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Zhu B, Guo Y, Lv S, Ling X, You S. Hepatic phenotypes of EFL1-related Shwachman-Diamond syndrome in a biopsy-validated study. J Hepatol 2024:S0168-8278(24)00328-3. [PMID: 38703831 DOI: 10.1016/j.jhep.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Affiliation(s)
- Bing Zhu
- Department of Liver Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | | | - Sa Lv
- Department of Liver Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | | | - Shaoli You
- Department of Liver Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China.
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2
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Wang M, Vulcano S, Xu C, Xie R, Peng W, Wang J, Liu Q, Jia L, Li Z, Li Y. Potentials of ribosomopathy gene as pharmaceutical targets for cancer treatment. J Pharm Anal 2024; 14:308-320. [PMID: 38618250 PMCID: PMC11010632 DOI: 10.1016/j.jpha.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 04/16/2024] Open
Abstract
Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality. Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenesis can result in different types of ribosomopathies in clinic, collectively known as ribosomopathy genes. Emerging data suggest that ribosomopathy patients exhibit a significantly heightened susceptibility to cancer. Abnormal ribosome biogenesis and dysregulation of some ribosomopathy genes have also been found to be intimately associated with cancer development. The correlation between ribosome biogenesis or ribosomopathy and the development of malignancies has been well established. This work aims to review the recent advances in the research of ribosomopathy genes among human cancers and meanwhile, to excavate the potential role of these genes, which have not or rarely been reported in cancer, in the disease development across cancers. We plan to establish a theoretical framework between the ribosomopathy gene and cancer development, to further facilitate the potential of these genes as diagnostic biomarker as well as pharmaceutical targets for cancer treatment.
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Affiliation(s)
- Mengxin Wang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Stephen Vulcano
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery New York, New York, NY, 10021, USA
| | - Changlu Xu
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Renjian Xie
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Weijie Peng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Qiaojun Liu
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhi Li
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Yumei Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
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Arai H, Matsui H, Chi S, Utsu Y, Masuda S, Aotsuka N, Minami Y. Germline Variants and Characteristic Features of Hereditary Hematological Malignancy Syndrome. Int J Mol Sci 2024; 25:652. [PMID: 38203823 PMCID: PMC10779750 DOI: 10.3390/ijms25010652] [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: 11/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the proliferation of genetic testing, pathogenic germline variants predisposing to hereditary hematological malignancy syndrome (HHMS) have been identified in an increasing number of genes. Consequently, the field of HHMS is gaining recognition among clinicians and scientists worldwide. Patients with germline genetic abnormalities often have poor outcomes and are candidates for allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT using blood from a related donor should be carefully considered because of the risk that the patient may inherit a pathogenic variant. At present, we now face the challenge of incorporating these advances into clinical practice for patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and optimizing the management and surveillance of patients and asymptomatic carriers, with the limitation that evidence-based guidelines are often inadequate. The 2016 revision of the WHO classification added a new section on myeloid malignant neoplasms, including MDS and AML with germline predisposition. The main syndromes can be classified into three groups. Those without pre-existing disease or organ dysfunction; DDX41, TP53, CEBPA, those with pre-existing platelet disorders; ANKRD26, ETV6, RUNX1, and those with other organ dysfunctions; SAMD9/SAMD9L, GATA2, and inherited bone marrow failure syndromes. In this review, we will outline the role of the genes involved in HHMS in order to clarify our understanding of HHMS.
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Affiliation(s)
- Hironori Arai
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, Tsukiji, Chuoku 104-0045, Japan;
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8665, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
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4
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Oyarbide U, Crane GM, Corey SJ. The metabolic basis of inherited neutropenias. Br J Haematol 2024; 204:45-55. [PMID: 38049194 DOI: 10.1111/bjh.19192] [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: 08/29/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Neutrophils are the shortest-lived blood cells, which requires a prodigious degree of proliferation and differentiation to sustain physiologically sufficient numbers and be poised to respond quickly to infectious emergencies. More than 107 neutrophils are produced every minute in an adult bone marrow-a process that is tightly regulated by a small group of cytokines and chemical mediators and dependent on nutrients and energy. Like granulocyte colony-stimulating factor, the primary growth factor for granulopoiesis, they stimulate signalling pathways, some affecting metabolism. Nutrient or energy deficiency stresses the survival, proliferation, and differentiation of neutrophils and their precursors. Thus, it is not surprising that monogenic disorders related to metabolism exist that result in neutropenia. Among these are pathogenic mutations in HAX1, G6PC3, SLC37A4, TAFAZZIN, SBDS, EFL1 and the mitochondrial disorders. These mutations perturb carbohydrate, lipid and/or protein metabolism. We hypothesize that metabolic disturbances may drive the pathogenesis of a subset of inherited neutropenias just as defects in DNA damage response do in Fanconi anaemia, telomere maintenance in dyskeratosis congenita and ribosome formation in Diamond-Blackfan anaemia. Greater understanding of metabolic pathways in granulopoiesis will identify points of vulnerability in production and may point to new strategies for the treatment of neutropenias.
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Affiliation(s)
- Usua Oyarbide
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
| | - Genevieve M Crane
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Seth J Corey
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
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5
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Kawashima N, Oyarbide U, Cipolli M, Bezzerri V, Corey SJ. Shwachman-Diamond syndromes: clinical, genetic, and biochemical insights from the rare variants. Haematologica 2023; 108:2594-2605. [PMID: 37226705 PMCID: PMC10543188 DOI: 10.3324/haematol.2023.282949] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Shwachman-Diamond syndrome is a rare inherited bone marrow failure syndrome characterized by neutropenia, exocrine pancreatic insufficiency, and skeletal abnormalities. In 10-30% of cases, transformation to a myeloid neoplasm occurs. Approximately 90% of patients have biallelic pathogenic variants in the SBDS gene located on human chromosome 7q11. Over the past several years, pathogenic variants in three other genes have been identified to cause similar phenotypes; these are DNAJC21, EFL1, and SRP54. Clinical manifestations involve multiple organ systems and those classically associated with the Shwachman-Diamond syndrome (bone, blood, and pancreas). Neurocognitive, dermatologic, and retinal changes may also be found. There are specific gene-phenotype differences. To date, SBDS, DNAJC21, and SRP54 variants have been associated with myeloid neoplasia. Common to SBDS, EFL1, DNAJC21, and SRP54 is their involvement in ribosome biogenesis or early protein synthesis. These four genes constitute a common biochemical pathway conserved from yeast to humans that involve early stages of protein synthesis and demonstrate the importance of this synthetic pathway in myelopoiesis.
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Affiliation(s)
- Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH
| | - Usua Oyarbide
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH
| | | | | | - Seth J Corey
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH.
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6
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Reddy T, Kotha R, M A. An Unusual Presentation of Extremely Early Neonatal Cirrhosis in Shwachman-Diamond Syndrome: A Case Report. Cureus 2023; 15:e38583. [PMID: 37288222 PMCID: PMC10241746 DOI: 10.7759/cureus.38583] [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] [Accepted: 05/05/2023] [Indexed: 06/09/2023] Open
Abstract
Exocrine pancreatic insufficiency, haematological dysfunction, and skeletal abnormalities are the three clinical characteristics of the rare inherited bone marrow failure syndrome (IBMFS), known as Shwachman-Diamond syndrome (SDS). Cirrhosis at a neonatal age is uncommon and is typically not documented, as in neonatal presentation. Here, we present a case of SDS in which bi-cytopenia with macro-nodular cirrhosis emerged before the age of one month. Utilising genetic testing on the infant and both parents, we were able to confirm the diagnosis. We were expecting a higher-level liver transplant set-up, but the infant passed away in the interim. Genetic studies play a significant part in the diagnosis of difficult cases.
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Affiliation(s)
- Tejaswy Reddy
- Department of Neonatology, Niloufer Hospital, Hyderabad, IND
| | - Rakesh Kotha
- Department of Neonatology, Osmania Medical College, Hyderabad, IND
| | - Alimelu M
- Department of Neonatology, Niloufer Hospital, Hyderabad, IND
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7
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Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.2022.11.001] [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: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
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Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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8
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Reilly CR, Shimamura A. Predisposition to myeloid malignancies in Shwachman-Diamond syndrome: biological insights and clinical advances. Blood 2023; 141:1513-1523. [PMID: 36542827 PMCID: PMC10082379 DOI: 10.1182/blood.2022017739] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) is an inherited multisystem ribosomopathy characterized by exocrine pancreatic deficiency, bone marrow failure, and predisposition to myeloid malignancies. The pathobiology of SDS results from impaired ribosomal maturation due to the deficiency of SBDS and the inability to evict the antiassociation factor eIF6 from the 60S ribosomal subunit. Clinical outcomes for patients with SDS who develop myeloid malignancies are extremely poor because of high treatment-related toxicities and a high rate of refractory disease/relapse even after allogeneic hematopoietic stem cell transplant (HSCT). Registry data indicate that outcomes are improved for patients with SDS who undergo routine bone marrow surveillance and receive an HSCT before developing an overt malignancy. However, the optimal approach to hematologic surveillance and the timing of HSCT for patients with SDS is not clearly established. Recent studies have elucidated distinct patterns of somatic blood mutations in patients with SDS that either alleviate the ribosome defect via somatic rescue (heterozygous EIF6 inactivation) or disrupt cellular checkpoints, resulting in increased leukemogenic potential (heterozygous TP53 inactivation). Genomic analysis revealed that most myeloid malignancies in patients with SDS have biallelic loss-of-function TP53 mutations. Single-cell DNA sequencing of SDS bone marrow samples can detect premalignant biallelic TP53-mutated clones before clinical diagnosis, suggesting that molecular surveillance may enhance the detection of incipient myeloid malignancies when HSCT may be most effective. Here, we review the clinical, genetic, and biologic features of SDS. In addition, we present evidence supporting the hematologic surveillance for patients with SDS that incorporates clinical, pathologic, and molecular data to risk stratify patients and prioritize transplant evaluation for patients with SDS with high-risk features.
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Affiliation(s)
- Christopher R. Reilly
- Division of Hematological Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Akiko Shimamura
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
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9
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Elliff J, Biswas A, Roshan P, Kuppa S, Patterson A, Mattice J, Chinnaraj M, Burd R, Walker SE, Pozzi N, Antony E, Bothner B, Origanti S. Dynamic states of eIF6 and SDS variants modulate interactions with uL14 of the 60S ribosomal subunit. Nucleic Acids Res 2023; 51:1803-1822. [PMID: 36651285 PMCID: PMC9976893 DOI: 10.1093/nar/gkac1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
Assembly of ribosomal subunits into active ribosomal complexes is integral to protein synthesis. Release of eIF6 from the 60S ribosomal subunit primes 60S to associate with the 40S subunit and engage in translation. The dynamics of eIF6 interaction with the uL14 (RPL23) interface of 60S and its perturbation by somatic mutations acquired in Shwachman-Diamond Syndrome (SDS) is yet to be clearly understood. Here, by using a modified strategy to obtain high yields of recombinant human eIF6 we have uncovered the critical interface entailing eight key residues in the C-tail of uL14 that is essential for physical interactions between 60S and eIF6. Disruption of the complementary binding interface by conformational changes in eIF6 disease variants provide a mechanism for weakened interactions of variants with the 60S. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) analyses uncovered dynamic configurational rearrangements in eIF6 induced by binding to uL14 and exposed an allosteric interface regulated by the C-tail of eIF6. Disrupting key residues in the eIF6-60S binding interface markedly limits proliferation of cancer cells, which highlights the significance of therapeutically targeting this interface. Establishing these key interfaces thus provide a therapeutic framework for targeting eIF6 in cancers and SDS.
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Affiliation(s)
- Jonah Elliff
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
- Department of Immunology, The University of Iowa, Iowa City, IA 52242, USA
| | - Aparna Biswas
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Poonam Roshan
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Jenna Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Mathivanan Chinnaraj
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Ryan Burd
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Sarah E Walker
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Nicola Pozzi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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10
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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11
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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12
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Ma D, Liu P, Wen J, Gu Y, Yang Z, Lan J, Fan H, Liu Z, Guo D. FCN3 inhibits the progression of hepatocellular carcinoma by suppressing SBDS-mediated blockade of the p53 pathway. Int J Biol Sci 2023; 19:362-376. [PMID: 36632465 PMCID: PMC9830510 DOI: 10.7150/ijbs.69784] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 11/07/2022] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third-leading cause of cancer deaths globally. Although considerable progress has been made in the treatment, clinical outcomes of HCC patients are still poor. Therefore, it is necessary to find novel prognostic factors upon which prevention and treatment strategies can be formulated. Ficolin-3 (FCN3) protein is a member of the human ficolin family. It activates complement through pathways associated with mannose-binding lectin-associated serine proteases. Herein, we identified that FCN3 was downregulated in HCC tissues and decreased FCN3 expression was closely related to poor prognosis. Overexpression of FCN3 induced apoptosis and inhibited cell proliferation via the p53 signaling pathway. Mechanistically, FCN3 modulated the nuclear translocation of eukaryotic initiation factor 6 (EIF6) by binding ribosome maturation factor (SBDS), which induced ribosomal stress and activation of the p53 pathway. In addition, Y-Box Binding Protein 1 (YBX1) involved in the transcription and translation level regulation of FCN3 to SBDS. Besides, a negative feedback loop in the downstream of FCN3 involving p53, YBX1 and SBDS was identified.
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Affiliation(s)
- Dong Ma
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.,Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qinghai University, Xining, 810000, P.R. China
| | - Pengpeng Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.,Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, P.R. China
| | - Junjun Wen
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China
| | - Yang Gu
- Department of Hepatobiliary and Pancreas, The First People's Hospital of Jingmen, Jingmen, 448000, P.R. China
| | - Zhangshuo Yang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China
| | - Jianwei Lan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.,Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, P.R. China
| | - Haining Fan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qinghai University, Xining, 810000, P.R. China.,✉ Corresponding authors: Deliang Guo. Tel.: +86-27-67812588; Fax: +86-27-8731935; E-mail: . Correspondence may also be addressed to Zhisu Liu. E-mail: and Haining Fan. E-mail:
| | - Zhisu Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.,✉ Corresponding authors: Deliang Guo. Tel.: +86-27-67812588; Fax: +86-27-8731935; E-mail: . Correspondence may also be addressed to Zhisu Liu. E-mail: and Haining Fan. E-mail:
| | - Deliang Guo
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.,✉ Corresponding authors: Deliang Guo. Tel.: +86-27-67812588; Fax: +86-27-8731935; E-mail: . Correspondence may also be addressed to Zhisu Liu. E-mail: and Haining Fan. E-mail:
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13
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Overcoming the Pitfalls of Next-Generation Sequencing-Based Molecular Diagnosis of Shwachman-Diamond Syndrome. J Mol Diagn 2022; 24:1240-1253. [PMID: 36162759 DOI: 10.1016/j.jmoldx.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/30/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is the second most common cause of exocrine pancreatic insufficiency, and 90% of patients carry mutations in the SBDS gene, the most common being the c.183_184delinsCT and c.258+2T>C variants. However, precise detection of these most contributory variants by conventional short-read next-generation sequencing data analysis is limited because of the SBDS/SBDSP1 highly homologous sequences. In this study, an efficient approach was established to infer the haplotype of SBDS based on the expectation-maximization algorithm. The workflow was retrospectively applied to detect the two most common SBDS variants in a Chinese SDS high-risk cohort, and a systematic comparison of variant detection results was performed between the workflow and conventional next-generation sequencing analysis based on Sanger sequencing validation. Among the Chinese SDS high-risk cohort (n = 47) and their available parents (n = 64), the established workflow improved the diagnostic rate for these two variants by 27.7% (95% CI, 15.6%-42.6%) compared with conventional analysis. For overall variant detection, the established workflow achieved 100% (95% CI, 92.5%-100%) concordance with Sanger sequencing, whereas conventional analysis showed only 65.8% accuracy; these results included 25.2% with missed variant calls, 7.2% with diagnosed but inaccurate variant calls, and 1.8% with false-positive calls. With its favorable result in both SDS patient diagnosis and carrier detection performance, the provided workflow showed its potential in clinical application for SDS molecular diagnosis.
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14
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Pérez-Juárez J, Tapia-Vieyra JV, Gutiérrez-Magdaleno G, Sánchez-Puig N. Altered Conformational Landscape upon Sensing Guanine Nucleotides in a Disease Mutant of Elongation Factor-like 1 (EFL1) GTPase. Biomolecules 2022; 12:biom12081141. [PMID: 36009035 PMCID: PMC9405973 DOI: 10.3390/biom12081141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
The final maturation step of the 60S ribosomal subunit requires the release of eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) to enter the pool of mature ribosomes capable of engaging in translation. This process is mediated by the concerted action of the Elongation Factor-like 1 (human EFL1, yeast Efl1) GTPase and its effector, the Shwachman-Bodian-Diamond syndrome protein (human SBDS, yeast Sdo1). Mutations in these proteins prevent the release of eIF6 and cause a disease known as Shwachman–Diamond Syndrome (SDS). While some mutations in EFL1 or SBDS result in insufficient proteins to meet the cell production of mature large ribosomal subunits, others do not affect the expression levels with unclear molecular defects. We studied the functional consequences of one such mutation using Saccharomyces cerevisiae Efl1 R1086Q, equivalent to human EFL1 R1095Q described in SDS patients. We characterised the enzyme kinetics and energetic basis outlining the recognition of this mutant to guanine nucleotides and Sdo1, and their interplay in solution. From our data, we propose a model where the conformational change in Efl1 depends on a long-distance network of interactions that are disrupted in mutant R1086Q, whereby Sdo1 and the guanine nucleotides no longer elicit the conformational changes previously described in the wild-type protein. These findings point to the molecular malfunction of an EFL1 mutant and its possible impact on SDS pathology.
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Affiliation(s)
- Jesús Pérez-Juárez
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
| | - Juana Virginia Tapia-Vieyra
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
| | - Gabriel Gutiérrez-Magdaleno
- División de Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpan Avenida Vasco de Quiroga 4871, Ciudad de Mexico 05348, Mexico
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Correspondence: ; Tel.: +52-55-56224468
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15
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Taha I, Foroni S, Valli R, Frattini A, Roccia P, Porta G, Zecca M, Bergami E, Cipolli M, Pasquali F, Danesino C, Scotti C, Minelli A. Case Report: Heterozygous Germline Variant in EIF6 Additional to Biallelic SBDS Pathogenic Variants in a Patient With Ribosomopathy Shwachman–Diamond Syndrome. Front Genet 2022; 13:896749. [PMID: 36035165 PMCID: PMC9411639 DOI: 10.3389/fgene.2022.896749] [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: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Shwachman–Diamond syndrome (SDS) is a rare autosomal recessive ribosomopathy mainly characterized by exocrine pancreatic insufficiency, skeletal alterations, neutropenia, and a relevant risk of hematological transformation. At least 90% of SDS patients have pathogenic variants in SBDS, the first gene associated with the disease with very low allelic heterogeneity; three variants, derived from events of genetic conversion between SBDS and its pseudogene, SBDSP1, provided the alleles observed in about 62% of SDS patients. Methods: We performed a reanalysis of the available WES files of a group of SDS patients with biallelic SBDS pathogenic variants, studying the results by next bioinformatic and protein structural analysis. Parallelly, careful clinical attention was given to the patient focused in this study. Results: We found and confirmed in one SDS patient a germline heterozygous missense variant (c.100T>C; p.Phe34Leu) in the EIF6 gene. This variant, inherited from his mother, has a very low frequency, and it is predicted as pathogenic, according to several in silico prediction tools. The protein structural analysis also envisages the variant could reduce the binding to the nascent 60S ribosomal. Conclusion: This study focused on the hypothesis that the EIF6 germline variant mimics the effect of somatic deletions of chromosome 20, always including the locus of this gene, and similarly may rescue the ribosomal stress and ribosomal dysfunction due to SBDS mutations. It is likely that this rescue may contribute to the stable and not severe hematological status of the proband, but a definite answer on the role of this EIF6 variant can be obtained only by adding a functional layer of evidence. In the future, these results are likely to be useful for selected cases in personalized medicine and therapy.
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Affiliation(s)
- Ibrahim Taha
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Selena Foroni
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Roberto Valli
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Annalisa Frattini
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Istituto di Ricerca Genetica e Biomedica, CNR, Milano, Italy
| | - Pamela Roccia
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giovanni Porta
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Marco Zecca
- Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico S, Matteo, Pavia, Italy
| | - Elena Bergami
- Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico S, Matteo, Pavia, Italy
| | - Marco Cipolli
- Centro Fibrosi Cistica, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Francesco Pasquali
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cesare Danesino
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Claudia Scotti
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Antonella Minelli
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- *Correspondence: Antonella Minelli,
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16
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Phenotypic Variation in Two Siblings Affected with Shwachman-Diamond Syndrome: The Use of Expert Variant Interpreter (eVai) Suggests Clinical Relevance of a Variant in the KMT2A Gene. Genes (Basel) 2022; 13:genes13081314. [PMID: 35893049 PMCID: PMC9394309 DOI: 10.3390/genes13081314] [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: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction. Shwachman-Diamond Syndrome (SDS) is an autosomal-recessive disorder characterized by neutropenia, pancreatic exocrine insufficiency, skeletal dysplasia, and an increased risk for leukemic transformation. Biallelic mutations in the SBDS gene have been found in about 90% of patients. The clinical spectrum of SDS in patients is wide, and variability has been noticed between different patients, siblings, and even within the same patient over time. Herein, we present two SDS siblings (UPN42 and UPN43) carrying the same SBDS mutations and showing relevant differences in their phenotypic presentation. Study aim. We attempted to understand whether other germline variants, in addition to SBDS, could explain some of the clinical variability noticed between the siblings. Methods. Whole-exome sequencing (WES) was performed. Human Phenotype Ontology (HPO) terms were defined for each patient, and the WES data were analyzed using the eVai and DIVAs platforms. Results. In UPN43, we found and confirmed, using Sanger sequencing, a novel de novo variant (c.10663G > A, p.Gly3555Ser) in the KMT2A gene that is associated with autosomal-dominant Wiedemann−Steiner Syndrome. The variant is classified as pathogenic according to different in silico prediction tools. Interestingly, it was found to be related to some of the HPO terms that describe UPN43. Conclusions. We postulate that the KMT2A variant found in UPN43 has a concomitant and co-occurring clinical effect, in addition to SBDS mutation. This dual molecular effect, supported by in silico prediction, could help to understand some of the clinical variations found among the siblings. In the future, these new data are likely to be useful for personalized medicine and therapy for selected cases.
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17
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A Comparative Molecular Dynamics Study of Selected Point Mutations in the Shwachman–Bodian–Diamond Syndrome Protein SBDS. Int J Mol Sci 2022; 23:ijms23147938. [PMID: 35887285 PMCID: PMC9320453 DOI: 10.3390/ijms23147938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 01/27/2023] Open
Abstract
The Shwachman–Diamond Syndrome (SDS) is an autosomal recessive disease whose majority of patients display mutations in a ribosome assembly protein named Shwachman–Bodian–Diamond Syndrome protein (SBDS). A specific therapy for treating this rare disease is missing, due to the lack of knowledge of the molecular mechanisms responsible for its pathogenesis. Starting from the observation that SBDS single-point mutations, localized in different domains of the proteins, are responsible for an SDS phenotype, we carried out the first comparative Molecular Dynamics simulations on three SBDS mutants, namely R19Q, R126T and I212T. The obtained 450-ns long trajectories were compared with those returned by both the open and closed forms of wild type SBDS and strongly indicated that two distinct conformations (open and closed) are both necessary for the proper SBDS function, in full agreement with recent experimental observations. Our study supports the hypothesis that the SBDS function is governed by an allosteric mechanism involving domains I and III and provides new insights into SDS pathogenesis, thus offering a possible starting point for a specific therapeutic option.
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18
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Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [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: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
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Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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19
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Jaako P, Faille A, Tan S, Wong CC, Escudero-Urquijo N, Castro-Hartmann P, Wright P, Hilcenko C, Adams DJ, Warren AJ. eIF6 rebinding dynamically couples ribosome maturation and translation. Nat Commun 2022; 13:1562. [PMID: 35322020 PMCID: PMC8943182 DOI: 10.1038/s41467-022-29214-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/03/2022] [Indexed: 02/05/2023] Open
Abstract
Protein synthesis is a cyclical process consisting of translation initiation, elongation, termination and ribosome recycling. The release factors SBDS and EFL1—both mutated in the leukemia predisposition disorder Shwachman-Diamond syndrome — license entry of nascent 60S ribosomal subunits into active translation by evicting the anti-association factor eIF6 from the 60S intersubunit face. We find that in mammalian cells, eIF6 holds all free cytoplasmic 60S subunits in a translationally inactive state and that SBDS and EFL1 are the minimal components required to recycle these 60S subunits back into additional rounds of translation by evicting eIF6. Increasing the dose of eIF6 in mice in vivo impairs terminal erythropoiesis by sequestering post-termination 60S subunits in the cytoplasm, disrupting subunit joining and attenuating global protein synthesis. These data reveal that ribosome maturation and recycling are dynamically coupled by a mechanism that is disrupted in an inherited leukemia predisposition disorder. Jaako et al. discover a conserved tier of translational control that dynamically couples ribosome assembly and recycling. This mechanism is corrupted in an inherited bone marrow failure disorder associated with an increased risk of blood cancer.
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Affiliation(s)
- Pekka Jaako
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Alexandre Faille
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Shengjiang Tan
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Chi C Wong
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Department of Pathology, Cambridge University Hospitals, Hills Road, Cambridge, CB2 0QQ, UK
| | - Norberto Escudero-Urquijo
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Pablo Castro-Hartmann
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Penny Wright
- Department of Pathology, Cambridge University Hospitals, Hills Road, Cambridge, CB2 0QQ, UK
| | - Christine Hilcenko
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK. .,Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
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20
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Revy P, Donadieu J. EFL1 deficiency: a little is better than nothing. Blood 2021; 138:2016-2018. [PMID: 34821936 DOI: 10.1182/blood.2021012724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/11/2021] [Indexed: 11/20/2022] Open
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21
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Lee S, Shin CH, Lee J, Jeong SD, Hong CR, Kim JD, Kim AR, Park B, Son SJ, Kokhan O, Yoo T, Ko JS, Sohn YB, Kim OH, Ko JM, Cho TJ, Wright NT, Seong JK, Jin SW, Kang HJ, Kim HH, Choi M. Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome. Blood 2021; 138:2117-2128. [PMID: 34115847 DOI: 10.1182/blood.2021010913] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS; OMIM #260400) is caused by variants in SBDS (Shwachman-Bodian-Diamond syndrome gene), which encodes a protein that plays an important role in ribosome assembly. Recent reports suggest that recessive variants in EFL1 are also responsible for SDS. However, the precise genetic mechanism that leads to EFL1-induced SDS remains incompletely understood. Here we present 3 unrelated Korean SDS patients who carry biallelic pathogenic variants in EFL1 with biased allele frequencies, resulting from a bone marrow-specific somatic uniparental disomy in chromosome 15. The recombination events generated cells that were homozygous for the relatively milder variant, allowing for the evasion of catastrophic physiologic consequences. However, the milder EFL1 variant was still solely able to impair 80S ribosome assembly and induce SDS features in cell line and animal models. The loss of EFL1 resulted in a pronounced inhibition of terminal oligopyrimidine element-containing ribosomal protein transcript 80S assembly. Therefore, we propose a more accurate pathogenesis mechanism of EFL1 dysfunction that eventually leads to aberrant translational control and ribosomopathy.
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Affiliation(s)
- Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Chang Hoon Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Jawon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Seong Dong Jeong
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Che Ry Hong
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jun-Dae Kim
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Ah-Ra Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Boryeong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Soo Jin Son
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, and
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, South Korea
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Sung Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University Hospital, Ajou University School of Medicine, Suwon, South Korea
| | - Ok-Hwa Kim
- Department of Pediatric Radiology, VIC 365 Children's Hospital, Incheon, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Tae-Joon Cho
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, and
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, South Korea
- Interdisciplinary Program for Bioinformatics-Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul, South Korea
| | - Suk-Won Jin
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Hyoung Jin Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
- Seoul National University Cancer Research Institute, Seoul, South Korea; and
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
- Institute for Future Medicine, Samsung Medical Center, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
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22
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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23
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Méndez-Godoy A, García-Montalvo D, Martínez-Castilla LP, Sánchez-Puig N. Evolutionary and functional relationships in the ribosome biogenesis SBDS and EFL1 protein families. Mol Genet Genomics 2021; 296:1263-1278. [PMID: 34453201 DOI: 10.1007/s00438-021-01814-w] [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: 03/17/2021] [Accepted: 08/15/2021] [Indexed: 11/25/2022]
Abstract
Nascent ribosomal 60S subunits undergo the last maturation steps in the cytoplasm. The last one involves removing the anti-association factor eIF6 from the 60S ribosomal surface by the joint action of the Elongation Factor-like 1 (EFL1) GTPase and the SBDS protein. Herein, we studied the evolutionary relationship of the EFL1 and EF-2 protein families and the functional conservation within EFL1 orthologues. Phylogenetic analysis demonstrated that the EFL1 proteins are exclusive of eukaryotes and share an evolutionary origin with the EF-2 and EF-G protein families. EFL1 proteins originated by gene duplication from the EF-2 proteins and specialized in ribosome maturation while the latter retained their function in translation. Some organisms have more than one EFL1 protein resulting from alternative splicing, while others are encoded in different genes originated by gene duplication. However, the function of these alternative EFL1 proteins is still unknown. We performed GTPase activity and complementation assays to study the functional conservation of EFL1 homologs alone and together with their SBDS counterparts. None of the orthologues or cross-species combinations could replace the function of the corresponding yeast EFL1•SBDS binomial. The complementation of SBDS interspecies chimeras indicates that domain 2 is vital for its function together with EFL1 and the 60S subunit. The results suggest a functional species-specificity and possible co-evolution between EFL1, SBDS, and the 60S ribosomal subunit. These findings set the basis for further studies directed to understand the molecular evolution of these proteins and their impact on ribosome biogenesis and disease.
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Affiliation(s)
- Alfonso Méndez-Godoy
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México.,Unit of Biochemistry, Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Daniel García-Montalvo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México
| | - León P Martínez-Castilla
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México.
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24
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Abstract
Indirect somatic genetic rescue (SGR) of a germline mutation is thought to be rare in inherited Mendelian disorders. Here, we establish that acquired mutations in the EIF6 gene are a frequent mechanism of SGR in Shwachman-Diamond syndrome (SDS), a leukemia predisposition disorder caused by a germline defect in ribosome assembly. Biallelic mutations in the SBDS or EFL1 genes in SDS impair release of the anti-association factor eIF6 from the 60S ribosomal subunit, a key step in the translational activation of ribosomes. Here, we identify diverse mosaic somatic genetic events (point mutations, interstitial deletion, reciprocal chromosomal translocation) in SDS hematopoietic cells that reduce eIF6 expression or disrupt its interaction with the 60S subunit, thereby conferring a selective advantage over non-modified cells. SDS-related somatic EIF6 missense mutations that reduce eIF6 dosage or eIF6 binding to the 60S subunit suppress the defects in ribosome assembly and protein synthesis across multiple SBDS-deficient species including yeast, Dictyostelium and Drosophila. Our data suggest that SGR is a universal phenomenon that may influence the clinical evolution of diverse Mendelian disorders and support eIF6 suppressor mimics as a therapeutic strategy in SDS.
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25
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van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol 2021; 16:e9828. [PMID: 32939983 PMCID: PMC7507402 DOI: 10.15252/msb.20209828] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole-genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane-associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line-specific essentiality in the Cancer Dependency Map (DepMap) project.
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Affiliation(s)
- Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Guihong Tan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jason Zi Wang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jing Hou
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Zhijian Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Maykel Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Andreia Dos Santos Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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26
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Kobar K, Collett K, Prykhozhij SV, Berman JN. Zebrafish Cancer Predisposition Models. Front Cell Dev Biol 2021; 9:660069. [PMID: 33987182 PMCID: PMC8112447 DOI: 10.3389/fcell.2021.660069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5-10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.
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Affiliation(s)
- Kim Kobar
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Keon Collett
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
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27
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Lv K, Gong C, Antony C, Han X, Ren JG, Donaghy R, Cheng Y, Pellegrino S, Warren AJ, Paralkar VR, Tong W. HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis. Cell Stem Cell 2021; 28:1275-1290.e9. [PMID: 33711283 DOI: 10.1016/j.stem.2021.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/28/2020] [Accepted: 02/05/2021] [Indexed: 01/28/2023]
Abstract
Impaired ribosome function is the underlying etiology in a group of bone marrow failure syndromes called ribosomopathies. However, how ribosomes are regulated remains poorly understood, as are approaches to restore hematopoietic stem cell (HSC) function loss because of defective ribosome biogenesis. Here we reveal a role of the E3 ubiquitin ligase HectD1 in regulating HSC function via ribosome assembly and protein translation. Hectd1-deficient HSCs exhibit a striking defect in transplantation ability and ex vivo maintenance concomitant with reduced protein synthesis and growth rate under stress conditions. Mechanistically, HectD1 ubiquitinates and degrades ZNF622, an assembly factor for the ribosomal 60S subunit. Hectd1 loss leads to accumulation of ZNF622 and the anti-association factor eIF6 on 60S, resulting in 60S/40S joining defects. Importantly, Znf622 depletion in Hectd1-deficient HSCs restored ribosomal subunit joining, protein synthesis, and HSC reconstitution capacity. These findings highlight the importance of ubiquitin-coordinated ribosome assembly in HSC regeneration.
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Affiliation(s)
- Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chujie Gong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charles Antony
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xu Han
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jian-Gang Ren
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan Donaghy
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ying Cheng
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Pellegrino
- Cambridge Institute for Medical Research, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Vikram R Paralkar
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Tong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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28
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Costantini A, Alm JJ, Tonelli F, Valta H, Huber C, Tran AN, Daponte V, Kirova N, Kwon YU, Bae JY, Chung WY, Tan S, Sznajer Y, Nishimura G, Näreoja T, Warren AJ, Cormier-Daire V, Kim OH, Forlino A, Cho TJ, Mäkitie O. Novel RPL13 Variants and Variable Clinical Expressivity in a Human Ribosomopathy With Spondyloepimetaphyseal Dysplasia. J Bone Miner Res 2021; 36:283-297. [PMID: 32916022 PMCID: PMC7988564 DOI: 10.1002/jbmr.4177] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/31/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022]
Abstract
Spondyloepimetaphyseal dysplasias (SEMDs) are a heterogeneous group of disorders with variable growth failure and skeletal impairments affecting the spine and long bone epiphyses and metaphyses. Here we report on four unrelated families with SEMD in which we identified two monoallelic missense variants and one monoallelic splice site variant in RPL13, encoding the ribosomal protein eL13. In two out of four families, we observed autosomal dominant inheritance with incomplete penetrance and variable clinical expressivity; the phenotypes of the mutation-positive subjects ranged from normal height with or without hip dysplasia to severe SEMD with severe short stature and marked skeletal dysplasia. In vitro studies on patient-derived dermal fibroblasts harboring RPL13 missense mutations demonstrated normal eL13 expression, with proper subcellular localization but reduced colocalization with eL28 (p < 0.001). Cellular functional defects in fibroblasts from mutation-positive subjects indicated a significant increase in the ratio of 60S subunits to 80S ribosomes (p = 0.007) and attenuated global translation (p = 0.017). In line with the human phenotype, our rpl13 mutant zebrafish model, generated by CRISPR-Cas9 editing, showed cartilage deformities at embryonic and juvenile stages. These findings extend the genetic spectrum of RPL13 mutations causing this novel human ribosomopathy with variable skeletal features. Our study underscores for the first time incomplete penetrance and broad phenotypic variability in SEMD-RPL13 type and confirms impaired ribosomal function. Furthermore, the newly generated rpl13 mutant zebrafish model corroborates the role of eL13 in skeletogenesis. © 2020 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR)..
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Affiliation(s)
- Alice Costantini
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jessica J Alm
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Tonelli
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Helena Valta
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Céline Huber
- Department of Clinical Genetics, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker Enfans Malades Hospital (AP-HP), Paris, France
| | - Anh N Tran
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Valentina Daponte
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Nadi Kirova
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yong-Uk Kwon
- Department of Orthopaedic Surgery, Busan Paik Hospital, Inje University College of Medicine, Busan, South Korea
| | - Jung Yun Bae
- Department of Orthopaedic Surgery, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, College of Medicine, Inje University, Busan, Republic of Korea
| | - Shengjiang Tan
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Yves Sznajer
- Centre de Génétique Humaine - CGH, Cliniques Universitaires St. Luc, UCL, Bruxelles, Belgium
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Tuomas Näreoja
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Alan J Warren
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valérie Cormier-Daire
- Department of Clinical Genetics, INSERM UMR 1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Necker Enfans Malades Hospital (AP-HP), Paris, France
| | - Ok-Hwa Kim
- Department of Radiology, I-Bone Hospital, Cheonan, Republic of Korea
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Tae-Joon Cho
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Folkhälsan Institute of Genetics, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
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29
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Gueiderikh A, Maczkowiak-Chartois F, Rouvet G, Souquère-Besse S, Apcher S, Diaz JJ, Rosselli F. Fanconi anemia A protein participates in nucleolar homeostasis maintenance and ribosome biogenesis. SCIENCE ADVANCES 2021; 7:7/1/eabb5414. [PMID: 33523834 PMCID: PMC7775781 DOI: 10.1126/sciadv.abb5414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/28/2020] [Indexed: 05/22/2023]
Abstract
Fanconi anemia (FA), the most common inherited bone marrow failure and leukemia predisposition syndrome, is generally attributed to alterations in DNA damage responses due to the loss of function of the DNA repair and replication rescue activities of the FANC pathway. Here, we report that FANCA deficiency, whose inactivation has been identified in two-thirds of FA patients, is associated with nucleolar homeostasis loss, mislocalization of key nucleolar proteins, including nucleolin (NCL) and nucleophosmin 1 (NPM1), as well as alterations in ribosome biogenesis and protein synthesis. FANCA coimmunoprecipitates with NCL and NPM1 in a FANCcore complex-independent manner and, unique among the FANCcore complex proteins, associates with ribosomal subunits, influencing the stoichiometry of the translational machineries. In conclusion, we have identified unexpected nucleolar and translational consequences specifically associated with FANCA deficiency that appears to be involved in both DNA damage and nucleolar stress responses, challenging current hypothesis on FA physiopathology.
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Affiliation(s)
- Anna Gueiderikh
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Frédérique Maczkowiak-Chartois
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Guillaume Rouvet
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Sylvie Souquère-Besse
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
- CNRS-UMS3655, 94805 Villejuif, France
| | - Sébastien Apcher
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
- INSERM-UMR1015, 94805 Villejuif, France
| | - Jean-Jacques Diaz
- Université Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, 69373 Lyon cedex 08, France
| | - Filippo Rosselli
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France.
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
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30
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Trottier AM, Godley LA. Inherited predisposition to haematopoietic malignancies: overcoming barriers and exploring opportunities. Br J Haematol 2020; 194:663-676. [PMID: 33615436 DOI: 10.1111/bjh.17247] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022]
Abstract
Inherited predisposition to haematopoietic malignancies, due to deleterious germline variants in a variety of genes, is an important clinical entity with implications for the health and management of patients and their family members. Unfortunately, there remain several common misconceptions in this field that can result in patients going unrecognised and/or having incomplete or improper testing including: the impression that inherited haematological malignancy syndromes are rare, that myeloid and lymphoid malignancy predisposition syndromes are mutually exclusive, and that solid tumour predisposition syndromes are unique and distinct from haematopoietic malignancy predisposition syndromes. In the present review, we challenge these ideas with our insights into germline genetic testing for these conditions with the hope that increased awareness and knowledge will overcome barriers and lead to improved diagnosis and management.
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Affiliation(s)
- Amy M Trottier
- Division of Hematology, Department of Medicine, QEII Health Sciences Centre/Dalhousie University, Halifax, NS, Canada
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
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31
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Delre P, Alberga D, Gijsbers A, Sánchez-Puig N, Nicolotti O, Saviano M, Siliqi D, Mangiatordi GF. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics. J Biomol Struct Dyn 2020; 38:5219-5229. [PMID: 31838967 DOI: 10.1080/07391102.2019.1704883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shwachman-Diamond Syndrome (SDS) is an autosomal recessive disorder whose patients present mutations in two ribosome assembly proteins, the Shwachman-Bodian-Diamond Syndrome protein (SBDS) and the Elongation Factor-Like 1 (EFL1). Due to the lack of knowledge of the molecular mechanisms responsible for SDS pathogenesis, current therapy is nonspecific and focuses only at alleviating the symptoms. Building on the recent observation that EFL1 single-point mutations clinically manifest as SDS-like phenotype, we carried out comparative Molecular Dynamics (MD) simulations on three mutants, T127A, M882K and R1095Q and wild type EFL1. As supported by small angle X-ray scattering experiments, the obtained data improve the static EFL1 model resulting from the Cryo-electron microscopy and clearly show that all the mutants experience a peculiar rotation, around the hinge region, of domain IV with respect to domains I and II leading to a different conformation respect to that of wild type protein. This study supports the notion that EFL1 function is governed by an allosteric mechanism involving the concerted action of GTPase domain (domain I) and the domain IV and can help point towards new approaches to SDS treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pietro Delre
- Dipartimento di Chimica, Università Degli Studi di Bari "Aldo Moro", Bari, Italy.,Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
| | | | - Abril Gijsbers
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Nuria Sánchez-Puig
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze Del Farmaco, Università̀ Degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Michele Saviano
- Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
| | - Dritan Siliqi
- Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
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32
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Tsai FD, Lindsley RC. Clonal hematopoiesis in the inherited bone marrow failure syndromes. Blood 2020; 136:1615-1622. [PMID: 32736377 PMCID: PMC7530647 DOI: 10.1182/blood.2019000990] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/20/2020] [Indexed: 12/16/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are characterized by ineffective hematopoiesis and increased risk for developing myeloid malignancy. The pathophysiologies of different IBMFSs are variable and can relate to defects in diverse biological processes, including DNA damage repair (Fanconi anemia), telomere maintenance (dyskeratosis congenita), and ribosome biogenesis (Diamond-Blackfan anemia, Shwachman-Diamond syndrome). Somatic mutations leading to clonal hematopoiesis have been described in IBMFSs, but the distinct mechanisms by which mutations drive clonal advantage in each disease and their associations with leukemia risk are not well understood. Clinical observations and laboratory models of IBMFSs suggest that the germline deficiencies establish a qualitatively impaired functional state at baseline. In this context, somatic alterations can promote clonal hematopoiesis by improving the competitive fitness of specific hematopoietic stem cell clones. Some somatic alterations relieve baseline fitness constraints by normalizing the underlying germline deficit through direct reversion or indirect compensation, whereas others do so by subverting senescence or tumor-suppressor pathways. Clones with normalizing somatic mutations may have limited transformation potential that is due to retention of functionally intact fitness-sensing and tumor-suppressor pathways, whereas those with mutations that impair cellular elimination may have increased risk for malignant transformation that is due to subversion of tumor-suppressor pathways. Because clonal hematopoiesis is not deterministic of malignant transformation, rational surveillance strategies will depend on the ability to prospectively identify specific clones with increased leukemic potential. We describe a framework by which an understanding of the processes that promote clonal hematopoiesis in IBMFSs may inform clinical surveillance strategies.
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Affiliation(s)
- Frederick D Tsai
- Division of Hematologic Neoplasia, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - R Coleman Lindsley
- Division of Hematologic Neoplasia, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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33
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Jain A, Nilatawong P, Mamak N, Jensen LT, Jensen AN. Disruption in iron homeostasis and impaired activity of iron-sulfur cluster containing proteins in the yeast model of Shwachman-Diamond syndrome. Cell Biosci 2020; 10:105. [PMID: 32944219 PMCID: PMC7488397 DOI: 10.1186/s13578-020-00468-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shwachman-Diamond syndrome (SDS) is a congenital disease that affects the bone marrow, skeletal system, and pancreas. The majority of patients with SDS have mutations in the SBDS gene, involved in ribosome biogenesis as well as other processes. A Saccharomyces cerevisiae model of SDS, lacking Sdo1p the yeast orthologue of SBDS, was utilized to better understand the molecular pathogenesis in the development of this disease. RESULTS Deletion of SDO1 resulted in a three-fold over-accumulation of intracellular iron. Phenotypes associated with impaired iron-sulfur (ISC) assembly, up-regulation of the high affinity iron uptake pathway, and reduced activities of ISC containing enzymes aconitase and succinate dehydrogenase, were observed in sdo1∆ yeast. In cells lacking Sdo1p, elevated levels of reactive oxygen species (ROS) and protein oxidation were reduced with iron chelation, using a cell impermeable iron chelator. In addition, the low activity of manganese superoxide dismutase (Sod2p) seen in sdo1∆ cells was improved with iron chelation, consistent with the presence of reactive iron from the ISC assembly pathway. In yeast lacking Sdo1p, the mitochondrial voltage-dependent anion channel (VDAC) Por1p is over-expressed and its deletion limits iron accumulation and increases activity of aconitase and succinate dehydrogenase. CONCLUSIONS We propose that oxidative stress from POR1 over-expression, resulting in impaired activity of ISC containing proteins and disruptions in iron homeostasis, may play a role in disease pathogenesis in SDS patients.
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Affiliation(s)
- Ayushi Jain
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok, 10400 Thailand
| | - Phubed Nilatawong
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok, 10400 Thailand
- Division of Biopharmacy, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani, 34190 Thailand
| | - Narinrat Mamak
- Toxicology Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
| | - Laran T. Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
| | - Amornrat Naranuntarat Jensen
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok, 10400 Thailand
- Pathology Information and Learning Center, Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand
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34
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Oyarbide U, Shah AN, Amaya-Mejia W, Snyderman M, Kell MJ, Allende DS, Calo E, Topczewski J, Corey SJ. Loss of Sbds in zebrafish leads to neutropenia and pancreas and liver atrophy. JCI Insight 2020; 5:134309. [PMID: 32759502 PMCID: PMC7526460 DOI: 10.1172/jci.insight.134309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 01/29/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is characterized by exocrine pancreatic insufficiency, neutropenia, and skeletal abnormalities. Biallelic mutations in SBDS, which encodes a ribosome maturation factor, are found in 90% of SDS cases. Sbds–/– mice are embryonic lethal. Using CRISPR/Cas9 editing, we created sbds-deficient zebrafish strains. Sbds protein levels progressively decreased and became undetectable at 10 days postfertilization (dpf). Polysome analysis revealed decreased 80S ribosomes. Homozygous mutant fish developed normally until 15 dpf. Mutant fish subsequently had stunted growth and showed signs of atrophy in pancreas, liver, and intestine. In addition, neutropenia occurred by 5 dpf. Upregulation of tp53 mRNA did not occur until 10 dpf, and inhibition of proliferation correlated with death by 21 dpf. Transcriptome analysis showed tp53 activation through upregulation of genes involved in cell cycle arrest, cdkn1a and ccng1, and apoptosis, puma and mdm2. However, elimination of Tp53 function did not prevent lethality. Because of growth retardation and atrophy of intestinal epithelia, we studied the effects of starvation on WT fish. Starved WT fish showed intestinal atrophy, zymogen granule loss, and tp53 upregulation — similar to the mutant phenotype. In addition, there was reduction in neutral lipid storage and ribosomal protein amount, similar to the mutant phenotype. Thus, loss of Sbds in zebrafish phenocopies much of the human disease and is associated with growth arrest and tissue atrophy, particularly of the gastrointestinal system, at the larval stage. A variety of stress responses, some associated with Tp53, contribute to pathophysiology of SDS. Loss of ribosome maturation factor sbds in the zebrafish phenocopies human Shwachman-Diamond syndrome and is associated with p53 activation, but lethality cannot be rescued by p53 mutation.
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Affiliation(s)
- Usua Oyarbide
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
| | - Arish N Shah
- Department of Biology and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wilmer Amaya-Mejia
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA
| | - Matthew Snyderman
- Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
| | - Margaret J Kell
- Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA
| | | | - Eliezer Calo
- Department of Biology and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacek Topczewski
- Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Seth J Corey
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
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35
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Koh AL, Bonnard C, Lim JY, Liew WK, Thoon KC, Thomas T, Ali NAB, Ng AYJ, Tohari S, Phua KB, Venkatesh B, Reversade B, Jamuar SS. Heterozygous missense variant in EIF6 gene: A novel form of Shwachman-Diamond syndrome? Am J Med Genet A 2020; 182:2010-2020. [PMID: 32657013 DOI: 10.1002/ajmg.a.61758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022]
Abstract
Shwachman-Diamond syndrome (SDS) is a rare multisystem ribosomal biogenesis disorder characterized by exocrine pancreatic insufficiency, hematologic abnormalities and bony abnormalities. About 90% of patients have biallelic mutations in SBDS gene. Three additional genes-EFL1, DNAJC21 and SRP54 have been reported in association with a SDS phenotype. However, the cause remains unknown for ~10% of patients. Herein, we report a 6-year-old Chinese boy, who presented in the neonatal period with pancytopenia, liver transaminitis with hepatosplenomegaly and developmental delay, and subsequently developed pancreatic insufficiency complicated by malabsorption and poor growth. Exome sequencing identified a novel de novo heterozygous variant in EIF6 (c.182G>T, p.Arg61Leu). EIF6 protein inhibits ribosomal maturation and is removed in the late steps of ribosomal maturation by SBDS and EFL1 protein. Given the interaction of EIF6 with SBDS and EFL1, we postulate heterozygous variants in EIF6 as a novel cause of Shwachman-Diamond-like phenotype. We compared the phenotype of our patient with those in patients with mutation in SBDS, EFL1, DNAJC21, and SRP54 genes to support this association. Identification of more cases of this novel phenotype would strengthen the association with the genetic etiology.
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Affiliation(s)
- Ai Ling Koh
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Carine Bonnard
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Jiin Ying Lim
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Woei Kang Liew
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore
| | - Koh Cheng Thoon
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Terrence Thomas
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | | | - Alvin Yu Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Kong Boo Phua
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | - Bruno Reversade
- Institute of Medical Biology, A*STAR, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore.,SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
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36
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Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes. Int J Mol Sci 2020; 21:ijms21134672. [PMID: 32630050 PMCID: PMC7369780 DOI: 10.3390/ijms21134672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman–Diamond syndrome (SDS), Diamond–Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.
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37
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Furutani E, Shah AS, Zhao Y, Andorsky D, Dedeoglu F, Geddis A, Zhou Y, Libermann TA, Myers KC, Shimamura A. Inflammatory manifestations in patients with Shwachman-Diamond syndrome: A novel phenotype. Am J Med Genet A 2020; 182:1754-1760. [PMID: 32293785 DOI: 10.1002/ajmg.a.61593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/27/2022]
Abstract
Shwachman-Diamond syndrome (SDS) is an autosomal recessive multisystem disorder characterized by exocrine pancreatic dysfunction, bone marrow failure, and leukemia predisposition. Approximately 90% of cases are due to biallelic mutations in the Shwachman-Bodian-Diamond (SBDS) gene. Additional phenotypic features variably associated with SDS include skeletal, neurologic, hepatic, cardiac, endocrine, and dental abnormalities. We report five subjects with SDS who developed a range of inflammatory manifestations. Three patients developed inflammatory eye conditions. Single cases of juvenile idiopathic arthritis, chronic recurrent multifocal osteomyelitis, and scleroderma were also noted. Clinical presentation and treatment responses are described. Proteomic analysis revealed increased inflammatory signatures in SDS subjects as compared to controls. Treatment of inflammatory manifestations in patients with SDS may be complicated by potential myelosuppressive toxicities of anti-rheumatic medications. Further research is needed to better understand the potential link between inflammatory disorders and SDS to inform effective treatment strategies.
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Affiliation(s)
- Elissa Furutani
- Dana-Farber and Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Ankoor S Shah
- Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yongdong Zhao
- Pediatric Rheumatology, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | | | - Fatma Dedeoglu
- Department of Medicine, Division of Immunology, Rheumatology Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Amy Geddis
- Department of Pediatric Hematology, Seattle Children's Hospital, Cancer and Blood Disorders Clinic, Seattle, Washington, USA
| | - Yu Zhou
- Dana-Farber and Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Towia A Libermann
- Beth Israel Deaconess Medical Center (BIDMC) Genomics and Proteomics Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kasiani C Myers
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Akiko Shimamura
- Dana-Farber and Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
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38
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Ford D. Ribosomal heterogeneity - A new inroad for pharmacological innovation. Biochem Pharmacol 2020; 175:113874. [PMID: 32105657 DOI: 10.1016/j.bcp.2020.113874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
The paradigm of ribosome usage in protein translation has shifted from a stance proposed as scientists began to unpick the genetic code that each mRNA was partnered by its own, unique ribosome to a rapid reversal of this view that ribosomes are completely interchangeable and simply recruited to mRNAs from a completely homogenous cellular pool. Evidence that the ribosomal proteome, ribosomal gene transcriptome and ribosome protein and RNA modifications differ between cells and tissues points to the fact that ribosomes are heterogeneous in their composition and have a degree of specialisation in their function. It has also been posited that the tissue-specificity of ribosome diseases provides an indication of functional ribosome heterogeneity, but there are substantial caveats to this interpretation. Only now have proteomic technologies developed to a level enabling accurate stoichiometric comparison of the abundance of specific ribosomal proteins in actively translating ribosomes and to measure protein in non-denatured ribosomes. This poises the field for the provocation that ribosome heterogeneity offers a novel and powerful inroad for the pharmacological targeting of disease. Such ribosome-targeted treatments may extend beyond specific ribosomopathies through strategies such as targeting features of ribosomes that are unique to diseased cells, particularly cancer cells, or to activated immune cells, as well as augmenting the action of other drugs through weakening the production of new proteins in target tissues. We may also be able to harness the potential power in ribosome diversity and specialism to better tune synthetic biology for the production of pharmaceutical proteins.
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Affiliation(s)
- Dianne Ford
- Northumbria University, Northumberland Building, Northumberland Road, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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