1
|
Loganathan T, Doss C GP. Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
Collapse
|
2
|
Aly KA, Moutaoufik MT, Phanse S, Zhang Q, Babu M. From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 2021; 24:102030. [PMID: 33521598 PMCID: PMC7820543 DOI: 10.1016/j.isci.2020.102030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial (mt) dysfunction is linked to rare diseases (RDs) such as respiratory chain complex (RCC) deficiency, MELAS, and ARSACS. Yet, how altered mt protein networks contribute to these ailments remains understudied. In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs. Accordingly, we discuss innovative untargeted label-free proteomics in identifying RD-specific mt or other macromolecular assemblies and mapping of protein networks in complex tissue, organoid, and stem cell-differentiated neurons. Furthermore, tag- and label-based proteomics, genealogical proteomics, and combinatorial affinity purification-mass spectrometry, along with advancements in detecting and integrating transient PPIs with single-cell proteomics and transcriptomics, collectively offer seminal follow-ups to enrich for RD-relevant networks, with implications in RD precision medicine.
Collapse
Affiliation(s)
- Khaled A. Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| |
Collapse
|
3
|
Abstract
Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.
Collapse
Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy.
| |
Collapse
|
4
|
Mäkitie RE, Hackl M, Niinimäki R, Kakko S, Grillari J, Mäkitie O. Altered MicroRNA Profile in Osteoporosis Caused by Impaired WNT Signaling. J Clin Endocrinol Metab 2018; 103:1985-1996. [PMID: 29506076 DOI: 10.1210/jc.2017-02585] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/26/2018] [Indexed: 12/16/2022]
Abstract
CONTEXT WNT signaling is fundamental to bone health, and its aberrant activation leads to skeletal pathologies. The heterozygous missense mutation p.C218G in WNT1, a key WNT pathway ligand, leads to severe early-onset and progressive osteoporosis with multiple peripheral and spinal fractures. Despite the severe skeletal manifestations, conventional bone turnover markers are normal in mutation-positive patients. OBJECTIVE This study sought to explore the circulating microRNA (miRNA) pattern in patients with impaired WNT signaling. DESIGN AND SETTING A cross-sectional cohort study at a university hospital. PARTICIPANTS Altogether, 12 mutation-positive (MP) subjects (median age, 39 years; range, 11 to 76 years) and 12 mutation-negative (MN) subjects (35 years; range, 9 to 59 years) from two Finnish families with WNT1 osteoporosis due to the heterozygous p.C218G WNT1 mutation. METHODS AND MAIN OUTCOME MEASURE Serum samples were screened for 192 miRNAs using quantitative polymerase chain reaction. Findings were compared between WNT1 MP and MN subjects. RESULTS The pattern of circulating miRNAs was significantly different in the MP subjects compared with the MN subjects, with two upregulated (miR-18a-3p and miR-223-3p) and six downregulated miRNAs (miR-22-3p, miR-31-5p, miR-34a-5p, miR-143-5p, miR-423-5p, and miR-423-3p). Three of these (miR-22-3p, miR-34a-5p, and miR-31-5p) are known inhibitors of WNT signaling: miR-22-3p and miR-34a-5p target WNT1 messenger RNA, and miR-31-5p is predicted to bind to WNT1 3'UTR. CONCLUSIONS The circulating miRNA pattern reflects WNT1 mutation status. The findings suggest that the WNT1 mutation disrupts feedback regulation between these miRNAs and WNT1, providing insights into the pathogenesis of WNT-related bone disorders. These miRNAs may have potential in the diagnosis and treatment of osteoporosis.
Collapse
Affiliation(s)
- Riikka E Mäkitie
- Folkhälsan Institute of Genetics and University of Helsinki, Helsinki, Finland
| | | | - Riitta Niinimäki
- Department of Children and Adolescents, Oulu University Hospital, and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Sakari Kakko
- Internal Medicine and Clinical Research Center, University of Oulu, Oulu, Finland
| | - Johannes Grillari
- Christian Doppler Laboratory on Biotechnology of Skin Aging, Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics and University of Helsinki, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
5
|
Le DH, Verbeke L, Son LH, Chu DT, Pham VH. Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs. BMC Bioinformatics 2017; 18:479. [PMID: 29137601 PMCID: PMC5686822 DOI: 10.1186/s12859-017-1924-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. RESULTS Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. CONCLUSIONS Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks.
Collapse
Affiliation(s)
- Duc-Hau Le
- Vinmec Research Institute of Stem Cell and Gene Technology, 458 Minh Khai, Hai Ba Trung, Hanoi, Vietnam
| | - Lieven Verbeke
- Department of Information Technology, Ghent University - imec, Ghent, Belgium
| | - Le Hoang Son
- VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam.,Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
| | - Van-Huy Pham
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| |
Collapse
|
6
|
Le D. Network-based ranking methods for prediction of novel disease associated microRNAs. Comput Biol Chem 2015; 58:139-48. [DOI: 10.1016/j.compbiolchem.2015.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 12/18/2022]
|
7
|
Taruscio D, Agresta L, Amato A, Bernardo G, Bernardo L, Braguti F, Carbone P, Carta C, Ceccarini M, Censi F, Coppola S, Crialese P, De Santis M, Diemoz S, Donati C, Gainotti S, Ferrari G, Floridia G, Frank C, Frazzica RG, Gentile AE, Granata O, Kodra Y, Latrofa M, Laricchiuta P, Magrelli A, Morciano C, Polizzi A, Razeto S, Salvatore M, Sanseverino A, Savini D, Torreri P, Tosto F, Villani F, Vincenti G, Vittozzi L. The Italian National Centre for Rare Diseases: where research and public health translate into action. Blood Transfus 2014; 12 Suppl 3:s591-605. [PMID: 24922300 DOI: 10.2450/2014.0040-14s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Sandoval J, Peiró-Chova L, Pallardó FV, García-Giménez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013; 13:457-71. [PMID: 23782253 DOI: 10.1586/erm.13.37] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics has emerged as a new and promising field in recent years. Lifestyle, stress, drugs, physiopathological situations and pharmacological interventions have a great impact on the epigenetic code of the cells by altering the methylome, miRNA expression and the covalent histone modifications. Since there exists a need to find new biomarkers and improve diagnosis for several diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. In this context, deciphering intricate epigenetic modifications involved in several molecular processes is a challenge that will be solved in the near future. In this review, the authors present an overview of the high-throughput technologies and laboratory techniques available for epigenetic studies, and also discuss which of them are more reliable to be used in a clinical diagnostic laboratory. In addition, the authors describe the most promising epigenetic biomarkers in lung, colorectal and prostate cancer, in which most advances have been achieved. Finally, the authors describe epigenetic biomarkers in some rare diseases; these rare syndromes are paradigms for a specific impaired molecular pathway, thus providing valuable information on the discovery of new epigenetic biomarkers.
Collapse
Affiliation(s)
- Juan Sandoval
- Epigenetics and Cancer Biology, Institut d'Investigació Biomèdica de Bellvitge IDIBELL, Barcelona, Spain
| | | | | | | |
Collapse
|
9
|
Kılıç P, Koçkaya G, Yemşen Ö, Tan C, Öztunca FH, Aksungur P, Kerman S. Orphan drug regulations in Turkey. Journal of Pharmaceutical Health Services Research 2013. [DOI: 10.1111/jphs.12018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pelin Kılıç
- Turkish Medicines and Medical Devices Agency (TİTCK); Turkey
| | | | - Ömer Yemşen
- Turkish Medicines and Medical Devices Agency (TİTCK); Turkey
| | - Celil Tan
- Alfa Farma Pharmaceuticals; Ankara Turkey
| | | | - Pelin Aksungur
- Turkish Medicines and Medical Devices Agency (TİTCK); Turkey
| | - Saim Kerman
- Turkish Medicines and Medical Devices Agency (TİTCK); Turkey
| |
Collapse
|
10
|
Dolled-Filhart MP, Lordemann A, Dahl W, Haraksingh RR, Ou-Yang CW, Lin JCH. Personalizing rare disease research: how genomics is revolutionizing the diagnosis and treatment of rare disease. Per Med 2012; 9:805-819. [DOI: 10.2217/pme.12.97] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A decade after the complete sequencing of the human genome, combined with recent advances in throughput and sequencing costs, the genetics of rare diseases has entered a new era. There has now been an explosion in the identification and mapping of rare diseases, with over 10,000 exomes having been sequenced to date. This article surveys the progress and development of technologies to understand rare disease; it provides a historical overview of traditional techniques such as karyotyping and homozygosity mapping, reviews current methods of whole-exome and -genome sequencing, and provides a future perspective on upcoming developments such as targeted drugs and gene therapy. This article will discuss the implications of these methods for rare disease research, along with a discussion of the success stories that provide great hope and optimism for patients and scientists alike.
Collapse
Affiliation(s)
| | - Amanda Lordemann
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - William Dahl
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Rajini Rani Haraksingh
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chih-Wen Ou-Yang
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Jimmy Cheng-Ho Lin
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| |
Collapse
|