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Ghosh S, Goswami D, Dutta R, Ghatak D, De R. A Comprehensive Pan-Cancer Analysis of Cytochrome C Oxidase Assembly Factor 1 (COA1) Reveals Instrumental Role of Mitochondrial Protein Assembly in Cancer that Modulates Disease Progression and Prognostic Outcome. Cell Biochem Biophys 2024:10.1007/s12013-024-01366-x. [PMID: 38907941 DOI: 10.1007/s12013-024-01366-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Cytochrome c oxidase assembly factor 1 (COA1), a mitochondrial respiratory chain complex assembly factor protein of inner mitochondrial membrane (IMM), is involved in translating many mitochondrial components and assembling nuclear-encoded components within mitochondria. Given the lack of extensive research on COA1 in cancer, this study undertakes a comprehensive pan-cancer analysis of COA1, which is overexpressed across various cancer types, shedding light on its multifaceted role in tumorigenesis, prognosis, and tumor microenvironment (TME) modulation. Leveraging bioinformatics tools and public databases, we elucidated its potential as a diagnostic cancer biomarker as well as a target for novel anti-cancer therapeutics. Gene expression analysis using "TIMER2.0", "UALCAN" and "GEPIA2" platforms, supported by protein expression data, revealed a significant correlation between COA1 upregulation and poor prognosis in Kaplan-Meir analysis, underscoring its clinical relevance. Additionally, genetic mutation analysis of COA1 with the help of "cBioPortal" warrants further exploration into its functional significance. Moreover, our investigation of the tumor microenvironment unveiled the interplay of COA1 with fibroblast and T cell infiltration implicating the role of COA1 in the tumor immune microenvironment. Furthermore, COA1-related gene enrichment study in "GeneMANIA" and pathway cross-talk analysis with Gene Ontology (GO) gene sets established comprehensive clarifications about the molecular pathways and protein networks associated with COA1 deregulation. Overall, this study lays a sturdy foundation to support future research endeavors targeting COA1, unraveling the molecular mechanisms underlying COA1 deregulation, and exploring its therapeutic potential in cancer.
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Affiliation(s)
- Sayak Ghosh
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Devyani Goswami
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Rittick Dutta
- Swami Vivekananda University, Kolkata, 700121, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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2
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Qu M, Zhang Y, Gao Z, Zhang Z, Liu Y, Wan S, Wang X, Yu H, Zhang H, Liu Y, Schneider R, Meyer A, Lin Q. The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2317-6. [PMID: 37204606 DOI: 10.1007/s11427-022-2317-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 05/20/2023]
Abstract
The leafy seadragon certainly is among evolution's most "beautiful and wonderful" species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat. However, limited information is known about the genetic basis of its phenotypes and conspicuous camouflage. Here, we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage, which allowed us to predict population dynamics for this species. Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes, suggesting adaptations to the highly specialized habitat. Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages, supporting a recent adaptive shift in camouflage appendage formation. Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish, implying its important function in bone formation. Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species. The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change. Therefore, taking climate change-induced range shifts into account while developing future protection strategies.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingyi Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Yuhong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Ralf Schneider
- Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118, Kiel, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China.
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Li J, Zhang X, Ren P, Wu Y, Wang Y, Zhou W, Wang Z, Chao P. Landscape of RNA-binding proteins in diagnostic utility, immune cell infiltration and PANoptosis features of heart failure. Front Genet 2022; 13:1004163. [PMID: 36313471 PMCID: PMC9614340 DOI: 10.3389/fgene.2022.1004163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Heart failure remains a global public health problem linked to rising morbidity and mortality. RNA-binding proteins (RBPs) are crucial regulators in post-transcriptionally determining gene expression. Our study aimed to comprehensively elucidate the diagnostic utility and biological roles of RBPs in heart failure. Methods: Genomic data of human failing and nonfailing left ventricular myocardium specimens were retrieved from the GEO datasets. Heart failure-specific RBPs were screened with differential expression analyses, and RBP-based subtypes were clustered with consensus clustering approach. GSEA was implemented for comparing KEGG pathways across subtypes. RBP-based subtype-related genes were screened with WGCNA. Afterwards, characteristic genes were selected through integrating LASSO and SVM-RFE approaches. A nomogram based on characteristic genes was established and verified through calibration curve, decision curve and clinical impact curve analyses. The abundance of immune cell types was estimated with CIBERSORT approach. Results: Heart failure-specific RBPs were determined, which were remarkably linked to RNA metabolism process. Three RBP-based subtypes (namely C1, C2, C3) were established, characterized by distinct pathway activities and PANoptosis gene levels. C2 subtype presented the highest abundance of immune cells, followed by C1 and C3. Afterwards, ten characteristic genes were selected, which enabled to reliably diagnose heart failure risk. The characteristic gene-based nomogram enabled to accurately predict risk of heart failure, with the excellent clinical utility. Additionally, characteristic genes correlated to immune cell infiltration and PANoptosis genes. Conclusion: Our findings comprehensively described the roles of RBPs in heart failure. Further research is required for verifying the effectiveness of RBP-based subtypes and characteristic genes in heart failure.
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Affiliation(s)
- Jie Li
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xueqin Zhang
- Department of Nephrology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Peng Ren
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yu Wu
- Department of Medical Administration, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yaoguo Wang
- Department of Information Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Wenzheng Zhou
- Department of Orthopaedics, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Zhao Wang
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
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Quiroga-Artigas G, de Jong D, Schnitzler CE. GNL3 is an evolutionarily conserved stem cell gene influencing cell proliferation, animal growth and regeneration in the hydrozoan Hydractinia. Open Biol 2022; 12:220120. [PMID: 36069077 PMCID: PMC9449814 DOI: 10.1098/rsob.220120] [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] [Indexed: 11/12/2022] Open
Abstract
Nucleostemin (NS) is a vertebrate gene preferentially expressed in stem and cancer cells, which acts to regulate cell cycle progression, genome stability and ribosome biogenesis. NS and its paralogous gene, GNL3-like (GNL3L), arose in the vertebrate clade after a duplication event from their orthologous gene, G protein Nucleolar 3 (GNL3). Research on invertebrate GNL3, however, has been limited. To gain a greater understanding of the evolution and functions of the GNL3 gene, we have performed studies in the hydrozoan cnidarian Hydractinia symbiolongicarpus, a colonial hydroid that continuously generates pluripotent stem cells throughout its life cycle and presents impressive regenerative abilities. We show that Hydractinia GNL3 is expressed in stem and germline cells. The knockdown of GNL3 reduces the number of mitotic and S-phase cells in Hydractinia larvae of different ages. Genome editing of Hydractinia GNL3 via CRISPR/Cas9 resulted in colonies with reduced growth rates, polyps with impaired regeneration capabilities, gonadal morphological defects, and low sperm motility. Collectively, our study shows that GNL3 is an evolutionarily conserved stem cell and germline gene involved in cell proliferation, animal growth, regeneration and sexual reproduction in Hydractinia, and sheds new light into the evolution of GNL3 and of stem cell systems.
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Affiliation(s)
- Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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5
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Lai B, Qian S, Zhang H, Zhang S, Kozlova A, Duan J, Xu J, He X. Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning. PLoS Comput Biol 2022; 18:e1010011. [PMID: 35576194 PMCID: PMC9135341 DOI: 10.1371/journal.pcbi.1010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/26/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomewide association studies (GWAS) have identified a large number of loci associated with neuropsychiatric traits, however, understanding the molecular mechanisms underlying these loci remains difficult. To help prioritize causal variants and interpret their functions, computational methods have been developed to predict regulatory effects of non-coding variants. An emerging approach to variant annotation is deep learning models that predict regulatory functions from DNA sequences alone. While such models have been trained on large publicly available dataset such as ENCODE, neuropsychiatric trait-related cell types are under-represented in these datasets, thus there is an urgent need of better tools and resources to annotate variant functions in such cellular contexts. To fill this gap, we collected a large collection of neurodevelopment-related cell/tissue types, and trained deep Convolutional Neural Networks (ResNet) using such data. Furthermore, our model, called MetaChrom, borrows information from public epigenomic consortium to improve the accuracy via transfer learning. We show that MetaChrom is substantially better in predicting experimentally determined chromatin accessibility variants than popular variant annotation tools such as CADD and delta-SVM. By combining GWAS data with MetaChrom predictions, we prioritized 31 SNPs for Schizophrenia, suggesting potential risk genes and the biological contexts where they act. In summary, MetaChrom provides functional annotations of any DNA variants in the neuro-development context and the general method of MetaChrom can also be extended to other disease-related cell or tissue types.
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Affiliation(s)
- Boqiao Lai
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Sheng Qian
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Hanwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Alena Kozlova
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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6
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Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet 2022; 109:116-135. [PMID: 34965383 DOI: 10.1016/j.ajhg.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022] Open
Abstract
The high-grade serous ovarian cancer (HGSOC) risk locus at chromosome 1p34.3 resides within a frequently amplified genomic region signifying the presence of an oncogene. Here, we integrate in silico variant-to-function analysis with functional studies to characterize the oncogenic potential of candidate genes in the 1p34.3 locus. Fine mapping of genome-wide association statistics identified candidate causal SNPs local to H3K27ac-demarcated enhancer regions that exhibit allele-specific binding for CTCF in HGSOC and normal fallopian tube secretory epithelium cells (FTSECs). SNP risk associations colocalized with eQTL for six genes (DNALI1, GNL2, RSPO1, SNIP1, MEAF6, and LINC01137) that are more highly expressed in carriers of the risk allele, and three (DNALI1, GNL2, and RSPO1) were upregulated in HGSOC compared to normal ovarian surface epithelium cells and/or FTSECs. Increased expression of GNL2 and MEAF6 was associated with shorter survival in HGSOC with 1p34.3 amplifications. Despite its activation of β-catenin signaling, RSPO1 overexpression exerted no effects on proliferation or colony formation in our study of ovarian cancer and FTSECs. Instead, GNL2, MEAF6, and SNIP1 silencing impaired in vitro ovarian cancer cell growth. Additionally, GNL2 silencing diminished xenograft tumor formation, whereas overexpression stimulated proliferation and colony formation in FTSECs. GNL2 influences 60S ribosomal subunit maturation and global protein synthesis in ovarian cancer and FTSECs, providing a potential mechanism of how GNL2 upregulation might promote ovarian cancer development and mediate genetic susceptibility of HGSOC.
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7
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Xia Z, Bi X, Yang S, Yang X, Song Z, Wei J, Xu P, Rink L, Min J, Wang F. Metal transporter Slc30a1 controls pharyngeal neural crest differentiation via the zinc-Snai2-Jag1 cascade. MedComm (Beijing) 2021; 2:778-797. [PMID: 34977877 PMCID: PMC8706747 DOI: 10.1002/mco2.91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
The pharyngeal arch (PA) is a neural crest (NC)-derived organ that is transiently developed during embryogenesis and is required for the subsequent development of various tissues. However, the role of zinc during PA differentiation from NC progenitor cells is unknown. Here, we found that the metal transporters Slc30a1a and Slc30a1b mediate zinc homeostasis during PA differentiation. Slc30a1-deficient zebrafish develop zinc accumulation in NC cells, with increased expression of stemness markers and PA dorsal genes, and SMART-seq analyses revealed that the genes snai2 and jag1b may serve as downstream targets. Furthermore, functional studies showed that knocking down either snai2 or jag1b rescues PA development in Slc30a1-deficient zebrafish. Notably, we identified the double zinc-finger domain in the transcription factor Snai2 as a zinc-responsive element that regulates jag1b expression. Our findings indicate that the Slc30a1/zinc-snai2-jag1b axis is an essential regulatory network controlling PA differentiation, shedding new light on the function of zinc homeostasis in maintaining NC cell stemness and multipotency in vertebrates.
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Affiliation(s)
- Zhidan Xia
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Xinying Bi
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangChina
| | - Sisi Yang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Xiu Yang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Zijun Song
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Jiayu Wei
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Pengfei Xu
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Lothar Rink
- Faculty of MedicineInstitute of ImmunologyRWTH Aachen UniversityAachenGermany
| | - Junxia Min
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Fudi Wang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangChina
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8
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Study of the G Protein Nucleolar 2 Value in Liver Hepatocellular Carcinoma Treatment and Prognosis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4873678. [PMID: 34337013 PMCID: PMC8315868 DOI: 10.1155/2021/4873678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/29/2021] [Indexed: 01/17/2023]
Abstract
LIHC (liver hepatocellular carcinoma) mostly occurs in patients with chronic liver disease. It is primarily induced by a vicious cycle of liver injury, inflammation, and regeneration that usually last for decades. The G protein nucleolar 2 (GNL2), as a protein-encoding gene, is also known as NGP1, Nog2, Nug2, Ngp-1, and HUMAUANTIG. Few reports are shown towards the specific biological function of GNL2. Meanwhile, it is still unclear whether it is related to the pathogenesis of carcinoma up to date. Here, our study attempts to validate the role and function of GNL2 in LIHC via multiple databases and functional assays. After analysis of gene expression profile from The Cancer Genome Atlas (TCGA) database, GNL2 was largely heightened in LIHC, and its overexpression displayed a close relationship with different stages and poor prognosis of carcinoma. After enrichment analysis, the data revealed that the genes coexpressed with GNL2 probably participated in ribosome biosynthesis which was essential for unrestricted growth of carcinoma. Cell functional assays presented that GNL2 knockdown by siRNA in LIHC cells MHCC97-H and SMCC-7721 greatly reduced cell proliferation, migration, and invasion ability. All in all, these findings capitulated that GNL2 could be a promising treatment target and prognosis biomarker for LIHC.
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9
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Lu M, Qiu S, Jiang X, Wen D, Zhang R, Liu Z. Development and Validation of Epigenetic Modification-Related Signals for the Diagnosis and Prognosis of Hepatocellular Carcinoma. Front Oncol 2021; 11:649093. [PMID: 34235075 PMCID: PMC8256693 DOI: 10.3389/fonc.2021.649093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022] Open
Abstract
Background Increasing evidence has indicated that abnormal epigenetic factors such as RNA m6A modification, histone modification, DNA methylation, RNA binding proteins and transcription factors are correlated with hepatocarcinogenesis. However, it is unknown how epigenetic modification-associated genes contribute to the occurrence and clinical outcome of hepatocellular carcinoma (HCC). Thus, we constructed the epigenetic modification-associated models that may enhance the diagnosis and prognosis of HCC. Methods In this study, we focused on the clinical value of epigenetic modification-associated genes for HCC. Our gene expression data were collected from TCGA and HCC data sets from the GEO database to ensure the reliability of the data. Their functions were analyzed by bioinformatics methods. We used lasso regression, Support vector machine (SVM), logistic regression and Cox regression to construct the diagnostic and prognostic models. We also constructed a nomogram of the practicability of the above-mentioned prognostic model. The above results were verified in an independent liver cancer data set from the ICGC database and clinical samples. Furthermore, we carried out pan-cancer analysis to verify the specificity of the above model and screened a wide range of drug candidates. Results Many epigenetic modification-associated genes were significantly different in HCC and normal liver tissues. The gene signatures showed a good ability to predict the occurrence and survival of HCC patients, as verified by DCA and ROC curve analysis. Conclusion Gene signatures based on epigenetic modification-associated genes can be used to identify the occurrence and prognosis of liver cancer.
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Affiliation(s)
- Maoqing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sheng Qiu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianyao Jiang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Diguang Wen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ronggui Zhang
- Department of Endocrinology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zuojin Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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10
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Lv M, Zhang Y, Liu K, Li C, Wang J, Fan G, Liu X, Yang H, Liu C, Mahboob S, Liu J, Shao C. A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. Front Genet 2020; 11:581161. [PMID: 33329719 PMCID: PMC7729161 DOI: 10.3389/fgene.2020.581161] [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] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Anglerfishes are a highly diverse group of species with unique characteristics. Here, we report the first chromosome-level genome of a species in the order Lophiiformes, the yellow goosefish (Lophius litulon), obtained by whole genome shotgun sequencing and high-throughput chromatin conformation capture. Approximately 97.20% of the assembly spanning 709.23 Mb could be anchored to 23 chromosomes with a contig N50 of 164.91 kb. The BUSCO value was 95.4%, suggesting that the quality of the assembly was high. A comparative gene family analysis identified expanded and contracted gene families, and these may be associated with adaptation to the benthic environment and the lack of scales in the species. A majority of positively selected genes were related to metabolic processes, suggesting that digestive and metabolic system evolution expanded the diversity of yellow goosefish prey. Our study provides a valuable genetic resource for understanding the mechanisms underlying the unique features of the yellow goosefish and for investigating anglerfish evolution.
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Affiliation(s)
- Meiqi Lv
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Changlin Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shahid Mahboob
- Department of Zoology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Covello G, Rossello FJ, Filosi M, Gajardo F, Duchemin A, Tremonti BF, Eichenlaub M, Polo JM, Powell D, Ngai J, Allende ML, Domenici E, Ramialison M, Poggi L. Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases. FASEB Bioadv 2020; 2:434-448. [PMID: 32676583 PMCID: PMC7354691 DOI: 10.1096/fba.2020-00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 12/21/2022] Open
Abstract
Expression of the bHLH transcription protein Atoh7 is a crucial factor conferring competence to retinal progenitor cells for the development of retinal ganglion cells. Several studies have emerged establishing ATOH7 as a retinal disease gene. Remarkably, such studies uncovered ATOH7 variants associated with global eye defects including optic nerve hypoplasia, microphthalmia, retinal vascular disorders, and glaucoma. The complex genetic networks and cellular decisions arising downstream of atoh7 expression, and how their dysregulation cause development of such disease traits remains unknown. To begin to understand such Atoh7-dependent events in vivo, we performed transcriptome analysis of wild-type and atoh7 mutant (lakritz) zebrafish embryos at the onset of retinal ganglion cell differentiation. We investigated in silico interplays of atoh7 and other disease-related genes and pathways. By network reconstruction analysis of differentially expressed genes, we identified gene clusters enriched in retinal development, cell cycle, chromatin remodeling, stress response, and Wnt pathways. By weighted gene coexpression network, we identified coexpression modules affected by the mutation and enriched in retina development genes tightly connected to atoh7. We established the groundwork whereby Atoh7-linked cellular and molecular processes can be investigated in the dynamic multi-tissue environment of the developing normal and diseased vertebrate eye.
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Affiliation(s)
- Giuseppina Covello
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Present address:
Department of BiologyUniversity of PadovaPadovaItaly
| | - Fernando J. Rossello
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
- Present address:
University of Melbourne Centre for Cancer ResearchUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Felipe Gajardo
- Center for Genome RegulationFacultad de Ciencias, SantiagoUniversidad de ChileSantiagoChile
| | | | - Beatrice F. Tremonti
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Michael Eichenlaub
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
| | - Jose M. Polo
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
- BDIMonash University Clayton VICClaytonAustralia
| | - David Powell
- Monash Bioinformatics PlatformMonash University Clayton VICClaytonAustralia
| | - John Ngai
- Department of Molecular and Cell Biology & Helen Wills Neuroscience InstituteUniversity of CaliforniaBerkeleyCAUSA
| | - Miguel L. Allende
- Center for Genome RegulationFacultad de Ciencias, SantiagoUniversidad de ChileSantiagoChile
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Fondazione The Microsoft Research ‐ University of Trento Centre for Computational and Systems BiologyTrentoItaly
| | - Mirana Ramialison
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
| | - Lucia Poggi
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Centre for Organismal StudyHeidelberg UniversityHeidelbergGermany
- Department of PhysiologyDevelopment and NeuroscienceUniversity of CambridgeCambridgeUnited Kingdom
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12
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Tkatchenko TV, Shah RL, Nagasaki T, Tkatchenko AV. Analysis of genetic networks regulating refractive eye development in collaborative cross progenitor strain mice reveals new genes and pathways underlying human myopia. BMC Med Genomics 2019; 12:113. [PMID: 31362747 PMCID: PMC6668126 DOI: 10.1186/s12920-019-0560-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Population studies suggest that genetic factors play an important role in refractive error development; however, the precise role of genetic background and the composition of the signaling pathways underlying refractive eye development remain poorly understood. METHODS Here, we analyzed normal refractive development and susceptibility to form-deprivation myopia in the eight progenitor mouse strains of the Collaborative Cross (CC). We used RNA-seq to analyze gene expression in the retinae of these mice and reconstruct genetic networks and signaling pathways underlying refractive eye development. We also utilized genome-wide gene-based association analysis to identify mouse genes and pathways associated with myopia in humans. RESULTS Genetic background strongly influenced both baseline refractive development and susceptibility to environmentally-induced myopia. Baseline refractive errors ranged from - 21.2 diopters (D) in 129S1/svlmj mice to + 22.0 D in CAST/EiJ mice and represented a continuous distribution typical of a quantitative genetic trait. The extent of induced form-deprivation myopia ranged from - 5.6 D in NZO/HILtJ mice to - 20.0 D in CAST/EiJ mice and also followed a continuous distribution. Whole-genome (RNA-seq) gene expression profiling in retinae from CC progenitor strains identified genes whose expression level correlated with either baseline refractive error or susceptibility to myopia. Expression levels of 2,302 genes correlated with the baseline refractive state of the eye, whereas 1,917 genes correlated with susceptibility to induced myopia. Genome-wide gene-based association analysis in the CREAM and UK Biobank human cohorts revealed that 985 of the above genes were associated with myopia in humans, including 847 genes which were implicated in the development of human myopia for the first time. Although the gene sets controlling baseline refractive development and those regulating susceptibility to myopia overlapped, these two processes appeared to be controlled by largely distinct sets of genes. CONCLUSIONS Comparison with data for other animal models of myopia revealed that the genes identified in this study comprise a well-defined set of retinal signaling pathways, which are highly conserved across different vertebrate species. These results identify major signaling pathways involved in refractive eye development and provide attractive targets for the development of anti-myopia drugs.
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Affiliation(s)
| | - Rupal L. Shah
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, UK
| | | | - Andrei V. Tkatchenko
- Department of Ophthalmology, Columbia University, New York, NY USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY USA
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13
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Sami MM, Hachim MY, Hachim IY, Elbarkouky AH, López-Ozuna VM. Nucleostemin expression in breast cancer is a marker of more aggressive phenotype and unfavorable patients' outcome: A STROBE-compliant article. Medicine (Baltimore) 2019; 98:e14744. [PMID: 30817632 PMCID: PMC6831441 DOI: 10.1097/md.0000000000014744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cancer stem cells (CSCs) are postulated to play significant role in the pathogenesis, progression as well as drug resistance of breast cancer. Nucleostemin (NS) is thought to be a key molecule for stemness, and the clinical impact of NS immunoreactivity in breast cancer can indicate its actual role and future therapeutic potentials.The current study is an observational study with an attempt to evaluate the correlation between NS expression (protein and gene expression levels) and different clinicopathological attributes of invasive breast cancer. For that reason, we investigated NS immunohistochemistry expression on commercial tissue microarray (TMA) of 102 patients and 51 archival specimens from patients admitted to Saqr Hospital, Ras Al Khaimah and diagnosed in Al Baraha Hospital, Dubai, UAE. In addition, the association between NS (GNL3) gene expression and different prognostic parameters as well as patient outcome was also evaluated using 2 large publicly available databases.Interestingly, we found NS expression to be associated with less differentiated and more advance stage. In addition, NS expression was significantly higher in larger size (P = .001) and LN-positive tumors (P = .007). Notably, NS expression was significantly correlated to P53 positive (P = .037) status. Furthermore, NS was found to be more expressed in the highly aggressive breast cancer subtypes including human epidermal growth factor receptor 2 (HER-2) and triple negative breast cancer (TNBC) subtypes. Moreover, our results also showed that high GNL3 gene expression to be associated with poor patient outcome and higher chances of tumor recurrence.Our results highlight NS expression as a marker of aggressive phenotype and poor outcome and indicate its possible use as a potential target for CSC-associated breast cancer management.
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Affiliation(s)
- Manal M. Sami
- Department of Pathology, Ras Al Khaimah College of Medical Sciences, Ras Al Khaimah Medical and Health Sciences University, United Arab Emirates
- Department of Pathology, Faculty of Medicine, Suez Canal University, Ismaillia, Egypt
| | - Mahmood Y. Hachim
- Sharjah Institute for Medical Research, University of Sharjah, United Arab Emirates
| | - Ibrahim Y. Hachim
- Department of Medicine, McGill University Health Center, Cancer Research Program, Montreal, Canada
| | - Ahmed H. Elbarkouky
- Department of Pathology, Al Baraha Hospital, Dubai, United Arab Emirates
- Department of Pathology, College of Medicine, Tanta University, Tanta, Gharbia, Egypt
| | - Vanessa M. López-Ozuna
- Segal Cancer Center, Lady Davis Institute of Medical Research, McGill University, Montreal, Quebec, Canada
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14
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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15
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Grigoryan EN, Markitantova YV. Cellular and Molecular Preconditions for Retinal Pigment Epithelium (RPE) Natural Reprogramming during Retinal Regeneration in Urodela. Biomedicines 2016; 4:E28. [PMID: 28536395 PMCID: PMC5344269 DOI: 10.3390/biomedicines4040028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 12/25/2022] Open
Abstract
Many regeneration processes in animals are based on the phenomenon of cell reprogramming followed by proliferation and differentiation in a different specialization direction. An insight into what makes natural (in vivo) cell reprogramming possible can help to solve a number of biomedical problems. In particular, the first problem is to reveal the intrinsic properties of the cells that are necessary and sufficient for reprogramming; the second, to evaluate these properties and, on this basis, to reveal potential endogenous sources for cell substitution in damaged tissues; and the third, to use the acquired data for developing approaches to in vitro cell reprogramming in order to obtain a cell reserve for damaged tissue repair. Normal cells of the retinal pigment epithelium (RPE) in newts (Urodela) can change their specialization and transform into retinal neurons and ganglion cells (i.e., actualize their retinogenic potential). Therefore, they can serve as a model that provides the possibility to identify factors of the initial competence of vertebrate cells for reprogramming in vivo. This review deals mainly with the endogenous properties of native newt RPE cells themselves and, to a lesser extent, with exogenous mechanisms regulating the process of reprogramming, which are actively discussed.
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Affiliation(s)
- Eleonora N Grigoryan
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia.
| | - Yuliya V Markitantova
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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16
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Sun X, Jia Y, Wei Y, Liu S, Yue B. Gene expression profiling of NB4 cells following knockdown of nucleostemin using DNA microarrays. Mol Med Rep 2016; 14:175-83. [PMID: 27374947 PMCID: PMC4918620 DOI: 10.3892/mmr.2016.5213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/18/2015] [Indexed: 11/05/2022] Open
Abstract
Nucleostemin (NS) is mainly expressed in stem and tumor cells, and is necessary for the maintenance of their self-renewal and proliferation. Originally, NS was thought to exert its effects through inhibiting p53, while recent studies have revealed that NS is also able to function independently of p53. The present study performed a gene expression profiling analysis of p53‑mutant NB4 leukeima cells following knockdown of NS in order to elucidate the p53‑independent NS pathway. NS expression was silenced using lentivirus‑mediated RNA interference technology, and gene expression profiling of NB4 cells was performed by DNA microarray analysis. A total of 1,953 genes were identified to be differentially expressed (fold change ≥2 or ≤0.5) following knockdown of NS expression. Furthermore, reverse‑transcription quantitative polymerase chain reaction analysis was used to detect the expression of certain candidate genes, and the results were in agreement with the micaroarray data. Pathway analysis indicated that aberrant genes were enhanced in endoplasmic, c‑Jun N‑terminal kinase and mineral absorption pathways. The present study shed light on the mechanisms of the p54‑independent NS pathway in NB4 cells and provided a foundation for the discovery of promising targets for the treatment of p53-mutant leukemia.
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Affiliation(s)
- Xiaoli Sun
- Department of Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yu Jia
- Department of Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yuanyu Wei
- Department of Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shuai Liu
- Department of Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Baohong Yue
- Department of Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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17
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Sia PI, Wood JP, Chidlow G, Sharma S, Craig J, Casson RJ. Role of the nucleolus in neurodegenerative diseases with particular reference to the retina: a review. Clin Exp Ophthalmol 2016; 44:188-95. [PMID: 26427048 DOI: 10.1111/ceo.12661] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 01/20/2023]
Abstract
The nucleolus has emerged as a key regulator of cellular growth and the response to stress, in addition to its traditionally understood function in ribosome biogenesis. The association between nucleolar function and neurodegenerative disease is increasingly being explored. There is also recent evidence indicating that the nucleolus may well be crucial in the development of the eye. In this present review, the role of the nucleolus in retinal development as well as in neurodegeneration with an emphasis on the retina is discussed.
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Affiliation(s)
- Paul I Sia
- Ophthalmic Research Laboratories, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - John Pm Wood
- Ophthalmic Research Laboratories, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Glyn Chidlow
- Ophthalmic Research Laboratories, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Jamie Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Robert J Casson
- Ophthalmic Research Laboratories, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
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18
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19
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Markitantova YV, Avdonin PP, Grigoryan EN. Identification of the gene encoding nucleostemin in the eye tissues of Pleurodeles waltl. BIOL BULL+ 2015. [DOI: 10.1134/s1062359015050088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Datta D, Anbarasu K, Rajabather S, Priya RS, Desai P, Mahalingam S. Nucleolar GTP-binding Protein-1 (NGP-1) Promotes G1 to S Phase Transition by Activating Cyclin-dependent Kinase Inhibitor p21 Cip1/Waf1. J Biol Chem 2015. [PMID: 26203195 DOI: 10.1074/jbc.m115.637280] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleolar GTP-binding protein (NGP-1) is overexpressed in various cancers and proliferating cells, but the functional significance remains unknown. In this study, we show that NGP-1 promotes G1 to S phase transition of cells by enhancing CDK inhibitor p21(Cip-1/Waf1) expression through p53. In addition, our results suggest that activation of the cyclin D1-CDK4 complex by NGP-1 via maintaining the stoichiometry between cyclin D1-CDK4 complex and p21 resulted in hyperphosphorylation of retinoblastoma protein at serine 780 (p-RB(Ser-780)) followed by the up-regulation of E2F1 target genes required to promote G1 to S phase transition. Furthermore, our data suggest that ribosomal protein RPL23A interacts with NGP-1 and abolishes NGP-1-induced p53 activity by enhancing Mdm2-mediated p53 polyubiquitination. Finally, reduction of p-RB(Ser-780) levels and E2F1 target gene expression upon ectopic expression of RPL23a resulted in arrest at the G1 phase of the cell cycle. Collectively, this investigation provides evidence that NGP-1 promotes cell cycle progression through the activation of the p53/p21(Cip-1/Waf1) pathway.
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Affiliation(s)
- Debduti Datta
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Kumaraswamy Anbarasu
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Suryaraja Rajabather
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Rangasamy Sneha Priya
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Pavitra Desai
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
| | - Sundarasamy Mahalingam
- From the Laboratory of Molecular Virology and Cell Biology, National Cancer Tissue Biobank, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai 600 036, India
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21
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Fantin A, Lampropoulou A, Gestri G, Raimondi C, Senatore V, Zachary I, Ruhrberg C. NRP1 Regulates CDC42 Activation to Promote Filopodia Formation in Endothelial Tip Cells. Cell Rep 2015; 11:1577-90. [PMID: 26051942 PMCID: PMC4528263 DOI: 10.1016/j.celrep.2015.05.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/23/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022] Open
Abstract
Sprouting blood vessels are led by filopodia-studded endothelial tip cells that respond to angiogenic signals. Mosaic lineage tracing previously revealed that NRP1 is essential for tip cell function, although its mechanistic role in tip cells remains poorly defined. Here, we show that NRP1 is dispensable for genetic tip cell identity. Instead, we find that NRP1 is essential to form the filopodial bursts that distinguish tip cells morphologically from neighboring stalk cells, because it enables the extracellular matrix (ECM)-induced activation of CDC42, a key regulator of filopodia formation. Accordingly, NRP1 knockdown and pharmacological CDC42 inhibition similarly impaired filopodia formation in vitro and in developing zebrafish in vivo. During mouse retinal angiogenesis, CDC42 inhibition impaired tip cell and vascular network formation, causing defects that resembled those due to loss of ECM-induced, but not VEGF-induced, NRP1 signaling. We conclude that NRP1 enables ECM-induced filopodia formation for tip cell function during sprouting angiogenesis.
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Affiliation(s)
- Alessandro Fantin
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Anastasia Lampropoulou
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Gaia Gestri
- UCL Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Claudio Raimondi
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Valentina Senatore
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Ian Zachary
- UCL Division of Medicine, University College London, 5 University Street, London WC1E 6JJ, UK
| | - Christiana Ruhrberg
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK.
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22
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Abstract
A quintessential trait of stem cells is embedded in their ability to self-renew without incurring DNA damage as a result of genome replication. One key self-renewal factor is the nucleolar GTP-binding protein nucleostemin (also known as guanine-nucleotide-binding protein-like 3, GNL3, in invertebrate species). Several studies have recently pointed to an unexpected role of nucleostemin in safeguarding the genome integrity of stem and cancer cells. Since its discovery, the predominant presence of nucleostemin in the nucleolus has led to the notion that it might function in the card-carrying event of the nucleolus--the biogenesis of ribosomes. As tantalizing as this might be, a ribosomal role of nucleostemin is refuted by evidence from recent studies, which argues that nucleostemin depletion triggers a primary event of DNA damage in S phase cells that then leads to ribosomal perturbation. Furthermore, there have been conflicting reports regarding the p53 dependency of nucleostemin activity and the cell cycle arrest profile of nucleostemin-depleted cells. In this Commentary, I propose a model that explains how the many contradictory observations surrounding nucleostemin can be reconciled and suggest that this protein might not be as multi-tasking as has been previously perceived. The story of nucleostemin highlights the complexity of the underlying molecular events associated with the appearance of any cell biological phenotype and also signifies a new understanding of the genome maintenance program in stem cells.
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Affiliation(s)
- Robert Y L Tsai
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
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23
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SUN XIAOLI, JIA YU, WEI YUANYU, LIU SHUAI, YUE BAOHONG. Gene expression profiling of HL-60 cells following knockdown of nucleostemin using DNA microarrays. Oncol Rep 2014; 32:739-47. [DOI: 10.3892/or.2014.3240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/29/2014] [Indexed: 11/05/2022] Open
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24
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Essers PB, Pereboom TC, Goos YJ, Paridaen JT, Macinnes AW. A comparative study of nucleostemin family members in zebrafish reveals specific roles in ribosome biogenesis. Dev Biol 2013; 385:304-15. [PMID: 24211311 DOI: 10.1016/j.ydbio.2013.10.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 01/05/2023]
Abstract
Nucleostemin (NS) is an essential protein for the growth and viability of developmental stem cells. Its functions are multi-faceted, including important roles in ribosome biogenesis and in the p53-induced apoptosis pathway. While NS has been well studied, the functions of its family members GNL2 and GNL3-like (GNL3L) remain relatively obscure despite a high degree of sequence and domain homology. Here, we use zebrafish lines carrying mutations in the ns family to compare and contrast their functions in vertebrates. We find the loss of zebrafish ns or gnl2 has a major impact on 60S large ribosomal subunit formation and/or function due to cleavage impairments at distinct sites of pre-rRNA transcript. In both cases this leads to a reduction of total protein synthesis. In contrast, gnl3l loss shows relatively minor rRNA processing delays that ultimately have no appreciable effects on ribosome biogenesis or protein synthesis. However, the loss of gnl3l still results in p53 stabilization, apoptosis, and lethality similarly to ns and gnl2 loss. The depletion of p53 in all three of the mutants led to partial rescues of the morphological phenotypes and surprisingly, a rescue of the 60S subunit collapse in the ns mutants. We show that this rescue is due to an unexpected effect of p53 loss that even in wild type embryos results in an increase of 60S subunits. Our study presents an in-depth description of the mechanisms through which ns and gnl2 function in vertebrate ribosome biogenesis and shows that despite the high degree of sequence and domain homology, gnl3l has critical functions in development that are unrelated to the ribosome.
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Affiliation(s)
- Paul B Essers
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Tamara C Pereboom
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Yvonne J Goos
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Judith T Paridaen
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
| | - Alyson W Macinnes
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
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25
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Janssens E, Gaublomme D, De Groef L, Darras VM, Arckens L, Delorme N, Claes F, Van Hove I, Moons L. Matrix metalloproteinase 14 in the zebrafish: an eye on retinal and retinotectal development. PLoS One 2013; 8:e52915. [PMID: 23326364 PMCID: PMC3541391 DOI: 10.1371/journal.pone.0052915] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/22/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Matrix metalloproteinases (MMPs) are members of the metzincin superfamily of proteinases that cleave structural elements of the extracellular matrix and many molecules involved in signal transduction. Although there is evidence that MMPs promote the proper development of retinotectal projections, the nature and working mechanisms of specific MMPs in retinal development remain to be elucidated. Here, we report a role for zebrafish Mmp14a, one of the two zebrafish paralogs of human MMP14, in retinal neurogenesis and retinotectal development. RESULTS Whole mount in situ hybridization and immunohistochemical stainings for Mmp14a in developing zebrafish embryos reveal expression in the optic tectum, in the optic nerve and in defined retinal cell populations, including retinal ganglion cells (RGCs). Furthermore, Mmp14a loss-of-function results in perturbed retinoblast cell cycle kinetics and consequently, in a delayed retinal neurogenesis, differentiation and lamination. These Mmp14a-dependent retinal defects lead to microphthalmia and a significantly reduced innervation of the optic tectum (OT) by RGC axons. Mmp14b, on the contrary, does not appear to alter retinal neurogenesis or OT innervation. As mammalian MMP14 is known to act as an efficient MMP2-activator, we also explored and found a functional link and a possible co-involvement of Mmp2 and Mmp14a in zebrafish retinotectal development. CONCLUSION Both the Mmp14a expression in the developing visual system and the Mmp14a loss-of-function phenotype illustrate a critical role for Mmp14a activity in retinal and retinotectal development.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/embryology
- Embryo, Nonmammalian/metabolism
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Gene Knockdown Techniques
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Immunohistochemistry
- In Situ Hybridization
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Matrix Metalloproteinase 14/genetics
- Matrix Metalloproteinase 14/metabolism
- Matrix Metalloproteinase 2/genetics
- Matrix Metalloproteinase 2/metabolism
- Microphthalmos/embryology
- Microphthalmos/genetics
- Microphthalmos/metabolism
- Microscopy, Confocal
- Neurogenesis/genetics
- Optic Lobe, Nonmammalian/cytology
- Optic Lobe, Nonmammalian/embryology
- Optic Lobe, Nonmammalian/metabolism
- Protein Binding
- Retina/embryology
- Retina/metabolism
- Retinal Ganglion Cells/metabolism
- Zebrafish/embryology
- Zebrafish/genetics
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Els Janssens
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Djoere Gaublomme
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Lies De Groef
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Veerle M. Darras
- Laboratory of Comparative Endocrinology, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Lut Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Nathalie Delorme
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Filip Claes
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Inge Van Hove
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Lieve Moons
- Research Group Neural Circuit Development and Regeneration, Department of Biology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
- * E-mail:
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26
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Liang YM, Wang X, Ramalingam R, So KY, Lam YW, Li ZF. Novel nucleolar isolation method reveals rapid response of human nucleolar proteomes to serum stimulation. J Proteomics 2012; 77:521-30. [DOI: 10.1016/j.jprot.2012.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 12/31/2022]
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27
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Abstract
Nucleoli are the sites where synthesis of rRNA and ribosomal assembly take place. Along with these "traditional" roles, the nucleolus controls cellular physiology and homeostasis. The cellular and molecular alterations associated with impaired nucleolar activity ("nucleolar stress") have just started to be systematically explored in the nervous system taking advantage of newly available animal models lacking rRNA synthesis in specific neurons. These studies showed that nucleolar function is necessary for neuronal survival and that its modality of action differs between and within cell types. Nucleolar function is also crucial in pathology as it controls mitochondrial activity and critical stress signaling pathways mimicking hallmarks of human neurodegenerative diseases. This mini-review will focus on the modes of action of nucleolar stress and discuss how the manipulation of nucleolar activity might underscore novel strategies to extend neuronal function and survival.
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Affiliation(s)
- Rosanna Parlato
- Department of Molecular Biology of the Cell I, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld, 581, 69120, Heidelberg, Germany.
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28
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Markitantova YV, Zinovieva RD. Expression of nucleostemin in proliferating and differentiating cells of the human retina during prenatal development. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2012; 445:244-6. [PMID: 22945526 DOI: 10.1134/s0012496612040084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Indexed: 11/23/2022]
Affiliation(s)
- Yu V Markitantova
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
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29
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Hutchinson SA, Tooke-Locke E, Wang J, Tsai S, Katz T, Trede NS. Tbl3 regulates cell cycle length during zebrafish development. Dev Biol 2012; 368:261-72. [PMID: 22659140 DOI: 10.1016/j.ydbio.2012.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 02/07/2023]
Abstract
The regulation of cell cycle rate is essential for the correct timing of proliferation and differentiation during development. Changes to cell cycle rate can have profound effects on the size, shape and cell types of a developing organ. We previously identified a zebrafish mutant ceylon (cey) that has a severe reduction in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we find that the cey phenotype is due to absence of the gene transducin (beta)-like 3 (tbl3). The tbl3 homolog in yeast regulates the cell cycle by maintaining rRNA levels and preventing p53-induced cell death. Zebrafish tbl3 is maternally expressed, but later in development its expression is restricted to specific tissues. Tissues expressing tbl3 are severely reduced in cey mutants, including HSPCs, the retina, exocrine pancreas, intestine, and jaw cartilage. Specification of these tissues is normal, suggesting the reduced size is due to a reduced number of differentiated cells. Tbl3 MO injection into either wild-type or p53-/- mutant embryos phenocopies cey, indicating that loss of tbl3 causes specific defects in cey. Progression of both hematopoietic and retinal development is delayed beginning at 3 day post fertilization due to a slowing of the cell cycle. In contrast to yeast, reduction of Tbl3 causes a slowing of the cell cycle without a corresponding increase in p53 induced cell death. These data suggest that tbl3 plays a tissue-specific role regulating cell cycle rate during development.
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Affiliation(s)
- Sarah A Hutchinson
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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