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Cheng X, Li X, Yang M, Zheng C, Li H, Qu L, Ning Z. Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens. BMC Genomics 2023; 24:704. [PMID: 37993775 PMCID: PMC10666442 DOI: 10.1186/s12864-023-09632-7] [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: 04/26/2023] [Accepted: 08/28/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determined the heritability of eggshell speckles and conducted a genome-wide association study (GWAS) on purebred Rhode Island Red (RIR) hens at 28 weeks to detect potential genomic loci and candidate genes associated with eggshell speckles. RESULTS The heritability of eggshell speckles was 0.35 at 28 weeks, and the speckle level is not related to other eggshell quality traits in terms of phenotypic correlation. We detected 311 SNPs (6 significantly, and 305 suggestively associated) and 39 candidate genes associated with eggshell speckles. Based on the pathway analysis, the 39 candidate genes were mainly involved in alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, GnRH signaling pathway, vascular smooth muscle contraction, and MAPK signaling pathway. Ultimately, ten genes, LOC423226, SPTBN5, EHD4, LOC77155, TYRO3, ITPKA, DLL4, PLA2G4B, PLA2G4EL5, and PLA2G4EL6 were considered the most promising genes associated with eggshell speckles that were implicated in immunoregulation, calcium transport, and phospholipid metabolism, while its function in laying hens requires further studies. CONCLUSIONS This study provides new insights into understanding the genetic basis of eggshell speckles and has practical application value for the genetic improvement of eggshell quality.
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Affiliation(s)
- Xue Cheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinghua Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mengyuan Yang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chuanwei Zheng
- Beijing Zhongnongbangyang Layer Breeding Co., Ltd, Beijing, 100083, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Panchalingam S, Kasivelu G, Jayaraman M, Kumar R, Kalimuthu S, Jeyaraman J. Differential gene expression analysis combined with molecular dynamics simulation study to elucidate the novel potential biomarker involved in pulmonary TB. Microb Pathog 2023; 182:106266. [PMID: 37482113 DOI: 10.1016/j.micpath.2023.106266] [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: 05/31/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
Tuberculosis (TB) is a lethal multisystem disease that attacks the lungs' first line of defense. A substantial threat to public health and a primary cause of death is pulmonary TB. This study aimed to identify and investigate the probable differentially expressed genes (DEGs) primarily involved in Pulmonary TB. Accordingly, three independent gene expression data sets, numbered GSE139825, GSE139871, and GSE54992, were utilized for this purpose. The identified DEGs were used for bioinformatics-based analysis, including physical gene interaction, Gene Ontology (GO), network analysis and pathway studies using the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). The computational analysis predicted that TNFAIP6 is the significant DEG in the gene expression profiling of TB datasets. According to gene ontology analysis, TNFAIP6 is also essential in injury and inflammation. Further, TNFA1P6 is strongly linked to arsenic poisoning, evident from the results of NetworkAnalyst, a comprehensive and interactive platform for gene expression profiling via network visual analytics. As a result, the TNFAIP6 gene was ultimately chosen as a candidate DEG and subsequently employed for in silico structural characterization studies. The tertiary structure of TNFAIP6 was modelled using the ROBETTA server, followed by validation with SAVES and ProSA webserver. Additionally, structural dynamic studies, including molecular dynamics simulation (MDS) and essential dynamics analysis, including principal component (PC) based free energy landscape (FEL) analysis, was used for checking the stability of TNFAIP6 models. The dynamics result established the structural rigidity of modelled TNFAIP6 through RMSD, RMSF and RoG results. The FEL analysis revealed the restricted conformational flexibility of TNFAIP6 by displaying a single minimum energy basin in the contour plot. The comprehensive computational analysis established that TNFAIP6 could serve as a viable biomarker to assess the severity of pulmonary TB.
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Affiliation(s)
- Santhiya Panchalingam
- Centre for Ocean Research, Sathyabama Institute of Science and Technology (Deemed to Be University), Chennai, 600 119, Tamil Nadu, India
| | - Govindaraju Kasivelu
- Centre for Ocean Research, Sathyabama Institute of Science and Technology (Deemed to Be University), Chennai, 600 119, Tamil Nadu, India.
| | - Manikandan Jayaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Rajalakshmi Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to Be University), Pillayarkuppam, Puducherry, 607 402, India
| | | | - Jeyakanthan Jeyaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India.
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3
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Chakraborty S, Bhat AM, Mushtaq I, Luan H, Kalluchi A, Mirza S, Storck MD, Chaturvedi N, Lopez-Guerrero JA, Llombart-Bosch A, Machado I, Scotlandi K, Meza JL, Ghosal G, Coulter DW, Jordan Rowley M, Band V, Mohapatra BC, Band H. EHD1-dependent traffic of IGF-1 receptor to the cell surface is essential for Ewing sarcoma tumorigenesis and metastasis. Commun Biol 2023; 6:758. [PMID: 37474760 PMCID: PMC10359273 DOI: 10.1038/s42003-023-05125-1] [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: 02/27/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
Overexpression of the EPS15 Homology Domain containing 1 (EHD1) protein has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown. We establish that EHD1 is overexpressed in Ewing sarcoma (EWS), with high EHD1 mRNA expression specifying shorter patient survival. ShRNA-knockdown and CRISPR-knockout with mouse Ehd1 rescue established a requirement of EHD1 for tumorigenesis and metastasis. RTK antibody arrays identified IGF-1R as a target of EHD1 regulation in EWS. Mechanistically, we demonstrate a requirement of EHD1 for endocytic recycling and Golgi to plasma membrane traffic of IGF-1R to maintain its surface expression and downstream signaling. Conversely, EHD1 overexpression-dependent exaggerated oncogenic traits require IGF-1R expression and kinase activity. Our findings define the RTK traffic regulation as a proximal mechanism of EHD1 overexpression-dependent oncogenesis that impinges on IGF-1R in EWS, supporting the potential of IGF-1R and EHD1 co-targeting.
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Affiliation(s)
- Sukanya Chakraborty
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Aaqib M Bhat
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Insha Mushtaq
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Incyte Corporation, Wilmington, DE, USA
| | - Haitao Luan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, UAE
| | - Matthew D Storck
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nagendra Chaturvedi
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | | | - Antonio Llombart-Bosch
- Department of Pathology, University of Valencia, Avd. Blasco Ibáñez 15, 46010, Valencia, Spain
| | - Isidro Machado
- Department of Pathology, University of Valencia, Avd. Blasco Ibáñez 15, 46010, Valencia, Spain
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Jane L Meza
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Gargi Ghosal
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Donald W Coulter
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Vimla Band
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Bhopal C Mohapatra
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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4
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Chakraborty S, Bhat AM, Mushtaq I, Luan H, Kalluchi A, Mirza S, Storck MD, Chaturvedi N, Lopez-Guerrero JA, Llombart-Bosch A, Machado I, Scotlandi K, Meza JL, Ghosal G, Coulter DW, Rowley JM, Band V, Mohapatra BC, Band H. EHD1-dependent traffic of IGF-1 receptor to the cell surface is essential for Ewing sarcoma tumorigenesis and metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.15.524130. [PMID: 36711452 PMCID: PMC9882098 DOI: 10.1101/2023.01.15.524130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Overexpression of EPS15 Homology Domain containing 1 (EHD1) has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown. We establish that EHD1 is overexpressed in Ewing sarcoma (EWS), with high EHD mRNA expression specifying shorter patient survival. ShRNA and CRISPR-knockout with mouse Ehd1 rescue established a requirement of EHD1 for tumorigenesis and metastasis. RTK antibody arrays identified the IGF-1R as a target of EHD1 regulation in EWS. Mechanistically, we demonstrate a requirement of EHD1 for endocytic recycling and Golgi to plasma membrane traffic of IGF-1R to maintain its surface expression and downstream signaling. Conversely, EHD1 overexpression-dependent exaggerated oncogenic traits require IGF-1R expression and kinase activity. Our findings define the RTK traffic regulation as a proximal mechanism of EHD1 overexpression-dependent oncogenesis that impinges on IGF-1R in EWS, supporting the potential of IGF-1R and EHD1 co-targeting.
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5
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Transcriptomic Analysis of Fish Hosts Responses to Nervous Necrosis Virus. Pathogens 2022; 11:pathogens11020201. [PMID: 35215144 PMCID: PMC8875540 DOI: 10.3390/pathogens11020201] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/24/2022] Open
Abstract
Nervous necrosis virus (NNV) has been responsible for mass mortalities in the aquaculture industry worldwide, with great economic and environmental impact. The present review aims to summarize the current knowledge of gene expression responses to nervous necrosis virus infection in different fish species based on transcriptomic analysis data. Four electronic databases, including PubMed, Web of Science, and SCOPUS were searched, and more than 500 publications on the subject were identified. Following the application of the appropriate testing, a total of 24 articles proved eligible for this review. NNV infection of different host species, in different developmental stages and tissues, presented in the eligible publications, are described in detail, revealing and highlighting genes and pathways that are most affected by the viral infection. Those transcriptome studies of NNV infected fish are oriented in elucidating the roles of genes/biomarkers for functions of special interest, depending on each study’s specific emphasis. This review presents a first attempt to provide an overview of universal host reaction mechanisms to viral infections, which will provide us with new perspectives to overcome NNV infection to build healthier and sustainable aquaculture systems.
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Evnouchidou I, Caillens V, Koumantou D, Saveanu L. The role of endocytic trafficking in antigen T Cell Receptor activation. Biomed J 2021; 45:310-320. [PMID: 34592497 PMCID: PMC9250096 DOI: 10.1016/j.bj.2021.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Antigen T cell receptors (TCR) recognize antigenic peptides displayed by the major histocompatibility complex (pMHC) and play a critical role in T cell activation. The levels of TCR complexes at the cell surface, where signaling is initiated, depend on the balance between TCR synthesis, recycling and degradation. Cell surface TCR interaction with pMHC leads to receptor clustering and formation of a tight T cell-APC contact, the immune synapse, from which the activated TCR is internalized. While TCR internalization from the immune synapse has been initially considered to arrest TCR signaling, recent evidence support the hypothesis that the internalized receptor continues to signal from specialized endosomes. Here, we review the molecular mechanisms of TCR endocytosis and recycling, both in steady state and after T cell activation. We then discuss the experimental evidence in favor of endosomal TCR signaling and its possible consequences on T cell activation.
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Affiliation(s)
- Irini Evnouchidou
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France.
| | - Vivien Caillens
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France
| | - Despoina Koumantou
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France
| | - Loredana Saveanu
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France.
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7
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Charpentier JC, King PD. Mechanisms and functions of endocytosis in T cells. Cell Commun Signal 2021; 19:92. [PMID: 34503523 PMCID: PMC8427877 DOI: 10.1186/s12964-021-00766-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/17/2021] [Indexed: 11/11/2022] Open
Abstract
Once thought of primarily as a means to neutralize pathogens or to facilitate feeding, endocytosis is now known to regulate a wide range of eukaryotic cell processes. Among these are regulation of signal transduction, mitosis, lipid homeostasis, and directed migration, among others. Less well-appreciated are the roles various forms of endocytosis plays in regulating αβ and, especially, γδ T cell functions, such as T cell receptor signaling, antigen discovery by trogocytosis, and activated cell growth. Herein we examine the contribution of both clathrin-mediated and clathrin-independent mechanisms of endocytosis to T cell biology. Video Abstract
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Affiliation(s)
- John C Charpentier
- Department of Microbiology and Immunology, University of Michigan Medical School, 6606 Med Sci II, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-5620, USA
| | - Philip D King
- Department of Microbiology and Immunology, University of Michigan Medical School, 6606 Med Sci II, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-5620, USA.
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Zhang L, Ding L, Li Y, Zhang F, Xu Y, Pan H, Wan X, Yan G, Yu F, Li R. EHD3 positively regulated by NR5A1 participates in testosterone synthesis via endocytosis. Life Sci 2021; 278:119570. [PMID: 33964295 DOI: 10.1016/j.lfs.2021.119570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 01/23/2023]
Abstract
AIMS Increasing evidence has shown that hormone secretion is regulated by endocytosis. Eps15 homology domain-containing protein 3 (EHD3) is an endocytic-trafficking regulatory protein, but whether EHD3 is associated with testosterone secretion is not clear. This work aims to explore the role of EHD3 in testosterone synthesis. MAIN METHODS Testosterone concentration was determined by ELISA. The effects of EHD3 on endocytosis were assessed by exosomes tracing assay and Immunofluorescence. Targeting relationship between EHD3 and NR5A1 was verified by chromatin immunoprecipitation (ChIP) and dual luciferase reporter gene assay in Leydig cells. For in vivo assessments, conditional NR5A1 knockout mouse model was established with CRISPR/Cas9 gene targeting technology. KEY FINDINGS EHD3 overexpression significantly increased the concentration of testosterone. EHD3 knockdown markedly decreased testosterone synthesis by reducing endocytosis. The activity of the EHD3 promoter was positively regulated by NR5A1, which occupied the conserved sequence "AGGTCA" in the EHD3 promoter. Furthermore, mice with a Leydig cell-specific conditional NR5A1 knockout displayed the blunted levels of EHD3 and clathrin (a key factor for endocytosis), and serum testosterone concentration compared with NR5A1f/f mice. SIGNIFICANCE This study suggests a potential molecular mechanism of testosterone synthesis to fully understand male reproductive health.
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Affiliation(s)
- Lingling Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China; NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China; Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Lijun Ding
- Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China; Clinical Center for Stem Cell Research, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yifan Li
- Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Fangxi Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China; NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Yanhong Xu
- Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Hongjie Pan
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Xiaofeng Wan
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Guijun Yan
- Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Fei Yu
- Center for Experimental Animal, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China.
| | - Runsheng Li
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China; NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China.
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Huang W, Chen J, Weng W, Xiang Y, Shi H, Shan Y. Development of cancer prognostic signature based on pan-cancer proteomics. Bioengineered 2020; 11:1368-1381. [PMID: 33200655 PMCID: PMC8291886 DOI: 10.1080/21655979.2020.1847398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Utilizing genomic data to predict cancer prognosis was insufficient. Proteomics can improve our understanding of the etiology and progression of cancer and improve the assessment of cancer prognosis. And the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated extensive proteomics data of the vast majority of tumors. Based on CPTAC, we can perform a proteomic pan-carcinoma analysis. We collected the proteomics data and clinical features of cancer patients from CPTAC. Then, we screened 69 differentially expressed proteins (DEPs) with R software in five cancers: hepatocellular carcinoma (HCC), children’s brain tumor tissue consortium (CBTTC), clear cell renal cell carcinoma (CCRC), lung adenocarcinoma (LUAD) and uterine corpus endometrial carcinoma (UCEC). GO and KEGG analysis were performed to clarify the function of these proteins. We also identified their interactions. The DEPs-based prognostic model for predicting over survival was identified by least absolute shrinkage and selection operator (LASSO)-Cox regression model in training cohort. Then, we used the time-dependent receiver operating characteristics analysis to evaluate the ability of the prognostic model to predict overall survival and validated it in validation cohort. The results showed that the DEPs-based prognostic model could accurately and effectively predict the survival rate of most cancers.
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Affiliation(s)
- Weiguo Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
| | - Jianhui Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
| | - Wanqing Weng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
| | - Yukai Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
| | - Hongqi Shi
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
| | - Yunfeng Shan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University , Wenzhou, China
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10
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EHD1 and RUSC2 Control Basal Epidermal Growth Factor Receptor Cell Surface Expression and Recycling. Mol Cell Biol 2020; 40:MCB.00434-19. [PMID: 31932478 DOI: 10.1128/mcb.00434-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/26/2019] [Indexed: 01/25/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is a prototype receptor tyrosine kinase and an oncoprotein in many solid tumors. Cell surface display of EGFR is essential for cellular responses to its ligands. While postactivation endocytic trafficking of EGFR has been well elucidated, little is known about mechanisms of basal/preactivation surface display of EGFR. Here, we identify a novel role of the endocytic regulator EHD1 and a potential EHD1 partner, RUSC2, in cell surface display of EGFR. EHD1 and RUSC2 colocalize with EGFR in vesicular/tubular structures and at the Golgi compartment. Inducible EHD1 knockdown reduced the cell surface EGFR expression with accumulation at the Golgi compartment, a phenotype rescued by exogenous EHD1. RUSC2 knockdown phenocopied the EHD1 depletion effects. EHD1 or RUSC2 depletion impaired the EGF-induced cell proliferation, demonstrating that the novel, EHD1- and RUSC2-dependent transport of unstimulated EGFR from the Golgi compartment to the cell surface that we describe is functionally important, with implications for physiologic and oncogenic roles of EGFR and targeted cancer therapies.
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11
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Ge H, Lin K, Zhou C, Lin Q, Zhang Z, Wu J, Zheng L, Yang Q, Wu S, Chen W, Wang Y. A multi-omic analysis of orange-spotted grouper larvae infected with nervous necrosis virus identifies increased adhesion molecules and collagen synthesis in the persistent state. FISH & SHELLFISH IMMUNOLOGY 2020; 98:595-604. [PMID: 32004615 DOI: 10.1016/j.fsi.2020.01.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Grouper (Epinephelus coioides) is an important commercial maricultural fish, which suffers from nervous necrosis virus (NNV) infection. The molecular mechanisms underlying the pathogenesis of the viral infection are not clear. In this study, we combined deep RNA sequencing and label-free mass spectrum for the first time to analyze the transcriptomic and proteomic profiles in infected/dead, infected/survival (persistent), and infection-free (control)orange-spotted groupers in the larval stage. Further analyses showed that the transcriptome and proteome changed dramatically among the three distinct groups, especially differentially-expressed genes in the infected/dead and infected/survival larvae enriched for pathways related to immune response. Notably, the overlapped genes between transcriptomes and proteomes identified that genes related to collagen synthesis and adhesion molecules were enhanced in the persistent (infected/survival) stage, which might contribute to suppressing the acute and lethal immune responses upon NNV infection. These transcriptomic and proteomic datasets enable the investigation of molecular mechanisms underlying NNV infection, thus may help further development of molecular breeding in marine fishery.
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Affiliation(s)
- Hui Ge
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China; Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Kebing Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China.
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Ziping Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350117, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Leyun Zheng
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Shuiqing Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361012, China
| | - Wei Chen
- Shanghai Applied Protein Technology Co., Ltd, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China.
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Onnis A, Baldari CT. Orchestration of Immunological Synapse Assembly by Vesicular Trafficking. Front Cell Dev Biol 2019; 7:110. [PMID: 31334230 PMCID: PMC6616304 DOI: 10.3389/fcell.2019.00110] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
Ligation of the T-cell antigen receptor (TCR) by cognate peptide bound to the Major Histocompatibility Complex on the surface of an antigen-presenting cell (APC) leads to the spatial reorganization of the TCR and accessory receptors to form a specialized area of intimate contact between T cell and APC, known as the immunological synapse (IS), where signals are deciphered, coordinated, and integrated to promote T cell activation. With the discovery that an endosomal TCR pool contributes to IS assembly and function by undergoing polarized recycling to the IS, recent years have witnessed a shift from a plasma membrane-centric view of the IS to the vesicular trafficking events that occur at this location following the TCR-dependent translocation of the centrosome toward the synaptic membrane. Here we will summarize our current understanding of the trafficking pathways that are responsible for the steady delivery of endosomal TCRs, kinases, and adapters to the IS to sustain signaling, as well as of the endocytic pathways responsible for signal termination. We will also discuss recent evidence highlighting a role for endosomes in sustaining TCR signaling after its internalization at the IS and identifying the IS as a site of formation and release of extracellular vesicles that allow for transcellular communication with the APC.
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Affiliation(s)
- Anna Onnis
- Department of Life Sciences, University of Siena, Siena, Italy
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Nakamura T, Nakajima K, Ohnishi T, Yoshikawa T, Nakanishi M, Takumi T, Tsuboi T, Kato T. Quantitative evaluation of incomplete preweaning lethality in mice by using the CRISPR/Cas9 system. Sci Rep 2018; 8:16025. [PMID: 30375401 PMCID: PMC6207718 DOI: 10.1038/s41598-018-34270-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/15/2018] [Indexed: 12/20/2022] Open
Abstract
Various molecular biology techniques implementing genome editing have made it possible to generate mouse mutants for nearly all known genes; as a result, the International Mouse Phenotyping Consortium (IMPC) database listing the phenotypes of genetically modified mice has been established. Among mouse phenotypes, lethality is crucial to evaluate the importance of genes in mouse survival. Although many genes are reported to show “preweaning lethality, incomplete penetrance” in the IMPC database, the survival rates of homozygous knockout mice are highly variable. Here, we propose the lethal allele index (LAI), the ratio of the observed number of mice with homozygous knockout (KO) to the theoretically predicted number of homozygous KO mice, as a simple quantitative indicator of preweaning lethality. Among the mice mutants registered as incompletely lethal in IMPC, the LAI calculated from the genotypes of F1 mice tended to be lower in disease-related genes, and correlated with the frequency of loss-of-function (LOF) alleles in humans. In genome-edited mice using CRISPR/Cas9, the number of mice with homozygous frameshift alleles seemed to be associated with lethality. We edited the Ehd1 gene in cell lines as well as mice using CRISPR/Cas9, and found that the genotype distribution was significantly different. The LAI calculated from these data was similar to the value calculated from the IMPC data. These findings support the potential usefulness of the LAI as an index of preweaning lethality in genome-edited mice.
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Affiliation(s)
- Takumi Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.,Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Kazuo Nakajima
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Tetsuo Ohnishi
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Moe Nakanishi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.
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