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Reghupaty SC, Dall NR, Svensson KJ. Hallmarks of the metabolic secretome. Trends Endocrinol Metab 2024; 35:49-61. [PMID: 37845120 PMCID: PMC10841501 DOI: 10.1016/j.tem.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
The identification of novel secreted factors is advancing at an unprecedented pace. However, there is a critical need to consolidate and integrate this knowledge to provide a framework of their diverse mechanisms, functional significance, and inter-relationships. Complicating this effort are challenges related to nonstandardized methods, discrepancies in sample handling, and inconsistencies in the annotation of unknown molecules. This Review aims to synthesize the rapidly expanding field of the metabolic secretome, encompassing the five major types of secreted factors: proteins, peptides, metabolites, lipids, and extracellular vesicles. By systematically defining the functions and detection of the components within the metabolic secretome, this Review provides a primer into the advances of the field, and how integration of the techniques discussed can provide a deeper understanding of the mechanisms underlying metabolic homeostasis and its disorders.
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Affiliation(s)
- Saranya C Reghupaty
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Nicholas R Dall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Katrin J Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA.
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2
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The human batokine EPDR1 regulates β-cell metabolism and function. Mol Metab 2022; 66:101629. [PMID: 36343918 PMCID: PMC9663883 DOI: 10.1016/j.molmet.2022.101629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/14/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE Ependymin-Related Protein 1 (EPDR1) was recently identified as a secreted human batokine regulating mitochondrial respiration linked to thermogenesis in brown fat. Despite that EPDR1 is expressed in human pancreatic β-cells and that glucose-stimulated mitochondrial metabolism is critical for stimulus-secretion coupling in β-cells, the role of EPDR1 in β-cell metabolism and function has not been investigated. METHODS EPDR1 mRNA levels in human pancreatic islets from non-diabetic (ND) and type 2 diabetes (T2D) subjects were assessed. Human islets, EndoC-βH1 and INS1 832/13 cells were transfected with scramble (control) and EPDR1 siRNAs (EPDR1-KD) or treated with human EPDR1 protein, and glucose-stimulated insulin secretion (GSIS) assessed by ELISA. Mitochondrial metabolism was investigated by extracellular flux analyzer, confocal microscopy and mass spectrometry-based metabolomics analysis. RESULTS EPDR1 mRNA expression was upregulated in human islets from T2D and obese donors and positively correlated to BMI of donors. In T2D donors, EPDR1 mRNA levels negatively correlated with HbA1c and positively correlated with GSIS. EPDR1 silencing in human islets and β-cell lines reduced GSIS whereas treatment with human EPDR1 protein increased GSIS. Epdr1 silencing in INS1 832/13 cells reduced glucose- and pyruvate- but not K+-stimulated insulin secretion. Metabolomics analysis in Epdr1-KD INS1 832/13 cells suggests diversion of glucose-derived pyruvate to lactate production and decreased malate-aspartate shuttle and the tricarboxylic acid (TCA) cycle activity. The glucose-stimulated rise in mitochondrial respiration and ATP/ADP-ratio was impaired in Epdr1-deficient cells. CONCLUSION These results suggests that to maintain glucose homeostasis in obese people, upregulation of EPDR1 may improve β-cell function via channelling glycolysis-derived pyruvate to the mitochondrial TCA cycle.
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Yang Y, Xu H, Zhu H, Yuan D, Zhang H, Liu Z, Zhao F, Liang G. EPDR1 levels and tumor budding predict and affect the prognosis of bladder carcinoma. Front Oncol 2022; 12:986006. [PMID: 36276104 PMCID: PMC9585273 DOI: 10.3389/fonc.2022.986006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Bladder carcinoma is a common malignancy of the urinary system. The previous study showed that EPDR1 expression was significantly related to the carcinogenesis and progression of bladder carcinoma Methods We retrospectively reviewed the records of 621 patients who were newly diagnosed with bladder carcinoma between January 2018 and August 2020 at The Affiliated Hospital of Zunyi Medical University. We conducted immunohistochemistry of EPDR1 in tumor tissues. Meanwhile, tumor budding evaluation was also carried out by 2 independent experienced pathologists. Results 80 patients were included in this study with a median age of 66 years (range; 42–88 years). 45% of the patients (36/80) were non-muscle-invasive bladder carcinoma patients, while 55% of muscle-invasive bladder carcinoma(44/80). The follow-up time was from 6 months to 36 months. We found that there were significant differences in expression of EPDR1 in the tumor pT stages(p<0.05), pM stages(p<0.05), and pN stages(p<0.05). Meanwhile, a higher expression of EPDR1 indicated a worse outcome for the patient(p<0.05). A tendency toward a worse status of the patient was accompanied by a high positive rate (p<0.001). Moreover, the IOD of EPDR1 had a positive relationship with TB (p<0.05). Furthermore, we found that EPDR1 and tumor budding could be crucial factors for affecting the prognosis of bladder carcinoma, even better than pTMN(Riskscore=(0.724)* pT_stage +(4.960) *EPDR1+(4.312)*TB). Conclusion In conclusion, bladder cancer patients with higher expression levels of EPDR1 had worse survival outcomes. The combination of TB and EPDR1 levels could predict the prognosis for muscle-invasive bladder cancer patients.
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Affiliation(s)
- Yue Yang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Urology, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
- Medical College of Soochow University, Suzhou, China
| | - Hong Xu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Han Zhu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Dan Yuan
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hanchao Zhang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Urology, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
- Medical College of Soochow University, Suzhou, China
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhengdao Liu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Medical College of Soochow University, Suzhou, China
| | - Faliang Zhao
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Medical College of Soochow University, Suzhou, China
| | - Guobiao Liang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Medical College of Soochow University, Suzhou, China
- *Correspondence: Guobiao Liang,
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4
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Evans TG, Bible JM, Maynard A, Griffith KR, Sanford E, Kültz D. Proteomic changes associated with predator-induced morphological defenses in oysters. Mol Ecol 2022; 31:4254-4270. [PMID: 35754098 DOI: 10.1111/mec.16580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
Abstract
Inducible prey defenses occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defenses. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defenses. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with up-regulation of calcium transport proteins that could influence biomineralization. Inducible defenses evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were down-regulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defense response evolved in oysters that co-occur with drills through modification of an existing mechanism.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Jillian M Bible
- Department of Environmental Science and Studies, Washington College, Chestertown, MD 21620, USA
| | - Ashley Maynard
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA
| | - Kaylee R Griffith
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
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Zhao Z, Wang Z, Wang P, Liu S, Li Y, Yang X. EPDR1, Which Is Negatively Regulated by miR-429, Suppresses Epithelial Ovarian Cancer Progression via PI3K/AKT Signaling Pathway. Front Oncol 2021; 11:751567. [PMID: 35004274 PMCID: PMC8733570 DOI: 10.3389/fonc.2021.751567] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the main pathological type of ovarian cancer. In this study, we found that ependymin-related 1 (EPDR1) was remarkably downregulated in EOC tissues, and low EPDR1 expression was associated with International Federation of Gynecology and Obstetrics (FIGO) stage, metastasis, and poor prognosis. We confirmed that EPDR1 overexpression dramatically suppressed EOC cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, EPDR1 inhibited EOC tumorigenesis and progression, at least in part, through the repression of the PI3K (Phosphoinositide 3-kinase)/AKT (AKT Serine/Threonine Kinase 1) signaling pathway. Furthermore, the expression and function of EPDR1 were regulated by miR-429, as demonstrated by luciferase reporter assays and rescue experiments. In conclusion, our study validated that EPDR1, negatively regulated by miR-429, played an important role as a tumor-suppressor gene in EOC development via inhibition of the PI3K/AKT pathway. The miR-429/EPDR1 axis might provide novel therapeutic targets for individualized treatment of EOC patients in the future.
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Affiliation(s)
- Zhendan Zhao
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Zhiling Wang
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Pengling Wang
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Shujie Liu
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
- Department of Obstetrics and Gynecology, Zibo Spring Hospital Co., Ltd., Zibo, China
| | - Yingwei Li
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
| | - Xingsheng Yang
- Department of Gynecology and Obstetrics, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Xingsheng Yang ,
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Chen H, Wang M, Zhang H, Wang H, Zhou L, Zhong Z, Cao L, Lian C, Sun Y, Li C. microRNAs facilitate comprehensive responses of Bathymodiolinae mussel against symbiotic and nonsymbiotic bacteria stimulation. FISH & SHELLFISH IMMUNOLOGY 2021; 119:420-431. [PMID: 34687882 DOI: 10.1016/j.fsi.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/08/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Bathymodiolinae mussels are dominant species in cold seeps and hydrothermal vents and could harbor endosymbionts in gill bacteriocytes. However, mechanisms underlying the symbiosis have remained largely undisclosed for years. In the present study, the global expression pattern of immune-related genes and miRNAs were surveyed in Gigantidas platifrons during bacterial challenges using enriched symbiotic methane oxidation bacteria MOBs or nonsymbiotic Vibrio. As a result, multiple pattern recognition receptors were found differentially expressed at 12 h and 24 h post bacteria challenges and distinctly clustered between stimulations. Dozens of immune effectors along with signal transducers were also modulated simultaneously during MOB or Vibrio challenge. A total of 459 miRNAs were identified in the gill while some were differentially expressed post MOB or nonsymbiotic bacteria challenge. A variety of immune-related genes were annotated as target genes of aforesaid differentially expressed miRNAs. As a result, biological processes including the immune recognition, lysosome activity and bacteria engulfment were suggested to be dynamically modulated by miRNAs in either symbiotic or nonsymbiotic bacteria challenge. It was suggested that G. platifrons mussels could maintain a robust immune response against invading pathogens while establishing symbiosis with chemosynthetic bacteria with the orchestra of immune-related genes and miRNAs.
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Affiliation(s)
- Hao Chen
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Zhou
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Lei Cao
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yan Sun
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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Yang Y, Zhang H, Liu Z, Zhao F, Liang G. EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker. BMC Urol 2021; 21:71. [PMID: 33902536 PMCID: PMC8077848 DOI: 10.1186/s12894-021-00843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Background Bladder cancer (BLCA) is a malignant urothelial carcinoma and has a high mortality rate. EPDR1 (ependymin related 1) is a type II transmembrane protein and related to calcium-dependent cell adhesion. Methods We explored the potential oncogenic roles of EPDR1 in BLCA basing on the multiple public datasets. Results We found that EPDR1 expression had a significant difference in BLCA and adjacent normal bladder tissues, and the level of EPDR1was up-regulated with advanced tumor stage and metastasis in BLCA. Meanwhile, the high expression group of EPDR1 had a shorter OS compared to the low or medium expression-group. Furthermore, EPDR1 expression was associated with tumor-infiltrating immune cells (TIICs), including NK cells, CD8 + T cells, CD4 + T cells, Macrophages cells, and so on. Moreover, EPDR1 also involved in several signaling pathways as well as PI3K/AKT pathway, Cytokine receptor interaction, and apoptosis. Conclusion EPDR1 can be used as a novel prognostic biomarker as well as an effective target for diagnosis and treatment in BLCA.
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Affiliation(s)
- Yue Yang
- Medical College of Soochow University, Suzhou, Jiangsu, China.,Urological Department, The Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China.,Urological Department, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Hanchao Zhang
- Medical College of Soochow University, Suzhou, Jiangsu, China.,Urological Department, The Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China.,Urological Department, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhengdao Liu
- Medical College of Soochow University, Suzhou, Jiangsu, China.,Urological Department, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Faliang Zhao
- Medical College of Soochow University, Suzhou, Jiangsu, China.,Urological Department, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Guobiao Liang
- Medical College of Soochow University, Suzhou, Jiangsu, China. .,Urological Department, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
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Kondkar AA. Updates on Genes and Genetic Mechanisms Implicated in Primary Angle-Closure Glaucoma. APPLICATION OF CLINICAL GENETICS 2021; 14:89-112. [PMID: 33727852 PMCID: PMC7955727 DOI: 10.2147/tacg.s274884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/18/2021] [Indexed: 12/29/2022]
Abstract
Primary angle-closure glaucoma (PACG) is estimated to affect over 30 million people worldwide by 2040 and is highly prevalent in the Asian population. PACG is more severe and carries three times the higher risk of blindness than primary open-angle glaucoma, thus representing a significant public health concern. High heritability and ethnic-specific predisposition to PACG suggest the involvement of genetic factors in disease development. In the recent past, genetic studies have led to the successful identification of several genes and loci associated with PACG across different ethnicities. The precise cellular and molecular roles of these multiple loci in the development and progression of PACG remains to be elucidated. Nonetheless, these studies have significantly increased our understanding of the emerging cellular processes and biological pathways that might provide more significant insights into the disease’s genetic etiology and may be valuable for future clinical applications. This review aims to summarize and update the current knowledge of PACG genetics analysis research.
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Affiliation(s)
- Altaf A Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
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9
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Chen R, Zhang Y. EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker. J Cell Mol Med 2020; 24:12107-12118. [PMID: 32935479 PMCID: PMC7579695 DOI: 10.1111/jcmm.15852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has high mortality rate and is a serious disease burden globally. EPDR1 (ependymin related 1) is a member of piscine brain glycoproteins and is involved in cell adhesion. The gene expression, prognostic, and clinicopathological related data for EPDR1 were obtained from multiple transcriptome databases. Protein level of EPDR1 in HCC was verified using human protein atlas and CPTAC databases. EPDR1 co‐expressed genes were identified using LinkedOmics. Functional analysis of the co‐expressed genes was performed using gene set enrichment analysis, Gene Ontology, and KEGG. Statistical analysis was conducted in R. The relationship between EPDR1 expression and immune cell infiltration was analyzed using TIMER and CIBERSORT. The expression of EPDR1 was found to be significantly higher in HCC than in normal tissues. Further, EPDR1 level was correlated with advanced stage of HCC. EPDR1 was associated with multiple signaling, as well as cancer and apoptotic pathways. Further, EPDR1 expression was significantly correlated with purity and infiltration levels of various immune cells as well as immune signatures. This is the first study to report the role of EPDR1 in HCC. EPDR1 can be used as a novel prognostic biomarker as well as an effective target for diagnosis and treatment in HCC.
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Affiliation(s)
- Ruochan Chen
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China.,Department of Infectious Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiya Zhang
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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10
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EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness. Sci Rep 2020; 10:3723. [PMID: 32111877 PMCID: PMC7048834 DOI: 10.1038/s41598-020-60476-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/03/2020] [Indexed: 12/15/2022] Open
Abstract
The finding of novel molecular markers for prediction or prognosis of invasiveness in colorectal cancer (CRC) constitutes an appealing challenge. Here we show the up-regulation of EPDR1 in a prospective cohort of 101 CRC patients, in a cDNA array of 43 patients and in in silico analyses. EPDR1 encodes a protein related to ependymins, a family of glycoproteins involved in intercellular contacts. A thorough statistical model allowed us to conclude that the gene is significantly up-regulated in tumour tissues when compared with normal mucosa. These results agree with those obtained by the analysis of three publicly available databases. EPDR1 up-regulation correlates with the TNM staging parameters, especially T and M. Studies with CRC cell lines revealed that the methylation of a CpG island controls EPDR1 expression. siRNA knocking-down and overexpression of the gene following transient plasmid transfection, showed that EPDR1 favours cell proliferation, migration, invasiveness and adhesion to type I collagen fibres, suggesting a role in epithelial to mesenchymal transition. Both statistical and functional analysis correlated EPDR1 overexpression with invasiveness and dissemination of tumour cells, supporting the inclusion of EPDR1 in panels of genes used to improve molecular subtyping of CRC. Eventually, EPDR1 may be an actionable target.
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Park JK, Kim KY, Sim YW, Kim YI, Kim JK, Lee C, Han J, Kim CU, Lee JE, Park S. Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder. IUCRJ 2019; 6:729-739. [PMID: 31316816 PMCID: PMC6608618 DOI: 10.1107/s2052252519007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation.
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Affiliation(s)
- Jeong Kuk Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Keon Young Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yeo Won Sim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yong-In Kim
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Cheol Lee
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jeongran Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - J. Eugene Lee
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
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12
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Wei Y, Xiong ZJ, Li J, Zou C, Cairo CW, Klassen JS, Privé GG. Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters. Commun Biol 2019; 2:52. [PMID: 30729188 PMCID: PMC6363788 DOI: 10.1038/s42003-018-0262-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
EPDR1, a member of the ependymin-related protein family, is a relatively uncharacterized protein found in the lysosomes and secretomes of most vertebrates. Despite having roles in human disease and health, the molecular functions of EPDR1 remain unknown. Here, we present crystal structures of human EPDR1 and reveal that the protein adopts a fold previously seen only in bacterial proteins related to the LolA lipoprotein transporter. EPDR1 forms a homodimer with an overall shape resembling a half-shell with two non-overlapping hydrophobic grooves on the flat side of the hemisphere. EPDR1 can interact with membranes that contain negatively charged lipids, including BMP and GM1, and we suggest that EPDR1 may function as a lysosomal activator protein or a lipid transporter. A phylogenetic analysis reveals that the fold is more widely distributed than previously suspected, with representatives identified in all branches of cellular life.
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Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
| | - Zi Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Jun Li
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Chunxia Zou
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Gilbert G. Privé
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7 ON Canada
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13
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McDougall C, Hammond MJ, Dailey SC, Somorjai IML, Cummins SF, Degnan BM. The evolution of ependymin-related proteins. BMC Evol Biol 2018; 18:182. [PMID: 30514200 PMCID: PMC6280359 DOI: 10.1186/s12862-018-1306-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/23/2018] [Indexed: 12/19/2022] Open
Abstract
Background Ependymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood. Results We undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar. Conclusions Our results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family. Electronic supplementary material The online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Australian Rivers Institute, Griffith University, Nathan, Queensland, 4111, Australia
| | - Michael J Hammond
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Simon C Dailey
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Ildiko M L Somorjai
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Scott F Cummins
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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14
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Eguía-Aguilar P, Gutiérrez-Castillo L, Pérezpeña-Díazconti M, García-Chéquer J, García-Quintana J, Chico-Ponce de León F, Gordillo-Domínguez L, Torres-García S, Arenas-Huertero F. Expression of microRNAs in tumors of the central nervous system in pediatric patients in México. Childs Nerv Syst 2017; 33:2117-2128. [PMID: 28815380 DOI: 10.1007/s00381-017-3569-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/04/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE MicroRNAs were identified as molecules that participate in gene regulation; alterations in their expression characterize central nervous system (CNS). Information in pediatrics is scarce, so the objective of this work was to determine and then compare the patterns of expression of microRNAs in astrocytomas, ependymomas, and medulloblastomas, as well as in non-neoplastic brain. METHODS Low-density arrays were utilized to evaluate 756 microRNAs in three samples of each type of tumor and non-neoplastic brain. The relative expression was calculated in order to identify the three microRNAs whose expression was modified notably. This was verified using RT-qPCR in more number of tumor samples. RESULTS The microRNAs selected for testing were miR-100-5p, miR-195-5p, and miR-770-5p. A higher expression of miR-100-5p was observed in the astrocytomas and ependymomas compared to the medulloblastomas: on average 3.8 times (p < 0.05). MiR-770-5p was expressed less in medulloblastomas compared to astrocytomas four times (p = 0.0162). MiR-195-5p had a low expression in medulloblastomas compared to non-neoplastic cerebellum (p = 0.049). In all three tumor types, expression of miR-770-5p was lower than in non-neoplastic brain (p < 0.001). CONCLUSIONS These microRNAs may represent potential markers in these tumors.
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Affiliation(s)
- Pilar Eguía-Aguilar
- Departmento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Lisette Gutiérrez-Castillo
- Departmento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México.,Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Ciudad de México, México
| | - Mario Pérezpeña-Díazconti
- Departmento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Jeanette García-Chéquer
- Departmento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Jorge García-Quintana
- Departmento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | | | - Luis Gordillo-Domínguez
- Departmento de Neurocirugía, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Samuel Torres-García
- Departmento de Neurocirugía, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Francisco Arenas-Huertero
- Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Ciudad de México, México. .,Laboratorio de Investigación en Patología Experimental, Hospital Infantil de México Federico Gómez-Instituto Nacional de Salud, Dr. Márquez 162, Colonia Doctores, Delegación Cuauhtémoc, 06720, Ciudad de México, México.
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15
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Dupuytren’s disease susceptibility gene, EPDR1, is involved in myofibroblast contractility. J Dermatol Sci 2016; 83:131-7. [DOI: 10.1016/j.jdermsci.2016.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/01/2016] [Accepted: 04/28/2016] [Indexed: 01/06/2023]
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16
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Tilli TM, Bellahcène A, Castronovo V, Gimba ERP. Changes in the transcriptional profile in response to overexpression of the osteopontin-c splice isoform in ovarian (OvCar-3) and prostate (PC-3) cancer cell lines. BMC Cancer 2014; 14:433. [PMID: 24928374 PMCID: PMC4075779 DOI: 10.1186/1471-2407-14-433] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/23/2014] [Indexed: 12/16/2022] Open
Abstract
Background Especially in human tumor cells, the osteopontin (OPN) primary transcript is subject to alternative splicing, generating three isoforms termed OPNa, OPNb and OPNc. We previously demonstrated that the OPNc splice variant activates several aspects of the progression of ovarian and prostate cancers. The goal of the present study was to develop cell line models to determine the impact of OPNc overexpression on main cancer signaling pathways and thus obtain insights into the mechanisms of OPNc pro-tumorigenic roles. Methods Human ovarian and prostate cancer cell lines, OvCar-3 and PC-3 cells, respectively, were stably transfected to overexpress OPNc. Transcriptomic profiling was performed on these cells and compared to controls, to identify OPNc overexpression-dependent changes in gene expression levels and pathways by qRT-PCR analyses. Results Among 84 genes tested by using a multiplex real-time PCR Cancer Pathway Array approach, 34 and 16, respectively, were differentially expressed between OvCar-3 and PC-3 OPNc-overexpressing cells in relation to control clones. Differentially expressed genes are included in all main hallmarks of cancer, and several interacting proteins have been identified using an interactome network analysis. Based on marked up-regulation of Vegfa transcript in response to OPNc overexpression, we partially validated the array data by demonstrating that conditioned medium (CM) secreted from OvCar-3 and PC-3 OPNc-overexpressing cells significantly induced endothelial cell adhesion, proliferation and migration, compared to CM secreted from control cells. Conclusions Overall, the present study elucidated transcriptional changes of OvCar-3 and PC-3 cancer cell lines in response to OPNc overexpression, which provides an assessment for predicting the molecular mechanisms by which this splice variant promotes tumor progression features.
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Affiliation(s)
| | | | | | - Etel R P Gimba
- Coordenação de Pesquisa, Programa de Carcinogênese Molecular, Instituto Nacional de Câncer (INCa)/Programa de Pós Graduação Stricto Sensu em Oncologia do INCa, Rio de Janeiro, RJ, Brazil.
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17
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Andreeva AM. Identification of some proteins of blood and tissue fluid in the fish with enciphered genome. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093013060029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Huang ZX, Chen ZS, Ke CH, Zhao J, You WW, Zhang J, Dong WT, Chen J. Pyrosequencing of Haliotis diversicolor transcriptomes: insights into early developmental molluscan gene expression. PLoS One 2012; 7:e51279. [PMID: 23236463 PMCID: PMC3517415 DOI: 10.1371/journal.pone.0051279] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/31/2012] [Indexed: 12/02/2022] Open
Abstract
Background The abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking. Methodology/Principal Findings In this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the ‘lock system’ in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae. Conclusion This study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.
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Affiliation(s)
- Zi-Xia Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Zhi-Sen Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Cai-Huan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jing Zhao
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Wei You
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jie Zhang
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Ting Dong
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jun Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
- * E-mail:
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19
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Ganss B, Hoffmann W. Calcium-induced conformational transition of trout ependymins monitored by tryptophan fluorescence. Open Biochem J 2009; 3:14-7. [PMID: 19401757 PMCID: PMC2669641 DOI: 10.2174/1874091x00903010014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 12/05/2008] [Accepted: 01/20/2009] [Indexed: 11/22/2022] Open
Abstract
Ependymins are secretory, calcium-binding sialoproteins which are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these regeneration-responsive glycoproteins is associated with collagen fibrils of the extracellular matrix. Here, the tryptophan fluorescence of ependymins was monitored at various Ca(2+) concentrations. Two distinct states were identified with a relatively sharp transition at about 1 mM Ca(2+). In agreement with previous circular dichroism measurements, this strongly supports the hypothesis that a calcium-induced conformational change is important for the interaction of ependymins with components of the extracellular matrix. Such interactions with constituents of various basal laminae would also explain the important roles of piscine ependymins as well as invertebrate and mammalian ependymin-related proteins for cell adhesion processes and cell migration.
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Affiliation(s)
- Bernhard Ganss
- Max-Planck-Institute for Psychiatry, Department of Neurochemistry, D-82152 Martinsried, Germany
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20
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Suárez-Castillo EC, García-Arrarás JE. Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol 2007; 7:23. [PMID: 17302986 PMCID: PMC1805737 DOI: 10.1186/1471-2148-7-23] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 02/15/2007] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. RESULTS Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the ependymin paralog groups is well supported and several amino acid positions are predicted to be critical for this divergence. CONCLUSION Ependymin proteins are present in vertebrates, invertebrate deuterostomes, and protostomes. Overall, our analyses suggest that the ependymin protein family is a suitable target to experimentally test subfunctionalization in gene copies that originated after gene or genome duplication events.
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Affiliation(s)
- Edna C Suárez-Castillo
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
| | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
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21
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Bouchut A, Coustau C, Gourbal B, Mitta G. Compatibility in the Biomphalaria glabrata/Echinostoma caproni model: new candidate genes evidenced by a suppressive subtractive hybridization approach. Parasitology 2006; 134:575-88. [PMID: 17096871 DOI: 10.1017/s0031182006001673] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 09/27/2006] [Accepted: 09/28/2006] [Indexed: 11/05/2022]
Abstract
In order to elucidate mechanisms underlying snail/echinostome compatibility, numerous molecular studies comparing transcripts and proteins of Biomphalaria glabrata susceptible or resistant to Echinostoma caproni were undertaken. These studies focused on plasma and haemocytes of the two strains and revealed that some transcripts and/or proteins were differentially expressed between strains. The aim of the present study was to develop a complementary transcriptomic approach by constructing subtractive libraries. This work revealed some candidate transcripts already identified in previous studies (calcium-binding proteins and glycolytic enzymes) as well as novel candidate transcripts that were differentially represented between strains of B. glabrata. Among these newly identified genes, we revealed several genes potentially involved in immune processes encoding proteases, protease inhibitors, a lectin, an aplysianin-like molecule, and cell adhesion molecules.
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Affiliation(s)
- A Bouchut
- Parasitologie Fonctionnelle et Evolutive, UMR 5555, CNRS Université de Perpignan Perpignan, France
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22
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Della Valle MC, Sleat DE, Sohar I, Wen T, Pintar JE, Jadot M, Lobel P. Demonstration of Lysosomal Localization for the Mammalian Ependymin-related Protein Using Classical Approaches Combined with a Novel Density Shift Method. J Biol Chem 2006; 281:35436-45. [PMID: 16954209 DOI: 10.1074/jbc.m606208200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most newly synthesized soluble lysosomal proteins are delivered to the lysosome via the mannose 6-phosphate (Man-6-P)-targeting pathway. The presence of the Man-6-P post-translational modification allows these proteins to be affinity-purified on immobilized Man-6-P receptors. This approach has formed the basis for a number of proteomic studies that identified multiple as yet uncharacterized Man-6-P glycoproteins that may represent new lysosomal proteins. Although the presence of Man-6-P is suggestive of lysosomal function, the subcellular localization of such candidates requires experimental verification. Here, we have investigated one such candidate, ependymin-related protein (EPDR). EPDR is a protein of unknown function with some sequence similarity to ependymin, a fish protein thought to play a role in memory consolidation and learning. Using classical subcellular fractionation on rat brain, EPDR co-distributes with lysosomal proteins, but there is significant overlap between lysosomal and mitochondrial markers. For more definitive localization, we have developed a novel approach based upon a selective buoyant density shift of the brain lysosomes in a mutant mouse lacking NPC2, a lysosomal protein involved in lipid transport. EPDR, in parallel with lysosomal markers, shows this density shift in gradient centrifugation experiments comparing mutant and wild type mice. This approach, combined with morphological analyses, demonstrates that EPDR resides in the lysosome. In addition, the lipidosis-induced density shift approach represents a valuable tool for identification and validation of both luminal and membrane lysosomal proteins that should be applicable to high throughput proteomic studies.
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Affiliation(s)
- Maria Cecilia Della Valle
- Center for Advanced Biotechnology and Medicine, Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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23
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Kouznetsova I, Chwieralski CE, Bälder R, Hinz M, Braun A, Krug N, Hoffmann W. Induced trefoil factor family 1 expression by trans-differentiating Clara cells in a murine asthma model. Am J Respir Cell Mol Biol 2006; 36:286-95. [PMID: 16990615 DOI: 10.1165/rcmb.2006-0008oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Asthma is a chronic inflammatory disease of the airways that is accompanied by goblet cell metaplasia and mucus hypersecretion. Trefoil factor family (TFF) peptides represent major secretory products of the respiratory tract and are synthesized together with mucins. In the murine lung, TFF2 is mainly expressed, whereas TFF1 transcripts represent only a minor species. TFF peptides are well known for their motogenic and anti-apoptotic effects, and they modulate the inflammatory response of bronchial epithelial cells. Here, an established mouse model of asthma was investigated (i.e., exposure to Aspergillus fumigatus [AF] antigens). RT-PCR analysis of lung tissue showed elevated levels particularly of TFF1 transcripts in AF-sensitized/challenged animals. In contrast, transcripts encoding Clara cell secretory protein (CCSP/CC10) were strongly diminished in these animals. For comparison, the expression of the goblet cell secretory granule marker mCLCA3/Gob-5, the mucins Muc1-Muc6 and Muc19, and the secretoglobins ScgB3A1 and ScgB3A2, as well as the mammalian ependymin-related gene MERP2, were monitored. Immunohistochemistry localized TFF1 mainly in cells with a mixed phenotype (e.g., TFF1-positive cells stain with the lectin wheat germ agglutinin (WGA), which recognizes mucins characteristic of goblet cells). In addition, these cells express CCSP/CC10, a Clara cell marker. When compared with mucins or CCSP/CC10, TFF1 was stored in a different population of secretory granules localized at the more basolateral portion of these cells. Thus, the results presented indicate for the first time that allergen exposure leads to the trans-differentiation of Clara cells toward a TFF1-expressing mucous phenotype.
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Affiliation(s)
- Irina Kouznetsova
- Institut für Molekularbiologie und Medizinische Chemie, Otto-von-Guericke-Universität, Magdeburg; and Fraunhofer-Institut für Toxikologie und Experimentelle Medizin, Hannover, Germany
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24
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Kollmann K, Mutenda KE, Balleininger M, Eckermann E, von Figura K, Schmidt B, Lübke T. Identification of novel lysosomal matrix proteins by proteome analysis. Proteomics 2006; 5:3966-78. [PMID: 16145712 DOI: 10.1002/pmic.200401247] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The lysosomal matrix is estimated to contain about 50 different proteins. Most of the matrix proteins are acid hydrolases that depend on mannose 6-phosphate receptors (MPR) for targeting to lysosomes. Here, we describe a comprehensive proteome analysis of MPR-binding proteins from mouse. Mouse embryonic fibroblasts defective in both MPR (MPR 46-/- and MPR 300-/-) are known to secrete the lysosomal matrix proteins. Secretions of these cells were affinity purified using an affinity matrix derivatized with MPR46 and MPR300. In the protein fraction bound to the affinity matrix and eluted with mannose 6-phosphate, 34 known lysosomal matrix proteins, 4 candidate proteins of the lysosomal matrix and 4 non-lysosomal contaminants were identified by mass spectrometry after separation by two-dimensional gel electrophoresis or by multidimensional protein identification technology. For 3 of the candidate proteins, mammalian ependymin-related protein-2 (MERP-2), retinoid-inducible serine carboxypeptidase (RISC) and the hypothetical 66.3-kDa protein we could verify that C-terminally tagged forms bound in an M6P-dependent manner to an MPR-affinity matrix and were internalized via MPR-mediated endocytosis. Hence these 3 proteins are likely to represent hitherto unrecognized lysosomal matrix proteins.
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Affiliation(s)
- Katrin Kollmann
- Zentrum Biochemie und Molekulare Zellbiologie, Abteilung Biochemie II, Georg-August Universität Göttingen, Göttingen, Germany
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Volz DC, Hinton DE, Law JM, Kullman SW. Dynamic gene expression changes precede dioxin-induced liver pathogenesis in medaka fish. Toxicol Sci 2005; 89:524-34. [PMID: 16267337 DOI: 10.1093/toxsci/kfj033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A major challenge for environmental genomics is linking gene expression to cellular toxicity and morphological alteration. Herein, we address complexities related to hepatic gene expression responses after a single injection of the aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) and illustrate an initial stress response followed by cytologic and adaptive changes in the teleost fish medaka. Using a custom 175-gene array, we find that overall hepatic gene expression and histological changes are strongly dependent on dose and time. The most pronounced dioxin-induced gene expression changes occurred early and preceded morphologic alteration in the liver. Following a systematic search for putative Ah response elements (AHREs) (5'-CACGCA-3') within 2000 bp upstream of the predicted transcriptional start site, the majority (87%) of genes screened in this study did not contain an AHRE, suggesting that gene expression was not solely dependent on AHRE-mediated transcription. Moreover, in the highest dosage, we observed gene expression changes associated with adaptation that persisted for almost two weeks, including induction of a gene putatively identified as ependymin that may function in hepatic injury repair. These data suggest that the cellular response to dioxin involves both AHRE- and non-AHRE-mediated transcription, and that coupling gene expression profiling with analysis of morphologic pathogenesis is essential for establishing temporal relationships between transcriptional changes, toxicity, and adaptation to hepatic injury.
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Affiliation(s)
- David C Volz
- Integrated Toxicology Program and Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina 27708, USA
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Suárez-Castillo EC, Medina-Ortíz WE, Roig-López JL, García-Arrarás JE. Ependymin, a gene involved in regeneration and neuroplasticity in vertebrates, is overexpressed during regeneration in the echinoderm Holothuria glaberrima. Gene 2004; 334:133-43. [PMID: 15256263 DOI: 10.1016/j.gene.2004.03.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Revised: 02/25/2004] [Accepted: 03/18/2004] [Indexed: 11/22/2022]
Abstract
We report the characterization of an ependymin-related gene (EpenHg) from a regenerating intestine cDNA library of the sea cucumber Holothuria glaberrima. This finding is remarkable because no ependymin sequence has ever been reported from invertebrates. Database comparisons of the conceptual translation of the EpenHg gene reveal 63% similarity (47% identity) with mammalian ependymin-related proteins (MERPs) and close relationship with the frog and piscine ependymins. We also report the partial sequences of ependymin representatives from another species of sea cucumber and from a sea urchin species. Conventional and real-time reverse transcriptase polymerase chain reaction (RT-PCRs) show that the gene is expressed in several echinoderm tissues, including esophagus, mesenteries, gonads, respiratory trees, hemal system, tentacles and body wall. Moreover, the ependymin product in the intestine is overexpressed during sea cucumber intestinal regeneration. The discovery of ependymins in echinoderms, a group well known for their regenerative capacities, can give us an insight on the evolution and roles of ependymin molecules.
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Affiliation(s)
- Edna C Suárez-Castillo
- Department of Biology, University of Puerto Rico, Room 220 JGD Building, Ponce de Leon Avenue, PO Box 23360, UPR Station, San Juan, PR 00931-3360, USA
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