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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey TC, Fillipakopoulos P, White R, Goding CR. DNA damage remodels the MITF interactome to increase melanoma genomic instability. Genes Dev 2024; 38:70-94. [PMID: 38316520 PMCID: PMC10903946 DOI: 10.1101/gad.350740.123] [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: 04/21/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA damage response (DDR) programs. However, some cells (for example, in skin) are normally exposed to high levels of DNA-damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Using melanoma as a model, we show here that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a nontranscriptional role in shaping the DDR. On exposure to DNA-damaging agents, MITF is phosphorylated at S325, and its interactome is dramatically remodeled; most transcription cofactors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement with this, high MITF levels are associated with increased single-nucleotide and copy number variant burdens in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of DNA-PKcs-phosphorylated MITF. Our data suggest that a nontranscriptional function of a lineage-restricted transcription factor contributes to a tissue-specialized modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Université Laval, Québec City, Québec G1V 4G2, Canada
- Endocrinology-Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec City, Québec G1V 4G2, Canada
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Sovan Sarkar
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Timothy C Humphrey
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom;
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Ploypetch S, Wongbandue G, Roytrakul S, Phaonakrop N, Prapaiwan N. Comparative Serum Proteome Profiling of Canine Benign Prostatic Hyperplasia before and after Castration. Animals (Basel) 2023; 13:3853. [PMID: 38136890 PMCID: PMC10740436 DOI: 10.3390/ani13243853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
BPH is the most prevalent prostatic condition in aging dogs. Nevertheless, clinical diagnosis and management remain inconsistent. This study employed in-solution digestion coupled with nano-liquid chromatography tandem mass spectrometry to assess serum proteome profiling of dogs with BPH and those dogs after castration. Male dogs were divided into two groups; control and BPH groups. In the BPH group, each dog was evaluated at two time points: Day 0 (BF subgroup) and Day 30 after castration (AT subgroup). In the BF subgroup, three proteins were significantly upregulated and associated with dihydrotestosterone: solute carrier family 5 member 5, tyrosine-protein kinase, and FRAT regulator of WNT signaling pathway 1. Additionally, the overexpression of polymeric immunoglobulin receptors in the BF subgroup hints at its potential as a novel protein linked to the BPH development process. Conversely, alpha-1-B glycoprotein (A1BG) displayed significant downregulation in the BF subgroup, suggesting A1BG's potential as a predictive protein for canine BPH. Finasteride was associated with increased proteins in the AT subgroup, including apolipoprotein C-I, apolipoprotein E, apolipoprotein A-II, TAO kinase 1, DnaJ homolog subfamily C member 16, PH domain and leucine-rich repeat protein phosphatase 1, neuregulin 1, and pseudopodium enriched atypical kinase 1. In conclusion, this pilot study highlighted alterations in various serum proteins in canine BPH, reflecting different pathological changes occurring in this condition. These proteins could be a source of potential non-invasive biomarkers for diagnosing this disease.
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Affiliation(s)
- Sekkarin Ploypetch
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Grisnarong Wongbandue
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Nawarus Prapaiwan
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
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Martínez-Rendón J, Hinojosa L, Xoconostle-Cázares B, Ramírez-Pool JA, Castillo A, Cereijido M, Ponce A. Ouabain Induces Transcript Changes and Activation of RhoA/ROCK Signaling in Cultured Epithelial Cells (MDCK). Curr Issues Mol Biol 2023; 45:7538-7556. [PMID: 37754259 PMCID: PMC10528288 DOI: 10.3390/cimb45090475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023] Open
Abstract
Ouabain, an organic compound with the ability to strengthen the contraction of the heart muscle, was originally derived from plants. It has been observed that certain mammalian species, including humans, naturally produce ouabain, leading to its classification as a new type of hormone. When ouabain binds to Na+/K+-ATPase, it elicits various physiological effects, although these effects are not well characterized. Previous studies have demonstrated that ouabain, within the concentration range found naturally in the body (10 nmol/L), affects the polarity of epithelial cells and their intercellular contacts, such as tight junctions, adherens junctions, and gap junctional communication. This is achieved by activating signaling pathways involving cSrc and Erk1/2. To further investigate the effects of ouabain within the hormonally relevant concentration range (10 nmol/L), mRNA-seq, a high-throughput sequencing technique, was employed to identify differentially expressed transcripts. The discovery that the transcript encoding MYO9A was among the genes affected prompted an exploration of whether RhoA and its downstream effector ROCK were involved in the signaling pathways through which ouabain influences cell-to-cell contacts in epithelial cells. Supporting this hypothesis, this study reveals the following: (1) Ouabain increases the activation of RhoA. (2) Treatment with inhibitors of RhoA activation (Y27) and ROCK (C3) eliminates the enhancing effect of ouabain on the tight junction seal and intercellular communication via gap junctions. These findings further support the notion that ouabain acts as a hormone to emphasize the epithelial phenotype.
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Affiliation(s)
- Jacqueline Martínez-Rendón
- Department of Physiology, Biophysics and Neurosciences, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico; (J.M.-R.); (L.H.); (A.C.); (M.C.)
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S., Campus UAZ Siglo XXI-L1, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Lorena Hinojosa
- Department of Physiology, Biophysics and Neurosciences, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico; (J.M.-R.); (L.H.); (A.C.); (M.C.)
| | - Beatriz Xoconostle-Cázares
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Ciudad de Mexico 07360, Mexico; (B.X.-C.); (J.A.R.-P.)
| | - José Abrahán Ramírez-Pool
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Ciudad de Mexico 07360, Mexico; (B.X.-C.); (J.A.R.-P.)
| | - Aída Castillo
- Department of Physiology, Biophysics and Neurosciences, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico; (J.M.-R.); (L.H.); (A.C.); (M.C.)
| | - Marcelino Cereijido
- Department of Physiology, Biophysics and Neurosciences, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico; (J.M.-R.); (L.H.); (A.C.); (M.C.)
| | - Arturo Ponce
- Department of Physiology, Biophysics and Neurosciences, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico; (J.M.-R.); (L.H.); (A.C.); (M.C.)
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Zhao M, Liu A, Mo L, Wan G, Lu F. The value of RPS15 and MRPS27 in ischemic stroke. Medicine (Baltimore) 2023; 102:e34706. [PMID: 37603533 PMCID: PMC10443774 DOI: 10.1097/md.0000000000034706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/21/2023] [Indexed: 08/23/2023] Open
Abstract
Ischemic stroke is caused by insufficient blood supply to the brain. It has acute onset, often disturbance of consciousness, and high mortality and disability rate. However, relationship between ribosomal proteins (RP)-S15 and mitochondrial ribosomal proteins (MRP)-S27 and ischemic stroke remains unclear. The ischemic stroke datasets GSE22255, GSE16561, and GSE199435 were downloaded from gene expression omnibus generated by GPL6883, GPL11154, and GPL570. Differentially expressed genes (DEGs) were screened, and the construction and analysis of protein-protein interaction network, functional enrichment analysis and gene set enrichment analysis were performed. The gene expression heat map was drawn. Comparative toxicogenomics database analysis were performed to find the disease most related to core gene. TargetScan screened miRNAs that regulated central DEGs. Five hundred DEGs were identified. According to gene ontology analysis, they were mainly enriched in leukocyte activation, myoid cell activation involved in immune response, cell membrane, mitochondria, secretory vesicles, catalytic activity, enzyme binding, ribonucleic acid binding, splicing. Gene set enrichment analysis showed that the enrichment items are similar to the enrichment items of differentially expressed genes. And 20 core genes were obtained. Comparative toxicogenomics database analysis showed that 6 genes (RPS15, RPS2, RPS3, MRPS27, POLR2A, MRPS26) were found to be associated with chemical and drug-induced liver injury, necrosis, delayed prenatal exposure, nephropathy, hepatomegaly and tumor. RPS15 and MRPS27 are the core genes of ischemic stroke and play an important role in ischemic stroke.
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Affiliation(s)
- Man Zhao
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing, China
| | - Aixian Liu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing, China
| | - Linhong Mo
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing, China
| | - Guiling Wan
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing, China
| | - Fang Lu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing, China
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Li XY, He XY, Zhao H, Qi L, Lu JJ. Identification of a novel therapeutic target for lung cancer: Mitochondrial ribosome protein L9. Pathol Res Pract 2023; 248:154625. [PMID: 37343379 DOI: 10.1016/j.prp.2023.154625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Lung cancer has a high fatality rate and incidence rate. At present, the initial and progress mechanism of lung cancer has not been completely elucidated and new therapeutic targets still need to be developed. In this study, the screening process was based on lung cancer expression profile data and survival analysis. Mitochondrial ribosome protein L9 (MRPL9) was upregulated in lung cancer tissues and related to the poor overall survival rate and recurrence-free survival rate of lung cancer patients. Knockdown of MRPL9 inhibited the proliferation, sphere-formation, and migration ability of lung cancer cells. MRPL9 was associated with the c-MYC signaling pathway, and lung cancer patients with high expression of both MRPL9 and MYC had a poor prognosis. Furthermore, c-MYC was associated with the epithelial-mesenchymal transition (EMT) regulatory protein zinc finger E-box binding homeobox 1 (ZEB1) by bioinformatics analysis. The relationship between ZEB1 and c-MYC was further confirmed by interfering with c-MYC expression. MRPL9 is a potential therapeutic target for lung cancer and exerts its biological functions by affecting the transcription factor c-MYC thereby regulating the EMT regulator ZEB1.
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Affiliation(s)
- Xin-Yuan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin-Yu He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hong Zhao
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Lu Qi
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, University of Macau, Macao, China.
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Del Giudice L, Pontieri P, Aletta M, Calcagnile M. Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's. BIOLOGY 2023; 12:972. [PMID: 37508402 PMCID: PMC10376763 DOI: 10.3390/biology12070972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Currently, numerous research endeavors are dedicated to unraveling the intricate nature of neurodegenerative diseases. These conditions are characterized by the gradual and progressive impairment of specific neuronal systems that exhibit anatomical or physiological connections. In particular, in the last twenty years, remarkable efforts have been made to elucidate neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, despite extensive research endeavors, no cure or effective treatment has been discovered thus far. With the emergence of studies shedding light on the contribution of mitochondria to the onset and advancement of mitochondrial neurodegenerative disorders, researchers are now directing their investigations toward the development of therapies. These therapies include molecules designed to protect mitochondria and neurons from the detrimental effects of aging, as well as mutant proteins. Our objective is to discuss and evaluate the recent discovery of three mitochondrial ribosomal proteins linked to Alzheimer's and Parkinson's diseases. These proteins represent an intermediate stage in the pathway connecting damaged genes to the two mitochondrial neurological pathologies. This discovery potentially could open new avenues for the production of medicinal substances with curative potential for the treatment of these diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | | | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, 73100 Lecce, Italy
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Silencing of the mitochondrial ribosomal protein L-24 gene activates the oxidative stress response in Caenorhabditis elegans. Biochim Biophys Acta Gen Subj 2023; 1867:130255. [PMID: 36265765 DOI: 10.1016/j.bbagen.2022.130255] [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: 05/20/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022]
Abstract
The mitochondrial translation machinery allows the synthesis of the mitochondrial-encoded subunits of the electron transport chain. Defects in this process lead to mitochondrial physiology failure; in humans, they are associated with early-onset, extremely variable and often fatal disorder. The use of a simple model to study the mitoribosomal defects is mandatory to overcome the difficulty to analyze the impact of pathological mutations in humans. In this paper we study in nematode Caenorhabditis elegans the silencing effect of the mrpl-24 gene, coding for the mitochondrial ribosomal protein L-24 (MRPL-24). This is a structural protein of the large subunit 39S of the mitoribosome and its effective physiological function is not completely elucidated. We have evaluated the nematode's fitness fault and investigated the mitochondrial defects associated with MRPL-24 depletion. The oxidative stress response activation due to the mitochondrial alteration has been also investigated as a compensatory physiological mechanism. For the first time, we demonstrated that MRPL-24 reduction increases the expression of detoxifying enzymes such as SOD-3 and GST-4 through the involvement of transcription factor SKN-1. BACKGROUND In humans, mutations in genes encoding mitochondrial ribosomal proteins (MRPs) often cause early-onset, severe, fatal and extremely variable clinical defects. Mitochondrial ribosomal protein L-24 (MRPL24) is a structural protein of the large subunit 39S of the mitoribosome. It is highly conserved in different species and its effective physiological function is not completely elucidated. METHODS We characterized the MRPL24 functionality using the animal model Caenorhabditis elegans. We performed the RNA mediated interference (RNAi) by exposing the nematodes' embryos to double-stranded RNA (dsRNA) specific for the MRPL-24 coding sequence. We investigated for the first time in C. elegans, the involvement of the MRPL-24 on the nematode's fitness and its mitochondrial physiology. RESULTS Mrpl-24 silencing in C. elegans negatively affected the larval development, progeny production and body bending. The analysis of mitochondrial functionality revealed loss of mitochondrial network and impairment of mitochondrial functionality, as the decrease of oxygen consumption rate and the ROS production, as well as reduction of mitochondrial protein synthesis. Finally, the MRPL-24 depletion activated the oxidative stress response, increasing the expression levels of two detoxifying enzymes, SOD-3 and GST-4. CONCLUSIONS In C. elegans the MRPL-24 depletion activated the oxidative stress response. This appears as a compensatory mechanism to the alteration of the mitochondrial functionality and requires the involvement of transcription factor SKN-1. GENERAL SIGNIFICANCE C. elegans resulted in a good model for the study of mitochondrial disorders and its use as a simple and pluricellular organism could open interesting perspectives to better investigate the pathologic mechanisms underlying these devastating diseases.
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Zhang HM, Li ZY, Dai ZT, Wang J, Li LW, Zong QB, Li JP, Zhang TC, Liao XH. Interaction of MRPL9 and GGCT Promotes Cell Proliferation and Migration by Activating the MAPK/ERK Pathway in Papillary Thyroid Cancer. Int J Mol Sci 2022; 23:ijms231911989. [PMID: 36233293 PMCID: PMC9570013 DOI: 10.3390/ijms231911989] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Thyroid cancer remains the most common endocrine malignancy worldwide, and its incidence has steadily increased over the past four years. Papillary Thyroid Cancer (PTC) is the most common differentiated thyroid cancer, accounting for 80–85% of all thyroid cancers. Mitochondrial proteins (MRPs) are an important part of the structural and functional integrity of the mitochondrial ribosomal complex. It has been reported that MRPL9 is highly expressed in liver cancer and promotes cell proliferation and migration, but it has not been reported in PTC. In the present study we found that MRPL9 was highly expressed in PTC tissues and cell lines, and lentivirus-mediated overexpression of MRPL9 promoted the proliferation and migration ability of PTC cells, whereas knockdown of MRPL9 had the opposite effect. The interaction between MRPL9 and GGCT (γ-glutamylcyclotransferase) was found by immunofluorescence and co-immunoprecipitation experiments (Co-IP). In addition, GGCT is highly expressed in PTC tissues and cell lines, and knockdown of GGCT/MRPL9 in vivo inhibited the growth of subcutaneous xenografts in nude mice and inhibited the formation of lung metastases. Mechanistically, we found that knockdown of GGCT/MRPL9 inhibited the MAPK/ERK signaling pathway. In conclusion, our study found that the interaction of GGCT and MRPL9 modulates the MAPK/ERK pathway, affecting the proliferation and migration of PTC cells. Therefore, GGCT/MRPL9 may serve as a potential biomarker for PTC monitoring and PTC treatment.
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Affiliation(s)
- Hui-Min Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Zi-Yi Li
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Zhou-Tong Dai
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Wang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Le-Wei Li
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Qi-Bei Zong
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Jia-Peng Li
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
| | - Tong-Cun Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
- Correspondence: (T.-C.Z.); (X.-H.L.)
| | - Xing-Hua Liao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430070, China
- Correspondence: (T.-C.Z.); (X.-H.L.)
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Koc EC, Koc FC, Kartal F, Tirona M, Koc H. Role of mitochondrial translation in remodeling of energy metabolism in ER/PR(+) breast cancer. Front Oncol 2022; 12:897207. [PMID: 36119536 PMCID: PMC9472243 DOI: 10.3389/fonc.2022.897207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Remodeling of mitochondrial energy metabolism is essential for the survival of tumor cells in limited nutrient availability and hypoxic conditions. Defects in oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis also cause a switch in energy metabolism from oxidative to aerobic glycolysis contributing to the tumor heterogeneity in cancer. Specifically, the aberrant expressions of mitochondrial translation components such as ribosomal proteins (MRPs) and translation factors have been increasingly associated with many different cancers including breast cancer. The mitochondrial translation is responsible for the synthesis 13 of mitochondrial-encoded OXPHOS subunits of complexes. In this study, we investigated the contribution of mitochondrial translation in the remodeling of oxidative energy metabolism through altered expression of OXPHOS subunits in 26 ER/PR(+) breast tumors. We observed a significant correlation between the changes in the expression of mitochondrial translation-related proteins and OXPHOS subunits in the majority of the ER/PR(+) breast tumors and breast cancer cell lines. The reduced expression of OXPHOS and mitochondrial translation components also correlated well with the changes in epithelial-mesenchymal transition (EMT) markers, E-cadherin (CHD1), and vimentin (VIM) in the ER/PR(+) tumor biopsies. Data mining analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) breast cancer proteome further supported the correlation between the reduced OXPHOS subunit expression and increased EMT and metastatic marker expression in the majority of the ER/PR(+) tumors. Therefore, understanding the role of MRPs in the remodeling of energy metabolism will be essential in the characterization of heterogeneity at the molecular level and serve as diagnostic and prognostic markers in breast cancer.
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Affiliation(s)
- Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
| | - Fatih C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Funda Kartal
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Maria Tirona
- Department of Medical Oncology, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Hasan Koc
- Department of Pharmaceutical Science, School of Pharmacy, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
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Oviya RP, Thangaretnam KP, Ramachandran B, Ramanathan P, Jayavelu S, Gopal G, Rajkumar T. Mitochondrial ribosomal small subunit (MRPS) MRPS23 protein-protein interaction reveals phosphorylation by CDK11-p58 affecting cell proliferation and knockdown of MRPS23 sensitizes breast cancer cells to CDK1 inhibitors. Mol Biol Rep 2022; 49:9521-9534. [PMID: 35962848 DOI: 10.1007/s11033-022-07842-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/04/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Post-translational modification of some mitoribosomal proteins has been found to regulate their functions. MRPS23 has been reported to be overexpressed in various cancers and has been predicted to be involved in increased cell proliferation. Furthermore, MRPS23 is a driver of luminal subtype breast cancer. However, its exact role and function in cancer remains unknown. METHODS AND RESULTS: Our previous study identified protein-protein interactions involving MRPS23 and CDK11A. In this study, we confirmed the interaction of MRPS23 with the p110 and p58 isoforms of CDK11A. Phosphoprotein enrichment studies and in vitro kinase assay using CDK11A/cyclin D3 followed by MALDI-ToF/ToF analysis confirmed the phosphorylation of MRPS23 at N-terminal serine 11 residue. Breast cancer cells expressing the MRPS23 (S11G) mutant showed increased cell proliferation, increased expression of PI3-AKT pathway proteins [p-AKT (Ser47), p-AKT (Thr308), p-PDK (Ser241) and p-GSK-3β (Ser9)] and increased antiapoptotic pathway protein expression [Bcl-2, Bcl-xL, p-Bcl2 (Ser70) and MCL-1] when compared with the MRPS23 (S11A) mutant-overexpressing cells. This finding indicated the role of MRPS23 phosphorylation in the proliferation and survival of breast cancer cells. The correlation of inconsistent MRPS23 phosphoserine 11 protein expression with CDK11A in the breast cancer cells suggested phosphorylation by other kinases. In vitro kinase assay showed that CDK1 kinase also phosphorylated MRPS23 and that inhibition using CDK1 inhibitors lowered phospho-MRPS23 (Ser11) levels. Additionally, modulating the expression of MRPS23 altered the sensitivity of the cells to CDK1 inhibitors. CONCLUSION In conclusion, phosphorylation of MRPS23 by mitotic kinases might potentially be involved in the proliferation of breast cancer cells. Furthermore, MRPS23 can be targeted for sensitizing the breast cancer cells to CDK1 inhibitors.
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Affiliation(s)
| | | | - Balaji Ramachandran
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Priya Ramanathan
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Subramani Jayavelu
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Gopisetty Gopal
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India. .,Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
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11
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Han J, Lee C. Antagonistic regulatory effects of a single cis-acting expression quantitative trait locus between transcription and translation of the MRPL43 gene. BMC Genom Data 2022; 23:42. [PMID: 35659240 PMCID: PMC9167510 DOI: 10.1186/s12863-022-01057-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/23/2022] [Indexed: 01/01/2023] Open
Abstract
Background Heterogeneity of expression quantitative trait locus (eQTL) effects have been shown across gene expression processes. Knowledge on how to produce the heterogeneity is quite limited. This study aims to examine fluctuations in differential gene expression by alleles of sequence variants across expression processes. Results Genome-wide eQTL analyses with transcriptome-wide gene expression data revealed 20 cis-acting eQTLs associated simultaneously with mRNA expression, ribosome occupancy, and protein abundance. A 97 kb-long eQTL signal for mitochondrial ribosomal protein L43 (MRPL43) covered the gene, showing a heterogeneous effect size on gene products across expression stages. One allele of the eQTL was associated with increased mRNA expression and ribosome occupancy but decreased protein abundance. We examined the heterogeneity and found that the eQTL can be attributed to the independent functions of three nucleotide variants, with a strong linkage. NC_000010.11:g.100987606G > T, upstream of MRPL43, may regulate the binding affinity of transcription factors. NC_000010.11:g.100986746C > G, 3 bp from an MRPL43 splice donor site, may alter the splice site. NC_000010.11:g.100978794A > G, in the isoform with a long 3′-UTR, may strengthen the binding affinity of the microRNA. Individuals with the TGG haplotype at these three variants had higher levels of mRNA expression and ribosome occupancy than individuals with the GCA haplotype but lower protein levels, producing the flipped effect throughout the expression process. Conclusions These findings suggest that multiple functional variants in a linkage exert their regulatory functions at different points in the gene expression process, producing a complexity of single eQTLs. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01057-7.
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Affiliation(s)
- Jooyeon Han
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978, South Korea
| | - Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978, South Korea.
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12
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C. Chi G, Liu Y, MacDonald JW, M. Reynolds L, Enquobahrie DA, L. Fitzpatrick A, Kerr KF, J. Budoff M, Lee SI, Siscovick D, D. Kaufman J. Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. Epigenetics 2022; 17:297-313. [PMID: 33818294 PMCID: PMC8920186 DOI: 10.1080/15592294.2021.1900028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Air pollution might affect atherosclerosis through DNA methylation changes in cells crucial to atherosclerosis, such as monocytes. We conducted an epigenome-wide study of DNA methylation in CD14+ monocytes and long-term ambient air pollution exposure in adults participating in the Multi-Ethnic Study of Atherosclerosis (MESA). We also assessed the association between differentially methylated signals and cis-gene expression. Using spatiotemporal models, one-year average concentrations of outdoor fine particulate matter (PM2.5) and oxides of nitrogen (NOX) were estimated at participants' homes. We assessed DNA methylation and gene expression using Illumina 450k and HumanHT-12 v4 Expression BeadChips, respectively (n = 1,207). We used bump hunting and site-specific approaches to identify differentially methylated signals (false discovery rate of 0.05) and used linear models to assess associations between differentially methylated signals and cis-gene expression. Four differentially methylated regions (DMRs) located on chromosomes 5, 6, 7, and 16 (within or near SDHAP3, ZFP57, HOXA5, and PRM1, respectively) were associated with PM2.5. The DMRs on chromosomes 5 and 6 also associated with NOX. The DMR on chromosome 5 had the smallest p-value for both PM2.5 (p = 1.4×10-6) and NOX (p = 7.7×10-6). Three differentially methylated CpGs were identified for PM2.5, and cg05926640 (near TOMM20) had the smallest p-value (p = 5.6×10-8). NOX significantly associated with cg11756214 within ZNF347 (p = 5.6×10-8). Several differentially methylated signals were also associated with cis-gene expression. The DMR located on chromosome 7 was associated with the expression of HOXA5, HOXA9, and HOXA10. The DMRs located on chromosomes 5 and 16 were associated with expression of MRPL36 and DEXI, respectively. The CpG cg05926640 was associated with expression of ARID4B, IRF2BP2, and TOMM20. We identified differential DNA methylation in monocytes associated with long-term air pollution exposure. Methylation signals associated with gene expression might help explain how air pollution contributes to cardiovascular disease.
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Affiliation(s)
- Gloria C. Chi
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,CONTACT Gloria C. Chi 1 DNA Way, South San Francisco, CA 94080
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Lindsay M. Reynolds
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Daniel A. Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Annette L. Fitzpatrick
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Family Medicine, School of Medicine, University of Washington, Seattle, Washington, USA,Department of Global Health, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Kathleen F. Kerr
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Matthew J. Budoff
- Division of Cardiology, Los Angeles Biomedical Research Institute at Harbor–UCLA Medical Center, Torrance, California, USA
| | - Su-in Lee
- Department of Computer Science & Engineering, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Joel D. Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
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13
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Del Giudice L, Alifano P, Calcagnile M, Di Schiavi E, Bertapelle C, Aletta M, Pontieri P. Mitochondrial ribosomal protein genes connected with Alzheimer's and tellurite toxicity. Mitochondrion 2022; 64:45-58. [PMID: 35218961 DOI: 10.1016/j.mito.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Mitochondrial diseases are a group of genetic disorders characterized by dysfunctional mitochondria. Within eukaryotic cells, mitochondria contain their own ribosomes, which synthesize small amounts of proteins, all of which are essential for the biogenesis of the oxidative phosphorylation system. The ribosome is an evolutionarily conserved macromolecular machine in nature both from a structural and functional point of view, universally responsible for the synthesis of proteins. Among the diseases afflicting humans, those of ribosomal origin - either cytoplasmic ribosomes (80S) or mitochondrial ribosomes (70S) - are relevant. These are inherited or acquired diseases most commonly caused by either ribosomal protein haploinsufficiency or defects in ribosome biogenesis. Here we review the scientific literature about the recent advances on changes in mitochondrial ribosomal structural and assembly proteins that are implicated in primary mitochondrial diseases and neurodegenerative disorders, and their possible connection with metalloid pollution and toxicity, with a focus on MRPL44, NAM9 (MNA6) and GEP3 (MTG3), whose lack or defect was associated with resistance to tellurite. Finally, we illustrate the suitability of yeast Saccharomyces cerevisiae (S.cerevisiae) and the nematode Caenorhabditis elegans (C.elegans) as model organisms for studying mitochondrial ribosome dysfunctions including those involved in human diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy.
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | | | | | | | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy
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14
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Trivedi A, Bade G, Madan K, Ahmed Bhat M, Guleria R, Talwar A. Effect of Smoking and Its Cessation on the Transcript Profile of Peripheral Monocytes in COPD Patients. Int J Chron Obstruct Pulmon Dis 2022; 17:65-77. [PMID: 35027824 PMCID: PMC8749770 DOI: 10.2147/copd.s337635] [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: 09/13/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Rationale Smoking is the primary cause of chronic obstructive pulmonary disease (COPD); however, only 10–20% of smokers develop the disease suggesting possible genomic association in the causation of the disease. In the present study, we aimed to explore the whole genome transcriptomics of blood monocytes from COPD smokers (COPD-S), COPD Ex-smokers (COPD-ExS), Control smokers (CS), and Control Never-smokers (CNS) to understand the differential effects of smoking, COPD and that of smoking cessation. Methods Exploratory analyses in form of principal component analysis (PCA) and hierarchical component analysis (uHCA) were performed to evaluate the similarity in gene expression patterns, while differential expression analyses of different supervised groups of smokers and never smokers were performed to study the differential effect of smoking, COPD and smoking cessation. Differentially expressed genes among groups were subjected to post-hoc enrichment analysis. Candidate genes were subjected to external validation by quantitative RT-PCR experiments. Results CNS made a cluster completely segregated from the other three subgroups (CS, COPDS and COPD-ExS). About 550, 8 and 5 genes showed differential expression, respectively, between CNS and CS, between CS and COPD-S, and between COPD-S and COPD-ExS. Apoptosis, immune response, cell adhesion, and inflammation were the top process networks identified in enrichment analysis. Two candidate genes (CASP9 and TNFRSF1A) found to be integral to several pathways in enrichment analysis were validated in an external validation experiment. Conclusion Control never smokers had formed a cluster distinctively separated from all smokers (COPDS, COPD-ExS, and CS), while amongst all smokers, control smokers had aggregated in a separate cluster. Smoking cessation appeared beneficial if started at an early stage as many genes altered due to smoking started reverting towards the baseline, whereas only a few COPD-related genes showed reversal after smoking cessation.
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Affiliation(s)
- Anjali Trivedi
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Geetanjali Bade
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Muzaffer Ahmed Bhat
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anjana Talwar
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
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15
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Yang QY, Hu YH, Guo HL, Xia Y, Zhang Y, Fang WR, Li YM, Xu J, Chen F, Wang YR, Wang TF. Vincristine-Induced Peripheral Neuropathy in Childhood Acute Lymphoblastic Leukemia: Genetic Variation as a Potential Risk Factor. Front Pharmacol 2021; 12:771487. [PMID: 34955843 PMCID: PMC8696478 DOI: 10.3389/fphar.2021.771487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
Vincristine (VCR) is the first-line chemotherapeutic medication often co-administered with other drugs to treat childhood acute lymphoblastic leukemia. Dose-dependent neurotoxicity is the main factor restricting VCR’s clinical application. VCR-induced peripheral neuropathy (VIPN) sometimes results in dose reduction or omission, leading to clinical complications or affecting the patient’s quality of life. With regard to the genetic basis of drug responses, preemptive pharmacogenomic testing and simultaneous blood level monitoring could be helpful for the transformation of various findings into individualized therapies. In this review, we discussed the potential associations between genetic variants in genes contributing to the pharmacokinetics/pharmacodynamics of VCR and VIPN incidence and severity in patients with acute lymphoblastic leukemia. Of note, genetic variants in the CEP72 gene have great potential to be translated into clinical practice. Such a genetic biomarker may help clinicians diagnose VIPN earlier. Besides, genetic variants in other genes, such as CYP3A5, ABCB1, ABCC1, ABCC2, TTPA, ACTG1, CAPG, SYNE2, SLC5A7, COCH, and MRPL47, have been reported to be associated with the VIPN, but more evidence is needed to validate the findings in the future. In fact, a variety of complex factors jointly determine the VIPN. In implementing precision medicine, the combination of genetic, environmental, and personal variables, along with therapeutic drug monitoring, will allow for a better understanding of the mechanisms of VIPN, improving the effectiveness of VCR treatment, reducing adverse reactions, and improving patients’ quality of life.
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Affiliation(s)
- Qing-Yan Yang
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China.,School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ya-Hui Hu
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Li Guo
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ying Xia
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Zhang
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei-Rong Fang
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yun-Man Li
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jing Xu
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yong-Ren Wang
- Department of Hematology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Teng-Fei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
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16
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Identification of the Upregulation of MRPL13 as a Novel Prognostic Marker Associated with Overall Survival Time and Immunotherapy Response in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1498924. [PMID: 34868337 PMCID: PMC8639240 DOI: 10.1155/2021/1498924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022]
Abstract
Mitochondrial ribosomal protein (MRPL) genes have been reported to participate in many cellular processes, such as cell proliferation, apoptosis, and cell cycle. Meanwhile, the occurrence rate of breast cancer (BRCA) in China steadily increased. Exploring the prognostic value of MRPL genes in BRCA could provide novel biomarkers for BRCA. In this study, to identify prognosis-related genes in breast cancer, the P value and the hazard ratio (HR) of all genes are analyzed with TCGA database. We revealed higher expression level of CEL, PGK1, WNT3A, USP41, LINC02037, PCMT1, LRP11, MCTS1, TCP1, TMEM31, STK4-AS1, STXBP5, LOC100287036, SLC16A2, MRPL13, DERL1, and TARS was correlated to shorter OS time in BRCA. However, higher expression level of JCHAIN, KLRB1, and TNFRSF14 was correlated to longer OS time in BRCA. The further analysis demonstrated MRPL13 was overexpressed in BRCA. Subtype analysis showed that MRPL13 was overexpressed in luminal, HER2-positive BRCA, and TNBC samples and was highest in TNBC samples. Moreover, we revealed higher expression of MRPL13 was significantly correlated to shorter OS time and higher TMB levels in BRCA. Pan-cancer analysis further revealed the prognostic value of MRPL13 in human cancers. MRPL13 expression was significantly increased in multiple human cancers, such as bladder cancer, colon cancer, liver cancer, and prostate cancer. Pan-cancer TMB and overall survival time showed dysregulation of MRPL13 is significantly related to the OS and TMB levels in various cancers. These results further proved that MRPL13 may be a pan-cancer biomarker for predicting prognosis and the response to immunotherapy.
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Kornicka-Garbowska K, Bourebaba L, Röcken M, Marycz K. Inhibition of protein tyrosine phosphatase improves mitochondrial bioenergetics and dynamics, reduces oxidative stress, and enhances adipogenic differentiation potential in metabolically impaired progenitor stem cells. Cell Commun Signal 2021; 19:106. [PMID: 34732209 PMCID: PMC8565043 DOI: 10.1186/s12964-021-00772-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/30/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Protein tyrosine phosphatase 1B (PTP1B) and low molecular weight protein tyrosine phosphatase (LMPTP) are implicated in the development of metabolic disorders. Yet, their role in progenitor stem cell adipogenic differentiation and modulation of mitochondrial dynamics remains elusive. METHODS In this study, we decided to investigate whether inhibition of PTP1B and LMPTP enhance adipogenic differentiation of metabolically impaired progenitor stem cells via modulation of mitochondrial bioenergetics and dynamics. Cells were cultured under adipogenic conditions in the presence of PTP1B and LMPTP inhibitors, and were subjected to the analysis of the main adipogenic-related and mitochondrial-related genes using RT-qPCR. Protein levels were established with western blot while mitochondrial morphology with MicroP software. RESULTS Selective inhibitors of both PTP1B and MPTP enhanced adipogenic differentiation of metabolically impaired progenitor stem cells. We have observed enhanced expression of PPARy and adiponectin in treated cells. What is more, increased antioxidative defence and alternations in mitochondrial bioenergetics were observed. We have found that inhibition of PTP1B as well as C23 activates oxidative phosphorylation and enhances mitochondrial fusion contributing to enhanced adipogenesis. CONCLUSIONS The presented data provides evidence that the application of PTP1B and LMPTP inhibitors enhances adipogenesis through the modulation of mitochondrial dynamics. Video abstract.
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Affiliation(s)
- Katarzyna Kornicka-Garbowska
- Department of Experimental Biology, Wroclaw University of Environmental and Life Sciences, Norwida 27B Street, A7 building, 50-375 Wroclaw, Poland
- International Institute of Translational Medicine, Malin, Jesionowa 11, 55-114 Wisznia Mała, Poland
| | - Lynda Bourebaba
- Department of Experimental Biology, Wroclaw University of Environmental and Life Sciences, Norwida 27B Street, A7 building, 50-375 Wroclaw, Poland
| | - Michael Röcken
- Faculty of Veterinary Medicine, Equine Clinic-Equine Surgery, Justus-Liebig University, 35392 Giessen, Germany
| | - Krzysztof Marycz
- Department of Experimental Biology, Wroclaw University of Environmental and Life Sciences, Norwida 27B Street, A7 building, 50-375 Wroclaw, Poland
- International Institute of Translational Medicine, Malin, Jesionowa 11, 55-114 Wisznia Mała, Poland
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18
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Blay C, Haffray P, D'Ambrosio J, Prado E, Dechamp N, Nazabal V, Bugeon J, Enez F, Causeur D, Eklouh-Molinier C, Petit V, Phocas F, Corraze G, Dupont-Nivet M. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. BMC Genomics 2021; 22:788. [PMID: 34732127 PMCID: PMC8564959 DOI: 10.1186/s12864-021-08062-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection. Results Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait. Conclusion This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08062-7.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Jonathan D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Enora Prado
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Virginie Nazabal
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | | | | | - David Causeur
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, Rennes, France
| | | | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR1419 NuMéA, St Pée sur, Nivelle, France
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A review on epidermal growth factor receptor's role in breast and non-small cell lung cancer. Chem Biol Interact 2021; 351:109735. [PMID: 34742684 DOI: 10.1016/j.cbi.2021.109735] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/28/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022]
Abstract
Epithelial growth factor receptor (EGFR) is a cell surface transmembrane receptor that mediates the tyrosine signaling pathway to carry the extracellular messages inside the cell and thereby alter the function of nucleus. This leads to the generation of various protein products to up or downregulate the cellular function. It is encoded by cell erythroblastosis virus oncogene B1, so called C-erb B1/ERBB2/HER-2 gene that acts as a proto-oncogene. It belongs to the HER-2 receptor-family in breast cancer and responds best with anti-Herceptin therapy (anti-tyrosine kinase monoclonal antibody). HER-2 positive breast cancer patient exhibits worse prognosis without Herceptin therapy. Similar incidence and prognosis are reported in other epithelial neoplasms like EGFR + lung non-small cell carcinoma and glioblastoma (grade IV brain glial tumor). Present study highlights the role and connectivity of EGF with various cancers via signaling pathways, cell surface receptors mechanism, macromolecules, mitochondrial genes and neoplasm. Present study describes the EGFR associated gene expression profiling (in breast cancer and NSCLC), relation between mitrochondrial genes and carcinoma, and several in vitro and in vivo models to screen the synergistic effect of various combination treatments. According to this study, although clinical studies including targeted treatments, immunotherapies, radiotherapy, TKi-EGFR combined targeted therapy have been carried out to investigate the synergism of combination therapy; however still there is a gap to apply the scenarios of experimental and clinical studies for further developments. This review will give an idea about the transition from experimental to most advanced clinical studies with different combination drug strategies to treat cancer.
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20
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Liu L, Zhang X, Ding H, Liu X, Cao D, Liu Y, Liu J, Lin C, Zhang N, Wang G, Hou J, Huang B, Zhang Y, Lu J. Arginine and lysine methylation of MRPS23 promotes breast cancer metastasis through regulating OXPHOS. Oncogene 2021; 40:3548-3563. [PMID: 33927350 DOI: 10.1038/s41388-021-01785-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 03/29/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) is a vital regulator of tumor metastasis. However, the mechanisms governing OXPHOS to facilitate tumor metastasis remain unclear. In this study, we discovered that arginine 21(R21) and lysine 108 (K108) of mitochondrial ribosomal protein S23 (MRPS23) was methylated by the protein arginine methyltransferase 7 (PRMT7) and SET-domain-containing protein 6 (SETD6), respectively. R21 methylation accelerated the poly-ubiquitin-dependent degradation of MRPS23 to a low level. The MRPS23 degradation inhibited OXPHOS with elevated mtROS level, which consequently increased breast cancer cell invasion and metastasis. In contrast, K108 methylation increased MRPS23 stability, and K108 methylation coordinated with R21 methylation to maintain a low level of MRPS23, which was in favor of supporting breast cancer cell survival through regulating OXPHOS. Consistently, R21 and K108 methylation was correlated with malignant breast carcinoma. Significantly, our findings unveil a unique mechanism of controlling OXPHOS by arginine and lysine methylation and point to the impact of the PRMT7-SETD6-MRPS23 axis during breast cancer metastasis.
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Affiliation(s)
- Lingxia Liu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiliu Zhang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Huayi Ding
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xin Liu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Donghui Cao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, China
| | - Yingqi Liu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Jiwei Liu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Cong Lin
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Na Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Guannan Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China
| | - Jingyao Hou
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Baiqu Huang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China.
| | - Jun Lu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China.
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21
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Menyhárt O, Fekete JT, Győrffy B. Gene expression-based biomarkers designating glioblastomas resistant to multiple treatment strategies. Carcinogenesis 2021; 42:804-813. [PMID: 33754151 PMCID: PMC8215594 DOI: 10.1093/carcin/bgab024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Despite advances in molecular characterization of glioblastoma multiforme (GBM), only a handful of predictive biomarkers exist with limited clinical relevance. We aimed to identify differentially expressed genes in tumor samples collected at surgery associated with response to subsequent treatment, including temozolomide (TMZ) and nitrosoureas. Gene expression was collected from multiple independent datasets. Patients were categorized as responders/nonresponders based on their survival status at 16 months postsurgery. For each gene, the expression was compared between responders and nonresponders with a Mann-Whitney U-test and receiver operating characteristic. The package 'roc' was used to calculate the area under the curve (AUC). The integrated database comprises 454 GBM patients from 3 independent datasets and 10 103 genes. The highest proportion of responders (68%) were among patients treated with TMZ combined with nitrosoureas, where FCGR2B upregulation provided the strongest predictive value (AUC = 0.72, P < 0.001). Elevated expression of CSTA and MRPS17 was associated with a lack of response to multiple treatment strategies. DLL3 upregulation was present in subsequent responders to any treatment combination containing TMZ. Three genes (PLSCR1, MX1 and MDM2) upregulated both in the younger cohort and in patients expressing low MGMT delineate a subset of patients with worse prognosis within a population generally associated with a favorable outcome. The identified transcriptomic changes provide biomarkers of responsiveness, offer avenues for preclinical studies and may enhance future GBM patient stratifications. The described methodology provides a reliable pipeline for the initial testing of potential biomarker candidates for future validation studies.
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Affiliation(s)
- Otília Menyhárt
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, Budapest, Hungary.,Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja, Budapest, Hungary
| | - János Tibor Fekete
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, Budapest, Hungary.,Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja, Budapest, Hungary
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, Budapest, Hungary.,Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja, Budapest, Hungary
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22
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Brady SW, Liu Y, Ma X, Gout AM, Hagiwara K, Zhou X, Wang J, Macias M, Chen X, Easton J, Mulder HL, Rusch M, Wang L, Nakitandwe J, Lei S, Davis EM, Naranjo A, Cheng C, Maris JM, Downing JR, Cheung NKV, Hogarty MD, Dyer MA, Zhang J. Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations. Nat Commun 2020; 11:5183. [PMID: 33056981 PMCID: PMC7560655 DOI: 10.1038/s41467-020-18987-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma is a pediatric malignancy with heterogeneous clinical outcomes. To better understand neuroblastoma pathogenesis, here we analyze whole-genome, whole-exome and/or transcriptome data from 702 neuroblastoma samples. Forty percent of samples harbor at least one recurrent driver gene alteration and most aberrations, including MYCN, ATRX, and TERT alterations, differ in frequency by age. MYCN alterations occur at median 2.3 years of age, TERT at 3.8 years, and ATRX at 5.6 years. COSMIC mutational signature 18, previously associated with reactive oxygen species, is the most common cause of driver point mutations in neuroblastoma, including most ALK and Ras-activating variants. Signature 18 appears early and is continuous throughout disease evolution. Signature 18 is enriched in neuroblastomas with MYCN amplification, 17q gain, and increased expression of mitochondrial ribosome and electron transport-associated genes. Recurrent FGFR1 variants in six patients, and ALK N-terminal structural alterations in five samples, identify additional patients potentially amenable to precision therapy.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Macias
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaohua Lei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Davis
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Arlene Naranjo
- Department of Biostatistics, University of Florida, Children's Oncology Group Statistics & Data Center, Gainesville, FL, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D Hogarty
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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23
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Franca R, Zudeh G, Lucafò M, Rabusin M, Decorti G, Stocco G. Genome wide association studies for treatment-related adverse effects of pediatric acute lymphoblastic leukemia. WIREs Mech Dis 2020; 13:e1509. [PMID: 33016644 DOI: 10.1002/wsbm.1509] [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: 03/07/2020] [Revised: 08/01/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy; notwithstanding the success of ALL therapy, severe adverse drugs effects represent a serious issue in pediatric oncology, because they could be both an additional life threatening condition for ALL patients per se and a reason to therapy delay or discontinuation with important fallouts on final outcome. Cancer treatment-related toxicities have generated a significant need of finding predictive pharmacogenomic markers for the a priori identification of at risk patients. In the era of precision medicine, high throughput genomic screening such as genome wide association studies (GWAS) might provide useful markers to tailor therapy intensity on patients' genetic profile. Furthermore, these findings could be useful in basic research for better understanding the mechanistic and regulatory pathways of the biological functions associated with ALL treatment toxicities. The purpose of this review is to give an overview of high throughput genomic screening of the last 10 years that had investigated the landscape of ALL treatment-associated toxicities. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Giulia Zudeh
- University of Trieste, PhD Course in Reproductive and Developmental Sciences, Trieste, Italy
| | - Marianna Lucafò
- Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Marco Rabusin
- Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
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24
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Maamari D, El-Khoury H, Saifi O, Muwakkit SA, Zgheib NK. Implementation of Pharmacogenetics to Individualize Treatment Regimens for Children with Acute Lymphoblastic Leukemia. Pharmgenomics Pers Med 2020; 13:295-317. [PMID: 32848445 PMCID: PMC7429230 DOI: 10.2147/pgpm.s239602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/20/2020] [Indexed: 12/28/2022] Open
Abstract
Despite major advances in the management and high cure rates of childhood acute lymphoblastic leukemia (ALL), patients still suffer from many drug-induced toxicities, sometimes necessitating dose reduction, or halting of cytotoxic drugs with a secondary risk of disease relapse. In addition, investigators have noted significant inter-individual variability in drug toxicities and disease outcomes, hence the role of pharmacogenetics (PGx) in elucidating genetic polymorphisms in candidate genes for the optimization of disease management. In this review, we present the PGx data in association with main toxicities seen in children treated for ALL in addition to efficacy, with a focus on the most plausible germline PGx variants. We then follow with a summary of the highest evidence drug-gene annotations with suggestions to move forward in implementing preemptive PGx for the individualization of treatment regimens for children with ALL.
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Affiliation(s)
- Dimitri Maamari
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Habib El-Khoury
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Omran Saifi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samar A Muwakkit
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
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25
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Di Nottia M, Marchese M, Verrigni D, Mutti CD, Torraco A, Oliva R, Fernandez-Vizarra E, Morani F, Trani G, Rizza T, Ghezzi D, Ardissone A, Nesti C, Vasco G, Zeviani M, Minczuk M, Bertini E, Santorelli FM, Carrozzo R. A homozygous MRPL24 mutation causes a complex movement disorder and affects the mitoribosome assembly. Neurobiol Dis 2020; 141:104880. [PMID: 32344152 DOI: 10.1016/j.nbd.2020.104880] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/04/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Mitochondrial ribosomal protein large 24 (MRPL24) is 1 of the 82 protein components of mitochondrial ribosomes, playing an essential role in the mitochondrial translation process. We report here on a baby girl with cerebellar atrophy, choreoathetosis of limbs and face, intellectual disability and a combined defect of complexes I and IV in muscle biopsy, caused by a homozygous missense mutation identified in MRPL24. The variant predicts a Leu91Pro substitution at an evolutionarily conserved site. Using human mutant cells and the zebrafish model, we demonstrated the pathological role of the identified variant. In fact, in fibroblasts we observed a significant reduction of MRPL24 protein and of mitochondrial respiratory chain complex I and IV subunits, as well a markedly reduced synthesis of the mtDNA-encoded peptides. In zebrafish we demonstrated that the orthologue gene is expressed in metabolically active tissues, and that gene knockdown induced locomotion impairment, structural defects and low ATP production. The motor phenotype was complemented by human WT but not mutant cRNA. Moreover, sucrose density gradient fractionation showed perturbed assembly of large subunit mitoribosomal proteins, suggesting that the mutation leads to a conformational change in MRPL24, which is expected to cause an aberrant interaction of the protein with other components of the 39S mitoribosomal subunit.
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Affiliation(s)
- Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Marchese
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Daniela Verrigni
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Naples, Italy
| | | | - Federica Morani
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Giulia Trani
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Anna Ardissone
- Child Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Molecular and Translational Medicine DIMET, University of Milan-Bicocca, Milan, Italy
| | - Claudia Nesti
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Gessica Vasco
- Department of Neurosciences, IRCCS Bambino Gesù Children Hospital, Rome, Italy
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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26
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Klæstad E, Opdahl S, Engstrøm MJ, Ytterhus B, Wik E, Bofin AM, Valla M. MRPS23 amplification and gene expression in breast cancer; association with proliferation and the non-basal subtypes. Breast Cancer Res Treat 2020; 180:73-86. [PMID: 31950385 PMCID: PMC7031208 DOI: 10.1007/s10549-020-05532-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/09/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE MRPS23 is recognized as a driver of proliferation in luminal breast cancer. The aims of the present study were to describe MRPS23 copy number change in breast cancer, and to assess associations between MRPS23 copy number change and molecular subtype, proliferation and prognosis, and between MRPS23 gene expression and molecular subtype and prognosis. METHODS Using fluorescence in situ hybridization (FISH), we examined MRPS23 and centromere 17 copy number in 590 formalin-fixed, paraffin-embedded primary tumours and 144 corresponding lymph node metastases from a cohort of Norwegian breast cancer patients. Furthermore, we analysed MRPS23 gene expression data in 1971 primary breast cancer tumours from the METABRIC dataset. We used Pearson's χ2 test to assess associations between MRPS23 copy number and molecular subtype and proliferation, and between MRPS23 expression and molecular subtype. We studied prognosis by estimating hazard ratios and cumulative incidence of death from breast cancer according to MRPS23 copy number and MRPS23 expression status. RESULTS We found MRPS23 amplification (mean MRPS23 copy number ≥ 6 and/or MRPS23/chromosome 17 ratio ≥ 2) in 8% of primary tumours. Copy number increase associated with non-basal subtypes and higher tumour cell proliferation (Ki67). Higher MRPS23 expression associated with the Luminal B subtype. We found no significant association between MRPS23 amplification or MRSP23 gene expression, and prognosis. CONCLUSION Amplification of MRPS23 is associated with higher proliferation and non-basal subtypes in breast cancer. High MRPS23 expression is associated with the Luminal B subtype.
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Affiliation(s)
- Elise Klæstad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gate, 7030, Trondheim, Norway.
| | - Signe Opdahl
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Monica Jernberg Engstrøm
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gate, 7030, Trondheim, Norway.,Department of Breast and Endocrine Surgery, St. Olav's Hospital, Trondheim University Hospital, 7006, Trondheim, Norway
| | - Borgny Ytterhus
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gate, 7030, Trondheim, Norway
| | - Elisabeth Wik
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, 5021, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5021, Bergen, Norway
| | - Anna Mary Bofin
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gate, 7030, Trondheim, Norway
| | - Marit Valla
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gate, 7030, Trondheim, Norway.,Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, 7006, Trondheim, Norway
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27
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Fu Z, Chen CT, Cagnone G, Heckel E, Sun Y, Cakir B, Tomita Y, Huang S, Li Q, Britton W, Cho SS, Kern TS, Hellström A, Joyal JS, Smith LE. Dyslipidemia in retinal metabolic disorders. EMBO Mol Med 2019; 11:e10473. [PMID: 31486227 PMCID: PMC6783651 DOI: 10.15252/emmm.201910473] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/10/2019] [Accepted: 08/15/2019] [Indexed: 12/24/2022] Open
Abstract
The light‐sensitive photoreceptors in the retina are extremely metabolically demanding and have the highest density of mitochondria of any cell in the body. Both physiological and pathological retinal vascular growth and regression are controlled by photoreceptor energy demands. It is critical to understand the energy demands of photoreceptors and fuel sources supplying them to understand neurovascular diseases. Retinas are very rich in lipids, which are continuously recycled as lipid‐rich photoreceptor outer segments are shed and reformed and dietary intake of lipids modulates retinal lipid composition. Lipids (as well as glucose) are fuel substrates for photoreceptor mitochondria. Dyslipidemia contributes to the development and progression of retinal dysfunction in many eye diseases. Here, we review photoreceptor energy demands with a focus on lipid metabolism in retinal neurovascular disorders.
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Affiliation(s)
- Zhongjie Fu
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA.,Manton Center for Orphan Disease, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Chuck T Chen
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Gael Cagnone
- Department of Pediatrics, Pharmacology and Ophthalmology, CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, University of Montreal, Montreal, QC, Canada
| | - Emilie Heckel
- Department of Pediatrics, Pharmacology and Ophthalmology, CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, University of Montreal, Montreal, QC, Canada
| | - Ye Sun
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Bertan Cakir
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Yohei Tomita
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Shuo Huang
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Qian Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - William Britton
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Steve S Cho
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Timothy S Kern
- Center for Translational Vision Research, Gavin Herbert Eye Institute, Irvine, CA, USA
| | - Ann Hellström
- Section for Ophthalmology, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Jean-Sébastien Joyal
- Department of Pediatrics, Pharmacology and Ophthalmology, CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, University of Montreal, Montreal, QC, Canada
| | - Lois Eh Smith
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
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28
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Liu AG, Xu KL, Wang WL, Zhou BK, Guo QG. Down-regulation of MRPS23 inhibits LPS-induced proliferation and invasion via regulation of the NF-κB signaling pathway in osteosarcoma cells. RSC Adv 2019; 9:10561-10568. [PMID: 35515333 PMCID: PMC9062464 DOI: 10.1039/c8ra08973f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/28/2019] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial ribosomal protein S23 (MRPS23), encoded by a nuclear gene, is a participant in the translation of mitochondrial proteins. Recently, MRPS23 has been reported to be overexpressed in many types of cancers and have a close association with cancer progression. However, the specific roles of MRPS23 in osteosarcoma (OS) remain unknown. In this study, we investigated the expression pattern and biological functions of MRPS23 in OS cells. Our results demonstrated that MRPS23 was up-regulated in OS tissues and cell lines. Down-regulation of MRPS23 significantly inhibited OS cell proliferation and invasion induced by lipopolysaccharide (LPS) in vitro. Furthermore, the in vivo experiments showed that MRPS23 down-regulation markedly suppressed OS cell growth and metastasis induced by LPS. Mechanistically, down-regulation of MRPS23 inhibited the activity of NF-κB signaling pathway in OS cells. In conclusion, these findings indicated that MRPS23 may be a potential therapeutic target for OS treatment. Mitochondrial ribosomal protein S23 (MRPS23), encoded by a nuclear gene, is a participant in the translation of mitochondrial proteins.![]()
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Affiliation(s)
- Ai-Guo Liu
- Department of Orthopaedics, The First Affiliated Hospital of Henan University Kaifeng 475000 China
| | - Ke-Lin Xu
- Department of Orthopaedics and Traumatology, Wuxi Hospital Affiliated to Nanjing University of Chinese Medicine No. 8 Zhongnan West Road Wuxi 214000 China +86-510-88859999 +86-510-88859999
| | - Wei-Lin Wang
- Department of Orthopaedics, The First Affiliated Hospital of Henan University Kaifeng 475000 China
| | - Bing-Kang Zhou
- Department of Orthopaedics, The First Affiliated Hospital of Henan University Kaifeng 475000 China
| | - Qing-Gong Guo
- Department of Orthopaedics, The First Affiliated Hospital of Henan University Kaifeng 475000 China
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29
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Zhang L, Lu P, Yan L, Yang L, Wang Y, Chen J, Dai J, Li Y, Kang Z, Bai T, Xi Y, Xu J, Sun G, Yang T. MRPL35 Is Up-Regulated in Colorectal Cancer and Regulates Colorectal Cancer Cell Growth and Apoptosis. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1105-1120. [PMID: 30862482 DOI: 10.1016/j.ajpath.2019.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 01/28/2019] [Accepted: 02/05/2019] [Indexed: 02/07/2023]
Abstract
Mitochondrial ribosome proteins (MRPs), which are encoded by the nuclear genomic DNA, are important for mitochondrial-encoded protein synthesis and mitochondrial function. Emerging evidence suggests that several MRPs also exhibit important extra-mitochondrial functions, such as involvement in apoptosis, protein biosynthesis, and signal transduction. In this study, we demonstrate a significant role of MRP L35 (MRPL35) in colorectal cancer (CRC). The expression of MRPL35 was higher in CRC tissues than in matched cancer-adjacent tissues and higher in CRC cells than in normal mucosal epithelial cells. Higher MRPL35 expression in CRC tissue correlated with shorter overall survival for CRC patients. In vitro, down-regulation of MRPL35 led to increased production of reactive oxygen species (ROS) together with DNA damage, loss of cell proliferation, G2/M arrest, a decrease in mitochondrial membrane potential, apoptosis, and autophagy induction. MRPL35 knockdown inhibited tumor proliferation in a CRC xenograft nude mouse model. Furthermore, overexpression of MRPL35 or treatment of cells with the ROS scavenger, N-acetyl cysteine, abrogated ROS production, cell cycle arrest, and apoptosis in vitro. These findings suggest that MRPL35 plays an essential role in the development of CRC and may be a potential therapeutic target for CRC.
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Affiliation(s)
- Litao Zhang
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Peifen Lu
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Lihong Yan
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Lijun Yang
- Department of Pharmacology, Shanxi Medical University, Taiyuan, China
| | - Yutao Wang
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Junjun Chen
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Jie Dai
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Yahui Li
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Zhiming Kang
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Tao Bai
- Department of Pathology, First Affiliated Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Provincial Cancer Hospital, Taiyuan, China
| | - Jun Xu
- Department of General Surgery, Shanxi Grand Hospital, Taiyuan, China
| | - Gongqin Sun
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island.
| | - Tao Yang
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China.
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30
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Pavlovic S, Kotur N, Stankovic B, Zukic B, Gasic V, Dokmanovic L. Pharmacogenomic and Pharmacotranscriptomic Profiling of Childhood Acute Lymphoblastic Leukemia: Paving the Way to Personalized Treatment. Genes (Basel) 2019; 10:E191. [PMID: 30832275 PMCID: PMC6471971 DOI: 10.3390/genes10030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine is focused on research disciplines which contribute to the individualization of therapy, like pharmacogenomics and pharmacotranscriptomics. Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. It is one of the pediatric malignancies with the highest cure rate, but still a lethal outcome due to therapy accounts for 1%⁻3% of deaths. Further improvement of treatment protocols is needed through the implementation of pharmacogenomics and pharmacotranscriptomics. Emerging high-throughput technologies, including microarrays and next-generation sequencing, have provided an enormous amount of molecular data with the potential to be implemented in childhood ALL treatment protocols. In the current review, we summarized the contribution of these novel technologies to the pharmacogenomics and pharmacotranscriptomics of childhood ALL. We have presented data on molecular markers responsible for the efficacy, side effects, and toxicity of the drugs commonly used for childhood ALL treatment, i.e., glucocorticoids, vincristine, asparaginase, anthracyclines, thiopurines, and methotrexate. Big data was generated using high-throughput technologies, but their implementation in clinical practice is poor. Research efforts should be focused on data analysis and designing prediction models using machine learning algorithms. Bioinformatics tools and the implementation of artificial i Lack of association of the CEP72 rs924607 TT genotype with intelligence are expected to open the door wide for personalized medicine in the clinical practice of childhood ALL.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Lidija Dokmanovic
- University Children's Hospital, 11000 Belgrade, Serbia.
- University of Belgrade, Faculty of Medicine, 11000 Belgrade, Serbia.
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31
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Guyatt AL, Brennan RR, Burrows K, Guthrie PAI, Ascione R, Ring SM, Gaunt TR, Pyle A, Cordell HJ, Lawlor DA, Chinnery PF, Hudson G, Rodriguez S. A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts. Hum Genomics 2019; 13:6. [PMID: 30704525 PMCID: PMC6357493 DOI: 10.1186/s40246-018-0190-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/27/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist. We undertook a GWAS of qPCR-assayed mtDNA CN in the Avon Longitudinal Study of Parents and Children (ALSPAC) and the UK Blood Service (UKBS) cohort. After validating and harmonising data, 5461 ALSPAC mothers (16-43 years at mtDNA CN assay) and 1338 UKBS females (17-69 years) were included in a meta-analysis. Sensitivity analyses restricted to females with white cell-extracted DNA and adjusted for estimated or assayed cell proportions. Associations were also explored in ALSPAC children and UKBS males. RESULTS A neutrophil-associated locus approached genome-wide significance (rs709591 [MED24], β (change in SD units of mtDNA CN per allele) [SE] - 0.084 [0.016], p = 1.54e-07) in the main meta-analysis of adult females. This association was concordant in magnitude and direction in UKBS males and ALSPAC neonates. SNPs in and around ABHD8 were associated with mtDNA CN in ALSPAC neonates (rs10424198, β [SE] 0.262 [0.034], p = 1.40e-14), but not other study groups. In a meta-analysis of unrelated individuals (N = 11,253), we replicated a published association in TFAM (β [SE] 0.046 [0.017], p = 0.006), with an effect size much smaller than that observed in the replication analysis of a previous in silico GWAS. CONCLUSIONS In a hypothesis-generating GWAS, we confirm an association between TFAM and mtDNA CN and present putative loci requiring replication in much larger samples. We discuss the limitations of our work, in terms of measurement error and cellular heterogeneity, and highlight the need for larger studies to better understand nuclear genomic control of mtDNA copy number.
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Affiliation(s)
- Anna L. Guyatt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca R. Brennan
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philip A. I. Guthrie
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Raimondo Ascione
- Bristol Heart Institute, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan M. Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
| | | | - Debbie A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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32
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Zhao X, Song X, Bai X, Tan Z, Ma X, Guo J, Zhang Z, Du Q, Huang Y, Tong D. microRNA-222 Attenuates Mitochondrial Dysfunction During Transmissible Gastroenteritis Virus Infection. Mol Cell Proteomics 2019; 18:51-64. [PMID: 30257878 PMCID: PMC6317483 DOI: 10.1074/mcp.ra118.000808] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/13/2018] [Indexed: 12/30/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a member of Coronaviridae family. Our previous research showed that TGEV infection could induce mitochondrial dysfunction and upregulate miR-222 level. Therefore, we presumed that miR-222 might be implicated in regulating mitochondrial dysfunction induced by TGEV infection. To verify the hypothesis, the effect of miR-222 on mitochondrial dysfunction was tested and we showed that miR-222 attenuated TGEV-induced mitochondrial dysfunction. To investigate the underlying molecular mechanism of miR-222 in TGEV-induced mitochondrial dysfunction, a quantitative proteomic analysis of PK-15 cells that were transfected with miR-222 mimics and infected with TGEV was performed. In total, 4151 proteins were quantified and 100 differentially expressed proteins were obtained (57 upregulated, 43 downregulated), among which thrombospondin-1 (THBS1) and cluster of differentiation 47 (CD47) were downregulated. THBS1 was identified as the target of miR-222. Knockdown of THBS1 and CD47 decreased mitochondrial Ca2+ level and increased mitochondrial membrane potential (MMP) level. Reversely, overexpression of THBS1 and CD47 elevated mitochondrial Ca2+ level and reduced mitochondrial membrane potential (MMP) level. Together, our data establish a significant role of miR-222 in regulating mitochondrial dysfunction in response to TGEV infection.
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Affiliation(s)
- Xiaomin Zhao
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xiangjun Song
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xiaoyuan Bai
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhanhang Tan
- §Huyi District Center for Animal Disease Control and Prevention, Xi'an, Shaanxi 710300, P.R. China
| | - Xuelian Ma
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jianxiong Guo
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhichao Zhang
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Qian Du
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yong Huang
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Dewen Tong
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China;.
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33
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Abaji R, Ceppi F, Patel S, Gagné V, Xu CJ, Spinella JF, Colombini A, Parasole R, Buldini B, Basso G, Conter V, Cazzaniga G, Leclerc JM, Laverdière C, Sinnett D, Krajinovic M. Genetic risk factors for VIPN in childhood acute lymphoblastic leukemia patients identified using whole-exome sequencing. Pharmacogenomics 2018; 19:1181-1193. [PMID: 30191766 DOI: 10.2217/pgs-2018-0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM To identify genetic markers associated with vincristine-induced peripheral neuropathy (VIPN) in childhood acute lymphoblastic leukemia. PATIENTS & METHODS Whole-exome sequencing data were combined with exome-wide association study to identify predicted-functional germline variants associated with high-grade VIPN. Genotyping was then performed for top-ranked signals (n = 237), followed by validation in independent replication group (n = 405). RESULTS Minor alleles of rs2781377/SYNE2 (p = 0.01) and rs10513762/MRPL47 (p = 0.01) showed increased risk, whereas that of rs3803357/BAHD1 had a protective effect (p = 0.007). Using a genetic model based on weighted genetic risk scores, an additive effect of combining these loci was observed (p = 0.003). The addition of rs1135989/ACTG1 further enhanced model performance (p = 0.0001). CONCLUSION Variants in SYNE2, MRPL47 and BAHD1 genes are putative new risk factors for VIPN in childhood acute lymphoblastic leukemia.
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Affiliation(s)
- Rachid Abaji
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Francesco Ceppi
- Pediatric Hematology-Oncology Unit & Pediatric Hematology-Oncology Research Laboratory, Division of Pediatrics, Department of Woman-Mother-Child, University Hospital of Lausanne, 1004 Lausanne, Switzerland
| | - Swati Patel
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Vincent Gagné
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Chang J Xu
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Jean-François Spinella
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Antonella Colombini
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Rosanna Parasole
- Department of Pediatric Hemato-Oncology, Santobono-Pausilipon Hospital, 80129 Naples, Italy
| | - Barbara Buldini
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Giuseppe Basso
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Valentino Conter
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
| | - Jean-Marie Leclerc
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Caroline Laverdière
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Daniel Sinnett
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Maja Krajinovic
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.,Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
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34
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Rovadoscki GA, Pertile SFN, Alvarenga AB, Cesar ASM, Pértille F, Petrini J, Franzo V, Soares WVB, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Lanna DPD, Coutinho LL, Mourão GB. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. BMC Genomics 2018; 19:375. [PMID: 29783944 PMCID: PMC5963081 DOI: 10.1186/s12864-018-4777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
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Affiliation(s)
- G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - S F N Pertile
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A B Alvarenga
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A S M Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - V Franzo
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - W V B Soares
- Institute of Zootechny (IZ), Nova Odessa, SP, Brazil
| | - G Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - L F B Pinto
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - G G P Carvalho
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - D P D Lanna
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil.
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35
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Graham PS, Kaidonis G, Abhary S, Gillies MC, Daniell M, Essex RW, Chang JH, Lake SR, Pal B, Jenkins AJ, Hewitt AW, Lamoureux EL, Hykin PG, Petrovsky N, Brown MA, Craig JE, Burdon KP. Genome-wide association studies for diabetic macular edema and proliferative diabetic retinopathy. BMC MEDICAL GENETICS 2018; 19:71. [PMID: 29739359 PMCID: PMC5941644 DOI: 10.1186/s12881-018-0587-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/19/2018] [Indexed: 02/07/2023]
Abstract
Background Diabetic macular edema (DME) and proliferative diabetic retinopathy (PDR) are sight-threatening complications of diabetes mellitus and leading causes of adult-onset blindness worldwide. Genetic risk factors for diabetic retinopathy (DR) have been described previously, but have been difficult to replicate between studies, which have often used composite phenotypes and been conducted in different populations. This study aims to identify genetic risk factors for DME and PDR as separate complications in Australians of European descent with type 2 diabetes. Methods Caucasian Australians with type 2 diabetes were evaluated in a genome-wide association study (GWAS) to compare 270 DME cases and 176 PDR cases with 435 non-retinopathy controls. All participants were genotyped by SNP array and after data cleaning, cases were compared to controls using logistic regression adjusting for relevant covariates. Results The top ranked SNP for DME was rs1990145 (p = 4.10 × 10− 6, OR = 2.02 95%CI [1.50, 2.72]) on chromosome 2. The top-ranked SNP for PDR was rs918519 (p = 3.87 × 10− 6, OR = 0.35 95%CI [0.22, 0.54]) on chromosome 5. A trend towards association was also detected at two SNPs reported in the only other reported GWAS of DR in Caucasians; rs12267418 near MALRD1 (p = 0.008) in the DME cohort and rs16999051 in the diabetes gene PCSK2 (p = 0.007) in the PDR cohort. Conclusion This study has identified loci of interest for DME and PDR, two common ocular complications of diabetes. These findings require replication in other Caucasian cohorts with type 2 diabetes and larger cohorts will be required to identify genetic loci with statistical confidence. There is considerable overlap in the patient cohorts with each retinopathy subtype, complicating the search for genes that contribute to PDR and DME biology. Electronic supplementary material The online version of this article (10.1186/s12881-018-0587-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia S Graham
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Georgia Kaidonis
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Sotoodeh Abhary
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Mark C Gillies
- Save Sight Institute, Clinical Ophthalmology and Eye Health, University of Sydney, Sydney, New South Wales, Australia
| | - Mark Daniell
- Department of Ophthalmology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Rohan W Essex
- Academic Unit of Ophthalmology, Australian National University, Canberra, Australia
| | - John H Chang
- School of Medical Sciences, University of NSW, Sydney, New South Wales, Australia.,Medical Retina Service, Moorfields Eye Hospital, London, UK
| | - Stewart R Lake
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Bishwanath Pal
- Medical Retina Service, Moorfields Eye Hospital, London, UK
| | - Alicia J Jenkins
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, New South Wales, Australia.,St Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Centre for Eye Research Australia, University of Melbourne, East Melbourne, Victoria, Australia
| | - Ecosse L Lamoureux
- Centre for Eye Research Australia, University of Melbourne, East Melbourne, Victoria, Australia.,Singapore Eye Research Institute, Singapore, Singapore
| | - Philip G Hykin
- Medical Retina Service, Moorfields Eye Hospital, London, UK
| | - Nikolai Petrovsky
- Department of Endocrinology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia. .,Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia.
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Yazd NKK, Patel RR, Dellavalle RP, Dunnick CA. Genetic Risk Factors for Development of Atopic Dermatitis: a Systematic Review. CURRENT DERMATOLOGY REPORTS 2017. [DOI: 10.1007/s13671-017-0199-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Pu M, Wang J, Huang Q, Zhao G, Xia C, Shang R, Zhang Z, Bian Z, Yang X, Tao K. High MRPS23 expression contributes to hepatocellular carcinoma proliferation and indicates poor survival outcomes. Tumour Biol 2017; 39:1010428317709127. [PMID: 28714366 DOI: 10.1177/1010428317709127] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma is one of the most prevalent neoplasms and the leading cause of cancer-related mortality worldwide. Mitochondrial ribosomal protein S23 is encoded by a nuclear gene and participates in mitochondrial protein translation. Mitochondrial ribosomal protein S23 overexpression has been found in many types of cancer. In this study, we explored mitochondrial ribosomal protein S23 expression in primary hepatocellular carcinoma tissues compared with matched adjacent non-tumoral liver tissues using mitochondrial ribosomal protein S23 messenger RNA and protein levels collected from public databases and clinical samples. Immunohistochemistry was performed to analyze the relationship between mitochondrial ribosomal protein S23 and various clinicopathological features. The results indicated that mitochondrial ribosomal protein S23 was significantly overexpressed in hepatocellular carcinoma. High mitochondrial ribosomal protein S23 expression was correlated with the tumor size and tumor–metastasis–node stage. Moreover, patients with high mitochondrial ribosomal protein S23 expression levels presented poorer survival rates. Mitochondrial ribosomal protein S23 was an independent prognostic factor for survival, especially at the early stage of hepatocellular carcinoma. In addition, the downregulation of mitochondrial ribosomal protein S23 decreased the proliferation of hepatocellular carcinoma in vitro and in vivo. In conclusion, we verified for the first time that mitochondrial ribosomal protein S23 expression was upregulated in hepatocellular carcinoma. High mitochondrial ribosomal protein S23 levels can predict poor clinical outcomes in hepatocellular carcinoma, and this protein plays a key role in tumor proliferation. Therefore, mitochondrial ribosomal protein S23 may be a potential therapeutic target for hepatocellular carcinoma.
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Affiliation(s)
- Meng Pu
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Jianlin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Qike Huang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Ge Zhao
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Congcong Xia
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Zhuochao Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Zhenyuan Bian
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Xishegn Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Kaishan Tao
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
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38
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Desaulniers AT, Cederberg RA, Lents CA, White BR. Expression and Role of Gonadotropin-Releasing Hormone 2 and Its Receptor in Mammals. Front Endocrinol (Lausanne) 2017; 8:269. [PMID: 29312140 PMCID: PMC5732264 DOI: 10.3389/fendo.2017.00269] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/26/2017] [Indexed: 11/13/2022] Open
Abstract
Gonadotropin-releasing hormone 1 (GnRH1) and its receptor (GnRHR1) drive mammalian reproduction via regulation of the gonadotropins. Yet, a second form of GnRH (GnRH2) and its receptor (GnRHR2) also exist in mammals. GnRH2 has been completely conserved throughout 500 million years of evolution, signifying high selection pressure and a critical biological role. However, the GnRH2 gene is absent (e.g., rat) or inactivated (e.g., cow and sheep) in some species but retained in others (e.g., human, horse, and pig). Likewise, many species (e.g., human, chimpanzee, cow, and sheep) retain the GnRHR2 gene but lack the appropriate coding sequence to produce a full-length protein due to gene coding errors; although production of GnRHR2 in humans remains controversial. Certain mammals lack the GnRHR2 gene (e.g., mouse) or most exons entirely (e.g., rat). In contrast, old world monkeys, musk shrews, and pigs maintain the coding sequence required to produce a functional GnRHR2. Like GnRHR1, GnRHR2 is a 7-transmembrane, G protein-coupled receptor that interacts with Gαq/11 to mediate cell signaling. However, GnRHR2 retains a cytoplasmic tail and is only 40% homologous to GnRHR1. A role for GnRH2 and its receptor in mammals has been elusive, likely because common laboratory models lack both the ligand and receptor. Uniquely, both GnRH2 and GnRHR2 are ubiquitously expressed; transcript levels are abundant in peripheral tissues and scarcely found in regions of the brain associated with gonadotropin secretion, suggesting a divergent role from GnRH1/GnRHR1. Indeed, GnRH2 and its receptor are not physiological modulators of gonadotropin secretion in mammals. Instead, GnRH2 and GnRHR2 coordinate the interaction between nutritional status and sexual behavior in the female brain. Within peripheral tissues, GnRH2 and its receptor are novel regulators of reproductive organs. GnRH2 and GnRHR2 directly stimulate steroidogenesis within the porcine testis. In the female, GnRH2 and its receptor may help mediate placental function, implantation, and ovarian steroidogenesis. Furthermore, both the GnRH2 and GnRHR2 genes are expressed in human reproductive tumors and represent emerging targets for cancer treatment. Thus, GnRH2 and GnRHR2 have diverse functions in mammals which remain largely unexplored.
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Affiliation(s)
- Amy T. Desaulniers
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Rebecca A. Cederberg
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Brett R. White
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
- *Correspondence: Brett R. White,
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Chintalapudi SR, Morales-Tirado VM, Williams RW, Jablonski MM. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells. FEBS J 2016; 283:678-93. [PMID: 26663874 DOI: 10.1111/febs.13620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vanessa M Morales-Tirado
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
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40
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Coughlin CR, Scharer GH, Friederich MW, Yu HC, Geiger EA, Creadon-Swindell G, Collins AE, Vanlander AV, Coster RV, Powell CA, Swanson MA, Minczuk M, Van Hove JLK, Shaikh TH. Mutations in the mitochondrial cysteinyl-tRNA synthase gene, CARS2, lead to a severe epileptic encephalopathy and complex movement disorder. J Med Genet 2015; 52:532-40. [PMID: 25787132 DOI: 10.1136/jmedgenet-2015-103049] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/26/2015] [Indexed: 11/03/2022]
Abstract
BACKGROUND Mitochondrial disease is often suspected in cases of severe epileptic encephalopathy especially when a complex movement disorder, liver involvement and progressive developmental regression are present. Although mutations in either mitochondrial DNA or POLG are often present, other nuclear defects in mitochondrial DNA replication and protein translation have been associated with a severe epileptic encephalopathy. METHODS AND RESULTS We identified a proband with an epileptic encephalopathy, complex movement disorder and a combined mitochondrial respiratory chain enzyme deficiency. The child presented with neurological regression, complex movement disorder and intractable seizures. A combined deficiency of mitochondrial complexes I, III and IV was noted in liver tissue, along with increased mitochondrial DNA content in skeletal muscle. Incomplete assembly of complex V, using blue native polyacrylamide gel electrophoretic analysis and complex I, using western blotting, suggested a disorder of mitochondrial transcription or translation. Exome sequencing identified compound heterozygous mutations in CARS2, a mitochondrial aminoacyl-tRNA synthetase. Both mutations affect highly conserved amino acids located within the functional ligase domain of the cysteinyl-tRNA synthase. A specific decrease in the amount of charged mt-tRNA(Cys) was detected in patient fibroblasts compared with controls. Retroviral transfection of the wild-type CARS2 into patient skin fibroblasts led to the correction of the incomplete assembly of complex V, providing functional evidence for the role of CARS2 mutations in disease aetiology. CONCLUSIONS Our findings indicate that mutations in CARS2 result in a mitochondrial translational defect as seen in individuals with mitochondrial epileptic encephalopathy.
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Affiliation(s)
- Curtis R Coughlin
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Gunter H Scharer
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, Colorado, USA Department of Pediatrics, Section of Clinical Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marisa W Friederich
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Hung-Chun Yu
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Geralyn Creadon-Swindell
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Abigail E Collins
- Department of Pediatrics, Section of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Arnaud V Vanlander
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | | | - Michael A Swanson
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Johan L K Van Hove
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, Colorado, USA
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41
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Zhang H, Singh KK. Global genetic determinants of mitochondrial DNA copy number. PLoS One 2014; 9:e105242. [PMID: 25170845 PMCID: PMC4149433 DOI: 10.1371/journal.pone.0105242] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/19/2014] [Indexed: 11/18/2022] Open
Abstract
Many human diseases including development of cancer is associated with depletion of mitochondrial DNA (mtDNA) content. These diseases are collectively described as mitochondrial DNA depletion syndrome (MDS). High similarity between yeast and human mitochondria allows genomic study of the budding yeast to be used to identify human disease genes. In this study, we systematically screened the pre-existing respiratory-deficient Saccharomyces cerevisiae yeast strains using fluorescent microscopy and identified 102 nuclear genes whose deletions result in a complete mtDNA loss, of which 52 are not reported previously. Strikingly, these genes mainly encode protein products involved in mitochondrial protein biosynthesis process (54.9%). The rest of these genes either encode protein products associated with nucleic acid metabolism (14.7%), oxidative phosphorylation (3.9%), or other protein products (13.7%) responsible for bud-site selection, mitochondrial intermembrane space protein import, assembly of cytochrome-c oxidase, vacuolar protein sorting, protein-nucleus import, calcium-mediated signaling, heme biosynthesis and iron homeostasis. Thirteen (12.7%) of the genes encode proteins of unknown function. We identified human orthologs of these genes, conducted the interaction between the gene products and linked them to human mitochondrial disorders and other pathologies. In addition, we screened for genes whose defects affect the nuclear genome integrity. Our data provide a systematic view of the nuclear genes involved in maintenance of mitochondrial DNA. Together, our studies i) provide a global view of the genes regulating mtDNA content; ii) provide compelling new evidence toward understanding novel mechanism involved in mitochondrial genome maintenance and iii) provide useful clues in understanding human diseases in which mitochondrial defect and in particular depletion of mitochondrial genome plays a critical role.
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Affiliation(s)
- Hengshan Zhang
- Hengshan Zhang, Department of Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Keshav K. Singh
- Departments of Genetics, Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, and Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, United States of America
- * E-mail:
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42
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Kemeny S, Pebrel-Richard C, Eymard-Pierre E, Gay-Bellile M, Gouas L, Goumy C, Tchirkov A, Francannet C, Vago P. Clinical and molecular description of a 17q21.33 microduplication in a girl with severe kyphoscoliosis and developmental delay. Eur J Med Genet 2014; 57:552-7. [PMID: 25106685 DOI: 10.1016/j.ejmg.2014.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/20/2014] [Indexed: 10/24/2022]
Abstract
High proportion of disease-associated copy number variant maps to chromosome 17. Genomic studies have provided an insight into its complex genomic structure such as relative abundance of segmental duplication and intercepted repetitive elements. 17q21.31, 17q11.2 and 17q12 loci are well known on this chromosome and are associated with microdeletion and microduplication syndrome. No syndrome associated with 17q21.33 locus have been described. We report clinical, cytogenetic and molecular investigations of a 13 years-old girl admitted for evaluation of microcephaly, scoliosis, skeletal defects and learning difficulties. We carried out detailed analysis of the clinical phenotype of this patient and investigated the genetic basis using Agilent 180K Array Comparative Genomic Hybridization. We identified a ∼0.9 Mb de novo microduplication on chromosome 17q21.33. Four genes, COL1A1, SGCA, PPP1R9B and CHAD located within the duplicated region are possible candidates for clinical features present in our patients. Gene expression studies by real-time RT-PCR assay only showed an overexpression of SGCA (P < 0.01), a component of the dystrophin glycoprotein complex. Defect of SGCA was previously shown to lead to severe childhood autosomal recessive muscular dystrophy (LGMD2D) which result in progressive muscle weakness and can also be associated with hyperlordosis or scoliosis. Further cases with similar duplications are expected to be diagnosed. This will contribute to the delineation of this potential new microduplication syndrome and to improve genetic counseling.
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Affiliation(s)
- Stéphan Kemeny
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Céline Pebrel-Richard
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Eléonore Eymard-Pierre
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Mathilde Gay-Bellile
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Laetitia Gouas
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Carole Goumy
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | - Andreï Tchirkov
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
| | | | - Philippe Vago
- Univ Clermont 1, UFR Médecine, Cytologie Histologie Embryologie Cytogénétique, Clermont-Ferrand, F-63001, France; CHU Estaing, Cytogénétique Médicale, Clermont-Ferrand, F-63003, France; ERTICa, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, F-63001, France.
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Lee KW, Bogenhagen DF. Assignment of 2'-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16 S ribosomal RNA (rRNA). J Biol Chem 2014; 289:24936-42. [PMID: 25074936 DOI: 10.1074/jbc.c114.581868] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Advances in proteomics and large scale studies of potential mitochondrial proteins have led to the identification of many novel mitochondrial proteins in need of further characterization. Among these novel proteins are three mammalian rRNA methyltransferase family members RNMTL1, MRM1, and MRM2. MRM1 and MRM2 have bacterial and yeast homologs, whereas RNMTL1 appears to have evolved later in higher eukaryotes. We recently confirmed the localization of the three proteins to mitochondria, specifically in the vicinity of mtDNA nucleoids. In this study, we took advantage of the ability of 2'-O-ribose modification to block site-specific cleavage of RNA by DNAzymes to show that MRM1, MRM2, and RNMTL1 are responsible for modification of human large subunit rRNA at residues G(1145), U(1369), and G(1370), respectively.
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Affiliation(s)
- Ken-Wing Lee
- From the Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
| | - Daniel F Bogenhagen
- From the Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
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44
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Varvagiannis K, Papoulidis I, Koromila T, Kefalas K, Ziegler M, Liehr T, Petersen MB, Gyftodimou Y, Manolakos E. De novo 393 kb microdeletion of 7p11.2 characterized by aCGH in a boy with psychomotor retardation and dysmorphic features. Meta Gene 2014; 2:274-82. [PMID: 25606410 PMCID: PMC4287824 DOI: 10.1016/j.mgene.2014.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/08/2014] [Accepted: 03/17/2014] [Indexed: 01/03/2023] Open
Abstract
We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features. We report in detail the clinical and cytogenetic findings of a 27-month old male. We compare our findings with current literature and online databases. We discuss the possible involvement of certain genes in our patient’s phenotype.
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Affiliation(s)
| | | | - Theodora Koromila
- Laboratory of Human Genetics, Department of Biology, University of Athens, Athens, Greece
| | | | - Monika Ziegler
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | | | | | - Emmanouil Manolakos
- Eurogenetica S.A., Laboratory of Genetics, Athens-Thessaloniki, Greece ; Cattedra di Genetica Medica, Ospedale Binaghi, Cagliari, Italy
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45
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Koc EC, Cimen H, Kumcuoglu B, Abu N, Akpinar G, Haque ME, Spremulli LL, Koc H. Identification and characterization of CHCHD1, AURKAIP1, and CRIF1 as new members of the mammalian mitochondrial ribosome. Front Physiol 2013; 4:183. [PMID: 23908630 PMCID: PMC3726836 DOI: 10.3389/fphys.2013.00183] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/26/2013] [Indexed: 11/17/2022] Open
Abstract
Defects in mitochondrial ribosomal proteins (MRPs) cause various diseases in humans. Because of the essential role of MRPs in synthesizing the essential subunits of oxidative phosphorylation (OXPHOS) complexes, identifying all of the protein components involved in the mitochondrial translational machinery is critical. Initially, we identified 79 MRPs; however, identifying MRPs with no clear homologs in bacteria and yeast mitochondria was challenging, due to limited availability of expressed sequence tags (ESTs) in the databases available at that time. With the improvement in genome sequencing and increased sensitivity of mass spectrometry (MS)-based technologies, we have established four previously known proteins as MRPs and have confirmed the identification of ICT1 (MRP58) as a ribosomal protein. The newly identified MRPs are MRPS37 (Coiled-coil-helix-coiled-coil-helix domain containing protein 1-CHCHD1), MRPS38 (Aurora kinase A interacting protein1, AURKAIP1), MRPS39 (Pentatricopeptide repeat-containing protein 3, PTCD3), in the small subunit and MRPL59 (CR-6 interacting factor 1, CRIF1) in the large subunit. Furthermore, we have demonstrated the essential roles of CHCHD1, AURKAIP1, and CRIF1in mitochondrial protein synthesis by siRNA knock-down studies, which had significant effects on the expression of mitochondrially encoded proteins.
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Affiliation(s)
- Emine C Koc
- Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall University Huntington, WV, USA
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Yazdi PG, Su H, Ghimbovschi S, Fan W, Coskun PE, Nalbandian A, Knoblach S, Resnick JL, Hoffman E, Wallace DC, Kimonis VE. Differential gene expression reveals mitochondrial dysfunction in an imprinting center deletion mouse model of Prader-Willi syndrome. Clin Transl Sci 2013; 6:347-55. [PMID: 24127921 DOI: 10.1111/cts.12083] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a genetic disorder caused by deficiency of imprinted gene expression from the paternal chromosome 15q11-15q13 and clinically characterized by neonatal hypotonia, short stature, cognitive impairment, hypogonadism, hyperphagia, morbid obesity, and diabetes. Previous clinical studies suggest that a defect in energy metabolism may be involved in the pathogenesis of PWS. We focused our attention on the genes associated with energy metabolism and found that there were 95 and 66 mitochondrial genes differentially expressed in PWS muscle and brain, respectively. Assessment of enzyme activities of mitochondrial oxidative phosphorylation complexes in the brain, heart, liver, and muscle were assessed. We found the enzyme activities of the cardiac mitochondrial complexes II+III were up-regulated in the PWS imprinting center deletion mice compared to the wild-type littermates. These studies suggest that differential gene expression, especially of the mitochondrial genes may contribute to the pathophysiology of PWS.
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Affiliation(s)
- Puya G Yazdi
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, California, USA
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Hass J, Walton E, Kirsten H, Liu J, Priebe L, Wolf C, Karbalai N, Gollub R, White T, Roessner V, Müller KU, Paus T, Smolka MN, Schumann G, Scholz M, Cichon S, Calhoun V, Ehrlich S. A Genome-Wide Association Study Suggests Novel Loci Associated with a Schizophrenia-Related Brain-Based Phenotype. PLoS One 2013; 8:e64872. [PMID: 23805179 PMCID: PMC3689744 DOI: 10.1371/journal.pone.0064872] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 04/12/2013] [Indexed: 01/05/2023] Open
Abstract
Patients with schizophrenia and their siblings typically show subtle changes of brain structures, such as a reduction of hippocampal volume. Hippocampal volume is heritable, may explain a variety of cognitive symptoms of schizophrenia and is thus considered an intermediate phenotype for this mental illness. The aim of our analyses was to identify single-nucleotide polymorphisms (SNP) related to hippocampal volume without making prior assumptions about possible candidate genes. In this study, we combined genetics, imaging and neuropsychological data obtained from the Mind Clinical Imaging Consortium study of schizophrenia (n = 328). A total of 743,591 SNPs were tested for association with hippocampal volume in a genome-wide association study. Gene expression profiles of human hippocampal tissue were investigated for gene regions of significantly associated SNPs. None of the genetic markers reached genome-wide significance. However, six highly correlated SNPs (rs4808611, rs35686037, rs12982178, rs1042178, rs10406920, rs8170) on chromosome 19p13.11, located within or in close proximity to the genes NR2F6, USHBP1, and BABAM1, as well as four SNPs in three other genomic regions (chromosome 1, 2 and 10) had p-values between 6.75×10(-6) and 8.3×10(-7). Using existing data of a very recently published GWAS of hippocampal volume and additional data of a multicentre study in a large cohort of adolescents of European ancestry, we found supporting evidence for our results. Furthermore, allelic differences in rs4808611 and rs8170 were highly associated with differential mRNA expression in the cis-acting region. Associations with memory functioning indicate a possible functional importance of the identified risk variants. Our findings provide new insights into the genetic architecture of a brain structure closely linked to schizophrenia. In silico replication, mRNA expression and cognitive data provide additional support for the relevance of our findings. Identification of causal variants and their functional effects may unveil yet unknown players in the neurodevelopment and the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Johanna Hass
- Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
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Jacobi A, Rauh J, Bernstein P, Liebers C, Zou X, Stiehler M. Comparative analysis of reference gene stability in human mesenchymal stromal cells during osteogenic differentiation. Biotechnol Prog 2013; 29:1034-42. [PMID: 23674393 DOI: 10.1002/btpr.1747] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/27/2013] [Indexed: 01/07/2023]
Abstract
Mesenchymal stromal cells (MSCs) are one of the most frequently used cell sources for tissue engineering strategies. Cultivation of osteogenic MSCs is a prerequisite for cell-based concepts that aim at bone regeneration. Quantitative real time reverse transcription polymerase chain reaction (qRT-PCR) analysis is a commonly used method for the examination of mRNA expression levels. However, data on suitable reference genes for osteogenically cultivated MSCs is scarce. Hence, the aim of the study was to compare the regulation of different potential reference genes in osteogenically stimulated MSCs. Human MSCs were isolated from bone marrow aspirates of N = 6 hematologically healthy individuals, expanded by polystyrene-adherence, and maintained with and without osteogenic supplements for 14 days. Cellular proliferation and osteogenic differentiation were assessed by total DNA quantification, cell-specific alkaline phosphatase (ALP) activity and by qualitative staining for ALP and alizarin red, respectively. mRNA expression levels of N = 32 potential reference genes were quantified using the human Endogenous Control TaqMan® assays. mRNA expression stability was calculated using geNorm. The combined use of the most stable reference genes and DNA-damage-inducible alpha, Pumilio homolog 1, and large ribosomal protein P0 significantly improved gene expression accuracy as compared to the use of the commonly used reference genes beta actin and glyceraldehyde-3-phosphate dehydrogenase during qRT-PCR-based target gene expression analysis of osteogenically stimulated MSCs.
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Affiliation(s)
- Angela Jacobi
- Dept. of Orthopaedics and Centre for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus, 01307, Dresden, Germany
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Imberg-Kazdan K, Ha S, Greenfield A, Poultney CS, Bonneau R, Logan SK, Garabedian MJ. A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells. Genome Res 2013; 23:581-91. [PMID: 23403032 PMCID: PMC3613576 DOI: 10.1101/gr.144774.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 01/31/2013] [Indexed: 01/22/2023]
Abstract
The androgen receptor (AR) is a mediator of both androgen-dependent and castration-resistant prostate cancers. Identification of cellular factors affecting AR transcriptional activity could in principle yield new targets that reduce AR activity and combat prostate cancer, yet a comprehensive analysis of the genes required for AR-dependent transcriptional activity has not been determined. Using an unbiased genetic approach that takes advantage of the evolutionary conservation of AR signaling, we have conducted a genome-wide RNAi screen in Drosophila cells for genes required for AR transcriptional activity and applied the results to human prostate cancer cells. We identified 45 AR-regulators, which include known pathway components and genes with functions not previously linked to AR regulation, such as HIPK2 (a protein kinase) and MED19 (a subunit of the Mediator complex). Depletion of HIPK2 and MED19 in human prostate cancer cells decreased AR target gene expression and, importantly, reduced the proliferation of androgen-dependent and castration-resistant prostate cancer cells. We also systematically analyzed additional Mediator subunits and uncovered a small subset of Mediator subunits that interpret AR signaling and affect AR-dependent transcription and prostate cancer cell proliferation. Importantly, targeting of HIPK2 by an FDA-approved kinase inhibitor phenocopied the effect of depletion by RNAi and reduced the growth of AR-positive, but not AR-negative, treatment-resistant prostate cancer cells. Thus, our screen has yielded new AR regulators including drugable targets that reduce the proliferation of castration-resistant prostate cancer cells.
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Affiliation(s)
- Keren Imberg-Kazdan
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Ha
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
| | - Alex Greenfield
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | | | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Susan K. Logan
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
- NYU Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Michael J. Garabedian
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
- NYU Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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Genome-wide analysis of gene and protein expression of dysplastic naevus cells. J Skin Cancer 2012; 2012:981308. [PMID: 23251804 PMCID: PMC3515917 DOI: 10.1155/2012/981308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 01/20/2023] Open
Abstract
Cutaneous melanoma, a type of skin tumor originating from melanocytes, often develops from premalignant naevoid lesions via a gradual transformation process driven by an accumulation of (epi)genetic lesions. These dysplastic naevi display altered morphology and often proliferation of melanocytes. Additionally, melanocytes in dysplastic naevi show structural mitochondrial and melanosomal alterations and have elevated reactive oxygen species (ROS) levels. For this study we performed genome-wide expression and proteomic analysis of melanocytes from dysplastic naevus (DNMC) and adjacent normal skin (MC) from 18 patients. Whole genome expression profiles of the DNMC and MC of each individual patient subjected to GO-based comparative statistical analysis yielded significantly differentially expressed GO classes including “organellar ribosome,” “mitochondrial ribosome,” “hydrogen ion transporter activity,” and “prefoldin complex.” Validation of 5 genes from these top GO classes revealed a heterogeneous differential expression pattern. Proteomic analysis demonstrated differentially expressed proteins in DNMC that are involved in cellular metabolism, detoxification, and cytoskeletal organization processes, such as GTP-binding Rho-like protein CDC42, glutathione-S-transferase omega-1 and prolyl 4-hydroxylase. Collectively these results point to deregulation of cellular processes, such as metabolism and protein synthesis, consistent with the observed elevated oxidative stress levels in DNMC potentially resulting in oxidative DNA damage in these cells.
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