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Lin Z, Zhang J, Chen Q, Zhang X, Zhang D, Lin J, Lin D. Transcriptome analysis of the adenoma-carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer. Front Vet Sci 2023; 10:1192525. [PMID: 38098990 PMCID: PMC10720982 DOI: 10.3389/fvets.2023.1192525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 12/17/2023] Open
Abstract
The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in canines is not clear. We collected transcriptome data from 8 normal colon tissues, 4 adenoma tissues, and 15 cancer tissues. Differential analysis was unable to determine the dynamic changes of genes but revealed that PFKFB3 may play a key role in this process. Enrichment analysis explained metabolic dysregulation, immunosuppression, and typical cancer pathways in canine colorectal tumors. MFuzz generated specific dynamic expression patterns of five differentially expressed genes (DEGs). Weighted correlation network analysis showed that DEGs in cluster 3 were associated with malignant tissues, revealing the key role of inflammatory and immune pathways in canine CRC, and the S100A protein family was also found to be involved in the malignant transformation of canine colorectal tumors. By comparing strategies between humans and dogs, we found five novel markers that may be drivers of CRC. Among them, GTBP4 showed excellent diagnostic and prognostic ability. This study was the first systematic exploration of transformation in canine CRC, complemented the molecular characteristics of the development and progression of canine CRC, and provided new potential biomarkers and comparative oncologic evidence for biomarker studies in human colorectal cancer.
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Affiliation(s)
- Zixiang Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiatong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohu Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiahao Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Degui Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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2
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Shimizu N, Shiraishi H, Hanada T. Zebrafish as a Useful Model System for Human Liver Disease. Cells 2023; 12:2246. [PMID: 37759472 PMCID: PMC10526867 DOI: 10.3390/cells12182246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Liver diseases represent a significant global health challenge, thereby necessitating extensive research to understand their intricate complexities and to develop effective treatments. In this context, zebrafish (Danio rerio) have emerged as a valuable model organism for studying various aspects of liver disease. The zebrafish liver has striking similarities to the human liver in terms of structure, function, and regenerative capacity. Researchers have successfully induced liver damage in zebrafish using chemical toxins, genetic manipulation, and other methods, thereby allowing the study of disease mechanisms and the progression of liver disease. Zebrafish embryos or larvae, with their transparency and rapid development, provide a unique opportunity for high-throughput drug screening and the identification of potential therapeutics. This review highlights how research on zebrafish has provided valuable insights into the pathological mechanisms of human liver disease.
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Affiliation(s)
- Nobuyuki Shimizu
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan;
| | | | - Toshikatsu Hanada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan;
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3
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Comerford SA, Hinnant EA, Chen Y, Hammer RE. Hepatic ribosomal protein S6 (Rps6) insufficiency results in failed bile duct development and loss of hepatocyte viability; a ribosomopathy-like phenotype that is partially p53-dependent. PLoS Genet 2023; 19:e1010595. [PMID: 36656901 PMCID: PMC9888725 DOI: 10.1371/journal.pgen.1010595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/31/2023] [Accepted: 12/26/2022] [Indexed: 01/20/2023] Open
Abstract
Defective ribosome biogenesis (RiBi) underlies a group of clinically diverse human diseases collectively known as the ribosomopathies, core manifestations of which include cytopenias and developmental abnormalities that are believed to stem primarily from an inability to synthesize adequate numbers of ribosomes and concomitant activation of p53. The importance of a correctly functioning RiBi machinery for maintaining tissue homeostasis is illustrated by the observation that, despite having a paucity of certain cell types in early life, ribosomopathy patients have an increased risk for developing cancer later in life. This suggests that hypoproliferative states trigger adaptive responses that can, over time, become maladaptive and inadvertently drive unchecked hyperproliferation and predispose to cancer. Here we describe an experimentally induced ribosomopathy in the mouse and show that a normal level of hepatic ribosomal protein S6 (Rps6) is required for proper bile duct development and preservation of hepatocyte viability and that its insufficiency later promotes overgrowth and predisposes to liver cancer which is accelerated in the absence of the tumor-suppressor PTEN. We also show that the overexpression of c-Myc in the liver ameliorates, while expression of a mutant hyperstable form of p53 partially recapitulates specific aspects of the hepatopathies induced by Rps6 deletion. Surprisingly, co-deletion of p53 in the Rps6-deficient background fails to restore biliary development or significantly improve hepatic function. This study not only reveals a previously unappreciated dependence of the developing liver on adequate levels of Rps6 and exquisitely controlled p53 signaling, but suggests that the increased cancer risk in ribosomopathy patients may, in part, stem from an inability to preserve normal tissue homeostasis in the face of chronic injury and regeneration.
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Affiliation(s)
- Sarah A. Comerford
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Elizabeth A. Hinnant
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yidong Chen
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas. United States of America
| | - Robert E. Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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Babu S, Takeuchi Y, Masai I. Banp regulates DNA damage response and chromosome segregation during the cell cycle in zebrafish retina. eLife 2022; 11:74611. [PMID: 35942692 PMCID: PMC9363121 DOI: 10.7554/elife.74611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Btg3-associated nuclear protein (Banp) was originally identified as a nuclear matrix-associated region (MAR)-binding protein and it functions as a tumor suppressor. At the molecular level, Banp regulates transcription of metabolic genes via a CGCG-containing motif called the Banp motif. However, its physiological roles in embryonic development are unknown. Here, we report that Banp is indispensable for the DNA damage response and chromosome segregation during mitosis. Zebrafish banp mutants show mitotic cell accumulation and apoptosis in developing retina. We found that DNA replication stress and tp53-dependent DNA damage responses were activated to induce apoptosis in banp mutants, suggesting that Banp is required for regulation of DNA replication and DNA damage repair. Furthermore, consistent with mitotic cell accumulation, chromosome segregation was not smoothly processed from prometaphase to anaphase in banp morphants, leading to a prolonged M-phase. Our RNA- and ATAC-sequencing identified 31 candidates for direct Banp target genes that carry the Banp motif. Interestingly, a DNA replication fork regulator, wrnip1, and two chromosome segregation regulators, cenpt and ncapg, are included in this list. Thus, Banp directly regulates transcription of wrnip1 for recovery from DNA replication stress, and cenpt and ncapg for chromosome segregation during mitosis. Our findings provide the first in vivo evidence that Banp is required for cell-cycle progression and cell survival by regulating DNA damage responses and chromosome segregation during mitosis. In order for a cell to divide, it must progress through a series of carefully controlled steps known as the cell cycle. First, the cell replicates its DNA and both copies get segregated to opposite ends. The cell then splits into two and each new cell receives a copy of the duplicated genetic material. If any of the stages in the cell cycle become disrupted or mis-regulated this can lead to uncontrolled divisions that may result in cancer. Researchers have often used a structure within the eye known as the retina to study the cell cycle in zebrafish and other animals as cells in the retina rapidly divide in a highly controlled manner. A protein called Banp is known to help stop tumors from growing in humans and mice, but its normal role in the body, particularly the cell cycle, has remained unclear. To investigate, Babu et al. studied the retina of mutant zebrafish that were unable to make the Banp protein. The experiments revealed that two stress responses indicating DNA damage or defects in copying DNA were active in the retinal cells of the mutant zebrafish. This suggested that Banp allows cell to progress through the cell cycle by repairing any DNA damage that may arise during replication. Banp does this by activating the gene for another protein called Wrnip1. Babu et al. also found that Banp helps segregate the two copies of DNA during cell division by promoting the activation of two other proteins called Cenpt and Ncapg. Further experiments identified 31 genes that were directly regulated by Banp. These findings demonstrate that Banp is required for zebrafish cells to be able to accurately copy their DNA and divide in to two new cells. In the future, the work of Babu et al. will provide a useful resource to investigate how tumors grow and spread around the body, and may contribute to the development of new treatments for cancer.
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Affiliation(s)
- Swathy Babu
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yuki Takeuchi
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Ichiro Masai
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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5
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Khendek L, Diaz C, Drouin E, Lallier M, Alvarez F, Paganelli M. Early predictors of unfavourable outcome in progressive cholestasis of northwestern Quebec. CANADIAN LIVER JOURNAL 2022; 5:402-410. [PMID: 36133898 PMCID: PMC9473563 DOI: 10.3138/canlivj-2021-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 08/30/2023]
Abstract
BACKGROUND Progressive cholestasis of northwestern Quebec (PCNQ) is a rare and severe form of cirrhosis affecting children from Quebec's First Nations. First described by our group in 1981 and historically named North American Indian childhood cirrhosis, such a condition often requires liver transplantation during the pediatric age. This study aimed at suggesting a more culturally sensitive name for the disease and identifying early prognostic factors for an unfavourable outcome. METHODS We retrospectively collected data of all 14 consecutive patients diagnosed with PCNQ over the last 20 years and compared children listed for liver transplant before 18 years of age (LT, n = 7) to those with milder disease progression (no-LT, n = 7). RESULTS Compared with the no-LT group, LT children developed serious complications with an unusually high incidence of gastrointestinal bleeding. Over the first 12 months from presentation, a greater increase of alanine aminotransferase plasma levels, decrease of total bilirubin, and increase of alanine aminotransferase-to-total bilirubin ratio was observed in the LT group. Bone mineral density was lower in LT children independently of vitamin D levels. Patients with PCNQ showed poorer bone health than age-matched children with other cholestatic disorders. CONCLUSIONS In the name of cultural sensitivity, PCNQ should be the preferred name for this condition. Variation of alanine aminotransferase and total bilirubin plasma levels over the first 12 months from presentation might be used for the early identification of children with PCNQ who are at higher risk of unfavourable outcomes. This might help optimize clinical management to populations that are underserved by health care services.
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Affiliation(s)
- Léticia Khendek
- Pediatric Gastroenterology, Hepatology and Nutrition, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Candice Diaz
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine Research Center, Université de Montréal, Montreal, Quebec, Canada
| | - Eric Drouin
- Pediatric Gastroenterology, Hepatology and Nutrition, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Michel Lallier
- Pediatric Surgery, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Fernando Alvarez
- Pediatric Gastroenterology, Hepatology and Nutrition, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Massimiliano Paganelli
- Pediatric Gastroenterology, Hepatology and Nutrition, CHU Sainte-Justine, Montreal, Quebec, Canada
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine Research Center, Université de Montréal, Montreal, Quebec, Canada
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6
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Zhang C, Huang R, Ma X, Chen J, Han X, Li L, Luo L, Ruan H, Huang H. The Ribosome Biogenesis Factor Ltv1 Is Essential for Digestive Organ Development and Definitive Hematopoiesis in Zebrafish. Front Cell Dev Biol 2021; 9:704730. [PMID: 34692673 PMCID: PMC8528963 DOI: 10.3389/fcell.2021.704730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome biogenesis is a fundamental activity in cells. Ribosomal dysfunction underlies a category of diseases called ribosomopathies in humans. The symptomatic characteristics of ribosomopathies often include abnormalities in craniofacial skeletons, digestive organs, and hematopoiesis. Consistently, disruptions of ribosome biogenesis in animals are deleterious to embryonic development with hypoplasia of digestive organs and/or impaired hematopoiesis. In this study, ltv1, a gene involved in the small ribosomal subunit assembly, was knocked out in zebrafish by clustered regularly interspaced short palindromic repeats (CRISPRs)/CRISPR associated protein 9 (Cas9) technology. The recessive lethal mutation resulted in disrupted ribosome biogenesis, and ltv1 Δ14/Δ14 embryos displayed hypoplastic craniofacial cartilage, digestive organs, and hematopoiesis. In addition, we showed that the impaired cell proliferation, instead of apoptosis, led to the defects in exocrine pancreas and hematopoietic stem and progenitor cells (HSPCs) in ltv1 Δ14/Δ14 embryos. It was reported that loss of function of genes associated with ribosome biogenesis often caused phenotypes in a P53-dependent manner. In ltv1 Δ14/Δ14 embryos, both P53 protein level and the expression of p53 target genes, Δ113p53 and p21, were upregulated. However, knockdown of p53 failed to rescue the phenotypes in ltv1 Δ14/Δ14 larvae. Taken together, our data demonstrate that LTV1 ribosome biogenesis factor (Ltv1) plays an essential role in digestive organs and hematopoiesis development in zebrafish in a P53-independent manner.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Rui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xirui Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xinlu Han
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Hua Ruan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
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7
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Fujimura A, Hayashi Y, Kato K, Kogure Y, Kameyama M, Shimamoto H, Daitoku H, Fukamizu A, Hirota T, Kimura K. Identification of a novel nucleolar protein complex required for mitotic chromosome segregation through centromeric accumulation of Aurora B. Nucleic Acids Res 2020; 48:6583-6596. [PMID: 32479628 PMCID: PMC7337965 DOI: 10.1093/nar/gkaa449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 04/24/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleolus is a membrane-less nuclear structure that disassembles when cells undergo mitosis. During mitosis, nucleolar factors are thus released from the nucleolus and dynamically change their subcellular localization; however, their functions remain largely uncharacterised. Here, we found that a nucleolar factor called nucleolar protein 11 (NOL11) forms a protein complex with two tryptophan-aspartic acid (WD) repeat proteins named WD-repeat protein 43 (WDR43) and Cirhin in mitotic cells. This complex, referred to here as the NWC (NOL11-WDR43-Cirhin) complex, exists in nucleoli during interphase and translocates to the periphery of mitotic chromosomes, i.e., perichromosomal regions. During mitotic progression, both the congression of chromosomes to the metaphase plate and sister chromatid cohesion are impaired in the absence of the NWC complex, as it is required for the centromeric enrichment of Aurora B and the associating phosphorylation of histone H3 at threonine 3. These results reveal the characteristics of a novel protein complex consisting of nucleolar proteins, which is required for regulating kinetochores and centromeres to ensure faithful chromosome segregation.
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Affiliation(s)
- Akiko Fujimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Yuki Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Kazashi Kato
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Yuichiro Kogure
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Mutsuro Kameyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Haruka Shimamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Toru Hirota
- Cancer Institute of the Japanese Foundation for Cancer Research, Division of Experimental Pathology, 3-8-1 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Keiji Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
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8
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Huang W, Chen F, Ma Q, Xin J, Li J, Chen J, Zhou B, Chen M, Li J, Peng J. Ribosome biogenesis gene DEF/UTP25 is essential for liver homeostasis and regeneration. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1651-1664. [PMID: 32303961 DOI: 10.1007/s11427-019-1635-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/17/2020] [Indexed: 12/19/2022]
Abstract
Hepatocytes are responsible for diverse metabolic activities in a liver. Proper ribosome biogenesis is essential to sustain the function of hepatocytes. There are approximately 200 factors involved in ribosome biogenesis; however, few studies have focused on the role of these factors in maintaining liver homeostasis. The digestive organ expansion factor (def) gene encodes a nucleolar protein Def that participates in ribosome biogenesis. In addition, Def forms a complex with cysteine protease Calpain3 (Capn3) and recruits Capn3 to the nucleolus to cleave protein targets. However, the function of Def has not been characterized in the mammalian digestive organs. In this report, we show that conditional knockout of the mouse def gene in hepatocytes causes cell morphology abnormality and constant infiltration of inflammatory cells in the liver. As age increases, the def conditional knockout liver displays multiple tissue damage foci and biliary hyperplasia. Moreover, partial hepatectomy leads to sudden acute death to the def conditional knockout mice and this phenotype is rescued by intragastric injection of the anti-inflammation drug dexamethasone one day before hepatectomy. Our results demonstrate that Def is essential for maintaining the liver homeostasis and liver regeneration capacity in mammals.
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Affiliation(s)
- Weidong Huang
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Quanxin Ma
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiaojiao Xin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jiaqi Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Minli Chen
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Jun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Jinrong Peng
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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10
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Bioinformatics‑based identification of key pathways and candidate genes for estrogen‑induced intrahepatic cholestasis using DNA microarray analysis. Mol Med Rep 2019; 20:303-311. [PMID: 31115536 DOI: 10.3892/mmr.2019.10256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/12/2019] [Indexed: 01/04/2023] Open
Abstract
Estrogen‑induced intrahepatic cholestasis (EIC) has increased incidence during pregnancy, and within women taking oral contraception and postmenopausal hormone replacement therapy. However, the pathology underlying EIC is not well understood. The aim of the present study was to identify key pathways and candidate genes in estrogen‑induced intrahepatic cholestasis (EIC) that may be potential targets for diagnosis and treatment. A whole‑genome microarray (4x44K) analysis of a 17α‑ethinylestradiol (EE)‑induced EIC rat liver model was performed. Bioinformatics‑based methods were used to identify key pathways and candidate genes associated with EIC. The candidate genes were validated using a reverse transcription quantitative polymerase chain reaction assay. A total of 455 genes were differentially expressed (P<0.05 and fold change >2.0) following EE treatment, including 225 downregulated genes and 230 upregulated genes. Sulfotransferase family 1E member 1, cytochrome P450 family 3 subfamily A member 2, carbonic anhydrase 3, leukotriene C4 synthase and ADAM metallopeptidase domain 8 were the 5 candidate genes identified to be differentially expressed and involved in the metabolism of estrogens and bile acids and the regulation of inflammation and oxidative stress. The Analyses of Gene Ontology enrichment, Kyoto Encyclopedia of Genes and Genomes pathways and protein‑protein interaction network associated‑modules identified several key pathways involved in the homeostasis of lipids and bile acids and in AMPK, p53 and Wnt signaling. These key pathways and candidate genes may have critical roles in the pathogenesis of EIC. In addition, reversing the abnormal expression of candidate genes or restoring the dysfunction of key pathways may provide therapeutic opportunities for patients with EIC.
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11
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Abstract
Cholestasis is a condition that impairs bile flow, resulting in retention of bile fluid in the liver. It may cause significant morbidity and mortality due to pruritus, malnutrition, and complications from portal hypertension secondary to biliary cirrhosis. The zebrafish (Danio rerio) has emerged as a valuable model organism for studying cholestasis that complements with the in vitro systems and rodent models. Its main advantages include conserved mechanisms of liver development and bile formation, rapid external development, ease of monitoring hepatobiliary morphology and function in live larvae, and accessibility to genetic and chemical manipulations. In this chapter, we provide an overview of the existing zebrafish models of cholestatic liver diseases. We discuss the strengths and limitations of using zebrafish to study cholestasis. We also provide step-by-step descriptions of the methodologies for analyzing cholestatic phenotypes in zebrafish.
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Affiliation(s)
- Duc-Hung Pham
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chunyue Yin
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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12
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Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus. Development 2018; 145:145/20/dev166181. [PMID: 30337486 DOI: 10.1242/dev.166181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]
Abstract
A growing number of tissue-specific inherited disorders are associated with impaired ribosome production, despite the universal requirement for ribosome function. Recently, mutations in RPSA, a protein component of the small ribosomal subunit, were discovered to underlie approximately half of all isolated congenital asplenia cases. However, the mechanisms by which mutations in this ribosome biogenesis factor lead specifically to spleen agenesis remain unknown, in part due to the lack of a suitable animal model for study. Here we reveal that RPSA is required for normal spleen development in the frog, Xenopus tropicalis Depletion of Rpsa in early embryonic development disrupts pre-rRNA processing and ribosome biogenesis, and impairs expression of the key spleen patterning genes nkx2-5, bapx1 and pod1 in the spleen anlage. Importantly, we also show that whereas injection of human RPSA mRNA can rescue both pre-rRNA processing and spleen patterning, injection of human mRNA bearing a common disease-associated mutation cannot. Together, we present the first animal model of RPSA-mediated asplenia and reveal a crucial requirement for RPSA in pre-rRNA processing and molecular patterning during early Xenopus development.
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Affiliation(s)
- John N Griffin
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Samuel B Sondalle
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Andrew Robson
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Gerald Griffin
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Saurabh S Kulkarni
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA .,Departments of Molecular Biophysics and Biochemistry, and Therapeutic Radiology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA .,Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
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13
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Abstract
Ribosomopathies are a group of human disorders most commonly caused by ribosomal protein haploinsufficiency or defects in ribosome biogenesis. These conditions manifest themselves as physiological defects in specific cell and tissue types. We review current molecular models to explain ribosomopathies and attempt to reconcile the tissue specificity of these disorders with the ubiquitous requirement for ribosomes in all cells. Ribosomopathies as a group are diverse in their origins and clinical manifestations; we use the well-described Diamond-Blackfan anemia (DBA) as a specific example to highlight some common features. We discuss ribosome homeostasis as an overarching principle that governs the sensitivity of specific cells and tissue types to ribosomal protein mutations. Mathematical models and experimental insights rationalize how even subtle shifts in the availability of ribosomes, such as those created by ribosome haploinsufficiency, can drive messenger RNA-specific effects on protein expression. We discuss recently identified roles played by ribosome rescue and recycling factors in regulating ribosome homeostasis.
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Affiliation(s)
- Eric W Mills
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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14
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2018; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
Abstract
Mutations that target the ubiquitous process of ribosome assembly paradoxically cause diverse tissue-specific disorders (ribosomopathies) that are often associated with an increased risk of cancer. Ribosomes are the essential macromolecular machines that read the genetic code in all cells in all kingdoms of life. Following pre-assembly in the nucleus, precursors of the large 60S and small 40S ribosomal subunits are exported to the cytoplasm where the final steps in maturation are completed. Here, I review the recent insights into the conserved mechanisms of ribosome assembly that have come from functional characterisation of the genes mutated in human ribosomopathies. In particular, recent advances in cryo-electron microscopy, coupled with genetic, biochemical and prior structural data, have revealed that the SBDS protein that is deficient in the inherited leukaemia predisposition disorder Shwachman-Diamond syndrome couples the final step in cytoplasmic 60S ribosomal subunit maturation to a quality control assessment of the structural and functional integrity of the nascent particle. Thus, study of this fascinating disorder is providing remarkable insights into how the large ribosomal subunit is functionally activated in the cytoplasm to enter the actively translating pool of ribosomes.
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MESH Headings
- Bone Marrow Diseases/metabolism
- Bone Marrow Diseases/pathology
- Cryoelectron Microscopy
- Exocrine Pancreatic Insufficiency/metabolism
- Exocrine Pancreatic Insufficiency/pathology
- Humans
- Lipomatosis/metabolism
- Lipomatosis/pathology
- Mutation
- Proteins/genetics
- Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Shwachman-Diamond Syndrome
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Affiliation(s)
- Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; The Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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15
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Probing the mechanisms underlying human diseases in making ribosomes. Biochem Soc Trans 2017; 44:1035-44. [PMID: 27528749 DOI: 10.1042/bst20160064] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 12/26/2022]
Abstract
Ribosomes are essential, highly complex machines responsible for protein synthesis in all growing cells. Because of their importance, the process of building these machines is intricately regulated. Although the proteins involved in regulating ribosome biogenesis are just beginning to be understood, especially in human cells, the consequences for dysregulating this process have been even less studied. Such interruptions in ribosome synthesis result in a collection of human disorders known as ribosomopathies. Ribosomopathies, which occur due to mutations in proteins involved in the global process of ribosome biogenesis, result in tissue-specific defects. The questions posed by this dichotomy and the steps taken to address these questions are therefore the focus of this review: How can tissue-specific disorders result from alterations in global processes? Could ribosome specialization account for this difference?
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16
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Pham DH, Zhang C, Yin C. Using zebrafish to model liver diseases-Where do we stand? CURRENT PATHOBIOLOGY REPORTS 2017; 5:207-221. [PMID: 29098121 DOI: 10.1007/s40139-017-0141-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Purpose of Review The liver is the largest internal organ and performs both exocrine and endocrine function that is necessary for survival. Liver failure is among the leading causes of death and represents a major global health burden. Liver transplantation is the only effective treatment for end-stage liver diseases. Animal models advance our understanding of liver disease etiology and hold promise for the development of alternative therapies. Zebrafish has become an increasingly popular system for modeling liver diseases and complements the rodent models. Recent Findings The zebrafish liver contains main cell types that are found in mammalian liver and exhibits similar pathogenic responses to environmental insults and genetic mutations. Zebrafish have been used to model neonatal cholestasis, cholangiopathies, such as polycystic liver disease, alcoholic liver disease, and non-alcoholic fatty liver disease. It also provides a unique opportunity to study the plasticity of liver parenchymal cells during regeneration. Summary In this review, we summarize the recent work of building zebrafish models of liver diseases. We highlight how these studies have brought new knowledge of disease mechanisms. We also discuss the advantages and challenges of using zebrafish to model liver diseases.
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Affiliation(s)
- Duc-Hung Pham
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Changwen Zhang
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Chunyue Yin
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
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17
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Guo F, Chen JJ, Tang WJ. CIRH1A augments the proliferation of RKO colorectal cancer cells. Oncol Rep 2017; 37:2375-2381. [PMID: 28350096 DOI: 10.3892/or.2017.5497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 01/18/2017] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence suggests that ribosomal proteins may have extraribosomal functions in various physiological and pathological processes, including cancer. We analyzed the expression of the CIRH1A ribosomal protein in colorectal carcinoma and para-carcinoma samples by bioinformatics analyses of data extracted from The Cancer Genome Atlas and in colorectal cancer cell lines in vitro by qPCR. CIRH1A was highly expressed in carcinoma samples and colorectal cancer cells. We also transduced the RKO colorectal cancer (CRC) cell line with lentivirus-mediated small interfering RNAs (siRNAs) and studied the impact that this knockdown of CIRH1A expression had on cell growth. RNA interference (RNAi)-mediated inhibition of CIRH1A expression significantly suppressed proliferation and increased apoptosis of transduced cells, and tended to arrest them in G1 phase. Our data suggest that CIRH1A plays a critical role in the proliferation, cell cycle distribution, and apoptosis of human malignant colorectal cells, and might therefore be a potential target for therapeutic strategies.
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Affiliation(s)
- Feng Guo
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Jian-Jun Chen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Wei-Jun Tang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
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18
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Tao T, Sondalle SB, Shi H, Zhu S, Perez-Atayde AR, Peng J, Baserga SJ, Look AT. The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma. Oncogene 2017; 36:3852-3867. [PMID: 28263972 PMCID: PMC5501763 DOI: 10.1038/onc.2016.527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/08/2016] [Accepted: 12/22/2016] [Indexed: 02/07/2023]
Abstract
The nucleolar factor, digestive organ expansion factor (DEF), has a key role in ribosome biogenesis, functioning in pre-ribosomal RNA (pre-rRNA) processing as a component of the small ribosomal subunit (SSU) processome. Here we show that the peripheral sympathetic nervous system (PSNS) is very underdeveloped in def-deficient zebrafish, and that def haploinsufficiency significantly decreases disease penetrance and tumor growth rate in a MYCN-driven transgenic zebrafish model of neuroblastoma that arises in the PSNS. Consistent with these findings, DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. Interestingly, overexpression of MYCN in zebrafish and in human neuroblastoma cells results in the appearance of intermediate pre-rRNAs species that reflect the processing of pre-rRNAs through Pathway 2, a pathway that processes pre-rRNAs in a different temporal order than the more often used Pathway 1. Our results indicate that DEF and possibly other components of the SSU processome provide a novel site of vulnerability in neuroblastoma cells that could be exploited for targeted therapy.
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Affiliation(s)
- T Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S B Sondalle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - H Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - S Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center and Mayo Clinic Center for Individualized Medicine, Rochester, MN, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center and Mayo Clinic Center for Individualized Medicine, Rochester, MN, USA
| | - A R Perez-Atayde
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - J Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - S J Baserga
- Departments of Molecular Biophysics &Biochemistry, Genetics and Therapeutic Radiology, Yale University and Yale University School of Medicine, New Haven, CT, USA
| | - A T Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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19
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Robson A, Owens NDL, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC DEVELOPMENTAL BIOLOGY 2016; 16:38. [PMID: 27784267 PMCID: PMC5081970 DOI: 10.1186/s12861-016-0138-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/07/2016] [Indexed: 11/17/2022]
Abstract
Background Because ribosomes are ubiquitously required for protein production, it was long assumed that any inherited defect in ribosome manufacture would be embryonically lethal. However, several human congenital diseases have been found to be associated with mutations in ribosome biogenesis factors. Surprisingly, despite the global requirement for ribosomes, these “ribosomopathies” are characterized by distinct and tissue specific phenotypes. The reasons for such tissue proclivity in ribosomopathies remain mysterious but may include differential expression of ribosome biogenesis factors in distinct tissues. Methods Here we use in situ hybridization of labeled antisense mRNA probes and ultra high temporal resolution RNA-Seq data to examine and compare expression of 13 disease associated ribosome biogenesis factors at six key stages in Xenopus tropicalis development. Results Rather than being ubiquitously expressed during development, mRNAs of all examined ribosome biogenesis factors were highly enriched in specific tissues, including the cranial neural crest and ventral blood islands. Interestingly, expression of ribosome biogenesis factors demonstrates clear differences in timing, transcript number and tissue localization. Conclusion Ribosome biogenesis factor expression is more spatiotemporally regulated during embryonic development than previously expected and correlates closely with many of the common ribosomopathy phenotypes. Our findings provide information on the dynamic use of ribosome production machinery components during development and advance our understanding of their roles in disease. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0138-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Robson
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Nick D L Owens
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, UK
| | - Susan J Baserga
- Departments of Genetics, Molecular Biophysics and Biochemistry, and Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - John N Griffin
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA.
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20
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Zhao X, Lorent K, Wilkins B, Marchione DM, Gillespie K, Waisbourd-Zinman O, So J, Koo KA, Shin D, Porter JR, Wells RG, Blair I, Pack M. Glutathione antioxidant pathway activity and reserve determine toxicity and specificity of the biliary toxin biliatresone in zebrafish. Hepatology 2016; 64:894-907. [PMID: 27102575 PMCID: PMC5251204 DOI: 10.1002/hep.28603] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/15/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
UNLABELLED Biliatresone is an electrophilic isoflavone isolated from Dysphania species plants that has been causatively linked to naturally occurring outbreaks of a biliary atresia (BA)-like disease in livestock. Biliatresone has selective toxicity for extrahepatic cholangiocytes (EHCs) in zebrafish larvae. To better understand its mechanism of toxicity, we performed transcriptional profiling of liver cells isolated from zebrafish larvae at the earliest stage of biliatresone-mediated biliary injury, with subsequent comparison of biliary and hepatocyte gene expression profiles. Transcripts encoded by genes involved in redox stress response, particularly those involved in glutathione (GSH) metabolism, were among the most prominently up-regulated in both cholangiocytes and hepatocytes of biliatresone-treated larvae. Consistent with these findings, hepatic GSH was depleted at the onset of biliary injury, and in situ mapping of the hepatic GSH redox potential using a redox-sensitive green fluorescent protein biosensor showed that it was significantly more oxidized in EHCs both before and after treatment with biliatresone. Pharmacological and genetic manipulation of GSH redox homeostasis confirmed the importance of GSH in modulating biliatresone-induced injury given that GSH depletion sensitized both EHCs and the otherwise resistant intrahepatic cholangiocytes to the toxin, whereas replenishing GSH level by N-acetylcysteine administration or activation of nuclear factor erythroid 2-like 2 (Nrf2), a transcriptional regulator of GSH synthesis, inhibited EHC injury. CONCLUSION These findings strongly support redox stress as a critical contributing factor in biliatresone-induced cholangiocyte injury, and suggest that variations in intrinsic stress responses underlie the susceptibility profile. Insufficient antioxidant capacity of EHCs may be critical to early pathogenesis of human BA. (Hepatology 2016;64:894-907).
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Affiliation(s)
- Xiao Zhao
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristin Lorent
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Wilkins
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dylan M. Marchione
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Gillespie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Orith Waisbourd-Zinman
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Juhoon So
- Department of Developmental Biology, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kyung Ah Koo
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104, USA
| | - Donghun Shin
- Department of Developmental Biology, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R. Porter
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104, USA
| | - Rebecca G. Wells
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Pack
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA., Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Danilova N, Gazda HT. Ribosomopathies: how a common root can cause a tree of pathologies. Dis Model Mech 2016; 8:1013-26. [PMID: 26398160 PMCID: PMC4582105 DOI: 10.1242/dmm.020529] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Defects in ribosome biogenesis are associated with a group of diseases called the ribosomopathies, of which Diamond-Blackfan anemia (DBA) is the most studied. Ribosomes are composed of ribosomal proteins (RPs) and ribosomal RNA (rRNA). RPs and multiple other factors are necessary for the processing of pre-rRNA, the assembly of ribosomal subunits, their export to the cytoplasm and for the final assembly of subunits into a ribosome. Haploinsufficiency of certain RPs causes DBA, whereas mutations in other factors cause various other ribosomopathies. Despite the general nature of their underlying defects, the clinical manifestations of ribosomopathies differ. In DBA, for example, red blood cell pathology is especially evident. In addition, individuals with DBA often have malformations of limbs, the face and various organs, and also have an increased risk of cancer. Common features shared among human DBA and animal models have emerged, such as small body size, eye defects, duplication or overgrowth of ectoderm-derived structures, and hematopoietic defects. Phenotypes of ribosomopathies are mediated both by p53-dependent and -independent pathways. The current challenge is to identify differences in response to ribosomal stress that lead to specific tissue defects in various ribosomopathies. Here, we review recent findings in this field, with a particular focus on animal models, and discuss how, in some cases, the different phenotypes of ribosomopathies might arise from differences in the spatiotemporal expression of the affected genes. Summary: This paper reviews recent data on Diamond Blackfan anemia and discusses them in connection with other ribosomopathies.
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Affiliation(s)
- Nadia Danilova
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Hanna T Gazda
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA Broad Institute, Cambridge, MA 02142, USA
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22
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Zhou H, Skolnick J. A knowledge-based approach for predicting gene-disease associations. Bioinformatics 2016; 32:2831-8. [PMID: 27283949 DOI: 10.1093/bioinformatics/btw358] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION Recent advances of next-generation sequence technologies have made it possible to rapidly and inexpensively identify gene variations. Knowing the disease association of these gene variations is important for early intervention to treat deadly diseases and provide possible targets to cure these diseases. Genome-wide association studies (GWAS) have identified many individual genes associated with common diseases. To exploit the large amount of data obtained from GWAS studies and leverage our understanding of common as well as rare diseases, we have developed a knowledge-based approach to predict gene-disease associations. We first derive gene-gene mutual information by utilizing the cooccurrence of genes in known gene-disease association data. Subsequently, the mutual information is combined with known protein-protein interaction networks by a boosted tree regression method. RESULTS The method called Know-GENE is compared with the method of random walking on the heterogeneous network using the same input data. For a set of 960 diseases, using the same training data in testing in 3-fold cross-validation, the average recall rate within the top ranked 100 genes by Know-GENE is 65.0% compared with 37.9% by the state of the art random walking on heterogeneous network. This significant improvement is mostly due to the inclusion of knowledge-based mutual information. AVAILABILITY AND IMPLEMENTATION Predictions for genes associated with the 960 diseases are available at http://cssb2.biology.gatech.edu/knowgene CONTACT : skolnick@gatech.edu.
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Affiliation(s)
- Hongyi Zhou
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeffrey Skolnick
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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23
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Bielczyk-Maczyńska E, Lam Hung L, Ferreira L, Fleischmann T, Weis F, Fernández-Pevida A, Harvey SA, Wali N, Warren AJ, Barroso I, Stemple DL, Cvejic A. The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish. PLoS Genet 2015; 11:e1005677. [PMID: 26624285 PMCID: PMC4666468 DOI: 10.1371/journal.pgen.1005677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
Ribosome biogenesis is a ubiquitous and essential process in cells. Defects in ribosome biogenesis and function result in a group of human disorders, collectively known as ribosomopathies. In this study, we describe a zebrafish mutant with a loss-of-function mutation in nol9, a gene that encodes a non-ribosomal protein involved in rRNA processing. nol9sa1022/sa1022 mutants have a defect in 28S rRNA processing. The nol9sa1022/sa1022 larvae display hypoplastic pancreas, liver and intestine and have decreased numbers of hematopoietic stem and progenitor cells (HSPCs), as well as definitive erythrocytes and lymphocytes. In addition, ultrastructural analysis revealed signs of pathological processes occurring in endothelial cells of the caudal vein, emphasizing the complexity of the phenotype observed in nol9sa1022/sa1022 larvae. We further show that both the pancreatic and hematopoietic deficiencies in nol9sa1022/sa1022 embryos were due to impaired cell proliferation of respective progenitor cells. Interestingly, genetic loss of Tp53 rescued the HSPCs but not the pancreatic defects. In contrast, activation of mRNA translation via the mTOR pathway by L-Leucine treatment did not revert the erythroid or pancreatic defects. Together, we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics. The use of this genetically tractable model will enhance our understanding of the tissue-specific mechanisms following impaired ribosome biogenesis in the context of an intact vertebrate.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Laure Lam Hung
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tobias Fleischmann
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Félix Weis
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Antonio Fernández-Pevida
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Steven A. Harvey
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan J. Warren
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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24
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Brombin A, Joly JS, Jamen F. New tricks for an old dog: ribosome biogenesis contributes to stem cell homeostasis. Curr Opin Genet Dev 2015; 34:61-70. [PMID: 26343009 DOI: 10.1016/j.gde.2015.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 01/21/2023]
Abstract
Although considered a 'house-keeping' function, ribosome biogenesis is regulated differently between cells and can be modulated in a cell-type-specific manner. These differences are required to generate specialized ribosomes that contribute to the translational control of gene expression by selecting mRNA subsets to be translated. Thus, differences in ribosome biogenesis between stem and differentiated cells indirectly contribute to determine cell identity. The concept of the existence of stem cell-specific mechanisms of ribosome biogenesis has progressed from an attractive theory to a useful working model with important implications for basic and medical research.
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Affiliation(s)
- Alessandro Brombin
- CASBAH Group, University Paris-Saclay, University Paris-Sud, UMR CNRS 9197, Neuroscience Paris-Saclay Institute (NeuroPSI), Bât. 32/33, 1 Avenue de la Terrasse, F-91190 Gif-sur-Yvette, France; INRA, USC 1126, F-91190 Gif-sur-Yvette, France
| | - Jean-Stéphane Joly
- CASBAH Group, University Paris-Saclay, University Paris-Sud, UMR CNRS 9197, Neuroscience Paris-Saclay Institute (NeuroPSI), Bât. 32/33, 1 Avenue de la Terrasse, F-91190 Gif-sur-Yvette, France; INRA, USC 1126, F-91190 Gif-sur-Yvette, France
| | - Françoise Jamen
- CASBAH Group, University Paris-Saclay, University Paris-Sud, UMR CNRS 9197, Neuroscience Paris-Saclay Institute (NeuroPSI), Bât. 32/33, 1 Avenue de la Terrasse, F-91190 Gif-sur-Yvette, France; INRA, USC 1126, F-91190 Gif-sur-Yvette, France.
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25
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Yelick PC, Trainor PA. Ribosomopathies: Global process, tissue specific defects. Rare Dis 2015; 3:e1025185. [PMID: 26442198 PMCID: PMC4590025 DOI: 10.1080/21675511.2015.1025185] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 01/01/2023] Open
Abstract
Disruptions in ribosomal biogenesis would be expected to have global and in fact lethal effects on a developing organism. However, mutations in ribosomal protein genes have been shown in to exhibit tissue specific defects. This seemingly contradictory finding - that globally expressed genes thought to play fundamental housekeeping functions can in fact exhibit tissue and cell type specific functions - provides new insight into roles for ribosomes, the protein translational machinery of the cell, in regulating normal development and disease. Furthermore it illustrates the surprisingly dynamic nature of processes regulating cell type specific protein translation. In this review, we discuss our current knowledge of a variety of ribosomal protein mutations associated with human disease, and models to better understand the molecular mechanisms associated with each. We use specific examples to emphasize both the similarities and differences between the effects of various human ribosomal protein mutations. Finally, we discuss areas of future study that are needed to further our understanding of the role of ribosome biogenesis in normal development, and possible approaches that can be used to treat debilitating ribosomopathy diseases.
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Affiliation(s)
| | - Paul A Trainor
- Stowers Institute ; Kansas City, MO USA ; University of Kansas Medical Center ; Kansas City, KS USA
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26
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Buszczak M, Signer RAJ, Morrison SJ. Cellular differences in protein synthesis regulate tissue homeostasis. Cell 2015; 159:242-51. [PMID: 25303523 DOI: 10.1016/j.cell.2014.09.016] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 12/12/2022]
Abstract
Although sometimes considered a "house-keeping" function, multiple aspects of protein synthesis are regulated differently among somatic cells, including stem cells, and can be modulated in a cell-type-specific manner. These differences are required to establish and maintain differences in cell identity, cell function, tissue homeostasis, and tumor suppression.
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Affiliation(s)
- Michael Buszczak
- Department of Molecular Biology, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert A J Signer
- Howard Hughes Medical Institute, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sean J Morrison
- Howard Hughes Medical Institute, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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27
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Armistead J, Triggs-Raine B. Diverse diseases from a ubiquitous process: the ribosomopathy paradox. FEBS Lett 2014; 588:1491-500. [PMID: 24657617 DOI: 10.1016/j.febslet.2014.03.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/08/2014] [Accepted: 03/12/2014] [Indexed: 01/03/2023]
Abstract
Collectively, the ribosomopathies are caused by defects in ribosome biogenesis. Although these disorders encompass deficiencies in a ubiquitous and fundamental process, the clinical manifestations are extremely variable and typically display tissue specificity. Research into this paradox has offered fascinating new insights into the role of the ribosome in the regulation of mRNA translation, cell cycle control, and signaling pathways involving TP53, MYC and mTOR. Several common features of ribosomopathies such as small stature, cancer predisposition, and hematological defects, point to how these diverse diseases may be related at a molecular level.
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Affiliation(s)
- Joy Armistead
- Department of Biochemistry and Medical Genetics, The University of Manitoba, 745 Bannatyne Ave., Winnipeg, MB R3E 0J9, Canada
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, The University of Manitoba, 745 Bannatyne Ave., Winnipeg, MB R3E 0J9, Canada; The Manitoba Institute of Child Health, 715 McDermot Ave., Winnipeg, MB R3E 3P4, Canada.
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28
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Cofer ZC, Matthews RP. Zebrafish Models of Biliary Atresia and Other Infantile Cholestatic Diseases. CURRENT PATHOBIOLOGY REPORTS 2014. [DOI: 10.1007/s40139-014-0040-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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A novel keratin18 promoter that drives reporter gene expression in the intrahepatic and extrahepatic biliary system allows isolation of cell-type specific transcripts from zebrafish liver. Gene Expr Patterns 2014; 14:62-8. [PMID: 24394404 DOI: 10.1016/j.gep.2013.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 12/05/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
Abstract
Heritable and acquired biliary disorders are an important cause of acute and chronic human liver disease. Biliary development and physiology have been studied extensively in rodent models and more recently, zebrafish have been used to uncover pathogenic mechanisms and potential therapies for these conditions. Here we report development of novel transgenic lines labeling the intrahepatic and extrahepatic biliary system of zebrafish larvae that can be used for lineage tracing and isolation of biliary-specific RNAs from mixed populations of liver cells. We show that GFP expression driven by a 4.4 kilobase promoter fragment from the zebrafish keratin18 (krt18) gene allows visualization of all components of the developing biliary system as early as 3 days post-fertilization. In addition, expression of a ribosomal fusion protein (EGFP-Rpl10a) in krt18:TRAP transgenic fish allows for enrichment of translated biliary cell mRNAs via translating ribosome affinity purification (TRAP). Future studies utilizing these reagents will enhance our understanding of the morphologic and molecular processes involved in biliary development and disease.
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