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Chen B, Weng Y, Li M, Bian Z, Tao Y, Zhou W, Lu H, He S, Liao R, Huang J, Wang Q, Xu M, Ge Y, Cao W, Lei M, Zhang Y. LINC02454-CCT complex interaction is essential for telomerase activity and cell proliferation in head and neck squamous cell carcinoma. Cancer Lett 2024; 588:216734. [PMID: 38401886 DOI: 10.1016/j.canlet.2024.216734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/03/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
Telomerase activity is upregulated in head and neck squamous cell carcinoma (HNSCC), yet its regulatory mechanisms remain unclear. Here, we identified a cancer-specific lncRNA (LINC02454) associated with poor prognosis by using LncRNA chip of our HNSCC cohorts and external datasets. Through employing negative-stain transmission electron microscopy (NS-TEM), we discovered an interaction between LINC02454 and CCT complex which would augment telomerase activity for maintaining telomere homeostasis. Supporting this, in the telomerase repeat amplification protocol (TRAP) assay and quantitative fluorescence in situ hybridization (Q-FISH) analysis, LINC02454 depletion significantly reduced telomerase activity and shortened telomere length. Consistently, pathways related to telomerase, mitosis, and apoptosis were significantly impacted upon LINC02454 knockdown in RNAseq analysis. Functionally, LINC02454-deficient cells exhibited a more significant senescence phenotype in β-galactosidase staining, cell cycle, and apoptosis assays. We further confirmed the role of LINC02454 in HNSCC proliferation through a combination of in vitro and in vivo experiments. The therapeutic potential of targeting LINC02454 was verified by adenovirus-shRNA approach in HNSCC patient-derived xenograft (PDX) models. In summary, our findings provided valuable insights into the molecular mechanisms of HNSCC tumorigenesis and potential targets for future treatment modalities.
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Affiliation(s)
- Biying Chen
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yue Weng
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mingyue Li
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhouliang Bian
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Ye Tao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenkai Zhou
- Department of Oral Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Hong Lu
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shufang He
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jie Huang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Wang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Ming Xu
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yunhui Ge
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wei Cao
- Department of Oral Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China.
| | - Ming Lei
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yanjie Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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Ling SF, Yap CF, Nair N, Bluett J, Morgan AW, Isaacs JD, Wilson AG, Hyrich KL, Barton A, Plant D. A proteomics study of rheumatoid arthritis patients on etanercept identifies putative biomarkers associated with clinical outcome measures. Rheumatology (Oxford) 2024; 63:1015-1021. [PMID: 37389432 PMCID: PMC10986807 DOI: 10.1093/rheumatology/kead321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/26/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
OBJECTIVES Biologic DMARDs (bDMARDs) are widely used in patients with RA, but response to bDMARDs is heterogeneous. The objective of this work was to identify pretreatment proteomic biomarkers associated with RA clinical outcome measures in patients starting bDMARDs. METHODS Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) was used to generate spectral maps of sera from patients with RA before and after 3 months of treatment with the bDMARD etanercept. Protein levels were regressed against RA clinical outcome measures, i.e. 28-joint DAS (DAS28) and its subcomponents and DAS28 <2.6 (i.e. remission). The proteins with the strongest evidence for association were analysed in an independent, replication dataset. Finally, subnetwork analysis was carried out using the Disease Module Detection algorithm and biological plausibility of identified proteins was assessed by enrichment analysis. RESULTS A total of 180 patients with RA were included in the discovery dataset and 58 in the validation dataset from a UK-based prospective multicentre study. Ten individual proteins were found to be significantly associated with RA clinical outcome measures. The association of T-complex protein 1 subunit η with DAS28 remission was replicated in an independent cohort. Subnetwork analysis of the 10 proteins from the regression analysis identified the ontological theme, with the strongest associations being with acute phase and acute inflammatory responses. CONCLUSION This longitudinal study of 180 patients with RA commencing etanercept has identified several putative protein biomarkers of treatment response to this drug, one of which was replicated in an independent cohort.
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Affiliation(s)
- Stephanie F Ling
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chuan Fu Yap
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - James Bluett
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Ann W Morgan
- School of Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- NIHR In Vitro Diagnostic Co-operative, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - John D Isaacs
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- Musculoskeletal Unit, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Anthony G Wilson
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Kimme L Hyrich
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Biomedical Research Centre Manchester, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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Zeng C, Han S, Pan Y, Huang Z, Zhang B, Zhang B. Revisiting the chaperonin T-complex protein-1 ring complex in human health and disease: A proteostasis modulator and beyond. Clin Transl Med 2024; 14:e1592. [PMID: 38363102 PMCID: PMC10870801 DOI: 10.1002/ctm2.1592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Disrupted protein homeostasis (proteostasis) has been demonstrated to facilitate the progression of various diseases. The cytosolic T-complex protein-1 ring complex (TRiC/CCT) was discovered to be a critical player in orchestrating proteostasis by folding eukaryotic proteins, guiding intracellular localisation and suppressing protein aggregation. Intensive investigations of TRiC/CCT in different fields have improved the understanding of its role and molecular mechanism in multiple physiological and pathological processes. MAIN BODY In this review, we embark on a journey through the dynamic protein folding cycle of TRiC/CCT, unraveling the intricate mechanisms of its substrate selection, recognition, and intriguing folding and assembly processes. In addition to discussing the critical role of TRiC/CCT in maintaining proteostasis, we detail its involvement in cell cycle regulation, apoptosis, autophagy, metabolic control, adaptive immunity and signal transduction processes. Furthermore, we meticulously catalogue a compendium of TRiC-associated diseases, such as neuropathies, cardiovascular diseases and various malignancies. Specifically, we report the roles and molecular mechanisms of TRiC/CCT in regulating cancer formation and progression. Finally, we discuss unresolved issues in TRiC/CCT research, highlighting the efforts required for translation to clinical applications, such as diagnosis and treatment. CONCLUSION This review aims to provide a comprehensive view of TRiC/CCT for researchers to inspire further investigations and explorations of potential translational possibilities.
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Affiliation(s)
- Chenglong Zeng
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Shenqi Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Binhao Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Clinical Medical Research Center of Hepatic Surgery at Hubei ProvinceWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreatic‐Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Organ Transplantation, Ministry of EducationWuhanChina
- Key Laboratory of Organ Transplantation, National Health CommissionWuhanChina
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical SciencesWuhanChina
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Yin T, Wen J, Xu S, Chen L, Zhang Z, Pan S, Zhou M, Guo X, Wang M, Gong J, Zhang H, Qin R. An E3 ubiquitin-proteasome gene signature for predicting prognosis in patients with pancreatic cancer. Front Immunol 2024; 14:1332626. [PMID: 38304253 PMCID: PMC10830689 DOI: 10.3389/fimmu.2023.1332626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
Pancreatic cancer is the seventh leading cause of cancer death worldwide, which is demonstrated with remarkable resistance to radiotherapy and chemotherapy. The identification of prognosis signature and novel prognostic markers will facilitate patient stratification and an individualized precision therapy strategy. In this study, TCGA-PAAD was used to screen prognostic E3 ubiquitin ligases and establish prognostic signatures, and GEO database was used to verify the accuracy of prognostic signatures. Functional analysis, in vitro experiments and clinical cohort studies were used to analyze the function and prognostic efficacy of the target gene. An E3 ligase-based signature of 9 genes and the nomogram were developed, and the signature was proved to accurately predict the prognosis of patients with pancreatic cancer. WDR37 might be the most prognostic E3 ubiquitin ligase in pancreatic cancer, and the clinical cohort analyses suggested a tumor-suppressive role. The results of functional analysis and in vitro experiments indicated that WDR37 may promote the degradation of TCP1 complex to inhibit tumor and improve immune cell infiltration. The E3 ligase-based signature accurately predicted the prognosis of patients with pancreatic cancer, so it can be used as a decision-making tool to guide the treatment of patients with pancreatic cancer. At the same time, WDR37, the main gene in E3PMP signature, can be used as the most prognostic E3 ubiquitin ligase in the treatment of pancreatic cancer.
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Affiliation(s)
- Taoyuan Yin
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jingjing Wen
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Simiao Xu
- Department of Endocrinology, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lin Chen
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhenxiong Zhang
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shutao Pan
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Min Zhou
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xingjun Guo
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Min Wang
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Gong
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hang Zhang
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Renyi Qin
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Klump BM, Schmidt JC. Advances in understanding telomerase assembly. Biochem Soc Trans 2023; 51:2093-2101. [PMID: 38108475 PMCID: PMC10754283 DOI: 10.1042/bst20230269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Telomerase is a complex ribonucleoprotein scaffolded by the telomerase RNA (TR). Telomere lengthening by telomerase is essential to maintain the proliferative potential of stem cells and germ cells, and telomerase is inappropriately activated in the majority of cancers. Assembly of TR with its 12 protein co-factors and the maturation of the 5'- and 3'-ends of TR have been the focus of intense research efforts over the past two decades. High-resolution Cryo-EM structures of human telomerase, high-throughput sequencing of the 3' end of TR, and live cell imaging of various telomerase components have significantly advanced our understanding of the molecular mechanisms that govern telomerase biogenesis, yet many important questions remain unaddressed. In this review, we will summarize these recent advances and highlight the remaining key questions with the ultimate goal of targeting telomerase assembly to suppress telomere maintenance in cancer cells or to promote telomerase activity in patients affected by telomere shortening disorders.
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Affiliation(s)
- Basma M. Klump
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, U.S.A
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, U.S.A
- Cell and Molecular Biology Graduate Program, College of Natural Sciences, Michigan State University, East Lansing, MI, U.S.A
| | - Jens C. Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, U.S.A
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, U.S.A
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Qiao H, Li H. PLP2 Could Be a Prognostic Biomarker and Potential Treatment Target in Glioblastoma Multiforme. Pharmgenomics Pers Med 2023; 16:991-1009. [PMID: 37964785 PMCID: PMC10642424 DOI: 10.2147/pgpm.s425251] [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: 07/09/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Objective This study aimed to discern the association between PLP2 expression, its biological significance, and the extent of immune infiltration in human GBM. Methods Utilizing the GEPIA2 and TCGA databases, we contrasted the expression levels of PLP2 in GBM against normal tissue. We utilized GEPIA2 and LinkedOmics for survival analysis, recognized genes co-expressed with PLP2 via cBioPortal and GEPIA2, and implemented GO and KEGG analyses. The STRING database facilitated the construction of protein-protein interaction networks. We evaluated the relationship of PLP2 with tumor immune infiltrates using ssGSEA and the TIMER 2.0 database. An IHC assay assessed PLP2 and PDL-1 expression in GBM tissue, and the Drugbank database aided in identifying potential PLP2-targeting compounds. Molecular docking was accomplished using Autodock Vina 1.2.2. Results PLP2 expression was markedly higher in GBM tissues in comparison to normal tissues. High PLP2 expression correlated with a decrease in overall survival across two databases. Functional analyses highlighted a focus of PLP2 functions within leukocyte. Discrepancies in PLP2 expression were evident in immune infiltration, impacting CD4+ T cells, neutrophils, myeloid dendritic cells, and macrophages. There was a concomitant increase in PLP2 and PD-L1 expression in GBM tissues, revealing a link between the two. Molecular docking with ethosuximide and praziquantel yielded scores of -7.441 and -4.295 kcal/mol, correspondingly. Conclusion PLP2's upregulation in GBM may adversely influence the lifespan of GBM patients. The involvement of PLP2 in pathways linked to leukocyte function is suggested. The positive correlation between PLP2 and PD-L1 could provide insights into PLP2's role in glioma modulation. Our research hints at PLP2's potential as a therapeutic target for GBM, with ethosuximide and praziquantel emerging as potential treatment candidates, especially emphasizing the potential of these compounds in GBM treatment targeting PLP2.
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Affiliation(s)
- Hao Qiao
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Huanting Li
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
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Iannello M, Forni G, Piccinini G, Xu R, Martelossi J, Ghiselli F, Milani L. Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution. Genome Biol Evol 2023; 15:evad159. [PMID: 37647860 PMCID: PMC10646442 DOI: 10.1093/gbe/evad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
Among Metazoa, bivalves have the highest lifespan disparity, ranging from 1 to 500+ years, making them an exceptional testing ground to understand mechanisms underlying aging and the evolution of extended longevity. Nevertheless, comparative molecular evolution has been an overlooked approach in this instance. Here, we leveraged transcriptomic resources spanning 30 bivalve species to unravel the signatures of convergent molecular evolution in four long-lived species: Margaritifera margaritifera, Elliptio complanata, Lampsilis siliquoidea, and Arctica islandica (the latter represents the longest-lived noncolonial metazoan known so far). We applied a comprehensive approach-which included inference of convergent dN/dS, convergent positive selection, and convergent amino acid substitution-with a strong focus on the reduction of false positives. Genes with convergent evolution in long-lived bivalves show more physical and functional interactions to each other than expected, suggesting that they are biologically connected; this interaction network is enriched in genes for which a role in longevity has been experimentally supported in other species. This suggests that genes in the network are involved in extended longevity in bivalves and, consequently, that the mechanisms underlying extended longevity are-at least partially-shared across Metazoa. Although we believe that an integration of different genes and pathways is required for the extended longevity phenotype, we highlight the potential central roles of genes involved in cell proliferation control, translational machinery, and response to hypoxia, in lifespan extension.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giobbe Forni
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ran Xu
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Jacopo Martelossi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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Brun C, Allain C, Ferron PJ, Younoussa H, Colicchio B, Jeandidier E, M’Kacher R, Guguen-Guillouzo C, Bertile F. Extended lifespan and improved genome stability in HepaRG-derived cell lines through reprogramming by high-density stress. Proc Natl Acad Sci U S A 2023; 120:e2219298120. [PMID: 37639591 PMCID: PMC10483629 DOI: 10.1073/pnas.2219298120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/31/2023] Open
Abstract
The characteristics and fate of cancer cells partly depend on their environmental stiffness, i.e., the local mechanical cues they face. HepaRG progenitors are liver carcinoma cells exhibiting transdifferentiation properties; however, the underlying mechanisms remain unknown. To evaluate the impact of external physical forces mimicking the tumor microenvironment, we seeded them at very high density for 20 h, keeping the cells round and unanchored to the substrate. Applied without corticoids, spatial confinement due to very high density induced reprogramming of HepaRG cells into stable replicative stem-like cells after replating at normal density. Redifferentiation of these stem-like cells into cells very similar to the original HepaRG cells was then achieved using the same stress but in the presence of corticoids. This demonstrates that the cells retained the memory required to run the complete hepatic differentiation program, after bypassing the Hayflick limit twice. We show that physical stress improved chromosome quality and genomic stability, through greater efficiency of DNA repair and restoration of telomerase activity, thus enabling cells to escape progression to a more aggressive cancer state. We also show the primary importance of high-density seeding, possibly triggering compressive stress, in these processes, rather than that of cell roundness or intracellular tensional signals. The HepaRG-derived lines established here considerably extend the lifespan and availability of this surrogate cell system for mature human hepatocytes. External physical stress is a promising way to create a variety of cell lines, and it paves the way for the development of strategies to improve cancer prognosis.
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Affiliation(s)
- Charlotte Brun
- Université de Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien UMR 7178, StrasbourgF-67000, France
- Proteomics French Infrastructure, FR2048, ProFI, StrasbourgF-67000, France
| | - Coralie Allain
- Université de Rennes 1, INSERM U1241, Nutrition, Métabolismes et Cancer, RennesF-35033, France
| | - Pierre-Jean Ferron
- Université de Rennes 1, INSERM U1241, Nutrition, Métabolismes et Cancer, RennesF-35033, France
| | | | - Bruno Colicchio
- Université de Haute-Alsace, Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, MulhouseF-68093, France
| | - Eric Jeandidier
- Groupe Hospitalier de la Région de Mulhouse et Sud Alsace Mulhouse, Service de génétique, MulhouseF-68070, France
| | - Radhia M’Kacher
- Cell Environment DNA Damage R&D, Genopole, EvryF-91058, France
| | | | - Fabrice Bertile
- Université de Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien UMR 7178, StrasbourgF-67000, France
- Proteomics French Infrastructure, FR2048, ProFI, StrasbourgF-67000, France
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Yagita Y, Zavodszky E, Peak-Chew SY, Hegde RS. Mechanism of orphan subunit recognition during assembly quality control. Cell 2023; 186:3443-3459.e24. [PMID: 37480851 PMCID: PMC10501995 DOI: 10.1016/j.cell.2023.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Cells contain numerous abundant molecular machines assembled from multiple subunits. Imbalances in subunit production and failed assembly generate orphan subunits that are eliminated by poorly defined pathways. Here, we determined how orphan subunits of the cytosolic chaperonin CCT are recognized. Several unassembled CCT subunits recruited the E3 ubiquitin ligase HERC2 using ZNRD2 as an adaptor. Both factors were necessary for orphan CCT subunit degradation in cells, sufficient for CCT subunit ubiquitination with purified factors, and necessary for optimal cell fitness. Domain mapping and structure prediction defined the molecular features of a minimal HERC2-ZNRD2-CCT module. The structural model, whose key elements were validated in cells using point mutants, shows why ZNRD2 selectively recognizes multiple orphaned CCT subunits without engaging assembled CCT. Our findings reveal how failures during CCT assembly are monitored and provide a paradigm for the molecular recognition of orphan subunits, the largest source of quality control substrates in cells.
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Affiliation(s)
- Yuichi Yagita
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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10
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Lottes EN, Ciger FH, Bhattacharjee S, Timmins-Wilde EA, Tete B, Tran T, Matta J, Patel AA, Cox DN. CCT and Cullin1 regulate the TORC1 pathway to promote dendritic arborization in health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551324. [PMID: 37577581 PMCID: PMC10418059 DOI: 10.1101/2023.07.31.551324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The development of cell-type-specific dendritic arbors is integral to the proper functioning of neurons within their circuit networks. In this study, we examine the regulatory relationship between the cytosolic chaperonin CCT, key insulin pathway genes, and an E3 ubiquitin ligase (Cullin1) in homeostatic dendritic development. CCT loss of function (LOF) results in dendritic hypotrophy in Drosophila Class IV (CIV) multidendritic larval sensory neurons, and CCT has recently been shown to fold components of the TOR (Target of Rapamycin) complex 1 (TORC1), in vitro. Through targeted genetic manipulations, we have confirmed that LOF of CCT and the TORC1 pathway reduces dendritic complexity, while overexpression of key TORC1 pathway genes increases dendritic complexity in CIV neurons. Both CCT and TORC1 LOF significantly reduce microtubule (MT) stability. CCT has been previously implicated in regulating proteinopathic aggregation, thus we examined CIV dendritic development in disease conditions as well. Expression of mutant Huntingtin leads to dendritic hypotrophy in a repeat-length-dependent manner, which can be rescued by TORC1 disinhibition via Cullin1 LOF. Together, our data suggest that Cullin1 and CCT influence dendritic arborization through regulation of TORC1 in both health and disease.
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Affiliation(s)
- Erin N. Lottes
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | - Feyza H. Ciger
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | | | | | - Benoit Tete
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | - Tommy Tran
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | - Jais Matta
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | - Atit A. Patel
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
| | - Daniel N. Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States
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11
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Xu W, Yao Z, Li Y, Wang K, Kong S, Wang Y, Xiang M, Zhu F, Wang F, Zhang H. Loss of PMFBP1 Disturbs Mouse Spermatogenesis by Downregulating HDAC3 Expression. J Assist Reprod Genet 2023:10.1007/s10815-023-02874-0. [PMID: 37423931 PMCID: PMC10371971 DOI: 10.1007/s10815-023-02874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/20/2023] [Indexed: 07/11/2023] Open
Abstract
PURPOSE Polyamine modulating factor 1 binding protein (PMFBP1) acts as a scaffold protein for the maintenance of sperm structure. The aim of this study was further to identify the new role and molecular mechanism of PMFBP1 during mouse spermatogenesis. METHODS AND RESULTS We identified a profile of proteins interacting with PMFBP1 by immunoprecipitation combined with mass spectrometry and demonstrated that class I histone deacetylases, particularly HDAC3 and chaperonin-containing TCP1 subunit 3 (CCT3), were potential interaction partners of PMFBP1 based on network analysis of protein-protein interactions and co-immunoprecipitation. Immunoblotting and immunochemistry assays showed that loss of Pmfbp1 would result in a decline in HDACs and change the proteomic profile of mouse testis, in which differently expressed proteins are associated with spermatogenesis and assembly of flagella, which was proved by proteomic analysis of testis tissue obtained from Pmfbp1-/- mice. After integrating with transcriptome data for Hdac3-/- and Sox30-/- round sperm obtained from a public database, RT-qPCR confirmed ring finger protein 151 (Rnf151) and ring finger protein 133 (Rnf133) were key downstream response factors of the Pmfbp1-Hdac axis affecting mouse spermatogenesis. CONCLUSION Taken together, this study indicates a previously unidentified molecular mechanism of PMFBP1 in spermatogenesis whereby PMFBP1 interacts with CCT3, affecting the expression of HDAC3, followed by the downregulation of RNF151 and RNF133, resulting in an abnormal phenotype of sperm beyond the headless sperm tails. These findings not only advance our understanding of the function of Pmfbp1 in mouse spermatogenesis but also provide a typical case for multi-omics analysis used in the functional annotation of specific genes.
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Affiliation(s)
- Weilong Xu
- School of Life Science, Anhui Medical University, Hefei, 230022, China
| | - Zhoujuan Yao
- School of Life Science, Anhui Medical University, Hefei, 230022, China
| | - Yunzhi Li
- School of Life Science, Anhui Medical University, Hefei, 230022, China
| | - Ke Wang
- School of Life Science, Anhui Medical University, Hefei, 230022, China
- Reproductive Medicine Center, Anhui No. 2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Shuai Kong
- School of Life Science, Anhui Medical University, Hefei, 230022, China
| | - Yu Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Mingfei Xiang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Fuxi Zhu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China.
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, 230032, Anhui, China.
| | - Fengsong Wang
- School of Life Science, Anhui Medical University, Hefei, 230022, China.
| | - Hui Zhang
- School of Life Science, Anhui Medical University, Hefei, 230022, China.
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12
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Klump BM, Perez GI, Patrick EM, Adams-Boone K, Cohen SB, Han L, Yu K, Schmidt JC. TCAB1 prevents nucleolar accumulation of the telomerase RNA to facilitate telomerase assembly. Cell Rep 2023; 42:112577. [PMID: 37267110 PMCID: PMC10569210 DOI: 10.1016/j.celrep.2023.112577] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/27/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023] Open
Abstract
Localization of a variety of RNAs to non-membrane-bound cellular compartments such as nucleoli and Cajal bodies is critical for their stability and function. The molecular mechanisms that underly the recruitment and exclusion of RNAs from these phase-separated organelles is incompletely understood. Telomerase is a ribonucleoprotein composed of the reverse transcriptase protein telomerase reverse transcriptase (TERT), the telomerase RNA (TR), and several auxiliary proteins, including TCAB1. Here we show that in the absence of TCAB1, a large fraction of TR is tightly bound to the nucleolus, while TERT is largely excluded from the nucleolus, reducing telomerase assembly. This suggests that nuclear compartmentalization by the non-membrane-bound nucleolus counteracts telomerase assembly, and TCAB1 is required to retain TR in the nucleoplasm. Our work provides insight into the mechanism and functional consequences of RNA recruitment to organelles formed by phase separation and demonstrates that TCAB1 plays an important role in telomerase assembly.
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Affiliation(s)
- Basma M Klump
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA; Cellular and Molecular Biology Graduate Program, College of Natural Sciences, Michigan State University, East Lansing, MI, USA
| | - Gloria I Perez
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Eric M Patrick
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Kate Adams-Boone
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Scott B Cohen
- Children's Medical Research Institute and University of Sydney, Westmead, NSW 2145, Australia
| | - Li Han
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA.
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13
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Lima TI, Laurila PP, Wohlwend M, Morel JD, Goeminne LJE, Li H, Romani M, Li X, Oh CM, Park D, Rodríguez-López S, Ivanisevic J, Gallart-Ayala H, Crisol B, Delort F, Batonnet-Pichon S, Silveira LR, Sankabattula Pavani Veera Venkata L, Padala AK, Jain S, Auwerx J. Inhibiting de novo ceramide synthesis restores mitochondrial and protein homeostasis in muscle aging. Sci Transl Med 2023; 15:eade6509. [PMID: 37196064 DOI: 10.1126/scitranslmed.ade6509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Disruption of mitochondrial function and protein homeostasis plays a central role in aging. However, how these processes interact and what governs their failure in aging remain poorly understood. Here, we showed that ceramide biosynthesis controls the decline in mitochondrial and protein homeostasis during muscle aging. Analysis of transcriptome datasets derived from muscle biopsies obtained from both aged individuals and patients with a diverse range of muscle disorders revealed that changes in ceramide biosynthesis, as well as disturbances in mitochondrial and protein homeostasis pathways, are prevalent features in these conditions. By performing targeted lipidomics analyses, we found that ceramides accumulated in skeletal muscle with increasing age across Caenorhabditis elegans, mice, and humans. Inhibition of serine palmitoyltransferase (SPT), the rate-limiting enzyme of the ceramide de novo synthesis, by gene silencing or by treatment with myriocin restored proteostasis and mitochondrial function in human myoblasts, in C. elegans, and in the skeletal muscles of mice during aging. Restoration of these age-related processes improved health and life span in the nematode and muscle health and fitness in mice. Collectively, our data implicate pharmacological and genetic suppression of ceramide biosynthesis as potential therapeutic approaches to delay muscle aging and to manage related proteinopathies via mitochondrial and proteostasis remodeling.
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Affiliation(s)
- Tanes I Lima
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Pirkka-Pekka Laurila
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Martin Wohlwend
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jean David Morel
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Ludger J E Goeminne
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Mario Romani
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Dohyun Park
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Sandra Rodríguez-López
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne 1005, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne 1005, Switzerland
| | - Barbara Crisol
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Florence Delort
- Laboratoire Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS and Université Paris Cité, Paris 8251, France
| | - Sabrina Batonnet-Pichon
- Laboratoire Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS and Université Paris Cité, Paris 8251, France
| | - Leonardo R Silveira
- Obesity and Comorbidities Research Center, University of Campinas, Campinas 13083-864, Brazil
| | | | - Anil K Padala
- Intonation Research Laboratories, Hyderabad 500076, India
| | - Suresh Jain
- Intonation Research Laboratories, Hyderabad 500076, India
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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14
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Wang S, Duan X, Wang S, Hao L, Zhang Y, Xu C, Yu Y, Xiang L, Jiang F, Heinlein M, Li T, Zhang W. A chaperonin containing T-complex polypeptide-1 facilitates the formation of the PbWoxT1-PbPTB3 ribonucleoprotein complex for long-distance RNA trafficking in Pyrus betulaefolia. THE NEW PHYTOLOGIST 2023; 238:1115-1128. [PMID: 36751904 DOI: 10.1111/nph.18789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Numerous plant endogenous mRNAs move via phloem and thus affect the growth and development of long-distant organs. mRNAs are transported with RNA-binding proteins forming a ribonucleoprotein complex. However, it remains elusive how such RNP complex assembles and facilitates mRNA trafficking. Protease digestion and RNA immunoprecipitation were used to investigate the RNP assembly function of the complete Chaperonin Containing T-complex Polypeptide-1. In situ hybridization, hairy root transformation, microprojectile bombardment, and grafting experiments demonstrate the role of CCT complex in the transport of a PbWoxT1-PbPTB3 RNP complex in Pyrus betulaefolia. PbCCT5 silenced caused defective movement of GFP-PbPTB3 and GFP-PbWoxT1 from hairy roots to new leaves via the phloem. PbCCT5 is shown to interact with PbPTB3. PbCCT complex enhanced PbPTB3 stabilization and permitted assembly of PbWoxT1 and PbPTB3 into an RNP complex. Furthermore, silencing of individual CCT subunits inhibited the intercellular movement of GFP-PbPTB3 and long-distance trafficking of PbWoxT1 and PbPTB3 in grafted plants. Taken together, the CCT complex assembles PbPTB3 and PbWoxT1 into an RNP complex in the phloem in order to facilitate the long-distance trafficking of PbWoxT1 in P. betulaefolia. This study therefore provides important insights into the mechanism of RNP complex formation and transport.
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Affiliation(s)
- Shengnan Wang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Xuwei Duan
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Shengyuan Wang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Li Hao
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Yi Zhang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Chaoran Xu
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Yunfei Yu
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Ling Xiang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Feng Jiang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Manfred Heinlein
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Tianzhong Li
- College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Wenna Zhang
- College of Horticulture, China Agricultural University, 100193, Beijing, China
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15
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Wang H, Zhang L, Liu B, Su J, Ni X. Role of CCT4/ErbB signaling in nephroblastoma: Implications for a biomarker of Wilms tumor. Medicine (Baltimore) 2023; 102:e33219. [PMID: 37058032 PMCID: PMC10101284 DOI: 10.1097/md.0000000000033219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/16/2023] [Indexed: 04/15/2023] Open
Abstract
Wilms tumor is a common abdominal malignant tumor in children. However, the molecular mechanism of Wilms tumor is unclear. GSE66405 and GSE197047 were obtained from the Gene Expression Omnibus database. To identify differentially expressed genes (DEGs) in Wilms tumor, the R package "limma" was used. Weighted gene co-expression network analysis was performed to identify the significant module. The list of DEGs was input into the Search Tool for the Retrieval of Interacting Genes database to construct a protein-protein interaction network for predicting core genes. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes analysis are computational methods for assessing gene function and biological pathways. The genome was analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes and developed by gene set enrichment analysis. Comparative Toxicogenomics Database analysis was performed to find the diseases most related to the core genes. TargetScan was used to screen for miRNAs that regulate hub genes. A total of 925 DEGs were identified. The differently expressed genes were mainly enriched in the metabolic pathway, AMPK signaling pathway, ErbB signaling pathway, mRNA detection pathway, and folded protein binding. A total of 16 core genes (HNRNPK, PABPC1, HNRNPD, NCL, YBX1, EIF4G1, KHDRBS1, HNRNPAB, HSPA4, EEF2, HSP90AA1, EEF1A1, A TP5A1, SDHA, CCT4, CCT5) were obtained. chaperonin containing TCP-1 subunit 4 (CCT4) was downregulated in tumor tissue samples, which may have reverse regulatory significance for Wilms tumor. CCT4, HSP90AA1, NCL, PABPC1, and YBX1 were found to be associated with kidney disease, acute kidney injury, edema, tumor metastasis, transitional cell carcinoma, necrosis, and inflammation. The research found that the related miRNA of the CCT4 gene was hsamiR-7-5p. CCT4 might play an essential role in the occurrence and development of Wilms tumor, and they may participate in the occurrence and development of Wilms tumor through the ERBB signal pathway. CCT4 may be a promising biomarker of Wilms tumor.
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Affiliation(s)
- Haoyuan Wang
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Lei Zhang
- Department of Urology Surgery, Fuxing Hospital Affiliated to Capital Medical University, Xicheng District, Beijing, PR China
| | - Bin Liu
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Jianzhi Su
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Xiaochen Ni
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
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16
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Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:ijms24055027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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Nelson N, Feurstein S, Niaz A, Truong J, Holien JK, Lucas S, Fairfax K, Dickinson J, Bryan TM. Functional genomics for curation of variants in telomere biology disorder associated genes: A systematic review. Genet Med 2023; 25:100354. [PMID: 36496180 DOI: 10.1016/j.gim.2022.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Patients with an underlying telomere biology disorder (TBD) have variable clinical presentations, and they can be challenging to diagnose clinically. A genomic diagnosis for patients presenting with TBD is vital for optimal treatment. Unfortunately, many variants identified during diagnostic testing are variants of uncertain significance. This complicates management decisions, delays treatment, and risks nonuptake of potentially curative therapies. Improved application of functional genomic evidence may reduce variants of uncertain significance classifications. METHODS We systematically searched the literature for published functional assays interrogating TBD gene variants. When possible, established likely benign/benign and likely pathogenic/pathogenic variants were used to estimate the assay sensitivity, specificity, positive predictive value, negative predictive value, and odds of pathogenicity. RESULTS In total, 3131 articles were screened and 151 met inclusion criteria. Sufficient data to enable a PS3/BS3 recommendation were available for TERT variants only. We recommend that PS3 and BS3 can be applied at a moderate and supportive level, respectively. PS3/BS3 application was limited by a lack of assay standardization and limited inclusion of benign variants. CONCLUSION Further assay standardization and assessment of benign variants are required for optimal use of the PS3/BS3 criterion for TBD gene variant classification.
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Affiliation(s)
- Niles Nelson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia; Department of Molecular Medicine, The Royal Hobart Hospital, Hobart, Tasmania, Australia; Department of Molecular Haematology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
| | - Simone Feurstein
- Section of Hematology, Oncology, and Rheumatology, Department of Internal Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Aram Niaz
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jia Truong
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Jessica K Holien
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Sionne Lucas
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Kirsten Fairfax
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Joanne Dickinson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
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18
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Chen Y, Kang J, Zhen R, Zhang L, Chen C. A genome-wide CRISPR screen identifies the CCT chaperonin as a critical regulator of vesicle trafficking. FASEB J 2023; 37:e22757. [PMID: 36607310 DOI: 10.1096/fj.202201580r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023]
Abstract
Vesicle trafficking is a fundamental cellular process that controls the transport of various proteins and cargos between cellular compartments in eukaryotes. Using a combination of genome-wide CRISPR screening in mammalian cells and RNAi screening in Caenorhabditis elegans, we identify chaperonin containing TCP-1 subunit 4 (CCT4) as a critical regulator of protein secretion and vesicle trafficking. In C. elegans, deficiency of cct-4 as well as other CCT subunits impairs the trafficking of endocytic markers in intestinal cells, and this defect resembles that of dyn-1 RNAi worms. Consistent with these findings, the silencing of CCT4 in human cells leads to defective endosomal trafficking, and this defect can be rescued by the dynamin activator Ryngo 1-23. These results suggest that the cytosolic chaperonin CCT may regulate vesicle trafficking by promoting the folding of dynamin in addition to its known substrate tubulin. Our findings establish an essential role for the CCT chaperonin in regulating vesicle trafficking, and provide new insights into the regulation of vesicle trafficking and the cellular function of the cytosolic chaperonin.
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Affiliation(s)
- Yongtian Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing Kang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ru Zhen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liyang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Caiyong Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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19
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Revy P, Kannengiesser C, Bertuch AA. Genetics of human telomere biology disorders. Nat Rev Genet 2023; 24:86-108. [PMID: 36151328 DOI: 10.1038/s41576-022-00527-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes that prevent the activation of DNA damage response and repair pathways. Numerous factors localize at telomeres to regulate their length, structure and function, to avert replicative senescence or genome instability and cell death. In humans, Mendelian defects in several of these factors can result in abnormally short or dysfunctional telomeres, causing a group of rare heterogeneous premature-ageing diseases, termed telomeropathies, short-telomere syndromes or telomere biology disorders (TBDs). Here, we review the TBD-causing genes identified so far and describe their main functions associated with telomere biology. We present molecular aspects of TBDs, including genetic anticipation, phenocopy, incomplete penetrance and somatic genetic rescue, which underlie the complexity of these diseases. We also discuss the implications of phenotypic and genetic features of TBDs on fundamental aspects related to human telomere biology, ageing and cancer, as well as on diagnostic, therapeutic and clinical approaches.
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Affiliation(s)
- Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Nationale contre le Cancer, Paris, France.
- Université Paris Cité, Imagine Institute, Paris, France.
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France
- Inserm U1152, Université Paris Cité, Paris, France
| | - Alison A Bertuch
- Departments of Paediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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20
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Sun Y, Liu C, Zhong H, Wang C, Xu H, Chen W. Screening of autoantibodies as biomarkers in the serum of renal cancer patients based on human proteome microarray. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1909-1916. [PMID: 36789694 PMCID: PMC10157637 DOI: 10.3724/abbs.2022189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
The autoantibody in patients' serum can act as a biomarker for diagnosing cancer, and the differences in autoantibodies are significantly correlated with the changes in their target proteins. In this study, 16 renal cancer (RC) patients were assigned to the disease group, and 16 healthy people were assigned to the healthy control (HC) group. The human proteome microarray consisting of>19,500 proteins was used to examine the differences in IgG and IgM autoantibodies in sera between RC and HC. The comparative analysis of the microarray results shows that 101 types of IgG and 25 types of IgM autoantibodies are significantly higher in RC than in HC. Highly responsive autoantibodies can be candidate biomarkers (e.g., anti-KCNAB2 IgG and anti-RCN1 IgM). Extensive enzyme-linked immunosorbent assay (ELISA) was performed to screen sera in 72 RC patients and 66 healthy volunteers to verify the effectiveness of the new autoantibodies. The AUCs of anti-KCNAB2 IgG and anti-GAPDH IgG were 0.833 and 0.753, respectively. KCNAB2 achieves high protein expression, and its high mRNA level is confirmed to be an unfavorable prognostic marker in clear cell renal cell carcinoma (ccRCC) tissues. This study suggests that the high-throughput human proteome microarray can effectively screen autoantibodies in serum as candidate biomarkers, and their corresponding target proteins can lay a basis for the in-depth investigation into renal cancer.
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Affiliation(s)
- Yangyang Sun
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Chengxi Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Food Safety and Technology Research Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Huidong Zhong
- Department of Medicinal ChemistryShantou University Medical CollegeShantou515041China
| | - Chenguang Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Haibo Xu
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Wei Chen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
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Alternative telomere maintenance mechanism in Alligator sinensis provides insights into aging evolution. iScience 2022; 26:105850. [PMID: 36636341 PMCID: PMC9829719 DOI: 10.1016/j.isci.2022.105850] [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: 02/07/2022] [Revised: 11/27/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
Lifespan is a life-history trait that undergoes natural selection. Telomeres are hallmarks of aging, and shortening rate predicts species lifespan, making telomere maintenance mechanisms throughout different lifespans a worthy topic for study. Alligators are suitable for the exploration of anti-aging molecular mechanisms, because they exhibit low or even negligible mortality in adults and no significant telomere shortening. Telomerase reverse transcriptase (TERT) expression is absent in the adult Alligator sinensis, as in humans. Selection analyses on telomere maintenance genes indicated that ATM, FANCE, SAMHD1, HMBOX1, NAT10, and MAP3K4 experienced positive selection on A. sinensis. Repressed pleiotropic ATM kinase in A. sinensis suggests their fitness optimum shift. In ATM downstream, Alternative Lengthening of Telomeres (ALT)-related genes were clustered in a higher expression pattern in A. sinensis, which covers 10-15% of human cancers showing no telomerase activities. In summary, we demonstrated how telomere shortening, telomerase activities, and ALT contributed to anti-aging strategies.
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22
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Udroiu I, Marinaccio J, Sgura A. Many Functions of Telomerase Components: Certainties, Doubts, and Inconsistencies. Int J Mol Sci 2022; 23:ijms232315189. [PMID: 36499514 PMCID: PMC9736166 DOI: 10.3390/ijms232315189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
A growing number of studies have evidenced non-telomeric functions of "telomerase". Almost all of them, however, investigated the non-canonical effects of the catalytic subunit TERT, and not the telomerase ribonucleoprotein holoenzyme. These functions mainly comprise signal transduction, gene regulation and the increase of anti-oxidative systems. Although less studied, TERC (the RNA component of telomerase) has also been shown to be involved in gene regulation, as well as other functions. All this has led to the publication of many reviews on the subject, which, however, are often disseminating personal interpretations of experimental studies of other researchers as original proofs. Indeed, while some functions such as gene regulation seem ascertained, especially because mechanistic findings have been provided, other ones remain dubious and/or are contradicted by other direct or indirect evidence (e.g., telomerase activity at double-strand break site, RNA polymerase activity of TERT, translation of TERC, mitochondrion-processed TERC). In a critical study of the primary evidence so far obtained, we show those functions for which there is consensus, those showing contradictory results and those needing confirmation. The resulting picture, together with some usually neglected aspects, seems to indicate a link between TERT and TERC functions and cellular stemness and gives possible directions for future research.
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23
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Gul H, Selvi S, Yilmaz F, Ozcelik G, Olfaz‐Aslan S, Yazan S, Tiryaki B, Gul S, Yurtseven A, Kavakli IH, Ozlu N, Ozturk N. Proteome analysis of the circadian clock protein PERIOD2. Proteins 2022; 90:1315-1330. [DOI: 10.1002/prot.26314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Huseyin Gul
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Saba Selvi
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Fatma Yilmaz
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Gozde Ozcelik
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Senanur Olfaz‐Aslan
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Seyma Yazan
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Busra Tiryaki
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
| | - Seref Gul
- Department of Biology Istanbul University Istanbul Turkey
| | - Ali Yurtseven
- Department of Molecular Biology and Genetics Koc University Istanbul Turkey
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics Koc University Istanbul Turkey
- Department of Chemical and Biological Engineering Koc University Istanbul Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics Koc University Istanbul Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics Gebze Technical University Gebze Kocaeli Turkey
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24
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Clair G, Bramer LM, Misra R, McGraw MD, Bhattacharya S, Kitzmiller JA, Feng S, Danna VG, Bandyopadhyay G, Bhotika H, Huyck HL, Deutsch GH, Mariani TJ, Carson JP, Whitsett JA, Pryhuber GS, Adkins JN, Ansong C. Proteomic Analysis of Human Lung Development. Am J Respir Crit Care Med 2022; 205:208-218. [PMID: 34752721 PMCID: PMC8787240 DOI: 10.1164/rccm.202008-3303oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Rationale: The current understanding of human lung development derives mostly from animal studies. Although transcript-level studies have analyzed human donor tissue to identify genes expressed during normal human lung development, protein-level analysis that would enable the generation of new hypotheses on the processes involved in pulmonary development are lacking. Objectives: To define the temporal dynamic of protein expression during human lung development. Methods: We performed proteomics analysis of human lungs at 10 distinct times from birth to 8 years to identify the molecular networks mediating postnatal lung maturation. Measurements and Main Results: We identified 8,938 proteins providing a comprehensive view of the developing human lung proteome. The analysis of the data supports the existence of distinct molecular substages of alveolar development and predicted the age of independent human lung samples, and extensive remodeling of the lung proteome occurred during postnatal development. Evidence of post-transcriptional control was identified in early postnatal development. An extensive extracellular matrix remodeling was supported by changes in the proteome during alveologenesis. The concept of maturation of the immune system as an inherent part of normal lung development was substantiated by flow cytometry and transcriptomics. Conclusions: This study provides the first in-depth characterization of the human lung proteome during development, providing a unique proteomic resource freely accessible at Lungmap.net. The data support the extensive remodeling of the lung proteome during development, the existence of molecular substages of alveologenesis, and evidence of post-transcriptional control in early postnatal development.
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Affiliation(s)
| | | | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Matthew D. McGraw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | | | - Joseph A. Kitzmiller
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati School of Medicine, Cincinnati, Ohio
| | | | | | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Harsh Bhotika
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Gail H. Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; and
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - James P. Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas
| | - Jeffrey A. Whitsett
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
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25
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Panner Selvam MK, Durairajanayagam D, Sikka SC. Molecular Interactions Associated with Oxidative Stress-Mediated Male Infertility: Sperm and Seminal Plasma Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1358:63-76. [DOI: 10.1007/978-3-030-89340-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Zhao L, Hutchison AT, Liu B, Yates CL, Teong XT, Wittert GA, Thompson CH, Nguyen L, Au J, Manoogian EN, Le HD, Williams AE, Panda S, Banks S, Heilbronn LK. Time restricted eating improves glycaemic control and dampens energy-consuming pathways in human adipose tissue. Nutrition 2022; 96:111583. [DOI: 10.1016/j.nut.2021.111583] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/03/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
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27
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Menarim BC, El-Sheikh Ali H, Loux SC, Scoggin KE, Kalbfleisch TS, MacLeod JN, Dahlgren LA. Transcriptional and Histochemical Signatures of Bone Marrow Mononuclear Cell-Mediated Resolution of Synovitis. Front Immunol 2021; 12:734322. [PMID: 34956173 PMCID: PMC8692379 DOI: 10.3389/fimmu.2021.734322] [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: 06/30/2021] [Accepted: 11/09/2021] [Indexed: 01/15/2023] Open
Abstract
Osteoarthritis (OA) may result from impaired ability of synovial macrophages to resolve joint inflammation. Increasing macrophage counts in inflamed joints through injection with bone marrow mononuclear cells (BMNC) induces lasting resolution of synovial inflammation. To uncover mechanisms by which BMNC may affect resolution, in this study, differential transcriptional signatures of BMNC in response to normal (SF) and inflamed synovial fluid (ISF) were analyzed. We demonstrate the temporal behavior of co-expressed gene networks associated with traits from related in vivo and in vitro studies. We also identified activated and inhibited signaling pathways and upstream regulators, further determining their protein expression in the synovium of inflamed joints treated with BMNC or DPBS controls. BMNC responded to ISF with an early pro-inflammatory response characterized by a short spike in the expression of a NF-ƙB- and mitogen-related gene network. This response was associated with sustained increased expression of two gene networks comprising known drivers of resolution (IL-10, IGF-1, PPARG, isoprenoid biosynthesis). These networks were common to SF and ISF, but more highly expressed in ISF. Most highly activated pathways in ISF included the mevalonate pathway and PPAR-γ signaling, with pro-resolving functional annotations that improve mitochondrial metabolism and deactivate NF-ƙB signaling. Lower expression of mevalonate kinase and phospho-PPARγ in synovium from inflamed joints treated with BMNC, and equivalent IL-1β staining between BMNC- and DPBS-treated joints, associates with accomplished resolution in BMNC-treated joints and emphasize the intricate balance of pro- and anti-inflammatory mechanisms required for resolution. Combined, our data suggest that BMNC-mediated resolution is characterized by constitutively expressed homeostatic mechanisms, whose expression are enhanced following inflammatory stimulus. These mechanisms translate into macrophage proliferation optimizing their capacity to counteract inflammatory damage and improving their general and mitochondrial metabolism to endure oxidative stress while driving tissue repair. Such effect is largely achieved through the synthesis of several lipids that mediate recovery of homeostasis. Our study reveals candidate mechanisms by which BMNC provide lasting improvement in patients with OA and suggests further investigation on the effects of PPAR-γ signaling enhancement for the treatment of arthritic conditions.
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Affiliation(s)
- Bruno C Menarim
- Department of Large Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States.,Theriogenology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Theodore S Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - James N MacLeod
- Gluck Equine Research Center, Department of Veterinary Sciences, College of Agricultural, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Linda A Dahlgren
- Department of Large Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
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28
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Liu J, Huang L, Zhu Y, He Y, Zhang W, Lei T, Xuan J, Xiao B, Li L, Zhou Q, Sun Z. Exploring the Expression and Prognostic Value of the TCP1 Ring Complex in Hepatocellular Carcinoma and Overexpressing Its Subunit 5 Promotes HCC Tumorigenesis. Front Oncol 2021; 11:739660. [PMID: 34676169 PMCID: PMC8525800 DOI: 10.3389/fonc.2021.739660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
T-complex protein-1 ring complex (TRiC), also known as Chaperonin Containing T-complex protein-1 (CCT), is a multisubunit chaperonin required for the folding of nascent proteins. Mounting evidence suggests that TRiC also contributes to the development and progression of tumors, but there are limited studies on pathogenic functions in hepatocellular carcinoma (HCC). We comprehensively evaluated the expression pattern and biological functions of TRiC subunits using The Cancer Genome Atlas and The Human Protein Atlas. Expression levels of TRiC subunits TCP1, CCT2/3/4/5/6A/7/8 were significantly upregulated in HCC tissues at both transcript and protein levels, which predicted shorter overall survival (OS). Moreover, high mutation rates were found in several CCT subunits, and patients with altered CCT genes exhibited poorer clinical outcomes. Functional enrichment analysis showed that co-regulated genes were preferentially involved in 'protein folding' and 'microtubule-based process', while genes co-expressed with CCT subunits were primarily involved in 'ribosome' and 'spliceosome'. Knockout of CCT5 in a HCC cell line reduced while overexpression enhanced proliferation rate, cycle transition, migration, and invasion. In conclusion, these findings suggest that subunits of the TRiC may be potential biomarkers for the diagnosis of HCC and play an important role in the occurrence and development of HCC.
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Affiliation(s)
- Jiahui Liu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ling Huang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yi Zhu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yongyin He
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Weiyun Zhang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ting Lei
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Junfeng Xuan
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Bin Xiao
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Linhai Li
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Quan Zhou
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Laboratory of Basic Medical Science, General Hospital of Southern Theater Command of PLA, Guangzhou, China
| | - Zhaohui Sun
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
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Gruber HJ, Semeraro MD, Renner W, Herrmann M. Telomeres and Age-Related Diseases. Biomedicines 2021; 9:biomedicines9101335. [PMID: 34680452 PMCID: PMC8533433 DOI: 10.3390/biomedicines9101335] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022] Open
Abstract
Telomeres are at the non-coding ends of linear chromosomes. Through a complex 3-dimensional structure, they protect the coding DNA and ensure appropriate separation of chromosomes. Aging is characterized by a progressive shortening of telomeres, which compromises their structure and function. Because of their protective function for genomic DNA, telomeres appear to play an important role in the development and progression of many age-related diseases, such as cardiovascular disease (CVD), malignancies, dementia, and osteoporosis. Despite substantial evidence that links telomere length with these conditions, the nature of these observations remains insufficiently understood. Therefore, future studies should address the question of causality. Furthermore, analytical methods should be further improved with the aim to provide informative and comparable results. This review summarize the actual knowledge of telomere biology and the possible implications of telomere dysfunction for the development and progression of age-related diseases. Furthermore, we provide an overview of analytical techniques for the measurement of telomere length and telomerase activity.
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30
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Hojka-Osinska A, Chlebowski A, Grochowska J, Owczarek EP, Affek K, Kłosowska-Kosicka K, Szczesny RJ, Dziembowski A. Landscape of functional interactions of human processive ribonucleases revealed by high-throughput siRNA screenings. iScience 2021; 24:103036. [PMID: 34541468 PMCID: PMC8437785 DOI: 10.1016/j.isci.2021.103036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Processive exoribonucleases are executors of RNA decay. In humans, their physical but not functional interactions were thoughtfully investigated. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their genetic interactions (GIs) with diverse pathways of RNA metabolism. We uncovered a complex network of positive interactions that buffer alterations in RNA degradation and reveal reciprocal cooperation with genes involved in transcription, RNA export, and splicing. Further, we evaluated the functional distinctness of nuclear DIS3 and cytoplasmic DIS3L using a library of all known genes associated with RNA metabolism. Our analysis revealed that DIS3 mutation suppresses RNA splicing deficiency, while DIS3L GIs disclose the interplay of cytoplasmic RNA degradation with nuclear RNA processing. Finally, genome-wide DIS3 GI map uncovered relations with genes not directly involved in RNA metabolism, like microtubule organization or regulation of telomerase activity.
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Affiliation(s)
- Anna Hojka-Osinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewelina P. Owczarek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kamila Affek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Roman J. Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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31
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PI3K-AKT, JAK2-STAT3 pathways and cell-cell contact regulate maspin subcellular localization. Cell Commun Signal 2021; 19:86. [PMID: 34391444 PMCID: PMC8364028 DOI: 10.1186/s12964-021-00758-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Background Maspin (SERPINB5) is a potential tumor suppressor gene with pleiotropic biological activities, including regulation of cell proliferation, death, adhesion, migration and gene expression. Several studies indicate that nuclear localization is essential for maspin tumor suppression activity. We have previously shown that the EGFR activation leads to maspin nuclear localization in MCF-10A cells. The present study investigated which EGFR downstream signaling molecules are involved in maspin nuclear localization and explored a possible role of cell–cell contact in this process. Methods MCF-10A cells were treated with pharmacological inhibitors against EGFR downstream pathways followed by EGF treatment. Maspin subcellular localization was determined by immunofluorescence. Proteomic and interactome analyses were conducted to identify maspin-binding proteins in EGF-treated cells only. To investigate the role of cell–cell contact these cells were either treated with chelating agents or plated on different cell densities. Maspin and E-cadherin subcellular localization was determined by immunofluorescence. Results We found that PI3K-Akt and JAK2-STAT3, but not MAP kinase pathway, regulate EGF-induced maspin nuclear accumulation in MCF-10A cells. We observed that maspin is predominantly nuclear in sparse cell culture, but it is redistributed to the cytoplasm in confluent cells even in the presence of EGF. Proteomic and interactome results suggest a role of maspin on post-transcriptional and translation regulation, protein folding and cell–cell adhesion. Conclusions Maspin nuclear accumulation is determined by an interplay between EGFR (via PI3K-Akt and JAK2-STAT3 pathways) and cell–cell contact.![]() Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00758-3.
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Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE, Kulej K, Dineen AS, Szeto JH, Garcia BA, Weitzman MD. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 2021; 22:e52145. [PMID: 34347354 DOI: 10.15252/embr.202052145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin-containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A-induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ariel S Dineen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia H Szeto
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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33
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DE Souza Dutra C, Martello CL, Cadore NA, Ferreira HB, Zaha A, Monteiro KM. Proteomic Analysis of the Non-genetic Response to Cisplatin in Lung Cancer Cells. CANCER DIAGNOSIS & PROGNOSIS 2021; 1:235-243. [PMID: 35399307 PMCID: PMC8962784 DOI: 10.21873/cdp.10032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/27/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Drug resistance is the main cause of therapy failure in advanced lung cancer. Although non-genetic mechanisms play important roles in tumor chemoresistance, drug-induced epigenetic reprogramming is still poorly understood. MATERIALS AND METHODS The A549 cell line was used to generate cells with non-genetic resistance to cisplatin (CDDP), namely A549/CDDP cells. Bioorthogonal non-canonical amino acid tagging (BONCAT) and mass spectrometry were used to identify proteins modulated by CDDP in A549 and A549/CDDP cells. RESULTS Proteins related to proteostasis, telomere maintenance, cell adhesion, cytoskeletal remodeling, and cell redox homeostasis were found enriched in both cell lines upon CDDP exposure. On the other hand, proteins involved in drug response, metabolic pathways and mRNA processing and splicing were up-regulated by CDDP only in A549/CDDP cells. CONCLUSION Our study revealed proteome dynamics involved in the non-genetic response to CDDP, pointing out potential targets to monitor and overcome epigenetic resistance in lung cancer.
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Affiliation(s)
- Cristine DE Souza Dutra
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carolina Lumertz Martello
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nathan Araujo Cadore
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Arnaldo Zaha
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Karina Mariante Monteiro
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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34
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Ghit A. Immunofluorescence studies to dissect the impact of Cockayne syndrome A alterations on the protein interaction and cellular localization. J Genet Eng Biotechnol 2021; 19:88. [PMID: 34132928 PMCID: PMC8208330 DOI: 10.1186/s43141-021-00190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/08/2021] [Indexed: 11/24/2022]
Abstract
Background Cockayne syndrome (CS), which was discovered by Alfred Cockayne nearly 75 years ago, is a rare autosomal recessive disorder characterized by growth failure, neurological dysfunction, premature aging, and other clinical features including microcephaly, ophthalmologic abnormalities, dental caries, and cutaneous photosensitivity. These alterations are caused by mutations in the CSA or CSB genes, both of which are involved in transcription-coupled nucleotide excision repair (TC-NER), the sub-pathway of NER that rapidly removes UV-induced DNA lesions which block the progression of the transcription machinery in the transcribed strand of active genes. Several studies assumed that CSA and CSB genes can play additional roles outside TC-NER, due to the wide variations in type and severity of the CS phenotype and the lack of a clear relationship between genotype and phenotype. To address this issue, our lab generated isogenic cell lines expressing wild type as well as different versions of mutated CSA proteins, fused at the C-terminus with the Flag and HA epitope tags (CSAFlag-HA). In unpublished data, the identity of the CSA-interacting proteins was determined by mass spectrometry. Among which three subunits (namely, CCT3, CCT8, and TCP1) of the TRiC/CCT complex appeared as novel interactors. TRiC is a chaperonin involved in the folding of newly synthesized or unfolded proteins. The aim of this study is directed to investigate by immunofluorescence analysis the impact of the selected CSA mutations on the subcellular localization of the CSA protein itself as well as on its novel interactors CCT3, CCT8, and TCP1. Results We showed that specific CSA mutations impair the proper cellular localization of the protein, but have no impact on the cellular distribution of the TRiC subunits or CSA/TRiC co-localization. Conclusion We suggested that the activity of the TRiC complex does not rely on the functionality of CSA. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00190-7.
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Affiliation(s)
- Amr Ghit
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy. .,Department of Biotechnology, Institute of Graduate Studies and Research (IGSR), Alexandria University, Alexandria, Egypt.
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35
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Vavouraki N, Tomkins JE, Kara E, Houlden H, Hardy J, Tindall MJ, Lewis PA, Manzoni C. Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. iScience 2021; 24:102484. [PMID: 34113825 PMCID: PMC8169945 DOI: 10.1016/j.isci.2021.102484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/01/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
The Hereditary Spastic Paraplegias are a group of neurodegenerative diseases characterized by spasticity and weakness in the lower body. Owing to the combination of genetic diversity and variable clinical presentation, the Hereditary Spastic Paraplegias are a strong candidate for protein-protein interaction network analysis as a tool to understand disease mechanism(s) and to aid functional stratification of phenotypes. In this study, experimentally validated human data were used to create a protein-protein interaction network based on the causative genes. Network evaluation as a combination of topological analysis and functional annotation led to the identification of core proteins in putative shared biological processes, such as intracellular transport and vesicle trafficking. The application of machine learning techniques suggested a functional dichotomy linked with distinct sets of clinical presentations, indicating that there is scope to further classify conditions currently described under the same umbrella-term of Hereditary Spastic Paraplegias based on specific molecular mechanisms of disease.
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Affiliation(s)
- Nikoleta Vavouraki
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK
| | | | - Eleanna Kara
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- UK Dementia Research Institute at UCL and Department of Neurodegenerative Disease, UCL IoN, UCL London, W1T 7NF UK
- Reta Lila Weston Institute, UCL IoN, 1 Wakefield Street, London, WC1N 1PJ, UK
- UCL Movement Disorders Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Marcus J. Tindall
- Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK
- Institute of Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, UK
| | - Patrick A. Lewis
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK
| | - Claudia Manzoni
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
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36
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Roberto J, Poulin KL, Parks RJ, Vacratsis PO. Label-free quantitative proteomic analysis of extracellular vesicles released from fibroblasts derived from patients with spinal muscular atrophy. Proteomics 2021; 21:e2000301. [PMID: 33893753 DOI: 10.1002/pmic.202000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/22/2021] [Accepted: 04/12/2021] [Indexed: 11/10/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disorder that represents a significant cause of infant mortality. SMA is characterized by reduced levels of the Survival Motor Neuron protein leading to the loss of alpha motor neurons in the spinal cord and brain stem as well as defects in peripheral tissues such as skeletal muscle and liver. With progress in promising therapies such as antisense oligonucleotide and gene replacement, there remains a need to better understand disease subtypes and develop biomarkers for improved diagnostics and therapeutic monitoring. In this study, we have examined the utility of extracellular vesicles as a source of biomarker discovery in patient-derived fibroblast cells. Proteome examination utilizing data-independent acquisition and ion mobility mass spectrometry identified 684 protein groups present in all biological replicates tested. Label-free quantitative analysis identified 116 statistically significant protein alterations compared to control cells, including several known SMA biomarkers. Protein level differences were also observed in regulators of Wnt signaling and Cajal bodies. Finally, levels of insulin growth factor binding protein-3 were validated as being significantly higher in extracellular vesicles isolated from SMA cells. We conclude that extracellular vesicles represent a promising source for SMA biomarker discovery as well as a relevant constituent for advancing our understanding of SMA pathophysiology.
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Affiliation(s)
- Justin Roberto
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Kathy L Poulin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Robin J Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Panayiotis O Vacratsis
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
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37
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Ilyinsky NS, Nesterov SV, Shestoperova EI, Fonin AV, Uversky VN, Gordeliy VI. On the Role of Normal Aging Processes in the Onset and Pathogenesis of Diseases Associated with the Abnormal Accumulation of Protein Aggregates. BIOCHEMISTRY (MOSCOW) 2021; 86:275-289. [PMID: 33838629 DOI: 10.1134/s0006297921030056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aging is a prime systemic cause of various age-related diseases, in particular, proteinopathies. In fact, most diseases associated with protein misfolding are sporadic, and their incidence increases with aging. This review examines the process of protein aggregate formation, the toxicity of such aggregates, the organization of cellular systems involved in proteostasis, and the impact of protein aggregates on important cellular processes leading to proteinopathies. We also analyze how manifestations of aging (mitochondrial dysfunction, dysfunction of signaling systems, changes in the genome and epigenome) facilitate pathogenesis of various proteinopathies either directly, by increasing the propensity of key proteins for aggregation, or indirectly, through dysregulation of stress responses. Such analysis might help in outlining approaches for treating proteinopathies and extending healthy longevity.
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Affiliation(s)
- Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Elizaveta I Shestoperova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexander V Fonin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Forschungszentrum Juelich, Juelich, 52428, Germany.,Institut de Biologie Structurale, Grenoble, 38000, France
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38
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Keysberg C, Hertel O, Schelletter L, Busche T, Sochart C, Kalinowski J, Hoffrogge R, Otte K, Noll T. Exploring the molecular content of CHO exosomes during bioprocessing. Appl Microbiol Biotechnol 2021; 105:3673-3689. [PMID: 33937930 PMCID: PMC8102462 DOI: 10.1007/s00253-021-11309-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 01/21/2023]
Abstract
Abstract In biopharmaceutical production, Chinese hamster ovary (CHO) cells derived from Cricetulus griseus remain the most commonly used host cell for recombinant protein production, especially antibodies. Over the last decade, in-depth multi-omics characterization of these CHO cells provided data for extensive cell line engineering and corresponding increases in productivity. However, exosomes, extracellular vesicles containing proteins and nucleic acids, are barely researched at all in CHO cells. Exosomes have been proven to be a ubiquitous mediator of intercellular communication and are proposed as new biopharmaceutical format for drug delivery, indicator reflecting host cell condition and anti-apoptotic factor in spent media. Here we provide a brief overview of different separation techniques and subsequently perform a proteome and regulatory, non-coding RNA analysis of exosomes, derived from lab-scale bioreactor cultivations of a CHO-K1 cell line, to lay out reference data for further research in the field. Applying bottom-up orbitrap shotgun proteomics and next-generation small RNA sequencing, we detected 1395 proteins, 144 micro RNA (miRNA), and 914 PIWI-interacting RNA (piRNA) species differentially across the phases of a batch cultivation process. The exosomal proteome and RNA data are compared with other extracellular fractions and cell lysate, yielding several significantly exosome-enriched species. Graphical Abstract ![]()
Key points • First-time comprehensive protein and miRNA characterization of CHO exosomes. • Isolation protocol and time point of bioprocess strongly affect quality of extracellular vesicles. • CHO-derived exosomes also contain numerous piRNA species of yet unknown function. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11309-8.
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Affiliation(s)
- Christoph Keysberg
- Bielefeld University, Bielefeld, Germany. .,University of Applied Sciences Biberach, Biberach, Germany.
| | - Oliver Hertel
- Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Louise Schelletter
- Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Raimund Hoffrogge
- Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kerstin Otte
- University of Applied Sciences Biberach, Biberach, Germany
| | - Thomas Noll
- Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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39
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Rai A, Poh QH, Fatmous M, Fang H, Gurung S, Vollenhoven B, Salamonsen LA, Greening DW. Proteomic profiling of human uterine extracellular vesicles reveal dynamic regulation of key players of embryo implantation and fertility during menstrual cycle. Proteomics 2021; 21:e2000211. [PMID: 33634576 DOI: 10.1002/pmic.202000211] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/22/2022]
Abstract
Endometrial extracellular vesicles (EVs) are emerging as important players in reproductive biology. However, how their proteome is regulated throughout the menstrual cycle is not known. Such information can provide novel insights into biological processes critical for embryo development, implantation, and successful pregnancy. Using mass spectrometry-based quantitative proteomics, we show that small EVs (sEVs) isolated from uterine lavage of fertile women (UL-sEV), compared to infertile women, are laden with proteins implicated in antioxidant activity (SOD1, GSTO1, MPO, CAT). Functionally, sEVs derived from endometrial cells enhance antioxidant function in trophectoderm cells. Moreover, there was striking enrichment of invasion-related proteins (LGALS1/3, S100A4/11) in fertile UL-sEVs in the secretory (estrogen plus progesterone-driven, EP) versus proliferative (estrogen-driven, E) phase, with several players downregulated in infertile UL-sEVs. Consistent with this, sEVs from EP- versus E-primed endometrial epithelial cells promote invasion of trophectoderm cells. Interestingly, UL-sEVs from fertile versus infertile women carry known players/predictors of embryo implantation (PRDX2, IDHC), endometrial receptivity (S100A4, FGB, SERPING1, CLU, ANXA2), and implantation success (CAT, YWHAE, PPIA), highlighting their potential to inform regarding endometrial status/pregnancy outcomes. Thus, this study provides novel insights into proteome reprograming of sEVs and soluble secretome in uterine fluid, with potential to enhance embryo implantation and hence fertility.
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Affiliation(s)
- Alin Rai
- Baker Heart and Diabetes Institute, Molecular Proteomics, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Qi Hui Poh
- Baker Heart and Diabetes Institute, Molecular Proteomics, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Monique Fatmous
- Baker Heart and Diabetes Institute, Molecular Proteomics, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Haoyun Fang
- Baker Heart and Diabetes Institute, Molecular Proteomics, Melbourne, Victoria, Australia
| | - Shanti Gurung
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Beverley Vollenhoven
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash IVF, Clayton, Victoria, Australia.,Women's and Newborn Program, Monash Health, Clayton, Victoria, Australia
| | - Lois A Salamonsen
- Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - David W Greening
- Baker Heart and Diabetes Institute, Molecular Proteomics, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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40
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Chen L, Roake CM, Galati A, Bavasso F, Micheli E, Saggio I, Schoeftner S, Cacchione S, Gatti M, Artandi SE, Raffa GD. Loss of Human TGS1 Hypermethylase Promotes Increased Telomerase RNA and Telomere Elongation. Cell Rep 2021; 30:1358-1372.e5. [PMID: 32023455 PMCID: PMC7156301 DOI: 10.1016/j.celrep.2020.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/09/2019] [Accepted: 12/31/2019] [Indexed: 02/08/2023] Open
Abstract
Biogenesis of the human telomerase RNA (hTR) involves a complex series of posttranscriptional modifications, including hypermethylation of the 5' mono-methylguanosine cap to a tri-methylguanosine cap (TMG). How the TMG cap affects hTR maturation is unknown. Here, we show that depletion of trimethylguanosine synthase 1 (TGS1), the enzyme responsible for cap hypermethylation, increases levels of hTR and telomerase. Diminished trimethylation increases hTR association with the cap-binding complex (CBC) and with Sm chaperone proteins. Loss of TGS1 causes an increase in accumulation of mature hTR in both the nucleus and the cytoplasm compared with controls. In TGS1 mutant cells, increased hTR assembles with telomerase reverse transcriptase (TERT) protein to yield elevated active telomerase complexes and increased telomerase activity, resulting in telomere elongation in cultured human cells. Our results show that TGS1-mediated hypermethylation of the hTR cap inhibits hTR accumulation, restrains levels of assembled telomerase, and limits telomere elongation.
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caitlin M Roake
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Emanuela Micheli
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Stefan Schoeftner
- Cancer Epigenetic Group, Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy; Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Roma, Italy
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Grazia D Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy.
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41
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Gene Co-Expression Analysis of Human RNASEH2A Reveals Functional Networks Associated with DNA Replication, DNA Damage Response, and Cell Cycle Regulation. BIOLOGY 2021; 10:biology10030221. [PMID: 33805806 PMCID: PMC7998727 DOI: 10.3390/biology10030221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 12/22/2022]
Abstract
Simple Summary RNASEH2A is the catalytic subunit of the ribonuclease (RNase) H2 ternary complex that plays an important role in maintaining DNA stability in cells. Recent studies have shown that the RNASEH2A subunit alone is highly expressed in certain cancer cell types. Via a series of bioinformatics approaches, we found that RNASEH2A is highly expressed in human proliferative tissues and many cancers. Our analyses reveal a possible involvement of RNASEH2A in cell cycle regulation in addition to its well established role in DNA replication and DNA repair. Our findings underscore that RNASEH2A could serve as a biomarker for cancer diagnosis and a therapeutic target. Abstract Ribonuclease (RNase) H2 is a key enzyme for the removal of RNA found in DNA-RNA hybrids, playing a fundamental role in biological processes such as DNA replication, telomere maintenance, and DNA damage repair. RNase H2 is a trimer composed of three subunits, RNASEH2A being the catalytic subunit. RNASEH2A expression levels have been shown to be upregulated in transformed and cancer cells. In this study, we used a bioinformatics approach to identify RNASEH2A co-expressed genes in different human tissues to underscore biological processes associated with RNASEH2A expression. Our analysis shows functional networks for RNASEH2A involvement such as DNA replication and DNA damage response and a novel putative functional network of cell cycle regulation. Further bioinformatics investigation showed increased gene expression in different types of actively cycling cells and tissues, particularly in several cancers, supporting a biological role for RNASEH2A but not for the other two subunits of RNase H2 in cell proliferation. Mass spectrometry analysis of RNASEH2A-bound proteins identified players functioning in cell cycle regulation. Additional bioinformatic analysis showed that RNASEH2A correlates with cancer progression and cell cycle related genes in Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA) Pan Cancer datasets and supported our mass spectrometry findings.
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Zhang YC, Bai YF, Yuan JF, Shen XL, Xu YL, Jian XX, Li S, Song ZQ, Hu HB, Li PY, Tu HQ, Han QY, Wang N, Li AL, Zhang XM, Wu M, Zhou T, Li HY. CEP55 promotes cilia disassembly through stabilizing Aurora A kinase. J Cell Biol 2021; 220:211702. [PMID: 33475699 PMCID: PMC7829976 DOI: 10.1083/jcb.202003149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/24/2020] [Accepted: 11/23/2020] [Indexed: 12/21/2022] Open
Abstract
Primary cilia protrude from the cell surface and have diverse roles during development and disease, which depends on the precise timing and control of cilia assembly and disassembly. Inactivation of assembly often causes cilia defects and underlies ciliopathy, while diseases caused by dysfunction in disassembly remain largely unknown. Here, we demonstrate that CEP55 functions as a cilia disassembly regulator to participate in ciliopathy. Cep55-/- mice display clinical manifestations of Meckel-Gruber syndrome, including perinatal death, polycystic kidneys, and abnormalities in the CNS. Interestingly, Cep55-/- mice exhibit an abnormal elongation of cilia on these tissues. Mechanistically, CEP55 promotes cilia disassembly by interacting with and stabilizing Aurora A kinase, which is achieved through facilitating the chaperonin CCT complex to Aurora A. In addition, CEP55 mutation in Meckel-Gruber syndrome causes the failure of cilia disassembly. Thus, our study establishes a cilia disassembly role for CEP55 in vivo, coupling defects in cilia disassembly to ciliopathy and further suggesting that proper cilia dynamics are critical for mammalian development.
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Affiliation(s)
- Yu-Cheng Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yun-Feng Bai
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jin-Feng Yuan
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xiao-Lin Shen
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yu-Ling Xu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xiao-Xiao Jian
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Sen Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Zeng-Qing Song
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Huai-Bin Hu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Pei-Yao Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China,School of Medicine, Tsinghua University, Beijing, China
| | - Hai-Qing Tu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Qiu-Ying Han
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Na Wang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xue-Min Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Min Wu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China,Min Wu:
| | - Tao Zhou
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China,Tao Zhou:
| | - Hui-Yan Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China,School of Basic Medical Sciences, Fudan University, Shanghai, China,Correspondence to Hui-Yan Li:
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43
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Tran JR, Paulson DI, Moresco JJ, Adam SA, Yates JR, Goldman RD, Zheng Y. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 2021; 220:e202002129. [PMID: 33306092 PMCID: PMC7737704 DOI: 10.1083/jcb.202002129] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3' UTR bias, a finding consistent with an observed bias toward longer 3' UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3' UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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Affiliation(s)
- Joseph R. Tran
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
| | - Danielle I. Paulson
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
- Horace Mann School, The Bronx, NY
| | - James J. Moresco
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Stephen A. Adam
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - John R. Yates
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Robert D. Goldman
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - Yixian Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
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44
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Li W, Liu J, Zhao H. Prognostic Power of a Chaperonin Containing TCP-1 Subunit Genes Panel for Hepatocellular Carcinoma. Front Genet 2021; 12:668871. [PMID: 33897772 PMCID: PMC8061729 DOI: 10.3389/fgene.2021.668871] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/15/2021] [Indexed: 02/05/2023] Open
Abstract
Chaperonin containing TCP-1 (T-complex protein 1) (CCT) is a large molecular weight complex that contains nine subunits (TCP1, CCT2, CCT3, CCT4, CCT5, CCT6A, CCT6B, CCT7, CCT8). This study aimed to reveal key genes which encode CCT subunits for prognosis and establish prognostic gene signatures based on CCT subunit genes. The data was downloaded from The Cancer Genome Atlas, International Cancer Genome Consortium and Gene Expression Omnibus. CCT subunit gene expression levels between tumor and normal tissues were compared. Corresponding Kaplan-Meier analysis displayed a distinct separation in the overall survival of CCT subunit genes. Correlation analysis, protein-protein interaction network, Gene Ontology analysis, immune cells infiltration analysis, and transcription factor network were performed. A nomogram was constructed for the prediction of prognosis. Based on multivariate Cox regression analysis and shrinkage and selection method for linear regression model, a three-gene signature comprising CCT4, CCT6A, and CCT6B was constructed in the training set and significantly associated with prognosis as an independent prognostic factor. The prognostic value of the signature was then validated in the validation and testing set. Nomogram including the signature showed some clinical benefit for overall survival prediction. In all, we built a novel three-gene signature and nomogram from CCT subunit genes to predict the prognosis of hepatocellular carcinoma, which may support the medical decision for HCC therapy.
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Affiliation(s)
- Wenli Li
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, China
| | - Jun Liu
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, China
| | - Hetong Zhao
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
- *Correspondence: Hetong Zhao
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45
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Grill S, Nandakumar J. Molecular mechanisms of telomere biology disorders. J Biol Chem 2021; 296:100064. [PMID: 33482595 PMCID: PMC7948428 DOI: 10.1074/jbc.rev120.014017] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mutations that affect telomerase function or telomere maintenance result in a variety of diseases collectively called telomeropathies. This wide spectrum of disorders, which include dyskeratosis congenita, pulmonary fibrosis, and aplastic anemia, is characterized by severely short telomeres, often resulting in hematopoietic stem cell failure in the most severe cases. Recent work has focused on understanding the molecular basis of these diseases. Mutations in the catalytic TERT and TR subunits of telomerase compromise activity, while others, such as those found in the telomeric protein TPP1, reduce the recruitment of telomerase to the telomere. Mutant telomerase-associated proteins TCAB1 and dyskerin and the telomerase RNA maturation component poly(A)-specific ribonuclease affect the maturation and stability of telomerase. In contrast, disease-associated mutations in either CTC1 or RTEL1 are more broadly associated with telomere replication defects. Yet even with the recent surge in studies decoding the mechanisms underlying these diseases, a significant proportion of dyskeratosis congenita mutations remain uncharacterized or poorly understood. Here we review the current understanding of the molecular basis of telomeropathies and highlight experimental data that illustrate how genetic mutations drive telomere shortening and dysfunction in these patients. This review connects insights from both clinical and molecular studies to create a comprehensive view of the underlying mechanisms that drive these diseases. Through this, we emphasize recent advances in therapeutics and pinpoint disease-associated variants that remain poorly defined in their mechanism of action. Finally, we suggest future avenues of research that will deepen our understanding of telomere biology and telomere-related disease.
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Affiliation(s)
- Sherilyn Grill
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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46
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Lavado-García J, González-Domínguez I, Cervera L, Jorge I, Vázquez J, Gòdia F. Molecular Characterization of the Coproduced Extracellular Vesicles in HEK293 during Virus-Like Particle Production. J Proteome Res 2020; 19:4516-4532. [PMID: 32975947 PMCID: PMC7640977 DOI: 10.1021/acs.jproteome.0c00581] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/22/2022]
Abstract
Vaccine therapies based on virus-like particles (VLPs) are currently in the spotlight due to their potential for generating high immunogenic responses while presenting fewer side effects than conventional vaccines. These self-assembled nanostructures resemble the native conformation of the virus but lack genetic material. They are becoming a promising platform for vaccine candidates against several diseases due to the ability of modifying their membrane with antigens from different viruses. The coproduction of extracellular vesicles (EVs) when producing VLPs is a key phenomenon currently still under study. In order to characterize this extracellular environment, a quantitative proteomics approach has been carried out. Three conditions were studied: non-transfected, transfected with an empty plasmid as control, and transfected with a plasmid coding for HIV-1 Gag polyprotein. A shift in EV biogenesis has been detected upon transfection, changing the production from large to small EVs. Another remarkable trait found was the presence of DNA being secreted within vesicles smaller than 200 nm. Studying the protein profile of these biological nanocarriers, it was observed that EVs were reflecting an overall energy homeostasis disruption via mitochondrial protein deregulation. Also, immunomodulatory proteins like ITGB1, ENO3, and PRDX5 were identified and quantified in VLP and EV fractions. These findings provide insight on the nature of the VLP extracellular environment defining the characteristics and protein profile of EVs, with potential to develop new downstream separation strategies or using them as adjuvants in viral therapies.
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Affiliation(s)
- Jesús Lavado-García
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Irene González-Domínguez
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Laura Cervera
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
| | - Inmaculada Jorge
- Laboratory
of Cardiovascular Proteomics, Centro Nacional
Investigaciones Cardiovasculares (CNIC), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
- Centro
de Investigación Biomédica en Red Enfermedades Cardiovasculares
(CIBERCV), Madrid, Spain
| | - Jesús Vázquez
- Laboratory
of Cardiovascular Proteomics, Centro Nacional
Investigaciones Cardiovasculares (CNIC), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
- Centro
de Investigación Biomédica en Red Enfermedades Cardiovasculares
(CIBERCV), Madrid, Spain
| | - Francesc Gòdia
- Grup
d’Enginyeria Cellular i Bioprocés, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola
del Vallès, 08193 Barcelona, Spain
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47
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Zhang X, Lin X, Qin C, Huang K, Sun X, Zhao L, Jin M. Avian Chaperonin Containing TCP1 Subunit 5 Supports Influenza A Virus Replication by Interacting With Viral Nucleoprotein, PB1, and PB2 Proteins. Front Microbiol 2020; 11:538355. [PMID: 33178142 PMCID: PMC7593399 DOI: 10.3389/fmicb.2020.538355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/26/2020] [Indexed: 11/30/2022] Open
Abstract
Humans and avian species are prone to influenza viral infection, which may cause serious clinical consequences. Many studies have documented the critical role of host factors in the influenza virus life cycle based on human models, but knowledge about their roles in birds is very limited. In this study, using immunoprecipitation coupled with mass spectrometry, a total of 72 potential interacting proteins of influenza nucleoprotein (NP) were identified in DF-1 cells. Among these proteins, avian chaperonin containing TCP1 subunit 5 (CCT5) was demonstrated to interact with influenza A virus (IAV) NP directly, as well as polymerase basic protein 1 (PB1) and polymerase basic protein 2 (PB2) but not with polymerase acidic protein (PA). Further investigation showed that viral infection profoundly elevated the expression level of cellular CCT5, whose expression, in turn, promoted the nuclear export of NP, as well as viral polymerase activity, thereby facilitating the replication of IAV. The obtained results suggested an important role of avian CCT5 in supporting influenza virus replication, which may serve as an anti-influenza target.
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Affiliation(s)
- Xiaohan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xian Lin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Chenghuang Qin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Kun Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Lianzhong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
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48
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Nagpal N, Agarwal S. Telomerase RNA processing: Implications for human health and disease. Stem Cells 2020; 38:10.1002/stem.3270. [PMID: 32875693 PMCID: PMC7917152 DOI: 10.1002/stem.3270] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/11/2020] [Indexed: 11/11/2022]
Abstract
Telomeres are composed of repetitive DNA sequences that are replenished by the enzyme telomerase to maintain the self-renewal capacity of stem cells. The RNA component of human telomerase (TERC) is the essential template for repeat addition by the telomerase reverse transcriptase (TERT), and also serves as a scaffold for several factors comprising the telomerase ribonucleoprotein (RNP). Unique features of TERC regulation and function have been informed not only through biochemical studies but also through human genetics. Disease-causing mutations impact TERC biogenesis at several levels including RNA transcription, post-transcriptional processing, folding, RNP assembly, and trafficking. Defects in TERC reduce telomerase activity and impair telomere maintenance, thereby causing a spectrum of degenerative diseases called telomere biology disorders (TBDs). Deciphering mechanisms of TERC dysregulation have led to a broader understanding of noncoding RNA biology, and more recently points to new therapeutic strategies for TBDs. In this review, we summarize over two decades of work revealing mechanisms of human telomerase RNA biogenesis, and how its disruption causes human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
| | - Suneet Agarwal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
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49
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Zhao J, Zhai X, Ma Y, Zhang T, Wang Z, Chong T. Anatomic characteristics of epididymis based on histology, proteomic, and 3D reconstruction. Andrology 2020; 8:1787-1794. [PMID: 32558146 DOI: 10.1111/andr.12842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/20/2020] [Accepted: 06/09/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND The epididymis is a popular research topic in urology and reproduction. OBJECTIVES To explore and identify the anatomical characteristics of the epididymis based on histology, proteomics, and 3D reconstruction of epididymal tubules. MATERIALS AND METHODS A 3D reconstruction of epididymal tubules was generated based on 7-μm-thick transverse serial sections of an epididymis. The proteins in the subcompartments of the epididymis were obtained and analyzed by non-labeled sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS). Protein function, signaling pathways, protein expression, and the histology in different subcompartments were analyzed. RESULTS The caput (Cap), corpus (Cor), and cauda (Cau) of the epididymis were divided into 6, 10, and 4 subcompartments, respectively, and the subcompartment between the Cap and Cor is mixed together. A total of 3411 proteins were identified, and 854 proteins were accurately quantified after screening. When the subcompartment Cap 5 transitioned to Cap 6 and Cap 6 to Cap 7, 87 and 52 proteins were upregulated and 14 and 7 proteins were downregulated, respectively. The Cor 9 transition to Cau 1 was marked by 230 proteins that were downregulated, while 74 proteins were upregulated. At the junction of the cauda and the vas deferens, 57 proteins were downregulated, and 410 proteins were upregulated. Cap 6 histology was consistent with that of Cor 1. DISCUSSION AND CONCLUSION The epididymis contains distinct connective tissue septa that can be identified under a surgical tabletop microscope, enabling it to be divided into 20 subcompartments.
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Affiliation(s)
- Jun Zhao
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaoqiang Zhai
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yubo Ma
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Tongdian Zhang
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Ziming Wang
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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50
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Ma J, Liu M, Wang Y, Xin C, Zhang H, Chen S, Zheng X, Zhang X, Xiao F, Yang S. Quantitative proteomics analysis of young and elderly skin with DIA mass spectrometry reveals new skin aging-related proteins. Aging (Albany NY) 2020; 12:13529-13554. [PMID: 32602849 PMCID: PMC7377841 DOI: 10.18632/aging.103461] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
Skin aging is a specific manifestation of the physiological aging process that occurs in virtually all organisms. In this study, we used data independent acquisition mass spectrometry to perform a comparative analysis of protein expression in volar forearm skin samples from of 20 healthy young and elderly Chinese individuals. Our quantitative proteomic analysis identified a total of 95 differentially expressed proteins (DEPs) in aged skin compared to young skin. Enrichment analyses of these DEPs (57 upregulated and 38 downregulated proteins) based on the GO, KEGG, and KOG databases revealed functional clusters associated with immunity and inflammation, oxidative stress, biosynthesis and metabolism, proteases, cell proliferation, cell differentiation, and apoptosis. We also found that GAPDH, which was downregulated in aged skin samples, was the top hub gene in a protein-protein interaction network analysis. Some of the DEPs identified herein had been previously correlated with aging of the skin and other organs, while others may represent novel age-related entities. Our non-invasive proteomics analysis of human epidermal proteins may guide future research on skin aging to help develop treatments for age-related skin conditions and rejuvenation.
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Affiliation(s)
- Jing Ma
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Mengting Liu
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Yaochi Wang
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Cong Xin
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Hui Zhang
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Shirui Chen
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Xiaodong Zheng
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Xuejun Zhang
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Fengli Xiao
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China.,The Center for Scientific Research of Anhui Medical University, Hefei, Anhui, China
| | - Sen Yang
- Department of Dermatology of First Affiliated Hospital, and Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
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