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Adisornkanj P, Chanprasit R, Eliason S, Fons JM, Intachai W, Tongsima S, Olsen B, Arold ST, Ngamphiw C, Amendt BA, Tucker AS, Kantaputra P. Genetic Variants in Protein Tyrosine Phosphatase Non-Receptor Type 23 Are Responsible for Mesiodens Formation. BIOLOGY 2023; 12:393. [PMID: 36979085 PMCID: PMC10045488 DOI: 10.3390/biology12030393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
A mesiodens is a supernumerary tooth located in the midline of the premaxilla. To investigate the genetic cause of mesiodens, clinical and radiographic examination were performed on 23 family members of a two-generation Hmong family. Whole exome sequencing (WES) or Sanger sequencing were performed in 22 family members and two unrelated Thai patients with mesiodens. WES in the Hmong family revealed a missense mutation (c.1807G>A;p.Glu603Lys) in PTPN23 in seven affected members and six unaffected members. The mode of inheritance was autosomal dominance with incomplete penetrance (53.84%). Two additional mutations in PTPN23, c.2248C>G;p.Pro750Ala and c.3298C>T;p.Arg1100Cys were identified in two unrelated patients with mesiodens. PTPN23 is a regulator of endosomal trafficking functioning to move activated membrane receptors, such as EGFR, from the endosomal sorting complex towards the ESCRT-III complex for multivesicular body biogenesis, lysosomal degradation, and subsequent downregulation of receptor signaling. Immunohistochemical study and RNAscope on developing mouse embryos showed broad expression of PTPN23 in oral tissues, while immunofluorescence showed that EGFR was specifically concentrated in the midline epithelium. Importantly, PTPN23 mutant protein was shown to have reduced phosphatase activity. In conclusion, mesiodens were associated with genetic variants in PTPN23, suggesting that mesiodens may form due to defects in endosomal trafficking, leading to disrupted midline signaling.
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Affiliation(s)
- Ploy Adisornkanj
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rajit Chanprasit
- Dental Department, Wiang Kaen Hospital, Wiang Kaen, Chiang Rai 57310, Thailand
| | - Steven Eliason
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Juan M. Fons
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Worrachet Intachai
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Bjorn Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard University, Boston, MA 02115, USA
| | - Stefan T. Arold
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Structural Biology, National Institute of Health and Medical Research, National Centre for Scientific Research, University of Montpellier, 34090 Montpellier, France
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Brad A. Amendt
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Abigail S. Tucker
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Piranit Kantaputra
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
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Khalaf-Nazzal R, Fasham J, Ubeyratna N, Evans DJ, Leslie JS, Warner TT, Al-Hijawi F, Alshaer S, Baker W, Turnpenny PD, Baple EL, Crosby AH. Final Exon Frameshift Biallelic PTPN23 Variants Are Associated with Microcephalic Complex Hereditary Spastic Paraplegia. Brain Sci 2021; 11:614. [PMID: 34064836 PMCID: PMC8151426 DOI: 10.3390/brainsci11050614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
The hereditary spastic paraplegias (HSPs) are a large clinically heterogeneous group of genetic disorders classified as 'pure' when the cardinal feature of progressive lower limb spasticity and weakness occurs in isolation and 'complex' when associated with other clinical signs. Here, we identify a homozygous frameshift alteration occurring in the last coding exon of the protein tyrosine phosphatase type 23 (PTPN23) gene in an extended Palestinian family associated with autosomal recessive complex HSP. PTPN23 encodes a catalytically inert non-receptor protein tyrosine phosphatase that has been proposed to interact with the endosomal sorting complex required for transport (ESCRT) complex, involved in the sorting of ubiquitinated cargos for fusion with lysosomes. In view of our data, we reviewed previously published candidate pathogenic PTPN23 variants to clarify clinical outcomes associated with pathogenic gene variants. This determined that a number of previously proposed candidate PTPN23 alterations are likely benign and revealed that pathogenic biallelic PTPN23 alterations cause a varied clinical spectrum comprising of complex HSP associated with microcephaly, which may occur without intellectual impairment or involve more severe neurological disease. Together, these findings highlight the importance of the inclusion of the PTPN23 gene on HSP gene testing panels globally.
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Affiliation(s)
- Reham Khalaf-Nazzal
- Biomedical Sciences Department, Faculty of Medicine, Arab American University of Palestine, Jenin P227, Palestine
| | - James Fasham
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Nishanka Ubeyratna
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - David J. Evans
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK;
| | - Joseph S. Leslie
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
| | - Thomas T. Warner
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK;
| | - Fida’ Al-Hijawi
- Paediatrics’ Community Outpatient Clinics, Palestinian Ministry of Health, Jenin P200, Palestine;
| | - Shurouq Alshaer
- Faculty of Graduate Studies, Arab American University, Ramallah P622, Palestine;
| | - Wisam Baker
- Paediatrics Department, Dr. Khalil Suleiman Government Hospital, Jenin P200, Palestine;
| | - Peter D. Turnpenny
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Emma L. Baple
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter EX1 2ED, UK
| | - Andrew H. Crosby
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; (J.F.); (N.U.); (J.S.L.); (P.D.T.)
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Jariwala N, Mendoza RG, Garcia D, Lai Z, Subler MA, Windle JJ, Mukhopadhyay ND, Fisher PB, Chen Y, Sarkar D. Posttranscriptional Inhibition of Protein Tyrosine Phosphatase Nonreceptor Type 23 by Staphylococcal Nuclease and Tudor Domain Containing 1: Implications for Hepatocellular Carcinoma. Hepatol Commun 2019; 3:1258-1270. [PMID: 31497746 PMCID: PMC6719750 DOI: 10.1002/hep4.1400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/16/2019] [Indexed: 01/12/2023] Open
Abstract
Oncoprotein staphylococcal nuclease and tudor domain containing 1 (SND1) regulates gene expression at a posttranscriptional level in multiple cancers, including hepatocellular carcinoma (HCC). Staphylococcal nuclease (SN) domains of SND1 function as a ribonuclease (RNase), and the tudor domain facilitates protein–oligonucleotide interaction. In the present study, we aimed to identify RNA interactome of SND1 to obtain enhanced insights into gene regulation by SND1. RNA interactome was identified by immunoprecipitation (IP) of RNA using anti‐SND1 antibody from human HCC cells followed by RNA immunoprecipitation sequencing (RIP‐Seq). Among RNA species that showed more than 10‐fold enrichment over the control, we focused on the tumor suppressor protein tyrosine phosphatase nonreceptor type 23 (PTPN23) because its regulation by SND1 and its role in HCC are not known. PTPN23 levels were down‐regulated in human HCC cells versus normal hepatocytes and in human HCC tissues versus normal adjacent liver, as revealed by immunohistochemistry. In human HCC cells, knocking down SND1 increased and overexpression of SND1 decreased PTPN23 protein. RNA binding and degradation assays revealed that SND1 binds to and degrades the 3′‐untranslated region (UTR) of PTPN23 messenger RNA (mRNA). Tetracycline‐inducible PTPN23 overexpression in human HCC cells resulted in significant inhibition in proliferation, migration, and invasion and in vivo tumorigenesis. PTPN23 induction caused inhibition in activation of tyrosine‐protein kinase Met (c‐Met), epidermal growth factor receptor (EGFR), Src, and focal adhesion kinase (FAK), suggesting that, as a putative phosphatase, PTPN23 inhibits activation of these oncogenic kinases. Conclusion: PTPN23 is a novel target of SND1, and our findings identify PTPN23 as a unique tumor suppressor for HCC. PTPN23 might function as a homeostatic regulator of multiple kinases, restraining their activation.
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Affiliation(s)
- Nidhi Jariwala
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA
| | - Rachel G Mendoza
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute University of Texas Health Science Center San Antonio San Antonio TX
| | - Zhao Lai
- Greehey Children's Cancer Research Institute University of Texas Health Science Center San Antonio San Antonio TX
| | - Mark A Subler
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA
| | - Jolene J Windle
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA.,Massey Cancer Center Virginia Commonwealth University Richmond VA
| | | | - Paul B Fisher
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA.,Massey Cancer Center Virginia Commonwealth University Richmond VA.,Virginia Commonwealth University Institute of Molecular Medicine Virginia Commonwealth University Richmond VA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute University of Texas Health Science Center San Antonio San Antonio TX.,Department of Epidemiology and Biostatistics University of Texas Health Science Center San Antonio San Antonio TX
| | - Devanand Sarkar
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA.,Massey Cancer Center Virginia Commonwealth University Richmond VA.,Virginia Commonwealth University Institute of Molecular Medicine Virginia Commonwealth University Richmond VA
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Desrochers G, Kazan JM, Pause A. Structure and functions of His domain protein tyrosine phosphatase in receptor trafficking and cancer. Biochem Cell Biol 2019; 97:68-72. [DOI: 10.1139/bcb-2017-0322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cell surface receptors trigger the activation of signaling pathways to regulate key cellular processes, including cell survival and proliferation. Internalization, sorting, and trafficking of activated receptors, therefore, play a major role in the regulation and attenuation of cell signaling. Efficient sorting of endocytosed receptors is performed by the ESCRT machinery, which targets receptors for degradation by the sequential establishment of protein complexes. These events are tightly regulated and malfunction of ESCRT components can lead to abnormal trafficking and sustained signaling and promote tumor formation or progression. In this review, we analyze the modular domain organization of the alternative ESCRT protein HD-PTP and its role in receptor trafficking and tumorigenesis.
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Affiliation(s)
- Guillaume Desrochers
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Jalal M. Kazan
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Arnim Pause
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
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Dissecting the role of His domain protein tyrosine phosphatase/PTPN23 and ESCRTs in sorting activated epidermal growth factor receptor to the multivesicular body. Biochem Soc Trans 2018; 46:1037-1046. [PMID: 30190330 PMCID: PMC6195633 DOI: 10.1042/bst20170443] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/31/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
Abstract
Sorting of activated epidermal growth factor receptor (EGFR) into intraluminal vesicles (ILVs) within the multivesicular body (MVB) is an essential step during the down-regulation of the receptor. The machinery that drives EGFR sorting attaches to the cytoplasmic face of the endosome and generates vesicles that bud into the endosome lumen, but somehow escapes encapsulation itself. This machinery is termed the ESCRT (endosomal sorting complexes required for transport) pathway, a series of multi-protein complexes and accessory factors first identified in yeast. Here, we review the yeast ESCRT pathway and describe the corresponding components in mammalian cells that sort EGFR. One of these is His domain protein tyrosine phosphatase (HD-PTP/PTPN23), and we review the interactions involving HD-PTP and ESCRTs. Finally, we describe a working model for how this ESCRT pathway might overcome the intrinsic topographical problem of EGFR sorting to the MVB lumen.
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Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. Int J Mol Sci 2017; 18:ijms18122761. [PMID: 29257115 PMCID: PMC5751360 DOI: 10.3390/ijms18122761] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs.
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Abstract
Cells respond to changes in their environment, to developmental cues, and to pathogen aggression through the action of a complex network of proteins. These networks can be decomposed into a multitude of signaling pathways that relay signals from the microenvironment to the cellular components involved in eliciting a specific response. Perturbations in these signaling processes are at the root of multiple pathologies, the most notable of these being cancer. The study of receptor tyrosine kinase (RTK) signaling led to the first description of a mechanism whereby an extracellular signal is transmitted to the nucleus to induce a transcriptional response. Genetic studies conducted in drosophila and nematodes have provided key elements to this puzzle. Here, we briefly discuss the somewhat lesser known contribution of these multicellular organisms to our understanding of what has come to be known as the prototype of signaling pathways. We also discuss the ostensibly much larger network of regulators that has emerged from recent functional genomic investigations of RTK/RAS/ERK signaling.
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Affiliation(s)
- Dariel Ashton-Beaucage
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7.
- Département de Pathologie et de Biologie Cellulaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada, H3C 3J7.
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Kundu K, Costa F, Huber M, Reth M, Backofen R. Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PLoS One 2013; 8:e62732. [PMID: 23690949 PMCID: PMC3656881 DOI: 10.1371/journal.pone.0062732] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023] Open
Abstract
Src homology 2 (SH2) domains are the largest family of the peptide-recognition modules (PRMs) that bind to phosphotyrosine containing peptides. Knowledge about binding partners of SH2-domains is key for a deeper understanding of different cellular processes. Given the high binding specificity of SH2, in-silico ligand peptide prediction is of great interest. Currently however, only a few approaches have been published for the prediction of SH2-peptide interactions. Their main shortcomings range from limited coverage, to restrictive modeling assumptions (they are mainly based on position specific scoring matrices and do not take into consideration complex amino acids inter-dependencies) and high computational complexity. We propose a simple yet effective machine learning approach for a large set of known human SH2 domains. We used comprehensive data from micro-array and peptide-array experiments on 51 human SH2 domains. In order to deal with the high data imbalance problem and the high signal-to-noise ration, we casted the problem in a semi-supervised setting. We report competitive predictive performance w.r.t. state-of-the-art. Specifically we obtain 0.83 AUC ROC and 0.93 AUC PR in comparison to 0.71 AUC ROC and 0.87 AUC PR previously achieved by the position specific scoring matrices (PSSMs) based SMALI approach. Our work provides three main contributions. First, we showed that better models can be obtained when the information on the non-interacting peptides (negative examples) is also used. Second, we improve performance when considering high order correlations between the ligand positions employing regularization techniques to effectively avoid overfitting issues. Third, we developed an approach to tackle the data imbalance problem using a semi-supervised strategy. Finally, we performed a genome-wide prediction of human SH2-peptide binding, uncovering several findings of biological relevance. We make our models and genome-wide predictions, for all the 51 SH2-domains, freely available to the scientific community under the following URLs: http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/SH2PepInt.tar.gz and http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/Genome-wide-predictions.tar.gz, respectively.
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Affiliation(s)
- Kousik Kundu
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Fabrizio Costa
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Michael Huber
- Institute of Biochemistry and Molecular Immunology, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Michael Reth
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Department of Molecular Immunology, Max Planck Institute of Immunology, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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