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Bhowmick C, Rahaman M, Bhattacharya S, Mukherjee M, Chakravorty N, Dutta PK, Mahadevappa M. Identification of hub genes to determine drug-disease correlation in breast carcinomas. Med Oncol 2023; 41:36. [PMID: 38153604 DOI: 10.1007/s12032-023-02246-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/11/2023] [Indexed: 12/29/2023]
Abstract
The exact molecular mechanism underlying the heterogeneous drug response against breast carcinoma remains to be fully understood. It is urgently required to identify key genes that are intricately associated with varied clinical response of standard anti-cancer drugs, clinically used to treat breast cancer patients. In the present study, the utility of transcriptomic data of breast cancer patients in discerning the clinical drug response using machine learning-based approaches were evaluated. Here, a computational framework has been developed which can be used to identify key genes that can be linked with clinical drug response and progression of cancer, offering an immense opportunity to predict potential prognostic biomarkers and therapeutic targets. The framework concerned utilizes DeSeq2, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape, and machine learning techniques to find these crucial genes. Total RNA extraction and qRT-PCR were performed to quantify relative expression of few hub genes selected from the networks. In our study, we have experimentally checked the expression of few key hub genes like APOA2, DLX5, APOC3, CAMK2B, and PAK6 that were predicted to play an immense role in breast cancer tumorigenesis and progression in response to anti-cancer drug Paclitaxel. However, further experimental validations will be required to get mechanistic insights of these genes in regulating the drug response and cancer progression which will likely to play pivotal role in cancer treatment and precision oncology.
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Affiliation(s)
- Chiranjib Bhowmick
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Motiur Rahaman
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Shatarupa Bhattacharya
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Mandrita Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Nishant Chakravorty
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Pranab Kumar Dutta
- Department of Electrical Engineering, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India
| | - Manjunatha Mahadevappa
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Medinipur, Kharagpur, West Bengal, 721302, India.
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2
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Lessey AJ, Mirczuk SM, Chand AN, Kurrasch DM, Korbonits M, Niessen SJM, McArdle CA, McGonnell IM, Fowkes RC. Pharmacological and Genetic Disruption of C-Type Natriuretic Peptide ( nppcl) Expression in Zebrafish ( Danio rerio) Causes Stunted Growth during Development. Int J Mol Sci 2023; 24:12921. [PMID: 37629102 PMCID: PMC10454581 DOI: 10.3390/ijms241612921] [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: 07/26/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Human patients with mutations within NPPC or NPR2 genes (encoding C-type natriuretic peptide (CNP) and guanylyl cyclase-B (GC-B), respectively) display clinical signs associated with skeletal abnormalities, such as overgrowth or short stature. Mice with induced models of Nppc or Npr2 deletion display profound achondroplasia, dwarfism and early death. Recent pharmacological therapies to treat short stature are utilizing long-acting CNP analogues, but the effects of manipulating CNP expression during development remain unknown. Here, we use Danio rerio (zebrafish) as a model for vertebrate development, employing both pharmacological and reverse genetics approaches to alter expression of genes encoding CNP in zebrafish. Four orthologues of CNP were identified in zebrafish, and spatiotemporal expression profiling confirmed their presence during development. Bioinformatic analyses suggested that nppcl is the most likely the orthologue of mammalian CNP. Exogenous CNP treatment of developing zebrafish embryos resulted in impaired growth characteristics, such as body length, head width and eye diameter. This reduced growth was potentially caused by increased apoptosis following CNP treatment. Expression of endogenous nppcl was downregulated in these CNP-treated embryos, suggesting that negative feedback of the CNP system might influence growth during development. CRISPR knock-down of endogenous nppcl in developing zebrafish embryos also resulted in impaired growth characteristics. Collectively, these data suggest that CNP in zebrafish is crucial for normal embryonic development, specifically with regard to growth.
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Affiliation(s)
- Andrew J. Lessey
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (A.J.L.); (S.M.M.); (A.N.C.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK
| | - Samantha M. Mirczuk
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (A.J.L.); (S.M.M.); (A.N.C.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK
| | - Annisa N. Chand
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (A.J.L.); (S.M.M.); (A.N.C.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK
| | - Deborah M. Kurrasch
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N2, Canada;
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Stijn J. M. Niessen
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK;
- Veterinary Specialist Consultations, Loosdrechtseweg 56, 1215 JX Hilversum, The Netherlands
| | - Craig A. McArdle
- Department of Translational Science, Bristol Medical School, University of Bristol, Whitson Street, Bristol BS1 3NY, UK;
| | - Imelda M. McGonnell
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK
| | - Robert C. Fowkes
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (A.J.L.); (S.M.M.); (A.N.C.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK
- Endocrine Signaling Group, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, Wilson Road, East Lansing, MI 48824, USA
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3
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García-Moreno JF, Lacerda R, da Costa PJ, Pereira M, Gama-Carvalho M, Matos P, Romão L. DIS3L2 knockdown impairs key oncogenic properties of colorectal cancer cells via the mTOR signaling pathway. Cell Mol Life Sci 2023; 80:185. [PMID: 37340282 DOI: 10.1007/s00018-023-04833-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
DIS3L2 degrades different types of RNAs in an exosome-independent manner including mRNAs and several types of non-coding RNAs. DIS3L2-mediated degradation is preceded by the addition of nontemplated uridines at the 3'end of its targets by the terminal uridylyl transferases 4 and 7. Most of the literature that concerns DIS3L2 characterizes its involvement in several RNA degradation pathways, however, there is some evidence that its dysregulated activity may contribute to cancer development. In the present study, we characterize the role of DIS3L2 in human colorectal cancer (CRC). Using the public RNA datasets from The Cancer Genome Atlas (TCGA), we found higher DIS3L2 mRNA levels in CRC tissues versus normal colonic samples as well as worse prognosis in patients with high DIS3L2 expression. In addition, our RNA deep-sequencing data revealed that knockdown (KD) of DIS3L2 induces a strong transcriptomic disturbance in SW480 CRC cells. Moreover, gene ontology (GO) analysis of significant upregulated transcripts displays enrichment in mRNAs encoding proteins involved in cell cycle regulation and cancer-related pathways, which guided us to evaluate which specific hallmarks of cancer are differentially regulated by DIS3L2. To do so, we employed four CRC cell lines (HCT116, SW480, Caco-2 and HT-29) differing in their mutational background and oncogenicity. We demonstrate that depletion of DIS3L2 results in reduced cell viability of highly oncogenic SW480 and HCT116 CRC cells, but had little or no impact in the more differentiated Caco-2 and HT-29 cells. Remarkably, the mTOR signaling pathway, crucial for cell survival and growth, is downregulated after DIS3L2 KD, whereas AZGP1, an mTOR pathway inhibitor, is upregulated. Furthermore, our results indicate that depletion of DIS3L2 disturbs metastasis-associated properties, such as cell migration and invasion, only in highly oncogenic CRC cells. Our work reveals for the first time a role for DIS3L2 in sustaining CRC cell proliferation and provides evidence that this ribonuclease is required to support the viability and invasive behavior of dedifferentiated CRC cells.
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Affiliation(s)
- Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafaela Lacerda
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Paulo J da Costa
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Marcelo Pereira
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Paulo Matos
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.
- Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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4
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Hujoel MLA, Sherman MA, Barton AR, Mukamel RE, Sankaran VG, Terao C, Loh PR. Influences of rare copy-number variation on human complex traits. Cell 2022; 185:4233-4248.e27. [PMID: 36306736 PMCID: PMC9800003 DOI: 10.1016/j.cell.2022.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
The human genome contains hundreds of thousands of regions harboring copy-number variants (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs have been ascertainable from SNP-array data generated by large biobanks. We developed a computational approach leveraging haplotype sharing in biobank cohorts to more sensitively detect CNVs. Applied to UK Biobank, this approach accounted for approximately half of all rare gene inactivation events produced by genomic structural variation. This CNV call set enabled a detailed analysis of associations between CNVs and 56 quantitative traits, identifying 269 independent associations (p < 5 × 10-8) likely to be causally driven by CNVs. Putative target genes were identifiable for nearly half of the loci, enabling insights into dosage sensitivity of these genes and uncovering several gene-trait relationships. These results demonstrate the ability of haplotype-informed analysis to provide insights into the genetic basis of human complex traits.
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Affiliation(s)
- Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA
| | - Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Marques P, Korbonits M. Approach to the Patient With Pseudoacromegaly. J Clin Endocrinol Metab 2022; 107:1767-1788. [PMID: 34792134 DOI: 10.1210/clinem/dgab789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/19/2022]
Abstract
Pseudoacromegaly encompasses a heterogeneous group of conditions in which patients have clinical features of acromegaly or gigantism, but no excess of GH or IGF-1. Acromegaloid physical features or accelerated growth in a patient may prompt referral to endocrinologists. Because pseudoacromegaly conditions are rare and heterogeneous, often with overlapping clinical features, the underlying diagnosis may be challenging to establish. As many of these have a genetic origin, such as pachydermoperiostosis, Sotos syndrome, Weaver syndrome, or Cantú syndrome, collaboration is key with clinical geneticists in the diagnosis of these patients. Although rare, awareness of these uncommon conditions and their characteristic features will help their timely recognition.
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Affiliation(s)
- Pedro Marques
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
- Endocrinology Department, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisboa, Portugal
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
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6
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [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: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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7
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Hoffmann S, Roeth R, Diebold S, Gogel J, Hassel D, Just S, Rappold GA. Identification and Tissue-Specific Characterization of Novel SHOX-Regulated Genes in Zebrafish Highlights SOX Family Members Among Other Genes. Front Genet 2021; 12:688808. [PMID: 34122528 PMCID: PMC8191631 DOI: 10.3389/fgene.2021.688808] [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: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 02/01/2023] Open
Abstract
SHOX deficiency causes a spectrum of clinical phenotypes related to skeletal dysplasia and short stature, including Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Turner syndrome, and idiopathic short stature. SHOX controls chondrocyte proliferation and differentiation, bone maturation, and cellular growth arrest and apoptosis via transcriptional regulation of its direct target genes NPPB, FGFR3, and CTGF. However, our understanding of SHOX-related pathways is still incomplete. To elucidate the underlying molecular mechanisms and to better understand the broad phenotypic spectrum of SHOX deficiency, we aimed to identify novel SHOX targets. We analyzed differentially expressed genes in SHOX-overexpressing human fibroblasts (NHDF), and confirmed the known SHOX target genes NPPB and FGFR among the most strongly regulated genes, together with 143 novel candidates. Altogether, 23 genes were selected for further validation, first by whole-body characterization in developing shox-deficient zebrafish embryos, followed by tissue-specific expression analysis in three shox-expressing zebrafish tissues: head (including brain, pharyngeal arches, eye, and olfactory epithelium), heart, and pectoral fins. Most genes were physiologically relevant in the pectoral fins, while only few genes were also significantly regulated in head and heart tissue. Interestingly, multiple sox family members (sox5, sox6, sox8, and sox18) were significantly dysregulated in shox-deficient pectoral fins together with other genes (nppa, nppc, cdkn1a, cdkn1ca, cyp26b1, and cy26c1), highlighting an important role for these genes in shox-related growth disorders. Network-based analysis integrating data from the Ingenuity pathways revealed that most of these genes act in a common network. Our results provide novel insights into the genetic pathways and molecular events leading to the clinical manifestation of SHOX deficiency.
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Affiliation(s)
- Sandra Hoffmann
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Sabrina Diebold
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Jasmin Gogel
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - David Hassel
- Department of Internal Medicine III - Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Steffen Just
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Estrada K, Froelich S, Wuster A, Bauer CR, Sterling T, Clark WT, Ru Y, Trinidad M, Nguyen HP, Luu AR, Wendt DJ, Yogalingam G, Yu GK, LeBowitz JH, Cardon LR. Identifying therapeutic drug targets using bidirectional effect genes. Nat Commun 2021; 12:2224. [PMID: 33850126 PMCID: PMC8044152 DOI: 10.1038/s41467-021-21843-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/12/2021] [Indexed: 01/15/2023] Open
Abstract
Prioritizing genes for translation to therapeutics for common diseases has been challenging. Here, we propose an approach to identify drug targets with high probability of success by focusing on genes with both gain of function (GoF) and loss of function (LoF) mutations associated with opposing effects on phenotype (Bidirectional Effect Selected Targets, BEST). We find 98 BEST genes for a variety of indications. Drugs targeting those genes are 3.8-fold more likely to be approved than non-BEST genes. We focus on five genes (IGF1R, NPPC, NPR2, FGFR3, and SHOX) with evidence for bidirectional effects on stature. Rare protein-altering variants in those genes result in significantly increased risk for idiopathic short stature (ISS) (OR = 2.75, p = 3.99 × 10-8). Finally, using functional experiments, we demonstrate that adding an exogenous CNP analog (encoded by NPPC) rescues the phenotype, thus validating its potential as a therapeutic treatment for ISS. Our results show the value of looking for bidirectional effects to identify and validate drug targets.
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Affiliation(s)
| | | | | | | | | | | | - Yuanbin Ru
- BioMarin Pharmaceutical Inc., Novato, CA, USA
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9
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Huang J, Deng X, Wang Y, Tang N, Zeng D. Analysis of Copy Number Variations by Low-Depth Whole-Genome Sequencing in Fetuses with Congenital Cardiovascular Malformations. Cytogenet Genome Res 2021; 160:643-649. [PMID: 33647914 DOI: 10.1159/000512605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
Abstract
Congenital cardiovascular malformations (CVMs) due to genomic mutations bring a greater risk of morbidity and comorbidity and increase the risks related to heart surgery. However, reports on CVMs induced by genomic mutations based on actual clinical data are still limited. In this study, 181 fetuses were screened by fetal echocardiography for prenatal diagnosis of congenital heart disease, including 146 cases without ultrasound extracardiac findings (Group A) and 35 cases with ultrasound extracardiac findings (Group B). All cases were analyzed by clinical data, karyotyping, and low-depth whole-genome sequencing. The rates of chromosomal abnormalities in Groups A and B were 4.8% (7/146) and 37.1% (13/35), respectively. There was a significant difference in the incidence of chromosomal abnormalities between Groups A and B (p < 0.001). In Group A, CNV-seq identified copy number variations (CNVs) in an additional 9.6% (14/146) of cases with normal karyotypes, including 7 pathogenic CNVs and 7 variations of uncertain clinical significance. In Group B, one pathogenic CNV was identified in a case with normal karyotype. Chromosomal abnormality is one of the most common causes of CVM with extracardiac defects. Low-depth whole-genome sequencing could effectively become a first approach for CNV diagnosis in fetuses with CVMs.
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Affiliation(s)
- Jiwei Huang
- Central Laboratory/Biobank, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Xine Deng
- Department of Perinatal Healthcare, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Yuanliu Wang
- Department of Perinatal Healthcare, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Ning Tang
- Central Laboratory/Biobank, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Dingyuan Zeng
- Department of Obstetrics and Gynecology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China,
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10
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Mirczuk SM, Scudder CJ, Read JE, Crossley VJ, Regan JT, Richardson KM, Simbi B, McArdle CA, Church DB, Fenn J, Kenny PJ, Volk HA, Wheeler-Jones CP, Korbonits M, Niessen SJ, McGonnell IM, Fowkes RC. Natriuretic Peptide Expression and Function in GH3 Somatolactotropes and Feline Somatotrope Pituitary Tumours. Int J Mol Sci 2021; 22:ijms22031076. [PMID: 33499110 PMCID: PMC7865297 DOI: 10.3390/ijms22031076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022] Open
Abstract
Patients harbouring mutations in genes encoding C-type natriuretic peptide (CNP; NPPC) or its receptor guanylyl cyclase B (GC-B, NPR2) suffer from severe growth phenotypes; loss-of-function mutations cause achondroplasia, whereas gain-of-function mutations cause skeletal overgrowth. Although most of the effects of CNP/GC-B on growth are mediated directly on bone, evidence suggests the natriuretic peptides may also affect anterior pituitary control of growth. Our previous studies described the expression of NPPC and NPR2 in a range of human pituitary tumours, normal human pituitary, and normal fetal human pituitary. However, the natriuretic peptide system in somatotropes has not been extensively explored. Here, we examine the expression and function of the CNP/GC-B system in rat GH3 somatolactotrope cell line and pituitary tumours from a cohort of feline hypersomatotropism (HST; acromegaly) patients. Using multiplex RT-qPCR, all three natriuretic peptides and their receptors were detected in GH3 cells. The expression of Nppc was significantly enhanced following treatment with either 100 nM TRH or 10 µM forskolin, yet only Npr1 expression was sensitive to forskolin stimulation; the effects of forskolin and TRH on Nppc expression were PKA- and MAPK-dependent, respectively. CNP stimulation of GH3 somatolactotropes significantly inhibited Esr1, Insr and Lepr expression, but dramatically enhanced cFos expression at the same time point. Oestrogen treatment significantly enhanced expression of Nppa, Nppc, Npr1, and Npr2 in GH3 somatolactotropes, but inhibited CNP-stimulated cGMP accumulation. Finally, transcripts for all three natriuretic peptides and receptors were expressed in feline pituitary tumours from patients with HST. NPPC expression was negatively correlated with pituitary tumour volume and SSTR5 expression, but positively correlated with D2R and GHR expression. Collectively, these data provide mechanisms that control expression and function of CNP in somatolactotrope cells, and identify putative transcriptional targets for CNP action in somatotropes.
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Affiliation(s)
- Samantha M. Mirczuk
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Christopher J. Scudder
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
| | - Jordan E. Read
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Victoria J. Crossley
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Jacob T. Regan
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
| | - Karen M. Richardson
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
| | - Bigboy Simbi
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Craig A. McArdle
- Department of Translational Science, Bristol Medical School, University of Bristol, Whitson Street, Bristol BS1 3NY, UK;
| | - David B. Church
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
| | - Joseph Fenn
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
| | - Patrick J. Kenny
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
- Small Animal Specialist Hospital, 1 Richardson Place, North Ryde, 2113 NSW, Australia
| | - Holger A. Volk
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Bünteweg 9, 30559 Hannover, Germany
| | - Caroline P. Wheeler-Jones
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Stijn J. Niessen
- Clinical Sciences & Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (D.B.C.); (J.F.); (P.J.K.); (H.A.V.); (S.J.N.)
| | - Imelda M. McGonnell
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
| | - Robert C. Fowkes
- Endocrine Signalling Group, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (S.M.M.); (C.J.S.); (J.E.R.); (V.J.C.); (J.T.R.); (K.M.R.)
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK; (B.S.); (C.P.W.-J.); (I.M.M.)
- Correspondence: ; Tel.: +11-44-207-468-1215
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Dis3L2 regulates cell proliferation and tissue growth through a conserved mechanism. PLoS Genet 2020; 16:e1009297. [PMID: 33370287 PMCID: PMC7793271 DOI: 10.1371/journal.pgen.1009297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 01/08/2021] [Accepted: 12/05/2020] [Indexed: 01/04/2023] Open
Abstract
Dis3L2 is a highly conserved 3’-5’ exoribonuclease which is mutated in the human overgrowth disorders Perlman syndrome and Wilms’ tumour of the kidney. Using Drosophila melanogaster as a model system, we have generated a new dis3L2 null mutant together with wild-type and nuclease-dead genetic lines in Drosophila to demonstrate that the catalytic activity of Dis3L2 is required to control cell proliferation. To understand the cellular pathways regulated by Dis3L2 to control proliferation, we used RNA-seq on dis3L2 mutant wing discs to show that the imaginal disc growth factor Idgf2 is responsible for driving the wing overgrowth. IDGFs are conserved proteins homologous to human chitinase-like proteins such as CHI3L1/YKL-40 which are implicated in tissue regeneration as well as cancers including colon cancer and non-small cell lung cancer. We also demonstrate that loss of DIS3L2 in human kidney HEK-293T cells results in cell proliferation, illustrating the conservation of this important cell proliferation pathway. Using these human cells, we show that loss of DIS3L2 results in an increase in the PI3-Kinase/AKT signalling pathway, which we subsequently show to contribute towards the proliferation phenotype in Drosophila. Our work therefore provides the first mechanistic explanation for DIS3L2-induced overgrowth in humans and flies and identifies an ancient proliferation pathway controlled by Dis3L2 to regulate cell proliferation and tissue growth. Regulation of cell proliferation is not only important during development but also required for repair of damaged tissues and during wound healing. Using human kidney cells as well as the fruit fly Drosophila we have recently discovered that cell proliferation can be regulated by a protein named Dis3L2. Depletion or removal of this protein results in excess proliferation. These results are relevant to human disease as DIS3L2 has been shown to be mutated in an overgrowth syndrome (Perlman syndrome) where affected children have abnormal enlargement of organs (e.g. kidneys) and susceptibility to Wilms’ tumour (a kidney cancer). Dis3L2 is an enzyme known to "chew up" mRNA molecules which instruct the cell to make particular proteins. Using state-of-the-art molecular methods in Drosophila, we have discovered that Dis3L2 targets a small subset of mRNAs, including an mRNA encoding a growth factor named 'imaginal disc growth factor 2' (idgf2). For human kidney cells in culture, we have found that depletion of DIS3L2 results in enhanced proliferation, and that this involves a well-known cellular pathway. Our results mean that we have discovered a new way of controlling cell proliferation, which could, in the future, be used in human therapies.
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P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Biosci Rep 2020; 39:221381. [PMID: 31789342 PMCID: PMC6914664 DOI: 10.1042/bsr20192114] [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: 06/20/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (ΔN and TA isoforms); both transcripts are also subjected to alternative splicing mechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development.
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De novo 2q36.3q37.1 deletion encompassing TRIP12 and NPPC yields distinct phenotypes. Hum Genome Var 2020; 7:19. [PMID: 32528716 PMCID: PMC7261772 DOI: 10.1038/s41439-020-0107-1] [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: 03/29/2020] [Accepted: 05/01/2020] [Indexed: 12/03/2022] Open
Abstract
We report a patient with developmental delay, extremely short stature, small hands, dysmorphic facial features, hearing loss, and epilepsy carrying a de novo 2.76-Mb deletion of 2q36.3q37.1, including TRIP12 and NPPC. TRIP12 haploinsufficiency causes developmental delay with isolated dysmorphic facial features, whereas NPPC haploinsufficiency causes short stature and small hands. This is the first report of a unique phenotype, which is secondary to a microdeletion encompassing TRIP12 and NPPC.
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Chen WX, Liu HH, Li RX, Mammadov G, Wang JJ, Liu FF, Samadli S, Wu YF, Zhang DD, Luo HH, Hu P. C-type natriuretic peptide stimulates osteoblastic proliferation and collagen-X expression but suppresses fibroblast growth factor-23 expression in vitro. Pediatr Rheumatol Online J 2020; 18:46. [PMID: 32517762 PMCID: PMC7285564 DOI: 10.1186/s12969-020-00441-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The effects of C-type natriuretic peptide (CNP) and fibroblast growth factor (FGF)-23 appear to oppose each other during the process of bone formation, whereas few studies exist on the interaction between CNP and FGF-23. The main objective of the present study is to probe whether CNP is directly responsible for the regulation of osteoblast or via antagonizing FGF-23. METHODS Osteoblasts were cultured in the absence or presence of CNP (0, 10, and 100 pmol/L) for 24 h, 48 h and 72 h, respectively. RESULTS The findings of the present study indicated that: (1) CNP significantly stimulated osteoblastic proliferation and collagen (Col)-X expression; (2) both osteoblastic (osteocalcin, procollagen type I carboxy-terminal propeptide, total alkaline phosphatase and bone-specific alkaline phosphatase) and osteolytic (tartrate-resistant acid phosphatase and cross-linked carboxyterminal telopeptide of type I collagen) bone turnover biomarkers were up-regulated by CNP in osteoblasts; (3) FGF-23 mRNA and protein were significantly down-regulated at 24 h by CNP in osteoblasts, but the expression of FGF receptor-1/Klotho had no significant change. CONCLUSIONS CNP stimulates osteoblastic proliferation and Col-X expression via the down-regulation of FGF-23 possibly in vitro. However, the specific mechanisms of the interaction between CNP and FGF-23 in osteoblasts are still unclear according to our findings. A further study on osteoblasts cultured with CNP and FGF-23 inhibitor will be undertaken in our laboratory.
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Affiliation(s)
- Wei Xia Chen
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Hui Hui Liu
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Rui Xue Li
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Goshgar Mammadov
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Jing Jing Wang
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Fei Fei Liu
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Sama Samadli
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Yang Fang Wu
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Dong Dong Zhang
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Huang Huang Luo
- grid.412679.f0000 0004 1771 3402Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province 230032 PR China
| | - Peng Hu
- Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, No. 218 Ji-Xi Road, Hefei, Anhui Province, 230032, PR China.
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15
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Espiner E, Prickett T, Olney R. Plasma C-Type Natriuretic Peptide: Emerging Applications in Disorders of Skeletal Growth. Horm Res Paediatr 2019; 90:345-357. [PMID: 30844819 DOI: 10.1159/000496544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/30/2018] [Indexed: 11/19/2022] Open
Abstract
Although studies in experimental animals show that blood levels of C-type natriuretic peptide (CNP) and its bioinactive aminoterminal propeptide (NTproCNP) are potential biomarkers of long bone growth, a lack of suitable assays and appropriate reference ranges has limited the application of CNP measurements in clinical practice. Plasma concentrations of the processed product of proCNP, NTproCNP - and to a lesser extent CNP itself - correlate with concurrent height velocity throughout all phases of normal skeletal growth, as well as during interventions known to affect skeletal growth in children. Since a change in levels precedes a measurable change in height velocity during interventions, measuring NTproCNP may have predictive value in clinical practice. Findings from a variety of genetic disorders affecting CNP signaling suggest that plasma concentrations of both peptides may be helpful in diagnosis, provided factors such as concurrent height velocity, feedback regulation of CNP, and differential changes in peptide clearance are considered when interpreting values. An improved understanding of factors affecting plasma levels, and the availability of commercial kits enabling accurate measurement using small volumes of plasma, can be expected to facilitate potential applications in growth disorders including genetic causes -affecting the CNP signaling pathway.
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Affiliation(s)
- Eric Espiner
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
| | - Tim Prickett
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand,
| | - Robert Olney
- Division of Endocrinology, Nemours Children's Specialty Care, Jacksonville, Florida, USA
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16
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Le TN, Williams SR, Alaimo JT, Elsea SH. Genotype and phenotype correlation in 103 individuals with 2q37 deletion syndrome reveals incomplete penetrance and supports HDAC4 as the primary genetic contributor. Am J Med Genet A 2019; 179:782-791. [PMID: 30848064 DOI: 10.1002/ajmg.a.61089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 01/02/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022]
Abstract
The 2q37 deletion syndrome, also described in the literature as brachydactyly-mental retardation syndrome (MIM 600430), is caused by deletion or haploinsufficiency of the HDAC4 gene, which encodes the histone deacetylase 4 protein. Although the most commonly described hallmark features of the 2q37 deletion syndrome include brachydactyly type E, developmental delay, obesity, autistic features, and craniofacial or skeletal dysmorphism, a literature review of 101 published cases plus two newly reported individuals indicates that there is a high degree of variability in the presence of some of the features that are considered the most characteristic of the syndrome: overweight and obesity (34%), cognitive-behavioral issues (79%), dysmorphic craniofacial features (86%), and type E brachydactyly (48%). These features overlap with other neurodevelopmental conditions, including Smith-Magenis syndrome (SMS), and may be incompletely penetrant or demonstrate variable expressivity, depending on the specific chromosomal anomaly. With the advent of fluorescence in situ hybridization (FISH), array-based comparative genomic hybridization, and next-generation DNA sequencing, more detailed molecular diagnoses are possible than in years past, enabling refined characterization of the genotype-phenotype correlation for subjects with 2q37 deletions. In addition, investigations into molecular and gene expression networks are expanding in neurodevelopmental conditions, and we surveyed HDAC4 downstream gene expression by quantitative real-time polymerase chain reaction, further implicating HDAC4 in its role in the regulation of RAI1. Correlation of clinical data defining the impact on downstream gene expression and the potential clinical associations across neurodevelopment will improve our understanding of these complex conditions and potentially lead to common therapeutic approaches.
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Affiliation(s)
- Trang N Le
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia.,Department of Internal Medicine, Division of Endocrinology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Stephen R Williams
- Department of Neurology, University of Virginia, Charlottesville, Virginia
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sarah H Elsea
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
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Hernandez Cordero AI, Carbonetto P, Riboni Verri G, Gregory JS, Vandenbergh DJ, P Gyekis J, Blizard DA, Lionikas A. Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines. Physiol Rep 2019; 6. [PMID: 29479840 PMCID: PMC6430048 DOI: 10.14814/phy2.13561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/02/2017] [Accepted: 12/05/2017] [Indexed: 12/14/2022] Open
Abstract
The genetics underlying variation in health‐related musculoskeletal phenotypes can be investigated in a mouse model. Quantitative trait loci (QTLs) affecting musculoskeletal traits in the LG/J and SM/J strain lineage remain to be refined and corroborated. The aim of this study was to map muscle and bone traits in males (n = 506) of the 50th filial generation of advanced intercross lines (LG/SM AIL) derived from the two strains. Genetic contribution to variation in all musculoskeletal traits was confirmed; the SNP heritability of muscle mass ranged between 0.46 and 0.56; and the SNP heritability of tibia length was 0.40. We used two analytical software, GEMMA and QTLRel, to map the underlying QTLs. GEMMA required substantially less computation and recovered all the QTLs identified by QTLRel. Seven significant QTLs were identified for muscle weight (Chr 1, 7, 11, 12, 13, 15, and 16), and two for tibia length, (Chr 1 and 13). Each QTL explained 4–5% of phenotypic variation. One muscle and both bone loci replicated previous findings; the remaining six were novel. Positional candidates for the replicated QTLs were prioritized based on in silico analyses and gene expression in muscle tissue. In summary, we replicated existing QTLs and identified novel QTLs affecting muscle weight, and replicated bone length QTLs in LG/SM AIL males. Heritability estimates substantially exceed the cumulative effect of the QTLs, hence a richer genetic architecture contributing to muscle and bone variability could be uncovered with a larger sample size.
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Affiliation(s)
- Ana I Hernandez Cordero
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Peter Carbonetto
- Research Computing Center and Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Gioia Riboni Verri
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Jennifer S Gregory
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - David J Vandenbergh
- Department of Biobehavioral Health, The Penn State Institute for the Neurosciences, Molecular and Cellular Integrative Biosciences Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Joseph P Gyekis
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania
| | - David A Blizard
- Department of Biobehavioral Health, The Penn State Institute for the Neurosciences, Molecular and Cellular Integrative Biosciences Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
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Luan S, Luo J, Liu H, Li Z. Regulation of RNA decay and cellular function by 3'-5' exoribonuclease DIS3L2. RNA Biol 2019; 16:160-165. [PMID: 30638126 DOI: 10.1080/15476286.2018.1564466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DIS3L2, in which mutations have been linked to Perlman syndrome, is an RNA-binding protein with 3'-5' exoribonuclease activity. It contains two CSD domains and one S1 domain, all of which are RNA-binding domains, and one RNB domain that is responsible for the exoribonuclease activity. The 3' polyuridine of RNA substrates can serve as a degradation signal for DIS3L2. Because DIS3L2 is predominantly localized in the cytoplasm, it can recognize, bind, and mediate the degradation of cytoplasmic uridylated RNA, including pre-microRNA, mature microRNA, mRNA, and some other non-coding RNAs. Therefore, DIS3L2 plays an important role in cytoplasmic RNA surveillance and decay. DIS3L2 is involved in multiple biological and physiological processes such as cell division, proliferation, differentiation, and apoptosis. Nonetheless, the function of DIS3L2, especially its association with cancer, remains largely unknown. We summarize here the RNA substrates degraded by DIS3L2 with its exonucleolytic activity, together with the corresponding biological functions it is implicated in. Furthermore, we discuss whether DIS3L2 can function independently of its 3'-5' exoribonuclease activity, as well as its potential tumor-suppressive or oncogenic roles during cancer progression.
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Affiliation(s)
- Siyu Luan
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Junyun Luo
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Hui Liu
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
| | - Zhaoyong Li
- a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University , Changsha , China
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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20
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Marques P, Korbonits M. Pseudoacromegaly. Front Neuroendocrinol 2019; 52:113-143. [PMID: 30448536 DOI: 10.1016/j.yfrne.2018.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023]
Abstract
Individuals with acromegaloid physical appearance or tall stature may be referred to endocrinologists to exclude growth hormone (GH) excess. While some of these subjects could be healthy individuals with normal variants of growth or physical traits, others will have acromegaly or pituitary gigantism, which are, in general, straightforward diagnoses upon assessment of the GH/IGF-1 axis. However, some patients with physical features resembling acromegaly - usually affecting the face and extremities -, or gigantism - accelerated growth/tall stature - will have no abnormalities in the GH axis. This scenario is termed pseudoacromegaly, and its correct diagnosis can be challenging due to the rarity and variability of these conditions, as well as due to significant overlap in their characteristics. In this review we aim to provide a comprehensive overview of pseudoacromegaly conditions, highlighting their similarities and differences with acromegaly and pituitary gigantism, to aid physicians with the diagnosis of patients with pseudoacromegaly.
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Affiliation(s)
- Pedro Marques
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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21
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Andrade AC, Jee YH, Nilsson O. New Genetic Diagnoses of Short Stature Provide Insights into Local Regulation of Childhood Growth
. Horm Res Paediatr 2018; 88:22-37. [PMID: 28334714 DOI: 10.1159/000455850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Idiopathic short stature is a common condition with a heterogeneous etiology. Advances in genetic methods, including genome sequencing techniques and bioinformatics approaches, have emerged as important tools to identify the genetic defects in families with monogenic short stature. These findings have contributed to the understanding of growth regulation and indicate that growth plate chondrogenesis, and therefore linear growth, is governed by a large number of genes important for different signaling pathways and cellular functions, including genetic defects in hormonal regulation, paracrine signaling, cartilage matrix, and fundamental cellular processes. In addition, mutations in the same gene can cause a wide phenotypic spectrum depending on the severity and mode of inheritance of the mutation.
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Affiliation(s)
- Anenisia C Andrade
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Youn Hee Jee
- Section of Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Örebro University and University Hospital, Örebro, Sweden
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22
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Mori F, Tanji K, Miki Y, Toyoshima Y, Sasaki H, Yoshida M, Kakita A, Takahashi H, Wakabayashi K. Immunohistochemical localization of exoribonucleases (DIS3L2 and XRN1) in intranuclear inclusion body disease. Neurosci Lett 2018; 662:389-394. [DOI: 10.1016/j.neulet.2017.10.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 12/27/2022]
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23
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Vidmar AP, Miyazaki B, Sanchez-Lara PA, Pitukcheewanont P. X-linked Hypophosphatemic Rickets, del(2)(q37.1;q37.3) Deletion Syndrome and Mosaic Turner Syndrome, mos 45,X/46,X, del(2)(q37.1;q37.3) in a 3-year-old Female. J Bone Metab 2017; 24:257-261. [PMID: 29259966 PMCID: PMC5734952 DOI: 10.11005/jbm.2017.24.4.257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/16/2017] [Accepted: 11/18/2017] [Indexed: 01/03/2023] Open
Abstract
There are currently no published cases that report concomitant Turner syndrome (TS), 2q37 deletion syndrome and X-linked hypophosphatemic rickets (XLH). Interestingly, since the clinical phenotypes of TS and 2q37 deletion syndrome overlap, the correct diagnosis may be missed without a standardized approach to genetic testing consisting of both karyotype and microarray. Both chromosome anomalies have been associated with short stature and a variety of skeletal abnormalities however to date no reports have associated these syndromes in association with a phosphate regulating endopeptidase homolog, X-linked (PHEX) gene deletion resulting in XLH. We report a 3-year-old female with 3 concurrent genetic disorders including a 9.98 Mb terminal deletion of chromosome 2: del(2)(q37.1;q37.3), XLH secondary to a small microdeletion of part of the PHEX gene, and mosaic TS (mos 45,X[32]/46,X[18]). This is the first case report of a patient with 2q37 deletion syndrome and mosaic TS (mos 45,X[32]/46,X[18]) found to have XLH secondary to an interstitial constitutional PHEX gene deletion. Her severe phenotype and multiple genotypic findings reinforce the importance of thorough genetic testing in the setting of complicated phenotypic presentations.
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Affiliation(s)
- Alaina P Vidmar
- Center for Endocrinology, Diabetes and Metabolism, Division of Endocrinology, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Brian Miyazaki
- Center for Endocrinology, Diabetes and Metabolism, Division of Endocrinology, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Pedro A Sanchez-Lara
- Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Pisit Pitukcheewanont
- Center for Endocrinology, Diabetes and Metabolism, Division of Endocrinology, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
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24
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The roles of the exoribonucleases DIS3L2 and XRN1 in human disease. Biochem Soc Trans 2017; 44:1377-1384. [PMID: 27911720 DOI: 10.1042/bst20160107] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 12/19/2022]
Abstract
RNA degradation is a vital post-transcriptional process which ensures that transcripts are maintained at the correct level within the cell. DIS3L2 and XRN1 are conserved exoribonucleases that are critical for the degradation of cytoplasmic RNAs. Although the molecular mechanisms of RNA degradation by DIS3L2 and XRN1 have been well studied, less is known about their specific roles in the development of multicellular organisms or human disease. This review focusses on the roles of DIS3L2 and XRN1 in the pathogenesis of human disease, particularly in relation to phenotypes seen in model organisms. The known diseases associated with loss of activity of DIS3L2 and XRN1 are discussed, together with possible mechanisms and cellular pathways leading to these disease conditions.
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25
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Hisado-Oliva A, Ruzafa-Martin A, Sentchordi L, Funari MFA, Bezanilla-López C, Alonso-Bernáldez M, Barraza-García J, Rodriguez-Zabala M, Lerario AM, Benito-Sanz S, Aza-Carmona M, Campos-Barros A, Jorge AAL, Heath KE. Mutations in C-natriuretic peptide (NPPC): a novel cause of autosomal dominant short stature. Genet Med 2017; 20:91-97. [PMID: 28661490 DOI: 10.1038/gim.2017.66] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/05/2017] [Indexed: 12/21/2022] Open
Abstract
PurposeC-type natriuretic peptide (CNP) and its principal receptor, natriuretic peptide receptor B (NPR-B), have been shown to be important in skeletal development. CNP and NPR-B are encoded by natriuretic peptide precursor-C (NPPC) and natriuretic peptide receptor 2 (NPR2) genes, respectively. While NPR2 mutations have been described in patients with skeletal dysplasias and idiopathic short stature (ISS), and several Npr2 and Nppc skeletal dysplasia mouse models exist, no mutations in NPPC have been described in patients to date.MethodsNPPC was screened in 668 patients (357 with disproportionate short stature and 311 with autosomal dominant ISS) and 29 additional ISS families in an ongoing whole-exome sequencing study.ResultsTwo heterozygous NPPC mutations, located in the highly conserved CNP ring, were identified. Both showed significant reductions in cyclic guanosine monophosphate synthesis, confirming their pathogenicity. Interestingly, one has been previously linked to skeletal abnormalities in the spontaneous Nppc mouse long-bone abnormality (lbab) mutant.ConclusionsOur results demonstrate, for the first time, that NPPC mutations cause autosomal dominant short stature in humans. The NPPC mutations cosegregated with a short stature and small hands phenotype. A CNP analog, which is currently in clinical trials for the treatment of achondroplasia, seems a promising therapeutic approach, since it directly replaces the defective protein.
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Affiliation(s)
- Alfonso Hisado-Oliva
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Alba Ruzafa-Martin
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Lucia Sentchordi
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain.,Department of Pediatrics, Hospital Universitario Infanta Leonor, Madrid, Spain
| | - Mariana F A Funari
- Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
| | | | - Marta Alonso-Bernáldez
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Jimena Barraza-García
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Maria Rodriguez-Zabala
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Antonio M Lerario
- Unidade de Endocrinologia Genetica (LIM25), Faculdade de Medicina da Universidade de São Paulo (USP), São Paulo, Brazil.,Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sara Benito-Sanz
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Miriam Aza-Carmona
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Angel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain
| | - Alexander A L Jorge
- Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil.,Unidade de Endocrinologia Genetica (LIM25), Faculdade de Medicina da Universidade de São Paulo (USP), São Paulo, Brazil
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain.,Multidisciplinary Skeletal Dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
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26
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Towler BP, Jones CI, Harper KL, Waldron JA, Newbury SF. A novel role for the 3'-5' exoribonuclease Dis3L2 in controlling cell proliferation and tissue growth. RNA Biol 2016; 13:1286-1299. [PMID: 27630034 PMCID: PMC5207379 DOI: 10.1080/15476286.2016.1232238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In a complex organism, cell proliferation and apoptosis need to be precisely controlled in order for tissues to develop correctly. Excessive cell proliferation can lead to diseases such as cancer. We have shown that the exoribonuclease Dis3L2 is required for the correct regulation of proliferation in a natural tissue within the model organism Drosophila melanogaster. Dis3L2 is a member of a highly conserved family of exoribonucleases that degrade RNA in a 3′-5′ direction. We show that knockdown of dis3L2 in the Drosophila wing imaginal discs results in substantial wing overgrowth due to increased cellular proliferation rather than an increase in cell size. Imaginal discs are specified in the embryo before proliferating and differentiating to form the adult structures of the fly. Using RNA-seq we identified a small set of mRNAs that are sensitive to Dis3L2 activity. Of the mRNAs which increase in levels and are therefore potential targets of Dis3L2, we identified 2 that change at the post-transcriptional level but not at the transcriptional level, namely CG2678 (a transcription factor) and pyrexia (a TRP cation channel). We also demonstrate a compensatory effect between Dis3L2 and the 5′-3′ exoribonuclease Pacman demonstrating that these 2 exoribonucleases function to regulate opposing pathways within the developing tissue. This work provides the first description of the molecular and developmental consequences of Dis3L2 inactivation in a non-human animal model. The work is directly relevant to the understanding of human overgrowth syndromes such as Perlman syndrome.
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Affiliation(s)
- Benjamin P Towler
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | | | - Kirsty L Harper
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | - Joseph A Waldron
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | - Sarah F Newbury
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
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27
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Hu P, Huang BY, Xia X, Xuan Q, Hu B, Qin YH. Therapeutic effect of CNP on renal osteodystrophy by antagonizing the FGF-23/MAPK pathway. J Recept Signal Transduct Res 2015; 36:213-9. [DOI: 10.3109/10799893.2015.1075041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Ko JM, Bae JS, Choi JS, Miura K, Lee HR, Kim OH, Kim NKD, Oh SK, Ozono K, Lee CK, Choi IH, Park WY, Cho TJ. Skeletal overgrowth syndrome caused by overexpression of C-type natriuretic peptide in a girl with balanced chromosomal translocation, t(1;2)(q41;q37.1). Am J Med Genet A 2015; 167A:1033-8. [PMID: 25728306 DOI: 10.1002/ajmg.a.36884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023]
Abstract
Chromosomal translocation of 2q37.1 just distal to the NPPC gene coding for C-type natriuretic peptide (CNP) and subsequent overproduction of CNP have been reported to cause a skeletal overgrowth syndrome. Loeys-Dietz syndrome (LDS) is one of marfanoid overgrowth syndromes, of which subtype IV is caused by haploinsufficiency of transforming growth factor beta 2 (TGFB2). We report on a girl with clinical phenotypes of overgrowth syndrome, including long and slim body habitus, macrodactyly of the big toe, scoliosis, ankle valgus deformity, coxa valga, slipped capital femoral epiphysis, and aortic root dilatation. Karyotyping revealed a balanced chromosomal translocation between 1q41 and 2q37.1, and the breakpoints could be mapped by targeted resequencing analysis. On chromosome 2q37.1, the translocation took place 200,365 bp downstream of NPPC, and serum level of the amino terminal of CNP was elevated. The contralateral site of translocation on chromosome 1q41 disrupted TGFB2 gene, presumed to cause its haploinsufficiency. This case supports the concept that NPPC is overexpressed because of the loss of a specific negative regulatory control in the normal chromosomal location, and demonstrates the effectiveness of targeted resequencing in the mapping of breakpoints.
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Affiliation(s)
- Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
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Peake NJ, Hobbs AJ, Pingguan-Murphy B, Salter DM, Berenbaum F, Chowdhury TT. Role of C-type natriuretic peptide signalling in maintaining cartilage and bone function. Osteoarthritis Cartilage 2014; 22:1800-7. [PMID: 25086404 DOI: 10.1016/j.joca.2014.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/16/2014] [Accepted: 07/22/2014] [Indexed: 02/02/2023]
Abstract
C-type natriuretic peptide (CNP) has been demonstrated in human and mouse models to play critical roles in cartilage homeostasis and endochondral bone formation. Indeed, targeted inactivation of the genes encoding CNP results in severe dwarfism and skeletal defects with a reduction in growth plate chondrocytes. Conversely, cartilage-specific overexpression of CNP was observed to rescue the phenotype of CNP deficient mice and significantly enhanced bone growth caused by growth plate expansion. In vitro studies reported that exogenous CNP influenced chondrocyte differentiation, proliferation and matrix synthesis with the response dependent on CNP concentration. The chondroprotective effects were shown to be mediated by natriuretic peptide receptor (Npr)2 and enhanced synthesis of cyclic guanosine-3',5'-monophosphate (cGMP) production. Recent studies also showed certain homeostatic effects of CNP are mediated by the clearance inactivation receptor, Npr3, highlighting several mechanisms in maintaining tissue homeostasis. However, the CNP signalling systems are complex and influenced by multiple factors that will lead to altered signalling and tissue dysfunction. This review will discuss the differential role of CNP signalling in regulating cartilage and bone homeostasis and how the pathways are influenced by age, inflammation or sex. Evidence indicates that enhanced CNP signalling may prevent growth retardation and protect cartilage in patients with inflammatory joint disease.
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Affiliation(s)
- N J Peake
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - A J Hobbs
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - B Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - D M Salter
- Centre for Genomics and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crew Road, Edinburgh EH4 2XU, UK
| | - F Berenbaum
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, INSERM UMRS 938, Assistance Publique-Hopitaux de Paris, Department of Rheumatology and DHU i2B, Hôpital Saint-Antoine, Paris, France
| | - T T Chowdhury
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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