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Omics Technologies in Rare Diseases
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Omics Technologies in Rare Diseases

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 9437

Special Issue Editors

Prof. Dr. María Luz Couce

E-Mail Website
Guest Editor
Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
Interests: inborn errors of metabolism; omic technologies; neonatal pathology
Dr. Emiliano González Vioque

E-Mail
Guest Editor
Metabolic Unit, University Hospital of Santiago de Compostela, Spain
Interests: genetics in rare diseases; mass sequencing techniques; transcriptomics; other omic technologies.

Special Issue Information

High-throughput sequencing has led to a revolution in genetic medicine, particularly in terms of improvements in both the diagnosis and knowledge of the molecular basis of the pathophysiology of rare diseases. However, DNA sequencing seems to be reaching its limit and new approaches and tools are needed to overcome its limitations. Transcriptomic, proteomic, metabolomic, and epigenomic approaches are emerging as useful tools in rare diseases field, allowing not only the identification of new disease mechanisms but also helping us to better understand the information generated by DNA sequencing. Ideally, the integrative use of these tools will change our traditional phenotype-genotype two-dimensional approach, improving our understanding of rare diseases and, therefore, our capacity to diagnose and treat them.

This Special Issue of IJMS aims to describe the actual use and future perspectives of the use of transcriptomic, proteomic, metabolomic, and epigenomic tools in rare diseases, with a special focus on integrative approaches.

Prof. Dr. María Luz Couce
Dr. Emiliano González Vioque
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rare diseases
  • RNA-seq
  • DNA methylation
  • histone modifications
  • proteomic
  • metabolomic
  • Integrative omics

Published Papers (3 papers)

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Research

21 pages, 5391 KiB  
Article
Plasma Proteomic Analysis in Morquio A Disease
by José V. Álvarez, Susana B. Bravo, María Pilar Chantada-Vázquez, Sofía Barbosa-Gouveia, Cristóbal Colón, Olalla López-Suarez, Shunji Tomatsu, Francisco J. Otero-Espinar and María L. Couce
Int. J. Mol. Sci. 2021, 22(11), 6165; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22116165 - 07 Jun 2021
Cited by 8 | Viewed by 2723
Abstract
Mucopolysaccharidosis type IVA (MPS IVA) is a lysosomal disease caused by mutations in the gene encoding the enzymeN-acetylgalactosamine-6-sulfate sulfatase (GALNS), and is characterized by systemic skeletal dysplasia due to excessive storage of keratan sulfate (KS) and chondroitin-6-sulfate in chondrocytes. Although improvements [...] Read more.
Mucopolysaccharidosis type IVA (MPS IVA) is a lysosomal disease caused by mutations in the gene encoding the enzymeN-acetylgalactosamine-6-sulfate sulfatase (GALNS), and is characterized by systemic skeletal dysplasia due to excessive storage of keratan sulfate (KS) and chondroitin-6-sulfate in chondrocytes. Although improvements in the activity of daily living and endurance tests have been achieved with enzyme replacement therapy (ERT) with recombinant human GALNS, recovery of bone lesions and bone growth in MPS IVA has not been demonstrated to date. Moreover, no correlation has been described between therapeutic efficacy and urine levels of KS, which accumulates in MPS IVA patients. The objective of this study was to assess the validity of potential biomarkers proposed by other authors and to identify new biomarkers. To identify candidate biomarkers of this disease, we analyzed plasma samples from healthy controls (n=6) and from untreated (n=8) and ERT-treated (n=5, sampled before and after treatment) MPS IVA patients using both qualitative and quantitative proteomics analyses. The qualitative proteomics approach analyzed the proteomic profile of the different study groups. In the quantitative analysis, we identified/quantified 215 proteins after comparing healthy control untreated, ERT-treated MPSIVA patients. We selected a group of proteins that were dysregulated in MPS IVA patients. We identified four potential protein biomarkers, all of which may influence bone and cartilage metabolism: fetuin-A, vitronectin, alpha-1antitrypsin, and clusterin. Further studies of cartilage and bone samples from MPS IVA patients will be required to verify the validity of these proteins as potential biomarkers of MPS IVA. Full article
(This article belongs to the Special Issue Omics Technologies in Rare Diseases)
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20 pages, 28921 KiB  
Article
Muscle Proteomic Profile before and after Enzyme Replacement Therapy in Late-Onset Pompe Disease
by Manuela Moriggi, Daniele Capitanio, Enrica Torretta, Pietro Barbacini, Cinzia Bragato, Patrizia Sartori, Maurizio Moggio, Lorenzo Maggi, Marina Mora and Cecilia Gelfi
Int. J. Mol. Sci. 2021, 22(6), 2850; https://doi.org/10.3390/ijms22062850 - 11 Mar 2021
Cited by 11 | Viewed by 3232
Abstract
Mutations in the acidic alpha-glucosidase (GAA) coding gene cause Pompe disease. Late-onset Pompe disease (LOPD) is characterized by progressive proximal and axial muscle weakness and atrophy, causing respiratory failure. Enzyme replacement therapy (ERT), based on recombinant human GAA infusions, is the only available [...] Read more.
Mutations in the acidic alpha-glucosidase (GAA) coding gene cause Pompe disease. Late-onset Pompe disease (LOPD) is characterized by progressive proximal and axial muscle weakness and atrophy, causing respiratory failure. Enzyme replacement therapy (ERT), based on recombinant human GAA infusions, is the only available treatment; however, the efficacy of ERT is variable. Here we address the question whether proteins at variance in LOPD muscle of patients before and after 1 year of ERT, compared withhealthy age-matched subjects (CTR), reveal a specific signature. Proteins extracted from skeletal muscle of LOPD patients and CTR were analyzed by combining gel based (two-dimensional difference gel electrophoresis) and label-free (liquid chromatography-mass spectrometry) proteomic approaches, and ingenuity pathway analysis. Upstream regulators targeting autophagy and lysosomal tethering were assessed by immunoblotting. 178 proteins were changed in abundance in LOPD patients, 47 of them recovered normal level after ERT. Defects in oxidative metabolism, muscle contractile protein regulation, cytoskeletal rearrangement, and membrane reorganization persisted. Metabolic changes, ER stress and UPR (unfolded protein response) contribute to muscle proteostasis dysregulation with active membrane remodeling (high levels of LC3BII/LC3BI) and accumulation of p62, suggesting imbalance in the autophagic process. Active lysosome biogenesis characterizes both LOPD PRE and POST, unparalleled by molecules involved in lysosome tethering (VAMP8, SNAP29, STX17, and GORASP2) and BNIP3. In conclusion this study reveals a specific signature that suggests ERT prolongation and molecular targets to ameliorate patient’s outcome. Full article
(This article belongs to the Special Issue Omics Technologies in Rare Diseases)
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22 pages, 2732 KiB  
Article
Characterization of New Proteomic Biomarker Candidates in Mucopolysaccharidosis Type IVA
by Víctor J. Álvarez, Susana B. Bravo, Maria Pilar Chantada-Vazquez, Cristóbal Colón, María J. De Castro, Montserrat Morales, Isidro Vitoria, Shunji Tomatsu, Francisco J. Otero-Espinar and María L. Couce
Int. J. Mol. Sci. 2021, 22(1), 226; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010226 - 28 Dec 2020
Cited by 11 | Viewed by 2768
Abstract
Mucopolysaccharidosis type IVA (MPS IVA) is a lysosomal storage disease caused by mutations in the N-acetylgalactosamine-6-sulfatase (GALNS) gene. Skeletal dysplasia and the related clinical features of MPS IVA are caused by disruption of the cartilage and its extracellular matrix, leading [...] Read more.
Mucopolysaccharidosis type IVA (MPS IVA) is a lysosomal storage disease caused by mutations in the N-acetylgalactosamine-6-sulfatase (GALNS) gene. Skeletal dysplasia and the related clinical features of MPS IVA are caused by disruption of the cartilage and its extracellular matrix, leading to a growth imbalance. Enzyme replacement therapy (ERT) with recombinant human GALNS has yielded positive results in activity of daily living and endurance tests. However, no data have demonstrated improvements in bone lesions and bone grow thin MPS IVA after ERT, and there is no correlation between therapeutic efficacy and urine levels of keratan sulfate, which accumulates in MPS IVA patients. Using qualitative and quantitative proteomics approaches, we analyzed leukocyte samples from healthy controls (n = 6) and from untreated (n = 5) and ERT-treated (n = 8, sampled before and after treatment) MPS IVA patients to identify potential biomarkers of disease. Out of 690 proteins identified in leukocytes, we selected a group of proteins that were dysregulated in MPS IVA patients with ERT. From these, we identified four potential protein biomarkers, all of which may influence bone and cartilage metabolism: lactotransferrin, coronin 1A, neutral alpha-glucosidase AB, and vitronectin. Further studies of cartilage and bone alterations in MPS IVA will be required to verify the validity of these proteins as potential biomarkers of MPS IVA. Full article
(This article belongs to the Special Issue Omics Technologies in Rare Diseases)
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