1
|
Chen F, Chen, Wang J, Zhang S, Chen M, Zhang X, Wu Z. Overexpression of SSR2 promotes proliferation of liver cancer cells and predicts prognosis of patients with hepatocellular carcinoma. J Cell Mol Med 2022; 26:3169-3182. [PMID: 35481617 PMCID: PMC9170819 DOI: 10.1111/jcmm.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022] Open
Abstract
Signal Sequence Receptor Subunit 2 (SSR2) is a key endoplasmic reticulum gene involved in protein folding and processing. Previous studies found that it was upregulated in several cancers, but its precise role in hepatocellular carcinoma (HCC) remains unclear. To have a better understanding of this gene in HCC, we examined the expression of SSR2 in HCC tissues by analysing The Cancer Genome Atlas (TCGA) data and immunohistochemistry. We also assessed the association between SSR2 expression and clinicopathological characteristics of HCC patients and patient survival. Potential function of SSR2 was predicted through GSEA and protein–protein interaction analysis. MTT, flowcytometry, transwell and a nude mice xenograft model were employed to investigate the biological functions in vivo and in vitro. The results showed that the expression of SSR2 was significantly increased in HCC tissues, and SSR2 expression was associated with several clinical characteristics. In addition, patients with higher SSR2 expression had poorer survival. Enrichment analysis suggested that SSR2 was probably involved in biological process or signalling pathways related to G2/M checkpoint, passive transmembrane transporter activity, ATF2_S_UP. V1_UP and ncRNA metabolic process. Further experimental study showed that SSR2 knockdown inhibited cell proliferation, migration and invasion ability and promoted apoptosis and cell cycle arrest in vitro. Moreover, downregulation of SSR2 also repressed the growth of HepG2 cells in vivo. In conclusion, our study suggests that SSR2 may act as an oncogene in HCC.
Collapse
Affiliation(s)
- Fengsui Chen
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Chen
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Jielong Wang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Shi'an Zhang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China
| | - Mengxue Chen
- Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, Fujian, P.R. China
| | - Xia Zhang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Zhixian Wu
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| |
Collapse
|
2
|
Fu J, Zhu W, Wang L, Luo M, Song F, Dong Z. Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis). BMC Genomics 2019; 20:781. [PMID: 31660854 PMCID: PMC6819325 DOI: 10.1186/s12864-019-6181-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish. RESULTS A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile. CONCLUSIONS The results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.
Collapse
Affiliation(s)
- Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Mingkun Luo
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| |
Collapse
|
3
|
Garg B, Pathria G, Wagner C, Maurer M, Wagner SN. Signal Sequence Receptor 2 is required for survival of human melanoma cells as part of an unfolded protein response to endoplasmic reticulum stress. Mutagenesis 2016; 31:573-82. [PMID: 27180333 DOI: 10.1093/mutage/gew023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Current therapy approaches in melanoma targeting have met with the development of resistance and tumour recurrence with a more aggressive phenotype. In a quest for alternative therapy targets, we had previously identified Signal Sequence Receptor 2 (SSR2) as a gene with high expression in a subgroup of human primary melanomas. Now we show that SSR2 exerts a prosurvival functionality in human melanoma cells and that high expression levels of SSR2 are associated with an unfavourable disease outcome in primary melanoma patients. Consistent with SSR's role in translocation of proteins from the ribosome across the endoplasmic reticulum (ER) membrane, our data supports induction of SSR2 as a part of the ER stress response. This response included SSR2 upregulation upon development of therapy resistance to BRAF inhibitors, as well as the dependency of cell survival of BRAF inhibitor-resistant melanoma cells on SSR2. Complementary gain and loss of function data showed the Unfolded Protein Response (UPR) to ER stress as an inducer of SSR2 via transcriptional regulation through X-Box Binding Protein 1s (XBP1s) and support an ER stress-UPR-Transcription Factor XBP1s-SSR2 response axis in human melanocytic cells. Together with its dispensability for survival in normal human cells, these data propose SSR2 as a potential therapeutic target in (therapy-resistant) human melanoma.
Collapse
Affiliation(s)
- Bhavuk Garg
- Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria
| | - Gaurav Pathria
- Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria, Present address: Biochemical-Pharmacological Center, University of Marburg, Karl-von-Frisch-Straße, Marburg 35032, Germany
| | - Christine Wagner
- Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria
| | - Margarita Maurer
- Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria
| | - Stephan N Wagner
- Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria,
| |
Collapse
|
4
|
Trikić MZ, Monk P, Roehl H, Partridge LJ. Regulation of zebrafish hatching by tetraspanin cd63. PLoS One 2011; 6:e19683. [PMID: 21625559 PMCID: PMC3098263 DOI: 10.1371/journal.pone.0019683] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 04/05/2011] [Indexed: 12/22/2022] Open
Abstract
Tetraspanins cause the clustering of membrane proteins into a level of organisation essential for cellular function. Given the importance and complicated nature of this mechanism, we attempted a novel approach to identify the function of a single component in a biologically relevant context. A morpholino knockdown strategy was used to investigate the role of cd63, a membrane protein associated with intracellular transport and a melanoma marker, in embryonic zebrafish. By using three separate morpholinos targeting cd63, we were able to identify a specific phenotype. Strikingly, morphant fish failed to hatch due to the lack of secreted proteolytic enzymes required for chorion-softening. The morphology of the hatching gland at both the cellular and intracellular levels was disorganised, suggesting a role for cd63 in the functioning of this organ. This work identifies a specific role for cd63 in the zebrafish embryo and provides evidence for the suitability of zebrafish as a model system for the investigation of tetraspanin enriched microdomains.
Collapse
Affiliation(s)
- Michael Z Trikić
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom.
| | | | | | | |
Collapse
|
5
|
Cerdà J, Bobe J, Babin PJ, Admon A, Lubzens E. Functional Genomics and Proteomic Approaches for the Study of Gamete Formation and Viability in Farmed Finfish. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802324685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
6
|
Mesbah K, Camus A, Babinet C, Barra J. Mutation in the Trapalpha/Ssr1 gene, encoding translocon-associated protein alpha, results in outflow tract morphogenetic defects. Mol Cell Biol 2006; 26:7760-71. [PMID: 17015483 PMCID: PMC1636874 DOI: 10.1128/mcb.00913-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Translocon-associated protein complex (TRAP) is thought to be required for efficient protein-specific translocation across the endoplasmic reticulum membrane. We created a mutation in the Trapalpha gene that leads to the synthesis of a truncated TRAPalpha protein fused to ShBle-beta-galactosidase. Analysis of Trapalpha cDNAs reveals that among three different messenger RNAs expressed in the mouse, one of them encodes a slightly larger protein that differs in its C-terminal end. This mRNA, specific for skeletal muscle and heart, is only expressed after birth. Homozygous Trapalpha mutant pups die at birth, likely as a result of severe cardiac defects. Indeed, the septation of the proximal part of the outflow tract is absent, resulting in a double-outlet right ventricle. Studies of protein secretion in transfected embryonic fibroblasts reveal that the TRAP complex does not function properly in homozygous mutant cells and confirm, in vivo, the involvement of TRAP in substrate-specific translocation. Our results provide the first in vivo demonstration that a member of the TRAP complex plays a crucial role in mammalian heart development and suggest that TRAPalpha could be involved in translocation of factors necessary for maturation of endocardial cushions.
Collapse
MESH Headings
- Aging/physiology
- Amino Acid Sequence
- Animals
- Base Sequence
- Calcium-Binding Proteins/chemistry
- Calcium-Binding Proteins/deficiency
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Cell Movement
- Conserved Sequence
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Embryo, Mammalian/cytology
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Gene Expression Regulation, Developmental
- Glycoside Hydrolases/genetics
- Glycoside Hydrolases/metabolism
- Heart/embryology
- Homozygote
- Humans
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/deficiency
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Knockout
- Molecular Sequence Data
- Mutation/genetics
- Myocardium/metabolism
- Neurons/cytology
- Neurons/metabolism
- RNA, Messenger/genetics
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/deficiency
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Peptide/chemistry
- Receptors, Peptide/deficiency
- Receptors, Peptide/genetics
- Receptors, Peptide/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Sequence Homology
Collapse
Affiliation(s)
- K Mesbah
- Laboratoire EGDM, CNRS URA 2578, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | | | | | | |
Collapse
|
7
|
Knoll-Gellida A, André M, Gattegno T, Forgue J, Admon A, Babin PJ. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. BMC Genomics 2006; 7:46. [PMID: 16526958 PMCID: PMC1488847 DOI: 10.1186/1471-2164-7-46] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 03/09/2006] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The ability of an oocyte to develop into a viable embryo depends on the accumulation of specific maternal information and molecules, such as RNAs and proteins. A serial analysis of gene expression (SAGE) was carried out in parallel with proteomic analysis on fully-grown ovarian follicles from zebrafish (Danio rerio). The data obtained were compared with ovary/follicle/egg molecular phenotypes of other animals, published or available in public sequence databases. RESULTS Sequencing of 27,486 SAGE tags identified 11,399 different ones, including 3,329 tags with an occurrence superior to one. Fifty-eight genes were expressed at over 0.15% of the total population and represented 17.34% of the mRNA population identified. The three most expressed transcripts were a rhamnose-binding lectin, beta-actin 2, and a transcribed locus similar to the H2B histone family. Comparison with the large-scale expressed sequence tags sequencing approach revealed highly expressed transcripts that were not previously known to be expressed at high levels in fish ovaries, like the short-sized polarized metallothionein 2 transcript. A higher sensitivity for the detection of transcripts with a characterized maternal genetic contribution was also demonstrated compared to large-scale sequencing of cDNA libraries. Ferritin heavy polypeptide 1, heat shock protein 90-beta, lactate dehydrogenase B4, beta-actin isoforms, tubulin beta 2, ATP synthase subunit 9, together with 40 S ribosomal protein S27a, were common highly-expressed transcripts of vertebrate ovary/unfertilized egg. Comparison of transcriptome and proteome data revealed that transcript levels provide little predictive value with respect to the extent of protein abundance. All the proteins identified by proteomic analysis of fully-grown zebrafish follicles had at least one transcript counterpart, with two exceptions: eosinophil chemotactic cytokine and nothepsin. CONCLUSION This study provides a complete sequence data set of maternal mRNA stored in zebrafish germ cells at the end of oogenesis. This catalogue contains highly-expressed transcripts that are part of a vertebrate ovarian expressed gene signature. Comparison of transcriptome and proteome data identified downregulated transcripts or proteins potentially incorporated in the oocyte by endocytosis. The molecular phenotype described provides groundwork for future experimental approaches aimed at identifying functionally important stored maternal transcripts and proteins involved in oogenesis and early stages of embryo development.
Collapse
Affiliation(s)
- Anja Knoll-Gellida
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Michèle André
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Tamar Gattegno
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Jean Forgue
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Patrick J Babin
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| |
Collapse
|
8
|
Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, Chalmel F, Fischer N, Strähle U. Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res 2004; 14:228-38. [PMID: 14718378 PMCID: PMC327098 DOI: 10.1101/gr.1819204] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for the identification of regulatory sequences in genomes. We tested this approach to identify regulatory sequences that control expression in the midline of the zebrafish embryo. We first isolated a set of genes that are coexpressed in the midline of the zebrafish embryo during somitogenesis stages by gene array analysis and subsequent rescreens by in situ hybridization. We subjected 45 of these genes to Compare and DotPlot analysis to detect conserved sequences in noncoding regions of orthologous loci in the zebrafish and Takifugu genomes. The regions of homology that were scored in nonconserved regions were inserted into expression vectors and tested for their regulatory activity by transient transgenesis in the zebrafish embryo. We identified one conserved region from the connective tissue growth factor gene (ctgf), which was able to drive expression in the midline of the embryo. This region shares sequence similarity with other floor plate/notochord-specific regulatory regions. Our results demonstrate that an unbiased comparative approach is a relevant method for the identification of tissue-specific cis-regulatory sequences in the zebrafish embryo.
Collapse
Affiliation(s)
- Thomas Dickmeis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142, F-67404 Illkirch Cedex, C.U. de Strasbourg, France
| | | | | | | | | | | | | | | |
Collapse
|