biol 2019; 431:3302-3311. [PMID: 31153905 DOI: 10.1016/j.jmb.2019.05.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/12/2019] [Accepted: 05/23/2019] [Indexed: 11/15/2022]
Abstract
RGS6 and RGS7 are regulators of G protein signaling (RGS) proteins that inactivate heterotrimeric (αβγ) G proteins and mediate diverse biological functions, such as cardiac and neuronal signaling. Uniquely, both RGS6 and RGS7 can discriminate between Gαo and Gαi1-two similar Gα subunits that belong to the same Gi sub-family. Here, we show that the isolated RGS domains of RGS6 and RGS7 are sufficient to achieve this specificity. We identified three specific RGS6/7 "disruptor residues" that can attenuate RGS interactions toward Gα subunits and demonstrated that their insertion into a representative high-activity RGS causes a significant, yet non-specific, reduction in activity. We further identified a unique "modulatory" residue that bypasses this negative effect, specifically toward Gαo. Hence, the exquisite specificity of RGS6 and RGS7 toward closely related Gα subunits is achieved via a two-tier specificity system, whereby a Gα-specific modulatory motif overrides the inhibitory effect of non-specific disruptor residues. Our findings expand the understanding of the molecular toolkit used by the RGS family to achieve specific interactions with selected Gα subunits-emphasizing the functional importance of the RGS domain in determining the activity and selectivity of RGS R7 sub-family members toward particular Gα subunits.
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Affiliation(s)
- Ran Israeli
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Ali Asli
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Meirav Avital-Shacham
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel.
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23
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Patil DN, Rangarajan ES, Novick SJ, Pascal BD, Kojetin DJ, Griffin PR, Izard T, Martemyanov KA. Structural organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex. eLife 2018; 7:42150. [PMID: 30540250 PMCID: PMC6310461 DOI: 10.7554/elife.42150] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 01/03/2023] Open
Abstract
Signaling by the G-protein-coupled receptors (GPCRs) plays fundamental role in a vast number of essential physiological functions. Precise control of GPCR signaling requires action of regulators of G protein signaling (RGS) proteins that deactivate heterotrimeric G proteins. RGS proteins are elaborately regulated and comprise multiple domains and subunits, yet structural organization of these assemblies is poorly understood. Here, we report a crystal structure and dynamics analyses of the multisubunit complex of RGS7, a major regulator of neuronal signaling with key roles in controlling a number of drug target GPCRs and links to neuropsychiatric disease, metabolism, and cancer. The crystal structure in combination with molecular dynamics and mass spectrometry analyses reveals unique organizational features of the complex and long-range conformational changes imposed by its constituent subunits during allosteric modulation. Notably, several intermolecular interfaces in the complex work in synergy to provide coordinated modulation of this key GPCR regulator.
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Affiliation(s)
- Dipak N Patil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, United States
| | - Erumbi S Rangarajan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Kirill A Martemyanov
- Department of Neuroscience, The Scripps Research Institute, Jupiter, United States
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24
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Squires KE, Montañez-Miranda C, Pandya RR, Torres MP, Hepler JR. Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease. Pharmacol Rev 2018; 70:446-474. [PMID: 29871944 DOI: 10.1124/pr.117.015354] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulators of G protein signaling (RGS) proteins modulate the physiologic actions of many neurotransmitters, hormones, and other signaling molecules. Human RGS proteins comprise a family of 20 canonical proteins that bind directly to G protein-coupled receptors/G protein complexes to limit the lifetime of their signaling events, which regulate all aspects of cell and organ physiology. Genetic variations account for diverse human traits and individual predispositions to disease. RGS proteins contribute to many complex polygenic human traits and pathologies such as hypertension, atherosclerosis, schizophrenia, depression, addiction, cancers, and many others. Recent analysis indicates that most human diseases are due to extremely rare genetic variants. In this study, we summarize physiologic roles for RGS proteins and links to human diseases/traits and report rare variants found within each human RGS protein exome sequence derived from global population studies. Each RGS sequence is analyzed using recently described bioinformatics and proteomic tools for measures of missense tolerance ratio paired with combined annotation-dependent depletion scores, and protein post-translational modification (PTM) alignment cluster analysis. We highlight selected variants within the well-studied RGS domain that likely disrupt RGS protein functions and provide comprehensive variant and PTM data for each RGS protein for future study. We propose that rare variants in functionally sensitive regions of RGS proteins confer profound change-of-function phenotypes that may contribute, in newly appreciated ways, to complex human diseases and/or traits. This information provides investigators with a valuable database to explore variation in RGS protein function, and for targeting RGS proteins as future therapeutic targets.
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Affiliation(s)
- Katherine E Squires
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Carolina Montañez-Miranda
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Rushika R Pandya
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Matthew P Torres
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - John R Hepler
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
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25
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Regulator of G-protein signaling 3 targeted by miR-126 correlates with poor prognosis in gastric cancer patients. Anticancer Drugs 2017; 28:161-169. [PMID: 27754994 DOI: 10.1097/cad.0000000000000446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Wnt/β-catenin signaling pathway dominates numerous cellular processes including cell proliferation, differentiation, and epithelial-mesenchymal transition, which play a crucial role in human cancer malignancies. Regulator of G-protein signaling 3 (RGS3) is a pivotal molecule involved in the Wnt/β-catenin signaling pathway, which is worthy of intensive research as a potential target in cancer treatment. In this study, we found that RGS3 is significantly upregulated in gastric cancer (GC) tumor samples compared with normal samples from the analysis of two independent GC mRNA microarray datasets in the NCBI public database. Further immunohistochemistry assay and western-blot experiments confirmed this finding on the basis of the results of our own 102 paired GC specimens and three GC cell lines. We found that a high expression of RGS3 is associated with advanced TNM stages and more aggressive malignant behaviors. In addition, the association of overexpression of RGS3 and poor overall survival and progression-free survival outcomes suggests that RGS3 has the potential to serve as a molecular therapy target for GC. Interestingly, our pathways analysis and the follow-up dual-luciferase reporter assay showed that there is a direct 3'-untranslated region binding site between RGS3 mRNA and microRNA-126, a GC inhibitor. On the basis of all the above evidences, our findings suggest that overexpressed RGS3 regulated by microRNA-126 through the post-transcriptional modulation is associated significantly with a poor prognosis of GC patients.
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26
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Sjögren B. The evolution of regulators of G protein signalling proteins as drug targets - 20 years in the making: IUPHAR Review 21. Br J Pharmacol 2017; 174:427-437. [PMID: 28098342 DOI: 10.1111/bph.13716] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/11/2016] [Accepted: 01/08/2017] [Indexed: 12/11/2022] Open
Abstract
Regulators of G protein signalling (RGS) proteins are celebrating the 20th anniversary of their discovery. The unveiling of this new family of negative regulators of G protein signalling in the mid-1990s solved a persistent conundrum in the G protein signalling field, in which the rate of deactivation of signalling cascades in vivo could not be replicated in exogenous systems. Since then, there has been tremendous advancement in the knowledge of RGS protein structure, function, regulation and their role as novel drug targets. RGS proteins play an important modulatory role through their GTPase-activating protein (GAP) activity at active, GTP-bound Gα subunits of heterotrimeric G proteins. They also possess many non-canonical functions not related to G protein signalling. Here, an update on the status of RGS proteins as drug targets is provided, highlighting advances that have led to the inclusion of RGS proteins in the IUPHAR/BPS Guide to PHARMACOLOGY database of drug targets.
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Affiliation(s)
- B Sjögren
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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27
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Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues. Sci Rep 2016; 6:39655. [PMID: 28000796 PMCID: PMC5175133 DOI: 10.1038/srep39655] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/24/2016] [Indexed: 12/23/2022] Open
Abstract
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a computational method to segregate DEPDCs and non-DEPDCs. First, we examined the Pfam numbers of the known DEPDCs and used the longest sequences for each Pfam to construct a phylogenetic tree. Subsequently, we extracted 188-dimensional (188D) and 20D features of DEPDCs and non-DEPDCs and classified them with random forest classifier. We also mined the motifs of human DEPDCs to find the related domains. Finally, we designed experimental verification methods of human DEPDC expression at the mRNA level in hepatocellular carcinoma (HCC) and adjacent normal tissues. The phylogenetic analysis showed that the DEPDCs superfamily can be divided into three clusters. Moreover, the 188D and 20D features can both be used to effectively distinguish the two protein types. Motif analysis revealed that the DEP and RhoGAP domain was common in human DEPDCs, human HCC and the adjacent tissues that widely expressed DEPDCs. However, their regulation was not identical. In conclusion, we successfully constructed a binary classifier for DEPDCs and experimentally verified their expression in human HCC tissues.
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