1
|
Fiore APZP, Maity S, Jeffery L, An D, Rendleman J, Iannitelli D, Choi H, Mazzoni E, Vogel C. Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons. Cell Rep 2024; 43:113885. [PMID: 38457337 PMCID: PMC11018139 DOI: 10.1016/j.celrep.2024.113885] [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: 03/06/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity.
Collapse
Affiliation(s)
| | - Shuvadeep Maity
- New York University, Department of Biology, New York, NY 10003, USA; Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lauren Jeffery
- New York University, Department of Biology, New York, NY 10003, USA
| | - Disi An
- New York University, Department of Biology, New York, NY 10003, USA
| | - Justin Rendleman
- New York University, Department of Biology, New York, NY 10003, USA
| | - Dylan Iannitelli
- New York University, Department of Biology, New York, NY 10003, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Esteban Mazzoni
- New York University, Department of Biology, New York, NY 10003, USA; Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Christine Vogel
- New York University, Department of Biology, New York, NY 10003, USA.
| |
Collapse
|
2
|
Wen S, Huang X, Xiong L, Zeng H, Wu S, An K, Bai J, Zhou Z, Yin T. WDR12/RAC1 axis promoted proliferation and anti-apoptosis in colorectal cancer cells. Mol Cell Biochem 2024:10.1007/s11010-024-04937-x. [PMID: 38341833 DOI: 10.1007/s11010-024-04937-x] [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: 07/17/2023] [Accepted: 01/09/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND WD repeat domain 12 (WDR12) plays a crucial role in the ribosome biogenesis pathway. However, its biological function in colorectal cancer (CRC) remains poorly understood. Therefore, this study aims to investigate the roles of WDR12 in the occurrence and progression of CRC, as well as its underlying mechanisms. METHODS The expression of WDR12 was assessed through The Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA) database. Functional experiments including Celigo assay, MTT assay, and Caspase-3/7 assay were conducted to validate the role of WDR12 in the malignant progression of CRC. Additionally, mRNA chip-sequencing and ingenuity pathway analysis (IPA) were performed to identify the molecular mechanism. RESULTS WDR12 expression was significantly upregulated in CRC tissues compared to normal colorectal tissues. Knockdown of WDR12 reduced proliferation and promoted apoptosis of CRC cell lines in vitro and in vivo experiments. Furthermore, WDR12 expression had a significantly inverse association with diseases and functions, including cancer, cell cycle, DNA replication, recombination, cellular growth, proliferation and repair, as revealed by IPA analysis of mRNA chip-sequencing data. Moreover, the activation of cell cycle checkpoint kinases proteins in the cell cycle checkpoint control signaling pathway was enriched in the WDR12 knockdown CRC cell lines. Additionally, downregulation of rac family small GTPase 1 (RAC1) occurred upon WDR12 knockdown, thereby facilitating the proliferation and anti-apoptosis of CRC cells. CONCLUSION Our study demonstrates that the WDR12/RAC1 axis promotes tumor progression in CRC. Therefore, WDR12 may serve as a novel oncogene and a potential target for individualized therapy in CRC. These findings provide an experimental foundation for the clinical development of drugs targeting the WDR12/RAC1 axis.
Collapse
Affiliation(s)
- Su Wen
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Xueqing Huang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Liping Xiong
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Hao Zeng
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Shuang Wu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Kangli An
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China
| | - Jing Bai
- Geneplus-Beijing Institute, Zhongguancun Life Science Park, Peking University Medical Industrial Park, Life Park Road No.8, Beijing, 102205, China
| | - Zhipeng Zhou
- Geneplus-Beijing Institute, Zhongguancun Life Science Park, Peking University Medical Industrial Park, Life Park Road No.8, Beijing, 102205, China
| | - Tiejun Yin
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road No.1095, Wuhan, 430030, Hubei, China.
| |
Collapse
|
3
|
Keer S, Neilson KM, Cousin H, Majumdar HD, Alfandari D, Klein SL, Moody SA. Bop1 is required to establish precursor domains of craniofacial tissues. Genesis 2024; 62:e23580. [PMID: 37974491 PMCID: PMC11021169 DOI: 10.1002/dvg.23580] [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: 09/19/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Bop1 can promote cell proliferation and is a component of the Pes1-Bop1-WDR12 (PeBoW) complex that regulates ribosomal RNA processing and biogenesis. In embryos, however, bop1 mRNA is highly enriched in the neural plate, cranial neural crest and placodes, and potentially may interact with Six1, which also is expressed in these tissues. Recent work demonstrated that during development, Bop1 is required for establishing the size of the tadpole brain, retina and cranial cartilages, as well as controlling neural tissue gene expression levels. Herein, we extend this work by assessing the effects of Bop1 knockdown at neural plate and larval stages. Loss of Bop1 expanded neural plate gene expression domains (sox2, sox11, irx1) and reduced neural crest (foxd3, sox9), placode (six1, sox11, irx1, sox9) and epidermal (dlx5) expression domains. At larval stages, Bop1 knockdown reduced the expression of several otic vesicle genes (six1, pax2, irx1, sox9, dlx5, otx2, tbx1) and branchial arch genes that are required for chondrogenesis (sox9, tbx1, dlx5). The latter was not the result of impaired neural crest migration. Together these observations indicate that Bop1 is a multifunctional protein that in addition to its well-known role in ribosomal biogenesis functions during early development to establish the craniofacial precursor domains.
Collapse
Affiliation(s)
- Stephanie Keer
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Karen M. Neilson
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Helene Cousin
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Himani D. Majumdar
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Steven L. Klein
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| |
Collapse
|
4
|
Li J, Hu W, Zhang R, Chen W, Li X, Tang Z. PDGF-C promotes cell proliferation partially via downregulating BOP1. Cell Biol Int 2023; 47:1942-1949. [PMID: 37615370 DOI: 10.1002/cbin.12082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/23/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
Platelet-derived growth factor C (PDGF-C) is a member of PDGF/VEGF family, which is well-known for important functions in the vascular system. It is widely reported that PDGF-C is able to modulate cell proliferation. However, it is still not very clear about this cell modulating mechanism at the molecular level. In a screening of factors regulated by PDGF-C protein, we fished out a factor called block of proliferation 1 (BOP1), which is a pivotal regulator of ribosome biogenesis and cell proliferation. In this study, we investigated the regulation of BOP1 by PDGF-C and its role in modulating cell proliferation. We found that BOP1 was downregulated at both mRNA and protein levels in cells treated with PDGF-C-containing conditioned medium. On the other hand, BOP1 was upregulated in PDGF-C deficient mice. Furthermore, we confirmed that overexpression of BOP1 inhibited HEK293A cell proliferation, whereas knockdown of BOP1 promoted cell proliferation. The mitogenic effect of PDGF-C could be attenuated by downregulation of BOP1. Our results demonstrate a clear PDGF-C-BOP1 signaling that modulates cell proliferation.
Collapse
Affiliation(s)
- Jiahui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenjie Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ruting Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wei Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhongshu Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| |
Collapse
|
5
|
Harold C. All these screens that we've done: how functional genetic screens have informed our understanding of ribosome biogenesis. Biosci Rep 2023; 43:BSR20230631. [PMID: 37335083 PMCID: PMC10329186 DOI: 10.1042/bsr20230631] [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: 04/09/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023] Open
Abstract
Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process is imperative to increase our understanding of basic biology, but also more critically, to provide novel therapeutic avenues for genetic and developmental diseases such as ribosomopathies and cancers which can arise when this process is impaired. In recent years, significant advances in technology have made identifying and characterizing novel human regulators of ribosome biogenesis via high-content, high-throughput screens. Additionally, screening platforms have been used to discover novel therapeutics for cancer. These screens have uncovered a wealth of knowledge regarding novel proteins involved in human ribosome biogenesis, from the regulation of the transcription of the ribosomal RNA to global protein synthesis. Specifically, comparing the discovered proteins in these screens showed interesting connections between large ribosomal subunit (LSU) maturation factors and earlier steps in ribosome biogenesis, as well as overall nucleolar integrity. In this review, a discussion of the current standing of screens for human ribosome biogenesis factors through the lens of comparing the datasets and discussing the biological implications of the areas of overlap will be combined with a look toward other technologies and how they can be adapted to discover more factors involved in ribosome synthesis, and answer other outstanding questions in the field.
Collapse
Affiliation(s)
- Cecelia M. Harold
- Department of Genetics, Yale School of Medicine, New Haven, CT, U.S.A
| |
Collapse
|
6
|
Ma N, Hua R, Yang Y, Liu ZC, Pan J, Yu BY, Sun YF, Xie D, Wang Y, Li ZG. PES1 reduces CD8 + T cell infiltration and immunotherapy sensitivity via interrupting ILF3-IL15 complex in esophageal squamous cell carcinoma. J Biomed Sci 2023; 30:20. [PMID: 36959575 PMCID: PMC10037800 DOI: 10.1186/s12929-023-00912-8] [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: 12/19/2022] [Accepted: 03/11/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Although immune checkpoint blockade (ICB) therapy has brought survival benefits to patients with specific cancer types, most of cancer patients remain refractory to the ICB therapy, which is largely attributed to the immunosuppressive tumor microenvironment. Thereby, it is urgent to profile key molecules and signal pathways responsible for modification of tumor microenvironment. METHODS Multiple databases of esophageal squamous cell carcinoma (ESCC) were integratively analyzed to screen candidate genes responsible for infiltration of CD8+ T cells. Expression of pescadillo ribosomal biogenesis factor 1 (PES1) in clinical ESCC samples was examined by qRT-PCR, western blotting, and immunohistochemistry. The mechanisms of PES1 were investigated via RNA sequencing and mass spectrometry followed by immunoprecipitation and proximity ligation assay. The clinical and therapeutic significance of PES1 in ESCC was comprehensively investigated using ESCC cells and mouse model. RESULTS PES1 was significantly upregulated and correlated with poor prognosis in ESCC patients. PES1 knockdown decreased ESCC cell growth in vitro and in vivo and enhanced the efficacy of ICB therapy in mouse model, which was established through subcutaneous inoculation with ESCC cells. Analyses on RNA sequencing and mass spectrometry suggested that PES1 expression was negatively correlated with IL15 and ILF3 was one of the PES1-associated proteins. It has been known that ILF3 interacts with and stabilizes IL15 mRNA to increase IL15 protein level. Our data further indicated that PES1 interfered with the interaction between ILF3 and IL15 mRNA and impaired ILF3-mediated stabilization of IL15 mRNA, which eventually reduced the protein level of IL15. Interestingly, the inhibitory effect of ICB therapy boosted by PES1 knockdown dramatically antagonized by knockdown of IL15, which suppressed the tumor-infiltrated CD8+ T cells in ESCC. Finally, we confirmed the relationships among PES1, IL15, and CD8+ T cell infiltration in 10 locally advanced ESCC patients receiving ICB neoadjuvant therapy and demonstrated that ICB therapy would be more effective in those with low expression of PES1. CONCLUSIONS Altogether, our findings herein provided novel insights on biological function and clinical significance of PES1 and suggested that high expression of PES1 could suppress ILF3-IL15 axis-mediated immunosurveillance and promote resistance to ICB through restraining tumor-infiltrated CD8+ T cells.
Collapse
Affiliation(s)
- Ning Ma
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Hua
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Chao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Pan
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo-Yao Yu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Feng Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yan Wang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
| | - Zhi-Gang Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
7
|
Zhang P, Tan P, Zhang L, Zhu W, Chen R, Wang L, Xu D. A Comparative Study on Growth Performance, Body Composition, and Liver Tissue Metabolism Rearing on Soybean Lecithin-Enriched Artemia Nauplii and Microdiet in Rock Bream ( Oplegnathus fasciatus) Larvae. AQUACULTURE NUTRITION 2023; 2023:5545898. [PMID: 36967811 PMCID: PMC10036177 DOI: 10.1155/2023/5545898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
This study is aimed at establishing optimal soybean lecithin (SL) enrichment protocols in Artemia nauplii and at comparing the growth performance, body composition, and liver tissue metabolism in rock bream (Oplegnathus fasciatus) larvae reared on SL-enriched Artemia nauplii or SL-enriched microdiet (MD). The enrichment protocol experiment results indicated 12 h enrichment, and 10 g SL/m3 seawater could obtain desirable results. Rock bream larvae (25 days posthatching (dph)) were fed Artemia nauplii or MD for 30 days with three replicates. At stage 1 (larval 25-40 dph), significantly higher growth performance was observed in larvae fed the live prey (P < 0.05). Conversely, at stage 2 (41-55 dph), feeding with MD significantly increased larval standard length, and specific growth rate compared with those of larvae fed live prey. Larvae fed a MD showed decreased lipolysis-related lipase activity as well as decreased amino acid catabolism-related alanine aminotransferase and aspartate aminotransferase enzyme activities in liver tissue. RNA sequencing revealed that feeding with the MD primarily increased the expression of lipogenesis-related genes and protein translation-related gene expression in the liver tissue. Notably, feeding with MD significantly increased ribosome biogenesis-related genes as well as mitochondria synthesis-related gene expression, indicating a high protein anabolism rate and high energy production in liver tissue. In conclusion, 10 g SL/m3 seawater and 12 h could effectively enrich SL in Artemia nauplii. Retard weaning onto MD led to lower growth performance, which was likely due to the diversity of lipid and protein metabolism.
Collapse
Affiliation(s)
- Pian Zhang
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Peng Tan
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lei Zhang
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Wenliang Zhu
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ruiyi Chen
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ligai Wang
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Dongdong Xu
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Marine and Fisheries Research Institute, Zhejiang Ocean University, Zhoushan 316022, China
| |
Collapse
|
8
|
Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
Collapse
Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
9
|
Eid RA, Eldeen MA, Soltan MA, Al-Shraim M, Aldehri M, Alqahtani LS, Alsharif G, Albogami S, Jafri I, Fayad E, Park MN, Bibi S, Behairy MY, Kim B, Zaki MSA. Integrative analysis of WDR12 as a potential prognostic and immunological biomarker in multiple human tumors. Front Genet 2023; 13:1008502. [PMID: 36726716 PMCID: PMC9885372 DOI: 10.3389/fgene.2022.1008502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Mammalian WD-repeat protein 12 (WDR12), a family member of proteins containing repeats of tryptophan-aspartic acid (WD), is a potential homolog of yeast Ytm1p and consists of seven repeats of WD. Aim of the study: This study aims to investigate the potential oncogenic effects of WDR12 in various human malignancies throughout a pan-cancer analysis that has been carried out to examine the various patterns in which this gene is expressed and behaves in tumor tissues. Methods: Herein, we used The Cancer Genome Atlas (TCGA) and various computational tools to explore expression profiles, prognostic relevance, genetic mutations, immune cell infiltration, as well as the functional characteristics of WDR12 in multiple human cancers. Results: We found that WDR12 was inconsistently expressed in various cancers and that variations in WDR12 expression predicted survival consequences for cancer patients. Furthermore, we observed a significant correlation between WDR12 gene mutation levels and the prognosis of some tumors. Furthermore, significant correlations were found between WDR12 expression patterns and cancer-associated fibroblast (CAF) infiltration, myeloid-derived suppressor cells (MDSCs), tumor mutation burden, microsatellite instability and immunoregulators. Ultimately, pathway enrichment analysis revealed that WDR12-related pathways are involved in carcinogenesis. Conclusions: The findings of our study are stisfactory, demonstrating that WDR12 could serve as a promising reliable prognostic biomarker, as well as a therapeutic target for novel cancer therapeutic approaches.
Collapse
Affiliation(s)
- Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig, Egypt,*Correspondence: Muhammad Alaa Eldeen, ; Bonglee Kim,
| | - Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
| | - Mubarak Al-Shraim
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Majed Aldehri
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Leena S. Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ghadi Alsharif
- College of Clinical Laboratory Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Moon Nyeo Park
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, China
| | - Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea,*Correspondence: Muhammad Alaa Eldeen, ; Bonglee Kim,
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia,Department of Histology and Cell Biology, College of Medicine, Zagazig University, Zagazig, Egypt
| |
Collapse
|
10
|
Demini L, Kervarrec C, Guillot L, Com E, Lavigne R, Kernanec PY, Primig M, Pineau C, Petit FG, Jamin SP. Inactivation of Exosc10 in the oocyte impairs oocyte development and maturation, leading to a depletion of the ovarian reserve in mice. Int J Biol Sci 2023; 19:1080-1093. [PMID: 36923944 PMCID: PMC10008699 DOI: 10.7150/ijbs.72889] [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: 03/15/2022] [Accepted: 01/01/2023] [Indexed: 02/05/2023] Open
Abstract
EXOSC10 is a catalytic subunit of the nuclear RNA exosome, and possesses a 3'-5' exoribonuclease activity. The enzyme processes and degrades different classes of RNAs. To delineate the role of EXOSC10 during oocyte growth, specific Exosc10 inactivation was performed in oocytes from the primordial follicle stage onward using the Gdf9-iCre; Exosc10 f/- mouse model (Exosc10 cKO(Gdf9)). Exosc10 cKO(Gdf9) female mice are infertile. The onset of puberty and the estrus cycle in mutants are initially normal and ovaries contain all follicle classes. By the age of eight weeks, vaginal smears reveal irregular estrus cycles and mutant ovaries are completely depleted of follicles. Mutant oocytes retrieved from the oviduct are degenerated, and occasionally show an enlarged polar body, which may reflect a defective first meiotic division. Under fertilization conditions, the mutant oocytes do not enter into an embryonic development process. Furthermore, we conducted a comparative proteome analysis of wild type and Exosc10 knockout mouse ovaries, and identified EXOSC10-dependent proteins involved in many biological processes, such as meiotic cell cycle progression and oocyte maturation. Our results unambiguously demonstrate an essential role for EXOSC10 in oogenesis and may serve as a model for primary ovarian insufficiency in humans. Data are available via ProteomeXchange with identifier PXD039417.
Collapse
Affiliation(s)
- Leïla Demini
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Christine Kervarrec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Laëtitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US 018, Protim core facility, F-35000 Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US 018, Protim core facility, F-35000 Rennes, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US 018, Protim core facility, F-35000 Rennes, France
| | - Pierre-Yves Kernanec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US 018, Protim core facility, F-35000 Rennes, France
| | - Fabrice G. Petit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- ✉ Corresponding authors: Contributed equally to this work. E-mail: ;
| | - Soazik P. Jamin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
- ✉ Corresponding authors: Contributed equally to this work. E-mail: ;
| |
Collapse
|
11
|
Kriachkov V, Ormsby AR, Kusnadi EP, McWilliam HE, Mintern JD, Amarasinghe SL, Ritchie ME, Furic L, Hatters DM. Arginine-rich C9ORF72 ALS proteins stall ribosomes in a manner distinct from a canonical ribosome-associated quality control substrate. J Biol Chem 2022; 299:102774. [PMID: 36481270 PMCID: PMC9830226 DOI: 10.1016/j.jbc.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Hexanucleotide expansion mutations in C9ORF72 are a frequent cause of amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPRs), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here, we explored the molecular features of DPR-induced stalling and examined whether known mechanisms such as ribosome quality control (RQC) regulate translation elongation on sequences that encode arginine-rich DPRs. We demonstrate that arginine-rich DPRs lead to stalling in a length-dependent manner, with lengths longer than 40 repeats invoking severe translation arrest. Mutational screening of 40×Gly-Xxx DPRs shows that stalling is most pronounced when Xxx is a charged amino acid (Arg, Lys, Glu, or Asp). Through a genome-wide knockout screen, we find that genes regulating stalling on polyadenosine mRNA coding for poly-Lys, a canonical RQC substrate, act differently in the case of arginine-rich DPRs. Indeed, these findings point to a limited scope for natural regulatory responses to resolve the arginine-rich DPR stalls, even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate arginine-rich DPR-mediated stalled ribosomes as a source of stress and toxicity and may be a crucial component in pathomechanisms.
Collapse
Affiliation(s)
- Viacheslav Kriachkov
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Angelique R. Ormsby
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eric P. Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Hamish E.G. McWilliam
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,Department of Microbiology and Immunology, Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine D. Mintern
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia,Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, Victoria, Australia
| | - Danny M. Hatters
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,For correspondence: Danny M. Hatters
| |
Collapse
|
12
|
McCool MA, Buhagiar AF, Bryant CJ, Ogawa LM, Abriola L, Surovtseva YV, Baserga SJ. Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing. RNA (NEW YORK, N.Y.) 2022; 29:rna.079149.122. [PMID: 36323459 PMCID: PMC9808572 DOI: 10.1261/rna.079149.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
In eukaryotes, the nucleolus is the site of ribosome biosynthesis, an essential process in all cells. While human ribosome assembly is largely evolutionarily conserved, many of the regulatory details underlying its control and function have not yet been well-defined. The nucleolar protein RSL24D1 was originally identified as a factor important for 60S ribosomal subunit biogenesis. In addition, the PeBoW (BOP1-PES1-WDR12) complex has been well-defined as required for pre-28S rRNA processing and cell proliferation. In this study, we show that RSL24D1 depletion impairs both pre-ribosomal RNA (pre-rRNA) transcription and mature 28S rRNA production, leading to decreased protein synthesis and p53 stabilization in human cells. Surprisingly, each of the PeBoW complex members is also required for pre-rRNA transcription. We demonstrate that RSL24D1 and WDR12 co-immunoprecipitate with the RNA polymerase I subunit, RPA194, and regulate its steady state levels. These results uncover the dual role of RSL24D1 and the PeBoW complex in multiple steps of ribosome biogenesis, and provide evidence implicating large ribosomal subunit biogenesis factors in pre-rRNA transcription control.
Collapse
|
13
|
Siddaway R, Milos S, Coyaud É, Yun HY, Morcos SM, Pajovic S, Campos EI, Raught B, Hawkins C. The in vivo Interaction Landscape of Histones H3.1 and H3.3. Mol Cell Proteomics 2022; 21:100411. [PMID: 36089195 PMCID: PMC9540345 DOI: 10.1016/j.mcpro.2022.100411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/10/2022] [Accepted: 09/06/2022] [Indexed: 01/18/2023] Open
Abstract
Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative interactomes for the replication-coupled (H3.1) and replication-independent (H3.3) histone H3 variants based on BioID proximity labeling, which allows interactions in intact, living cells to be detected. Along with a significant proportion of previously reported interactions detected by affinity purification followed by mass spectrometry, three quarters of the 608 histone-associated proteins that we identified are new, uncharacterized histone associations. The data reveal important biological nuances not captured by traditional biochemical means. For example, we found that the chromatin assembly factor-1 histone chaperone not only deposits the replication-coupled H3.1 histone variant during S-phase but also associates with H3.3 throughout the cell cycle in vivo. We also identified other variant-specific associations, such as with transcription factors, chromatin regulators, and with the mitotic machinery. Our proximity-based analysis is thus a rich resource that extends the H3 interactome and reveals new sets of variant-specific associations.
Collapse
Affiliation(s)
- Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Milos
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Université de Lille, Lille, France
| | - Hwa Young Yun
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shahir M. Morcos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sanja Pajovic
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric I. Campos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,For correspondence: Cynthia Hawkins
| |
Collapse
|
14
|
Functions of block of proliferation 1 during anterior development in Xenopus laevis. PLoS One 2022; 17:e0273507. [PMID: 36007075 PMCID: PMC9409556 DOI: 10.1371/journal.pone.0273507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
Block of proliferation 1 (Bop1) is a nucleolar protein known to be necessary for the assembly of the 60S subunit of ribosomes. Here, we show a specific bop1 expression in the developing anterior tissue of the South African clawed frog Xenopus laevis. Morpholino oligonucleotide-mediated knockdown approaches demonstrated that Bop1 is required for proper development of the cranial cartilage, brain, and the eyes. Furthermore, we show that bop1 knockdown leads to impaired retinal lamination with disorganized cell layers. Expression of neural crest-, brain-, and eye-specific marker genes was disturbed. Apoptotic and proliferative processes, which are known to be affected during ribosomal biogenesis defects, are not hindered upon bop1 knockdown. Because early Xenopus embryos contain a large store of maternal ribosomes, we considered if Bop1 might have a role independent of de novo ribosomal biogenesis. At early embryonic stages, pax6 expression was strongly reduced in bop1 morphants and synergy experiments indicate a common signaling pathway of the two molecules, Bop1 and Pax6. Our studies imply a novel function of Bop1 independent of ribosomal biogenesis.
Collapse
|
15
|
Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Mol Cell 2022; 82:2900-2911.e7. [PMID: 35905735 PMCID: PMC9662605 DOI: 10.1016/j.molcel.2022.06.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/08/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022]
Abstract
Proteogenomic identification of translated small open reading frames has revealed thousands of previously unannotated, largely uncharacterized microproteins, or polypeptides of less than 100 amino acids, and alternative proteins (alt-proteins) that are co-encoded with canonical proteins and are often larger. The subcellular localizations of microproteins and alt-proteins are generally unknown but can have significant implications for their functions. Proximity biotinylation is an attractive approach to define the protein composition of subcellular compartments in cells and in animals. Here, we developed a high-throughput technology to map unannotated microproteins and alt-proteins to subcellular localizations by proximity biotinylation with TurboID (MicroID). More than 150 microproteins and alt-proteins are associated with subnuclear organelles. One alt-protein, alt-LAMA3, localizes to the nucleolus and functions in pre-rRNA transcription. We applied MicroID in a mouse model, validating expression of a conserved nuclear microprotein, and establishing MicroID for discovery of microproteins and alt-proteins in vivo.
Collapse
Affiliation(s)
- Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Shu-Jian Zheng
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Ken H Loh
- Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Amber F Buhagiar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
| |
Collapse
|
16
|
Lavering ED, Petros IN, Weeks DL. Component analysis of nucleolar protein compartments using Xenopus laevis oocytes. Dev Growth Differ 2022; 64:306-317. [PMID: 35607824 PMCID: PMC9474603 DOI: 10.1111/dgd.12794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022]
Abstract
The nucleolus is a multi‐compartment, non‐membrane‐bound organelle within the nucleus. Nucleolar assembly is influenced by proteins capable of phase separation. Xenopus laevis oocytes contain hundreds of large nucleoli that provide experimental access for nucleoli that is unavailable in other systems. Here we detail methods to streamline the in vivo analysis of the compartmentalization of nucleolar proteins that are suspected of phase separation. The nucleolus is the main hub of ribosome biogenesis and here we present data supporting the division of proteins into nucleolar domains based on their function in ribosome biogenesis. We also describe the use of vital dyes such as Hoechst 33342 and Thioflavin T in nucleolar staining. Additionally, we quantify nucleolar morphology changes induced by heat shock and actinomycin D treatments. We suggest these approaches will be valuable in a variety of studies that seek to better understand the nucleolus, particularly those regarding phase separation. These approaches may also be instructive for other studies on phase separation, especially in the nucleus.
Collapse
Affiliation(s)
- Emily D Lavering
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Irini N Petros
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Daniel L Weeks
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
17
|
Okamoto T, Natsume Y, Doi M, Nosato H, Iwaki T, Yamanaka H, Yamamoto M, Kawachi H, Noda T, Nagayama S, Sakanashi H, Yao R. Integration of human inspection and AI-based morphological typing of PDOs reveals inter-patient heterogeneity of colorectal cancer. Cancer Sci 2022; 113:2693-2703. [PMID: 35585758 PMCID: PMC9357621 DOI: 10.1111/cas.15396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogenous disease, and patients have differences in therapeutic response. However, the mechanisms underlying inter-patient heterogeneity in the response to chemotherapeutic agents remain to be elucidated, and molecular tumor characteristics are required to select patients for specific therapies. Patient-derived organoids (PDOs) established from CRCs recapitulate various biological characteristics of tumor tissues, including cellular heterogeneity and the response to chemotherapy. PDOs established from CRCs exhibit various morphologies, but there are no criteria for defining these morphologies, which hampers the analysis of their biological significance. Here, we developed an artificial intelligence (AI)-based classifier to categorize PDOs based on microscopic images according to their similarity in appearance and classified tubular adenocarcinoma-derived PDOs into six types. Transcriptome analysis identified differential expression of genes related to cell adhesion in some of the morphological types. Genes involved in ribosome biogenesis were also differentially expressed and were most highly expressed in morphological types exhibiting CRC stem cell properties. We identified an RNA polymerase I inhibitor, CX-5641, to be an upstream regulator of these type-specific gene sets. Notably, PDO types with increased expression of genes involved in ribosome biogenesis were resistant to CX-5461 treatment. Taken together, these results uncover the biological significance of the morphology of PDOs and provide novel indicators by which to categorize CRCs. Therefore, the AI-based classifier is a useful tool to support PDO-based cancer research.
Collapse
Affiliation(s)
- Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hirokazu Nosato
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Toshiyuki Iwaki
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Mayuko Yamamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute; Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Director's office, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Hidenori Sakanashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| |
Collapse
|
18
|
Jiaze Y, Sinan H, Minjie Y, Yongjie Z, Nan D, Liangwen W, Wen Z, Jianjun L, Zhiping Y. Rcl1 suppresses tumor progression of hepatocellular carcinoma: a comprehensive analysis of bioinformatics and in vitro experiments. Cancer Cell Int 2022; 22:114. [PMID: 35264160 PMCID: PMC8905783 DOI: 10.1186/s12935-022-02533-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background RNA 3’-terminal phosphate cyclase-like protein (Rcl1) is involved in pre-rRNA processing, but its implication in cancers remains unclear. Methods RCL1 expressions in 21 malignancies was examinated through GEPIA website portal. Clinical implication data related to RCL1 level in Hepatocellular Carcinoma (HCC) samples were downloaded through TCGA, ICGC, GEO databases. Survival analysis and gene function enrichment analyses were performed through R software. The correlation between RCL1 expression and tumor immune infiltration was assessed via the TIMER2.0 database. The effects of Rcl1 overexpression or knockdown on cell growth and metastasis was evaluated by CCK8, transwell, and cell cycle assays. Results RCL1 expression is commonly down-regulated in HCC. The lower expression of RCL1 is associated with higher tumor stage, higher AFP level, vascular invasion, and poor prognosis. RCL1 expression has a significant correlation with immune cells infiltration in HCC, especially myeloid-derived suppressor cell (MDSC). Moreover, it was further identified that Rcl1 expression was reduced in HCC cell lines and negatively correlated with invasion of HCC cell lines. Immunofluorescence (IF) analysis revealed that the level of Rcl1 expression in the cytoplasm of HCC cells is significantly lower than that in the cytoplasm of L-02 cell. Moreover, both gain- and loss-of-function studies demonstrated that Rcl1 inhibited the growth and metastasis of HCC cells and regulated cell cycle progression in vitro. Conclusions Rcl1 may serve as a novel tumor suppressor in HCC, and its biological effect needs further study. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02533-x. Rcl1 mRNA expression is down-regulated within HCC tissues and associated with poor prognosis and disease progression. Anti-cancer effects of Rcl1 on HCC were confirmed in vitro. Rcl1 may be a potential tumor suppressor in HCC.
Collapse
Affiliation(s)
- Yu Jiaze
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Hou Sinan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Yang Minjie
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Zhou Yongjie
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Du Nan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Wang Liangwen
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Zhang Wen
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China. .,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China. .,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China.
| | - Luo Jianjun
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China. .,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China. .,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China.
| | - Yan Zhiping
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China. .,National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China. .,Shanghai Institution of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China.
| |
Collapse
|
19
|
Li YZ, Zhang C, Pei JP, Zhang WC, Zhang CD, Dai DQ. The functional role of Pescadillo ribosomal biogenesis factor 1 in cancer. J Cancer 2022; 13:268-277. [PMID: 34976188 PMCID: PMC8692700 DOI: 10.7150/jca.58982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Tumors are neogrowths formed by the growth of normal cells or tissues through complex mechanisms under the influence of many factors. The occurrence and development of tumors are affected by many factors. Pescadillo ribosomal biogenesis factor 1 (PES1) has been identified as a cancer-related gene. The study of these genes may open up new avenues for early diagnosis, treatment and prognosis of tumors. As a nucleolar protein and part of the Pes1/Bop1/WDR12 (PeBoW) complex, PES1 is involved in ribosome biogenesis and DNA replication. Many studies have shown that high expression of PES1 is often closely related to the occurrence, proliferation, invasion, metastasis, prognosis and sensitivity to chemotherapeutics of various human malignant tumors through a series of molecular mechanisms and signaling pathways. The molecules that regulate the expression of PES1 include microRNA (miRNA), circular RNA (circRNA), c-Jun, bromodomain-containing protein 4 (BRD4) and nucleolar phosphoprotein B23. However, the detailed pathogenic mechanisms of PES1 overexpression in human malignancies remains unclear. This article summarizes the role of PES1 in the carcinogenesis, prognosis and treatment of multiple tumors, and introduces the molecular mechanisms and signal transduction pathways related to PES1.
Collapse
Affiliation(s)
- Yong-Zhi Li
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Jun-Peng Pei
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Wan-Chuan Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Chun-Dong Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| |
Collapse
|
20
|
Nucleolar Stress Functions Upstream to Stimulate Expression of Autophagy Regulators. Cancers (Basel) 2021; 13:cancers13246220. [PMID: 34944838 PMCID: PMC8699128 DOI: 10.3390/cancers13246220] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/04/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Ribosome biogenesis takes place in nucleoli and is essential for cellular survival and proliferation. In case this function is disturbed, either due to defects in regulatory factors or the structure of the nucleolus, nucleolar stress is provoked. Consequently, cells classically undergo cell cycle arrest and apoptosis. Induction of nucleolar stress is known to eliminate cells in the background of cancer therapy and paradoxically is also associated with increased cancer formation. Recent reports demonstrated that nucleolar stress triggers autophagy, a conserved pathway responsible for recycling endogenous material. Thus, it was suggested that autophagy might serve as compensatory pro-survival response. However, the mechanisms how nucleolar stress triggers autophagy are poorly understood. Here we show that induction of nucleolar stress by depleting ribosome biogenesis factors or by interfering with RNA polymerase I function, triggers expression of various key autophagy regulators. Moreover, we demonstrate that RNA pol I inhibition by CX-5461 correlates with increased ATG7 and ATGL16L1 levels, essential factors for generating autophagosomes, and stimulates autophagic flux. Abstract Ribosome biogenesis is essential for protein synthesis, cell growth and survival. The process takes places in nucleoli and is orchestrated by various proteins, among them RNA polymerases I–III as well as ribosome biogenesis factors. Perturbation of ribosome biogenesis activates the nucleolar stress response, which classically triggers cell cycle arrest and apoptosis. Nucleolar stress is utilized in modern anti-cancer therapies, however, also contributes to the development of various pathologies, including cancer. Growing evidence suggests that nucleolar stress stimulates compensatory cascades, for instance bulk autophagy. However, underlying mechanisms are poorly understood. Here we demonstrate that induction of nucleolar stress activates expression of key autophagic regulators such as ATG7 and ATG16L1, essential for generation of autophagosomes. We show that knockdown of the ribosomopathy factor SBDS, or of key ribosome biogenesis factors (PPAN, NPM, PES1) is associated with enhanced levels of ATG7 in cancer cells. The same holds true when interfering with RNA polymerase I function by either pharmacological inhibition (CX-5461) or depletion of the transcription factor UBF-1. Moreover, we demonstrate that RNA pol I inhibition by CX-5461 stimulates autophagic flux. Together, our data establish that nucleolar stress affects transcriptional regulation of autophagy. Given the contribution of both axes in propagation or cure of cancer, our data uncover a connection that might be targeted in future.
Collapse
|
21
|
Mi L, Qi Q, Ran H, Chen L, Li D, Xiao D, Wu J, Cai Y, Zhang S, Li Y, Li B, Xie J, Huang H, Li T, Zhou T, Li A, Qi J, Li F, Man J. Suppression of Ribosome Biogenesis by Targeting WD Repeat Domain 12 (WDR12) Inhibits Glioma Stem-Like Cell Growth. Front Oncol 2021; 11:751792. [PMID: 34868955 PMCID: PMC8633585 DOI: 10.3389/fonc.2021.751792] [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: 08/02/2021] [Accepted: 10/26/2021] [Indexed: 01/05/2023] Open
Abstract
Glioma stem-like cells (GSCs) are a subset of tumor cells that initiate malignant growth and promote the therapeutic resistance of glioblastoma, the most lethal primary brain tumor. Ribosome biogenesis is an essential cellular process to maintain cell growth, but its regulatory mechanism in GSCs remains largely unknown. Here, we show that WD repeat domain 12 (WDR12), a component of the Pes1-Bop1 complex (PeBoW), is required for ribosome biogenesis in GSCs. WDR12 is preferentially expressed in GSCs compared to non-stem tumor cells and normal brain cells. High levels of WDR12 are associated with glioblastoma progression and poor prognosis. Silencing WDR12 results in the degradation of PeBoW complex components and prevents the maturation of 28S rRNA, thereby inhibiting ribosome biogenesis in GSCs. Subsequently, WDR12 depletion compromises GSC proliferation, inhibits GSC-derived orthotopic tumor growth, and extends animal survival. Together, our results suggest that WDR12 is crucial for ribosome biogenesis in GSCs, and is thus a potential target for GSC-directed therapy of glioblastoma.
Collapse
Affiliation(s)
- Lanjuan Mi
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Qinghui Qi
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Haowen Ran
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Lishu Chen
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Da Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Dake Xiao
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jiaqi Wu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yan Cai
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Songyang Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yuanyuan Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Bohan Li
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Jiong Xie
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Haohao Huang
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, China
| | - Tao Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Tao Zhou
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Ailing Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Ji Qi
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Fangye Li
- Department of Neurosurgery, First Medical Center of PLA General Hospital, Beijing, China
| | - Jianghong Man
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| |
Collapse
|
22
|
Chen J, Zhang J, Zhang Z. Upregulation of GTPBP4 Promotes the Proliferation of Liver Cancer Cells. JOURNAL OF ONCOLOGY 2021; 2021:1049104. [PMID: 34712323 PMCID: PMC8548153 DOI: 10.1155/2021/1049104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023]
Abstract
RESULTS The GTPBP4 has upregulated expression in liver cancer patients (P < 0.01), but there was no difference in its expression in patients with different clinicopathological stages. The expression of GTPBP4 increased with the increase of cancer metastasis in lymph nodes (P < 0.01). Liver cancer patients with upregulated expression of GTPBP4 showed a shorter overall survival rate (P=0.02). GTPBP4 is closely related to genes such as NIFK, WDR12, and RPF2, and these genes are involved in life processes such as GTP binding and rRNA processing. The upregulated expression of GTPBP4 promotes the proliferation of liver cancer cells and promotes the growth of tumors in mice, while the downregulated expression of GTPBP4 inhibits the proliferation of liver cancer cells and inhibits the growth of tumors in mice. CONCLUSION The expression of GTPBP4 is upregulated in liver cancer patients and affects the overall survival rate of patients. The upregulated expression of GTPBP4 promotes the proliferation of liver cancer cells and the growth of tumors.
Collapse
Affiliation(s)
- Jia Chen
- Cancer Research Institute of Hengyang Medical College, University of South China, Hengyang, China
- Physical Examination Center, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jie Zhang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China, Hengyang, China
| |
Collapse
|
23
|
BOP1 Used as a Novel Prognostic Marker and Correlated with Tumor Microenvironment in Pan-Cancer. JOURNAL OF ONCOLOGY 2021; 2021:3603030. [PMID: 34603446 PMCID: PMC8481050 DOI: 10.1155/2021/3603030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023]
Abstract
Previous studies have indicated the important role of block of proliferation 1 (BOP1) in the progression of several malignant tumors; no comprehensive pan-cancer analysis of BOP1 has been performed. Here, we aim to systematically identify the expression, prognostic value, and potential immunological functions of BOP1 in 33 malignancies. We obtained the gene expression data and clinical information from multiple public databases to assess the expression level and prognostic value of BOP1 in 33 cancers. We also analyzed the relationship between BOP1 expression and DNA methylation, tumor microenvironment (TME), microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Moreover, we conducted gene set enrichment analysis (GSEA) to investigate the biological function and signal transduction pathways of BOP1 in different types of tumors. Finally, we validated the expression of BOP1 in lung cancer cell line and detected the influence of BOP1 on lung cancer cell migration and the expression of epithelial-mesenchymal transition- (EMT-) related genes. Collectively, our findings elucidated that BOP1 has the potential to be a promising molecular prognostic biomarker for predicting poor survival in various malignant tumors, as well as a cancer-promoting gene involved in tumorigenesis and tumor immunity.
Collapse
|
24
|
Ianniello Z, Sorci M, Ceci Ginistrelli L, Iaiza A, Marchioni M, Tito C, Capuano E, Masciarelli S, Ottone T, Attrotto C, Rizzo M, Franceschini L, de Pretis S, Voso MT, Pelizzola M, Fazi F, Fatica A. New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia. Cell Death Dis 2021; 12:870. [PMID: 34561421 PMCID: PMC8463696 DOI: 10.1038/s41419-021-04169-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the presence of tyrosine kinase BCR-ABL1 fusion protein, which deregulate transcription and mRNA translation. Tyrosine kinase inhibitors (TKIs) are the first-choice treatment. However, resistance to TKIs remains a challenge to cure CML patients. Here, we reveal that the m6A methyltransferase complex METTL3/METTL14 is upregulated in CML patients and that is required for proliferation of primary CML cells and CML cell lines sensitive and resistant to the TKI imatinib. We demonstrate that depletion of METTL3 strongly impairs global translation efficiency. In particular, our data show that METTL3 is crucial for the expression of genes involved in ribosome biogenesis and translation. Specifically, we found that METTL3 directly regulates the level of PES1 protein identified as an oncogene in several tumors. We propose a model in which nuclear METTL3/METTL14 methyltransferase complex modified nascent transcripts whose translation is enhanced by cytoplasmic localization of METTL3, independently from its catalytic activity. In conclusion, our results point to METTL3 as a novel relevant oncogene in CML and as a promising therapeutic target for TKI resistant CML.
Collapse
Affiliation(s)
- Zaira Ianniello
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Melissa Sorci
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Lavinia Ceci Ginistrelli
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Alessia Iaiza
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Marcella Marchioni
- Institute of Biology, Molecular Medicine and Nanobiotechnology, CNR, Sapienza University of Rome, Rome, Italy
| | - Claudia Tito
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Ernestina Capuano
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy.,Histology and Embryology Section, Department of Life Science and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia, Laboratorio di Neuro-Oncoematologia, Rome, Italy
| | - Cristina Attrotto
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Stefano de Pretis
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia, Laboratorio di Neuro-Oncoematologia, Rome, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy. .,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy.
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
| |
Collapse
|
25
|
Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far. Noncoding RNA 2021; 7:ncrna7030042. [PMID: 34287370 PMCID: PMC8293466 DOI: 10.3390/ncrna7030042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 12/26/2022] Open
Abstract
Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.
Collapse
|
26
|
Li S, Wu H, Huang X, Jian Y, Kong L, Xu H, Ouyang Y, Chen X, Wu G, Yu L, Wang X. BOP1 confers chemoresistance of triple-negative breast cancer by promoting CBP-mediated β-catenin acetylation. J Pathol 2021; 254:265-278. [PMID: 33797754 DOI: 10.1002/path.5676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/03/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Chemoresistance is a major obstacle to the treatment of triple-negative breast cancer (TNBC), which has a poor prognosis. Increasing evidence has demonstrated the essential role of cancer stem cells (CSCs) in the process of TNBC chemoresistance. However, the underlying mechanism remains unclear. In the present study, we report that block of proliferation 1 (BOP1) serves as a key regulator of chemoresistance in TNBC. BOP1 expression was significantly upregulated in chemoresistant TNBC tissues, and high expression of BOP1 correlated with shorter overall survival and relapse-free survival in patients with TNBC. BOP1 overexpression promoted, while BOP1 downregulation inhibited the drug resistance and CSC-like phenotype of TNBC cells in vitro and in vivo. Moreover, BOP1 activated Wnt/β-catenin signaling by increasing the recruitment of cyclic AMP response element-binding protein (CBP) to β-catenin, enhancing CBP-mediated acetylation of β-catenin, and increasing the transcription of downstream stemness-related genes CD133 and ALDH1A1. Notably, treating with the β-catenin/CBP inhibitor PRI-724 induced an enhancement of chemotherapeutic response of paclitaxel in BOP1-overexpressing TNBC cells. These findings indicate that BOP1 is involved in chemoresistance development and might serve as a prognostic marker and therapeutic target in TNBC. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Siqi Li
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Haoming Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | | | - Yunting Jian
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Lingzhi Kong
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Hongyi Xu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Ouyang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Xiangfu Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Geyan Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Liang Yu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Xi Wang
- Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| |
Collapse
|
27
|
Wang X, Zhang H, Sapio R, Yang J, Wong J, Zhang X, Guo JY, Pine S, Van Remmen H, Li H, White E, Liu C, Kiledjian M, Pestov DG, Steven Zheng XF. SOD1 regulates ribosome biogenesis in KRAS mutant non-small cell lung cancer. Nat Commun 2021; 12:2259. [PMID: 33859191 PMCID: PMC8050259 DOI: 10.1038/s41467-021-22480-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
SOD1 is known as the major cytoplasmic superoxide dismutase and an anticancer target. However, the role of SOD1 in cancer is not fully understood. Herein we describe the generation of an inducible Sod1 knockout in KRAS-driven NSCLC mouse model. Sod1 knockout markedly reduces tumor burden in vivo and blocks growth of KRAS mutant NSCLC cells in vitro. Intriguingly, SOD1 is enriched in the nucleus and notably in the nucleolus of NSCLC cells. The nuclear and nucleolar, not cytoplasmic, form of SOD1 is essential for lung cancer cell proliferation. Moreover, SOD1 interacts with PeBoW complex and controls its assembly necessary for pre-60S ribosomal subunit maturation. Mechanistically, SOD1 regulates co-localization of PeBoW with and processing of pre-rRNA, and maturation of cytoplasmic 60S ribosomal subunits in KRAS mutant lung cancer cells. Collectively, our study unravels a nuclear SOD1 function essential for ribosome biogenesis and proliferation in KRAS-driven lung cancer.
Collapse
Affiliation(s)
- Xiaowen Wang
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Hong Zhang
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Russell Sapio
- Department of Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Jun Yang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Justin Wong
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Xin Zhang
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jessie Y Guo
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Sharon Pine
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Holly Van Remmen
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hong Li
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chen Liu
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Megerditch Kiledjian
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA.
| | - X F Steven Zheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| |
Collapse
|
28
|
Yang YP, Qin RH, Zhao JJ, Qin XY. BOP1 Silencing Suppresses Gastric Cancer Proliferation through p53 Modulation. Curr Med Sci 2021; 41:287-296. [PMID: 33877544 DOI: 10.1007/s11596-021-2345-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/26/2020] [Indexed: 10/21/2022]
Abstract
Block of proliferation 1 (BOP1) is a key protein involved in ribosome maturation and affects cancer progression. However, its role in gastric cancer (GC) remains unknown. This study aimed to explore the expression of BOP1 in GC and its potential mechanisms in regulating GC growth, and the relationship between BOP1 level in cancer tissues and survival was also analyzed. The expression of BOP1 was examined by immunohistochemistry (IHC) in a cohort containing 387 patients with primary GC. Cultured GC cells were treated by siRNA to knock down the BOP1 expression, and examined by CCK-8 assay and plate clone formation to assess cell proliferation in vitro. Apoptotic rate of cultured GC cells was detected by flow cytometry with double staining of AnnxinV/PI. The xenografted mouse model was used to assess GC cell proliferation in vivo. Western blot and IHC were also performed to detect the expression levels of BOP1, p53 and p21. Patients with higher level of BOP1 in cancer tissues had significantly poorer survival. BOP1 silencing significantly suppressed GC cell proliferation both in vitro and in vivo. It blocked cell cycle at G0/G1 phase and led to apoptosis of GC cells via upregulating p53 and p21. BOP1 silencing-induced suppression of cell proliferation was partly reversed by pifithrin-α (a p53 inhibitor). Our study demonstrated that BOP1 up-regulation may be a hallmark of GC and it may regulate proliferation of GC cells by activating p53. BOP1 might be considered a novel biomarker of GC proliferation, and could be a potential indicator of prognosis of GC patients. BOP1 might also be a potential target for the treatment of GC patients if further researched.
Collapse
Affiliation(s)
- Yu-Peng Yang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Rui-Huan Qin
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Jun-Jie Zhao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xin-Yu Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
29
|
BOP1 Knockdown Attenuates Neointimal Hyperplasia by Activating p53 and Inhibiting Nascent Protein Synthesis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5986260. [PMID: 33510838 PMCID: PMC7826231 DOI: 10.1155/2021/5986260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/18/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022]
Abstract
The rate of ribosome biogenesis plays a vital role in cell cycle progression and proliferation and is strongly connected with coronary restenosis and atherosclerosis. Blocking of proliferation 1 (BOP1) has been found as an evolutionarily conserved gene and a pivotal regulator of ribosome biogenesis and cell proliferation. However, little is known about its role in neointimal formation and its relationship with vascular smooth muscle cell (VSMC) proliferation and migration. The present study mainly explores the effect of BOP1 on VSMCs, the progression of neointimal hyperplasia, and the pathogenic mechanism. The expression of BOP1 was found to be significantly elevated during neointimal formation in human coronary samples and the rat balloon injury model. BOP1 knockdown inspires the nucleolus stress, which subsequently activates the p53-dependent stress response pathway, and inhibits the nascent protein synthesis, which subsequently inhibits the proliferation and migration of VSMCs. Knockdown ribosomal protein L11 (RPL11) by transfecting with siRNA or inhibiting p53 by pifithrin-α (PFT-α) partly reserved the biological effects induced by BOP1 knockdown. The present study revealed that BOP1 deletion attenuates VSMC proliferation and migration by activating the p53-dependent nucleolus stress response pathway and inhibits the synthesis of nascent proteins. BOP1 may become a novel biological target for neointimal hyperplasia.
Collapse
|
30
|
Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
Collapse
Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| |
Collapse
|
31
|
Chen B, Dragomir MP, Fabris L, Bayraktar R, Knutsen E, Liu X, Tang C, Li Y, Shimura T, Ivkovic TC, De los Santos MC, Anfossi S, Shimizu M, Shah MY, Ling H, Shen P, Multani AS, Pardini B, Burks JK, Katayama H, Reineke LC, Huo L, Syed M, Song S, Ferracin M, Oki E, Fromm B, Ivan C, Bhuvaneshwar K, Gusev Y, Mimori K, Menter D, Sen S, Matsuyama T, Uetake H, Vasilescu C, Kopetz S, Parker-Thornburg J, Taguchi A, Hanash SM, Girnita L, Slaby O, Goel A, Varani G, Gagea M, Li C, Ajani JA, Calin GA. The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. Gastroenterology 2020; 159:2146-2162.e33. [PMID: 32805281 PMCID: PMC7725986 DOI: 10.1053/j.gastro.2020.08.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.
Collapse
Affiliation(s)
- Baoqing Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China,Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Xu Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Yongfeng Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadanobu Shimura
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA
| | - Tina Catela Ivkovic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mireia Cruz De los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maitri Y. Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Asha S. Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,present address: Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,present address: Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Longfei Huo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muddassir Syed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Catalin Vasilescu
- Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,“Carol Davila University of Medicine and Pharmacy”, Bucharest, Romania
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Parker-Thornburg
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institute and Karolinska University Hospital, SE-171 647 Stockholm, Sweden
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA.,present address: Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston Texas 77030, USA
| | - Chunlai Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Lead Contact
| |
Collapse
|
32
|
Dannheisig DP, Bächle J, Tasic J, Keil M, Pfister AS. The Wnt/β-Catenin Pathway is Activated as a Novel Nucleolar Stress Response. J Mol Biol 2020; 433:166719. [PMID: 33221336 DOI: 10.1016/j.jmb.2020.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022]
Abstract
Ribosomes are mandatory for growth and survival. The complex process of ribosome biogenesis is located in nucleoli and requires action of the RNA polymerases I-III, together with a multitude of processing factors involved in rRNA cleavage and maturation. Impaired ribosome biogenesis and loss of nucleolar integrity triggers nucleolar stress, which classically stabilizes the tumor suppressor p53 and induces cell cycle arrest and apoptosis. Nucleolar stress is implemented in modern anti-cancer therapies, however, also emerges as contributor to diverse pathological conditions. These include ribosomopathies, such as the Shwachman Bodian Diamond Syndrome (SBDS), which are not only characterized by nucleolar stress, but paradoxically also increased cancer incidence. Wnt signaling is tightly coupled to cell proliferation and is constitutively activated in various tumor types. In addition, the Wnt/β-Catenin pathway regulates ribosome formation. Here, we demonstrate that induction of nucleolar stress by different strategies stimulates the Wnt/β-Catenin pathway. We show that depletion of the key ribosomopathy factor SBDS, or the nucleolar factors Nucleophosmin (NPM), Pescadillo 1 (PES1) or Peter Pan (PPAN) by si RNA-mediated knockdown or CRISPR/Cas9 strategy activates Wnt/β-Catenin signaling in a β-Catenin-dependent manner and stabilizes β-Catenin in human cancer cells. Moreover, triggering nucleolar stress by the chemotherapeutic agents Actinomycin D or the RNA polymerase I inhibitor CX-5461 stimulates expression of Wnt/β-Catenin targets, which is followed by the p53 target CDKN1A (p21). As PPAN expression is induced by Wnt/β-Catenin signaling, our data establish a novel feedback mechanism and reveal that nucleolar stress over-activates the Wnt/β-Catenin pathway, which most likely serves as compensatory mechanism to sustain ribosome biogenesis.
Collapse
Affiliation(s)
- David P Dannheisig
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Jana Bächle
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Jasmin Tasic
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Marina Keil
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Astrid S Pfister
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.
| |
Collapse
|
33
|
Nait Slimane S, Marcel V, Fenouil T, Catez F, Saurin JC, Bouvet P, Diaz JJ, Mertani HC. Ribosome Biogenesis Alterations in Colorectal Cancer. Cells 2020; 9:E2361. [PMID: 33120992 PMCID: PMC7693311 DOI: 10.3390/cells9112361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
Many studies have focused on understanding the regulation and functions of aberrant protein synthesis in colorectal cancer (CRC), leaving the ribosome, its main effector, relatively underappreciated in CRC. The production of functional ribosomes is initiated in the nucleolus, requires coordinated ribosomal RNA (rRNA) processing and ribosomal protein (RP) assembly, and is frequently hyperactivated to support the needs in protein synthesis essential to withstand unremitting cancer cell growth. This elevated ribosome production in cancer cells includes a strong alteration of ribosome biogenesis homeostasis that represents one of the hallmarks of cancer cells. None of the ribosome production steps escape this cancer-specific dysregulation. This review summarizes the early and late steps of ribosome biogenesis dysregulations described in CRC cell lines, intestinal organoids, CRC stem cells and mouse models, and their possible clinical implications. We highlight how this cancer-related ribosome biogenesis, both at quantitative and qualitative levels, can lead to the synthesis of ribosomes favoring the translation of mRNAs encoding hyperproliferative and survival factors. We also discuss whether cancer-related ribosome biogenesis is a mere consequence of cancer progression or is a causal factor in CRC, and how altered ribosome biogenesis pathways can represent effective targets to kill CRC cells. The association between exacerbated CRC cell growth and alteration of specific steps of ribosome biogenesis is highlighted as a key driver of tumorigenesis, providing promising perspectives for the implementation of predictive biomarkers and the development of new therapeutic drugs.
Collapse
Affiliation(s)
- Sophie Nait Slimane
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Virginie Marcel
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Tanguy Fenouil
- Institute of Pathology EST, Hospices Civils de Lyon, Site-Est Groupement Hospitalier- Est, 69677 Bron, France;
| | - Frédéric Catez
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Christophe Saurin
- Gastroenterology and Genetic Department, Edouard Herriot Hospital, Hospices Civils de Lyon, 69008 Lyon, France;
| | - Philippe Bouvet
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Hichem C. Mertani
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| |
Collapse
|
34
|
Determining the Clinical Value and Critical Pathway of GTPBP4 in Lung Adenocarcinoma Using a Bioinformatics Strategy: A Study Based on Datasets from The Cancer Genome Atlas. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5171242. [PMID: 33134380 PMCID: PMC7593728 DOI: 10.1155/2020/5171242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide, and the most common histologic subtype is lung adenocarcinoma (LUAD). Due to the significant mortality and morbidity rates among patients with LUAD, the identification of novel biomarkers to guide diagnosis, prognosis, and therapy is urgent. Guanosine triphosphate-binding protein 4 (GTPBP4) has been found to be associated with tumorigenesis in recent years, but the underlying molecular mechanism remains to be elucidated. In the present study, we demonstrate that GTPBP4 is significantly overexpressed in LUAD primary tumors. A total of 55 genes were identified as potential targets of GTPBP4. GO enrichment analysis identified the top 25 pathways among these target genes, among which, ribosome biogenesis was shown to be the most central. Each target gene demonstrated strong and complex interactions with other genes. Of the potential target genes, 12 abnormally expressed candidates were associated with survival probability and correlated with GTPBP4 expression. These findings suggest that GTPBP4 is associated with LUAD progression. Finally, we highlight the importance of the role of GTPBP4 in LUAD in vitro. GTPBP4 knockdown in LUAD cells inhibited proliferation and metastasis, promoted apoptosis, and enhanced sensitivity to TP. Overall, we conclude that GTPBP4 may be considered as a potential biomarker of LUAD.
Collapse
|
35
|
Vellky JE, Ricke EA, Huang W, Ricke WA. Expression, Localization, and Function of the Nucleolar Protein BOP1 in Prostate Cancer Progression. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 191:168-179. [PMID: 33039351 DOI: 10.1016/j.ajpath.2020.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 01/04/2023]
Abstract
Differentiating between indolent and aggressive prostate cancers (CaP) is important to decrease overtreatment and increase survival for men with the aggressive disease. Nucleolar prominence is a histologic hallmark of CaP; however, the expression, localization, and functional significance of specific nucleolar proteins have not been investigated thoroughly. The nucleolar protein block of proliferation 1 (BOP1) is associated with multiple cancers but has not been implicated in CaP thus far. Meta-analysis of publicly available data showed increased BOP1 expression in metastatic CaP and recurrent CaP, and was inversely associated with overall survival. Multiplexed immunohistochemistry was used to analyze expression and localization of BOP1 and nucleolar protein 56 in human tissue samples from various stages of CaP progression. Here, increased BOP1 expression was observed at later stages of CaP progression, coinciding with a localization change from nuclear to cytoplasmic. In patient samples, cytoplasmic BOP1 was also inversely associated with overall survival. In models of prostate cancer progression, BOP1 expression showed expression and localization similar to that in human patient samples. The functional significance of BOP1 in metastatic CaP was assessed by genetic knockdown, where BOP1 knockdown resulted in decreased proliferation and motility compared with control. Taken together, these data suggest prognostic significance of BOP1 expression and localization in CaP progression and provide a foundation for further investigation into the functional role of nucleolar proteins in advanced CaP.
Collapse
Affiliation(s)
- Jordan E Vellky
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Cancer Biology Graduate Program, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Emily A Ricke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; George M. O'Brien Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Wei Huang
- George M. O'Brien Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - William A Ricke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; George M. O'Brien Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
| |
Collapse
|
36
|
Li JL, Chen C, Chen W, Zhao LF, Xu XK, Li Y, Yuan HY, Lin JR, Pan JP, Jin BL, Li FC. Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma. J Cell Physiol 2020; 235:7344-7355. [PMID: 32180229 DOI: 10.1002/jcp.29635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 01/09/2020] [Indexed: 01/16/2023]
Abstract
Glioblastoma (GBM) is the most malignant primary brain tumor in adults. Due to its invasive nature, it cannot be thoroughly eliminated. WD repeat domain 12 (WDR12) processes the 32S precursor rRNA but cannot affect the synthesis of the 45S/47S primary transcript. In this study, we found that WDR12 is highly expressed in GBM according to the analysis results of mRNA expression by The Cancer Genome Atlas database. The high expression level of WDR12 is dramatically related to shorter overall survival and reduced disease-free survival. Next, we knocked down WDR12 and found that knockdown of WDR12 promoted the apoptosis and inhibited the proliferation by cell biology experiments. Differential expression genes in gene-chip revealed that WDR12 knockdown mainly inhibited cell cycle. Finally, we also found that WDR12 is associated with PLK1 and EZH2 in cell proliferation of GBM. Resumptively, this report showed a possible evidence that WDR12 drove malignant behavior of GBM, whose expression may present a neoteric independent prognostic biomarker in GBM.
Collapse
Affiliation(s)
- Jun-Liang Li
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Cheng Chen
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Wei Chen
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ling-Feng Zhao
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin-Ke Xu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yang Li
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Hong-Yao Yuan
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jin-Rong Lin
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jun-Ping Pan
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Bi-Lian Jin
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Fang-Cheng Li
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| |
Collapse
|
37
|
Pham KTM, Li Z. Regulated protein stabilization underpins the functional interplay among basal body components in Trypanosoma brucei. J Biol Chem 2020; 295:729-742. [PMID: 31819011 DOI: 10.1074/jbc.ra119.011352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/03/2019] [Indexed: 11/06/2022] Open
Abstract
The basal body in the human parasite Trypanosoma brucei is structurally equivalent to the centriole in animals and functions in the nucleation of axonemal microtubules in the flagellum. T. brucei lacks many evolutionarily conserved centriolar protein homologs and constructs the basal body through unknown mechanisms. Two evolutionarily conserved centriole/basal body cartwheel proteins, TbSAS-6 and TbBLD10, and a trypanosome-specific protein, BBP65, play essential roles in basal body biogenesis in T. brucei, but how they cooperate in the regulation of basal body assembly remains elusive. Here using RNAi, endogenous epitope tagging, immunofluorescence microscopy, and 3D-structured illumination super-resolution microscopy, we identified a new trypanosome-specific protein named BBP164 and found that it has an essential role in basal body biogenesis in T. brucei Further investigation of the functional interplay among BBP164 and the other three regulators of basal body assembly revealed that BBP164 and BBP65 are interdependent for maintaining their stability and depend on TbSAS-6 and TbBLD10 for their stabilization in the basal body. Additionally, TbSAS-6 and TbBLD10 are independent from each other and from BBP164 and BBP65 for maintaining their stability in the basal body. These findings demonstrate that basal body cartwheel proteins are required for stabilizing other basal body components and uncover that regulation of protein stability is an unusual control mechanism for assembly of the basal body in T. brucei.
Collapse
Affiliation(s)
- Kieu T M Pham
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| |
Collapse
|
38
|
Regulated protein stabilization underpins the functional interplay among basal body components in Trypanosoma brucei. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49931-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
39
|
Fu Z, Jiao Y, Li YQ, Ke JJ, Xu YH, Jia BX, Liu B. PES1 In Liver Cancer: A Prognostic Biomarker With Tumorigenic Roles. Cancer Manag Res 2019; 11:9641-9653. [PMID: 31814761 PMCID: PMC6861535 DOI: 10.2147/cmar.s226471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/01/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose Liver cancer has a high incidence of mortality. DNA replication and posttranscriptional modifications play important roles in the development of liver cancer. Pescadillo (PES1) is a nuclear protein that is involved in embryonic development, ribosome synthesis, DNA replication, and cell cycle progression. Recently, abnormal PES1 expression was reported in several tumors, including neuroblastoma, colon cancer, gastric cancer, and breast cancer. Based on bio-informatic analysis, cell experiments and animal models, the aim of this study is to investigate the expression patterns and specific roles of PES1 in liver cancer. Patients and methods PES1 expression was represented by boxplots. The correlation between PES1 expression and clinical features was assessed by the chi-squared test and Fisher's exact tests. Kaplan-Meier curves compared overall survival between different levels of PES1 expression, and Cox analysis selected potential variables associated with overall survival. The MTT assay investigated the proliferation rate, the scratch assay assessed the migratory ability, and the Transwell assay evaluated the invasion capacity of tumor cells in vitro. Animal models were used to confirm the tumorigenic roles of PES1 in vivo. GSEA illustrated the molecular mechanisms that PES1 participated in. Results We found that PES1 was highly expressed in liver cancer tissues, served as a diagnostic marker, and correlated with poor overall survival (OS) and relapse-free survival (RFS) in patients. In vitro studies indicated that PES1 promoted tumor cell proliferation (P=0.0034), migration (P=0.0026), and invasion (P=0.0008), and this tumorigenic role was confirmed in animal models. GSEA further illuminated molecular mechanisms that PES1 participated in liver cancer occurrence and progression. Conclusion This study suggested that PES1 was upregulated in liver cancer and correlated with poor prognosis, by promoting tumor cell proliferation, migration, and invasion, and PES1 may be a novel diagnostic and prognostic bio-marker and a promising therapeutic target in liver cancer.
Collapse
Affiliation(s)
- Zhuo Fu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Yan Jiao
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Yan-Qing Li
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Jian-Ji Ke
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Yan-Hui Xu
- Department of Digestive, China-Japan Union Hospital Affiliated to Jilin University, Changchun, Jilin 130033, People's Republic of China
| | - Bao-Xing Jia
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Bin Liu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| |
Collapse
|
40
|
Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis. Biomolecules 2019; 9:biom9110715. [PMID: 31703473 PMCID: PMC6920918 DOI: 10.3390/biom9110715] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.
Collapse
|
41
|
Cui K, Liu C, Li X, Zhang Q, Li Y. Comprehensive characterization of the rRNA metabolism-related genes in human cancer. Oncogene 2019; 39:786-800. [PMID: 31548613 DOI: 10.1038/s41388-019-1026-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
Although rRNA metabolism-related genes have been reported to be associated with human cancer, a systematic assessment of rRNA metabolism-related genes across human cancers is lacking. Thus, we performed a Pan-cancer analysis of rRNA metabolism-related genes across 20 human cancers. Here, we examined mRNA expression, mutation, DNA methylation, copy number variation (CNV) and clinical landscape of rRNA metabolism-related genes in more than 8600 patients across 20 human cancers from The Cancer Genome Atlas (TCGA) dataset. Besides, ten independent Gene Expression Omnibus (GEO) datasets, Cancer Cell Line Encyclopedia (CCLE) dataset and Project Achilles dataset were used to verify our study. A landscape of rRNA metabolism-related genes was established across 20 human cancers. The results suggest that rRNA metabolism-related genes are upregulated in multiple cancers, particularly in digestive and respiratory system cancers. Most of the upregulated genes were driven by CNV gain rather than mutation or DNA hypomethylation. We systematically identified CNV-driven rRNA metabolism-related genes with clinical relevance, including EXOSC8. Finally, functional experiments confirmed the oncogenic roles of EXOSC8 in colorectal carcinoma. Our study highlights the important roles of rRNA metabolism-related genes in tumorigenesis as prognostic biomarkers.
Collapse
Affiliation(s)
- Kaisa Cui
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Cheng Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xu Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qiang Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Youjun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
42
|
Gaviraghi M, Vivori C, Tonon G. How Cancer Exploits Ribosomal RNA Biogenesis: A Journey beyond the Boundaries of rRNA Transcription. Cells 2019; 8:cells8091098. [PMID: 31533350 PMCID: PMC6769540 DOI: 10.3390/cells8091098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 02/06/2023] Open
Abstract
The generation of new ribosomes is a coordinated process essential to sustain cell growth. As such, it is tightly regulated according to cell needs. As cancer cells require intense protein translation to ensure their enhanced growth rate, they exploit various mechanisms to boost ribosome biogenesis. In this review, we will summarize how oncogenes and tumor suppressors modulate the biosynthesis of the RNA component of ribosomes, starting from the description of well-characterized pathways that converge on ribosomal RNA transcription while including novel insights that reveal unexpected regulatory networks hacked by cancer cells to unleash ribosome production.
Collapse
Affiliation(s)
- Marco Gaviraghi
- Experimental Imaging Center; Ospedale San Raffaele, 20132 Milan, Italy.
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
- Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
| |
Collapse
|
43
|
Sáez-Vásquez J, Delseny M. Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors. THE PLANT CELL 2019; 31:1945-1967. [PMID: 31239391 PMCID: PMC6751116 DOI: 10.1105/tpc.18.00874] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/28/2019] [Accepted: 06/25/2019] [Indexed: 05/11/2023]
Abstract
The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants.
Collapse
Affiliation(s)
- Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michel Delseny
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| |
Collapse
|
44
|
Rohrmoser M, Kluge M, Yahia Y, Gruber-Eber A, Maqbool MA, Forné I, Krebs S, Blum H, Greifenberg AK, Geyer M, Descostes N, Imhof A, Andrau JC, Friedel CC, Eick D. MIR sequences recruit zinc finger protein ZNF768 to expressed genes. Nucleic Acids Res 2019; 47:700-715. [PMID: 30476274 PMCID: PMC6344866 DOI: 10.1093/nar/gky1148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
Mammalian-wide interspersed repeats (MIRs) are retrotransposed elements of mammalian genomes. Here, we report the specific binding of zinc finger protein ZNF768 to the sequence motif GCTGTGTG (N20) CCTCTCTG in the core region of MIRs. ZNF768 binding is preferentially associated with euchromatin and promoter regions of genes. Binding was observed for genes expressed in a cell type-specific manner in human B cell line Raji and osteosarcoma U2OS cells. Mass spectrometric analysis revealed binding of ZNF768 to Elongator components Elp1, Elp2 and Elp3 and other nuclear factors. The N-terminus of ZNF768 contains a heptad repeat array structurally related to the C-terminal domain (CTD) of RNA polymerase II. This array evolved in placental animals but not marsupials and monotreme species, displays species-specific length variations, and possibly fulfills CTD related functions in gene regulation. We propose that the evolution of MIRs and ZNF768 has extended the repertoire of gene regulatory mechanisms in mammals and that ZNF768 binding is associated with cell type-specific gene expression.
Collapse
Affiliation(s)
- Michaela Rohrmoser
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Michael Kluge
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Yousra Yahia
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Anita Gruber-Eber
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Muhammad Ahmad Maqbool
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Ignasi Forné
- Biomedical Center Munich, ZFP, Großhadener Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA) at the Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA) at the Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Ann Katrin Greifenberg
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.,Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Axel Imhof
- Biomedical Center Munich, ZFP, Großhadener Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| |
Collapse
|
45
|
Ghasemi H, Sabati Z, Ghaedi H, Salehi Z, Alipoor B. Circular RNAs in β-cell function and type 2 diabetes-related complications: a potential diagnostic and therapeutic approach. Mol Biol Rep 2019; 46:5631-5643. [PMID: 31302804 DOI: 10.1007/s11033-019-04937-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022]
Abstract
Recent investigations have indicated that altered expression of non-coding RNAs (ncRNAs) could be associated with human diseases such as type 2 diabetes (T2D). Circular RNAs (circRNAs) are a new discovered class of ncRNAs with unique structural characteristics that involved in several molecular and cellular functions. Exploring of the circulating circRNAs as a reliable non-invasive biomarker for monitoring and diagnosing of human diseases has grown significantly. However, the molecular functions and clinical relevance of circRNAs are not yet well clarified in T2D. Accordingly, in this review, the involvement of circRNAs in the β-cell function and T2D-related complications is highlighted. The study also shed light on the possibility of using circRNAs as a biomarker for T2D diagnosis.
Collapse
Affiliation(s)
- Hassan Ghasemi
- Department of Clinical Biochemistry, Abadan Faculty of Medical Sciences, Abadan, Iran
| | - Zolfaghar Sabati
- Student Research Committee, Abadan Faculty of Medical Sciences, Abadan, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zaker Salehi
- Department of Radiation Sciences, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Behnam Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran.
| |
Collapse
|
46
|
Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019; 38:e100278. [PMID: 31268599 PMCID: PMC6600647 DOI: 10.15252/embj.2018100278] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
The essential cellular process of ribosome biogenesis is at the nexus of various signalling pathways that coordinate protein synthesis with cellular growth and proliferation. The fact that numerous diseases are caused by defects in ribosome assembly underscores the importance of obtaining a detailed understanding of this pathway. Studies in yeast have provided a wealth of information about the fundamental principles of ribosome assembly, and although many features are conserved throughout eukaryotes, the larger size of human (pre-)ribosomes, as well as the evolution of additional regulatory networks that can modulate ribosome assembly and function, have resulted in a more complex assembly pathway in humans. Notably, many ribosome biogenesis factors conserved from yeast appear to have subtly different or additional functions in humans. In addition, recent genome-wide, RNAi-based screens have identified a plethora of novel factors required for human ribosome biogenesis. In this review, we discuss key aspects of human ribosome production, highlighting differences to yeast, links to disease, as well as emerging concepts such as extra-ribosomal functions of ribosomal proteins and ribosome heterogeneity.
Collapse
Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Markus T Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
- Göttingen Center for Molecular BiosciencesGeorg‐August UniversityGöttingenGermany
| |
Collapse
|
47
|
Abnormal Ribosome Biogenesis Partly Induced p53-Dependent Aortic Medial Smooth Muscle Cell Apoptosis and Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7064319. [PMID: 31210846 PMCID: PMC6532287 DOI: 10.1155/2019/7064319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/30/2019] [Accepted: 04/14/2019] [Indexed: 12/19/2022]
Abstract
Ribosome biogenesis is a crucial biological process related to cell proliferation, redox balance, and muscle contractility. Aortic smooth muscle cells (ASMCs) show inhibition of proliferation and apoptosis, along with high levels of oxidative stress in aortic dissection (AD). Theoretically, ribosome biogenesis should be enhanced in the ASMCs at its proliferative state but suppressed during apoptosis and oxidative stress. However, the exact status and role of ribosome biogenesis in AD are unknown. We therefore analyzed the expression levels of BOP1, a component of the PeBoW complex which is crucial to ribosome biogenesis, in AD patients and a murine AD model and its influence on the ASMCs. BOP1 was downregulated in the aortic tissues of AD patients compared to healthy donors. In addition, overexpression of BOP1 in human aortic smooth muscle cells (HASMCs) inhibited apoptosis and accumulation of p53 under hypoxic conditions, while knockdown of BOP1 decreased the protein synthesis rate and motility of HASMCs. The RNA polymerase I inhibitor cx-5461 induced apoptosis, ROS production, and proliferative inhibition in the HASMCs, which was partly attenuated by p53 knockout. Furthermore, cx-5461 aggravated the severity of AD in vivo, but a p53-/- background extended the life-span and lowered AD incidence in the mice. Taken together, decreased ribosome biogenesis in ASMCs resulting in p53-dependent proliferative inhibition, oxidative stress, and apoptosis is one of the underlying mechanisms of AD.
Collapse
|
48
|
Yin Y, Zhou L, Zhan R, Zhang Q, Li M. Identification of WDR12 as a novel oncogene involved in hepatocellular carcinoma propagation. Cancer Manag Res 2018; 10:3985-3993. [PMID: 30310320 PMCID: PMC6166768 DOI: 10.2147/cmar.s176268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignant cancer worldwide. Importantly, the precise mechanisms causing HCC pathogenicity are still unknown. The identification of potential oncogenes plays significant roles in finding novel therapeutic targets for human HCC. Purpose WDR12 (WD repeat protein 12), a member of WD repeats family, plays crucial roles in the ribosome biogenesis pathway. However, Whether WDR12 contributes to HCC development remains unknown. The objective of this study was to elucidate the role of WDR12 in HCC development. Methods The expression level of WDR12 in HCC tissues and adjacent non-tumor tissues were detected form Gene Expression Omnibus (GEO) database. The expression level of WDR12 in HCC cell lines were examined by RT-PCR and western blot. Kaplan-Meier analysis were used to analyze the effect of WDR12 level on overall and disease-free survival of HCC patients. To examine whether WDR12 supports development of HCC, we inhibited expression of WDR12 by using an shRNA-encoding lentivirus system. Effects of WDR12 knockdown were evaluated on cell-growth, cell-proliferation and cell-migration. The mechanisms involved in HCC cells growth, proliferation and migration were analyzed by western blot assay. Results In silico analysis of HCC data sets showed that elevated expression of WDR12 correlated with high serum AFP level, high vascular invasion, high histologic grade and high TNM stage in HCC patients. Furthermore, up-regulated expression of WDR12 significantly correlated with the short overall survival and recurrence time of HCC patients. The shRNA-mediated knockdown of WDR12 expression resulted in reduced proliferation and migration of HepG2 and Huh-7 cells. Notably, inhibition of WDR12 resulted in decreased phosphorylation of AKT, mTOR and S6K1. Conclusion Our study indicates that WDR12 contributes to HCC propagation, and indicates that suppression of WDR12 may be a potential strategy for human HCC treatment.
Collapse
Affiliation(s)
- Yancun Yin
- Taishan Scholar Immunology Program, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, Shandong, China
| | - Ling Zhou
- The Key Laboratory of Traditional Chinese Medicine Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine, School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong, China
| | - Renhui Zhan
- Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai 264003, Shandong, China,
| | - Qiang Zhang
- Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai 264003, Shandong, China,
| | - Minjing Li
- Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai 264003, Shandong, China,
| |
Collapse
|
49
|
Holdt LM, Kohlmaier A, Teupser D. Molecular functions and specific roles of circRNAs in the cardiovascular system. Noncoding RNA Res 2018; 3:75-98. [PMID: 30159442 PMCID: PMC6096412 DOI: 10.1016/j.ncrna.2018.05.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 12/25/2022] Open
Abstract
As part of the superfamily of long noncoding RNAs, circular RNAs (circRNAs) are emerging as a new type of regulatory molecules that partake in gene expression control. Here, we review the current knowledge about circRNAs in cardiovascular disease. CircRNAs are not only associated with different types of cardiovascular disease, but they have also been identified as intracellular effector molecules for pathophysiological changes in cardiovascular tissues, and as cardiovascular biomarkers. This evidence is put in the context of the current understanding of general circRNA biogenesis and of known interactions of circRNAs with DNA, RNA, and proteins.
Collapse
Affiliation(s)
- Lesca M. Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Germany
| | | | | |
Collapse
|
50
|
Wang L, Meng X, Li G, Zhou Q, Xiao J. Circular RNAs in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1087:191-204. [DOI: 10.1007/978-981-13-1426-1_15] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|