1
|
Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci 2024; 25:6168. [PMID: 38892355 PMCID: PMC11172855 DOI: 10.3390/ijms25116168] [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: 05/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder, predominantly of the motor system. Although some genetic components and cellular mechanisms of Parkinson's have been identified, much is still unknown. In recent years, emerging evidence has indicated that non-DNA-sequence variation (in particular epigenetic mechanisms) is likely to play a crucial role in the development and progression of the disease. Here, we present an up-to-date overview of epigenetic processes including DNA methylation, DNA hydroxymethylation, histone modifications and non-coding RNAs implicated in the brain of those with Parkinson's disease. We will also discuss the limitations of current epigenetic research in Parkinson's disease, the advantages of simultaneously studying genetics and epigenetics, and putative novel epigenetic therapies.
Collapse
Affiliation(s)
| | - Anna Migdalska-Richards
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK;
| |
Collapse
|
2
|
Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
Collapse
Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
| |
Collapse
|
3
|
Słowikowski B, Owecki W, Jeske J, Jezierski M, Draguła M, Goutor U, Jagodziński PP, Kozubski W, Dorszewska J. Epigenetics and the neurodegenerative process. Epigenomics 2024; 16:473-491. [PMID: 38511224 DOI: 10.2217/epi-2023-0416] [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] [Indexed: 03/22/2024] Open
Abstract
Neurological diseases are multifactorial, genetic and environmental. Environmental factors such as diet, physical activity and emotional state are epigenetic factors. Environmental markers are responsible for epigenetic modifications. The effect of epigenetic changes is increased inflammation of the nervous system and neuronal damage. In recent years, it has been shown that epigenetic changes may cause an increased risk of neurological disorders but, currently, the relationship between epigenetic modifications and neurodegeneration remains unclear. This review summarizes current knowledge about neurological disorders caused by epigenetic changes in diseases such as Alzheimer's disease, Parkinson's disease, stroke and epilepsy. Advances in epigenetic techniques may be key to understanding the epigenetics of central changes in neurological diseases.
Collapse
Affiliation(s)
- Bartosz Słowikowski
- Department of Biochemistry & Molecular Biology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Wojciech Owecki
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Jan Jeske
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Michał Jezierski
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Michał Draguła
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Ulyana Goutor
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry & Molecular Biology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Wojciech Kozubski
- Chair & Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| | - Jolanta Dorszewska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, 61-701, Poland
| |
Collapse
|
4
|
Chen Q, Zhang L, Liu Y, Qin Z, Zhao T. PUTransGCN: identification of piRNA-disease associations based on attention encoding graph convolutional network and positive unlabelled learning. Brief Bioinform 2024; 25:bbae144. [PMID: 38581419 PMCID: PMC10998538 DOI: 10.1093/bib/bbae144] [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: 01/25/2024] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a crucial role in various biological processes and are implicated in disease. Consequently, there is an escalating demand for computational tools to predict piRNA-disease interactions. Although there have been computational methods proposed for the detection of piRNA-disease associations, the problem of imbalanced and sparse dataset has brought great challenges to capture the complex relationships between piRNAs and diseases. In response to this necessity, we have developed a novel computational architecture, denoted as PUTransGCN, which uses heterogeneous graph convolutional networks to uncover potential piRNA-disease associations. Additionally, the attention mechanism was used to adjust the weight parameters of aggregation heterogeneous node features automatically. For tackling the imbalanced dataset problem, the combined positive unlabelled learning (PUL) method comprising PU bagging, two-step and spy technique was applied to select reliable negative associations. The features of piRNAs and diseases were derived from three distinct biological sources by PUTransGCN, including information on piRNA sequences, semantic terms related to diseases and the existing network of piRNA-disease associations. In the experiment, PUTransGCN performs in 5-fold cross-validation with an AUC of 0.93 and 0.95 on two datasets, respectively, which outperforms the other six state-of-the-art models. We compared three different PUL methods, and the results of the ablation experiment indicate that the combined PUL method yields the best results. The PUTransGCN could serve as a valuable piRNA-disease prediction tool for upcoming studies in the biomedical field. The code for PUTransGCN is available at https://github.com/chenqiuhao/PUTransGCN.
Collapse
Affiliation(s)
- Qiuhao Chen
- Institute of Bioinformatics, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Liyuan Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Yaojia Liu
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Zhonghao Qin
- State Key Laboratory of Robotics and System, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Tianyi Zhao
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| |
Collapse
|
5
|
Huang X, Wang C, Zhang T, Li R, Chen L, Leung KL, Lakso M, Zhou Q, Zhang H, Wong G. PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease. Nat Commun 2023; 14:6137. [PMID: 37783675 PMCID: PMC10545829 DOI: 10.1038/s41467-023-41881-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that regulate gene expression, yet their molecular functions in neurobiology are unclear. While investigating neurodegeneration mechanisms using human α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg pan-neuronal overexpressing strains, we unexpectedly observed dysregulation of piRNAs. RNAi screening revealed that knock down of piRNA biogenesis genes improved thrashing behavior; further, a tofu-1 gene deletion ameliorated phenotypic deficits in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg transgenic strains. piRNA expression was extensively downregulated and H3K9me3 marks were decreased after tofu-1 deletion in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg strains. Dysregulated piRNAs targeted protein degradation genes suggesting that a decrease of piRNA expression leads to an increase of degradation ability in C. elegans. Finally, we interrogated piRNA expression in brain samples from PD patients. piRNAs were observed to be widely overexpressed at late motor stage. In this work, our results provide evidence that piRNAs are mediators in pathogenesis of Lewy body diseases and suggest a molecular mechanism for neurodegeneration in these and related disorders.
Collapse
Affiliation(s)
- Xiaobing Huang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, China
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, 510799, China
| | - Tianjiao Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Rongzhen Li
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China
| | - Ka Lai Leung
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Merja Lakso
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Qinghua Zhou
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, China
| | - Hongjie Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China.
| |
Collapse
|
6
|
Menon R, Petrucci L, Lohrer B, Zhang J, Schulze M, Schichor C, Winner B, Winkler J, Riemenschneider MJ, Kühn R, Falk S, Karow M. Human Induced Pluripotent Stem Cell-Derived Pericytes as Scalable and Editable Source to Study Direct Lineage Reprogramming Into Induced Neurons. Cell Reprogram 2023; 25:212-223. [PMID: 37366790 DOI: 10.1089/cell.2023.0008] [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] [Indexed: 06/28/2023] Open
Abstract
Studying human somatic cell-to-neuron conversion using primary brain-derived cells as starting cell source is hampered by limitations and variations in human biopsy material. Thus, delineating the molecular variables that allow changing the identity of somatic cells, permit adoption of neuronal phenotypes, and foster maturation of induced neurons (iNs) is challenging. Based on our previous results that pericytes derived from the adult human cerebral cortex can be directly converted into iNs (Karow et al., 2018; Karow et al., 2012), we here introduce human induced pluripotent stem cell (hiPSC)-derived pericytes (hiPSC-pericytes) as a versatile and more uniform tool to study the pericyte-to-neuron conversion process. This strategy enables us to derive scalable cell numbers and allows for engineering of the starting cell population such as introducing reporter tools before differentiation into hiPSC-pericytes and subsequent iN conversion. Harvesting the potential of this approach, we established hiPSC-derived human-human neuronal cocultures that not only allow for independent manipulation of each coculture partner but also resulted in morphologically more mature iNs. In summary, we exploit hiPSC-based methods to facilitate the analysis of human somatic cell-to-neuron conversion.
Collapse
Affiliation(s)
- Radhika Menon
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Linda Petrucci
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Benjamin Lohrer
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jingzhong Zhang
- Genome Engineering and Disease Models, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Markus Schulze
- Department of Neuropathology, Regensburg University Hospital, Regensburg, Germany
| | - Christian Schichor
- Department of Neurosurgery, Ludwig Maximilians University, Munich, Germany
| | - Beate Winner
- Department of Stem Cell Biology, and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Center of Rare Diseases Erlangen (ZSEER), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Winkler
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Ralf Kühn
- Genome Engineering and Disease Models, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sven Falk
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marisa Karow
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
7
|
Zhang K, Li Y, Huang Y, Sun K. PiRNA in Cardiovascular Disease: Focus on Cardiac Remodeling and Cardiac Protection. J Cardiovasc Transl Res 2023; 16:768-777. [PMID: 37407865 DOI: 10.1007/s12265-023-10353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/08/2023] [Indexed: 07/07/2023]
Abstract
Cardiovascular diseases (CVDs) are common causes of death, which take about 18.6 million lives worldwide every year. Currently, exploring strategies that delay ventricular remodeling, reduce cardiomyocyte death, and promote cardiomyocyte regeneration has been the hotspot and difficulty of the ischemic heart disease (IHD) research field. Previous studies indicate that piwi-interacting RNA (piRNA) plays a vital role in the occurrence and development of cardiac remodeling and may offer novel therapeutic strategies for cardiac repair. The best-known biological function of piRNA is to silence transposons in cells. In the cardiovascular system, piRNA is known to participate in cardiac progenitor cell proliferation, AKT pathway regulation, and cardiac remodeling and decompensation. In this review, we systematically discuss the research progress on piRNA in CVDs, especially the mechanism of cardiac remodeling and the potential functions in cardiac protection, which provides new insights for the progress and treatment of cardiovascular diseases. Piwi-interacting RNA (piRNA) is one of the noncoding RNAs, with the best -known biological function to silence transposons in cells. Now piRNA is found to participate in cardiac progenitor cell proliferation, AKT pathway regulation, cardiac remodeling and decompensation, which implies the potential of piRNA in the diagnosis and treatment of cardiovascular diseases. Over expression of piRNA could promote cardiac apoptosis and cardiac hypertrophy, thus targeted therapy which inhibits expression of associated piRNA may reduce cardiac remodeling and reduce inflammation caused by necrotic cardiomyocytes. PiRNA is also speculated to participate in the proliferation of cardiac progenitor cells, implying the potential to induce cardiac regeneration th erapy, which provides new insights for treatment of cardiovascular diseases. At present, the treatment strategy of cardiac remodeling emphasizes the control of risk factors, prevention of disease progression and individualized treatment. With further studies in mechanism of piRNA, potential therapies above may come true and more therapies in cardiovascular diseases may be found.
Collapse
Affiliation(s)
- Kaiyu Zhang
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Yafei Li
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Ying Huang
- Central Laboratory, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Kangyun Sun
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China.
| |
Collapse
|
8
|
Ramakrishna K, Nalla LV, Naresh D, Venkateswarlu K, Viswanadh MK, Nalluri BN, Chakravarthy G, Duguluri S, Singh P, Rai SN, Kumar A, Singh V, Singh SK. WNT-β Catenin Signaling as a Potential Therapeutic Target for Neurodegenerative Diseases: Current Status and Future Perspective. Diseases 2023; 11:89. [PMID: 37489441 PMCID: PMC10366863 DOI: 10.3390/diseases11030089] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/26/2023] Open
Abstract
Wnt/β-catenin (WβC) signaling pathway is an important signaling pathway for the maintenance of cellular homeostasis from the embryonic developmental stages to adulthood. The canonical pathway of WβC signaling is essential for neurogenesis, cell proliferation, and neurogenesis, whereas the noncanonical pathway (WNT/Ca2+ and WNT/PCP) is responsible for cell polarity, calcium maintenance, and cell migration. Abnormal regulation of WβC signaling is involved in the pathogenesis of several neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), and spinal muscular atrophy (SMA). Hence, the alteration of WβC signaling is considered a potential therapeutic target for the treatment of neurodegenerative disease. In the present review, we have used the bibliographical information from PubMed, Google Scholar, and Scopus to address the current prospects of WβC signaling role in the abovementioned neurodegenerative diseases.
Collapse
Affiliation(s)
- Kakarla Ramakrishna
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Lakshmi Vineela Nalla
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Dumala Naresh
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Kojja Venkateswarlu
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, IIT BHU, Varanasi 221005, India
| | - Matte Kasi Viswanadh
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Buchi N Nalluri
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Guntupalli Chakravarthy
- KL College of Pharmacy, Koneru Lakshmaiah Education Foundation Deemed to be University (KLU), Green Fields, Vaddeswaram, Guntur 522502, India
| | - Sajusha Duguluri
- Department of Biotechnology, Bharathi Institute of Higher Education and Research, Chennai 600073, India
| | - Payal Singh
- Department of Zoology, Mahila Maha Vidyalaya, Banaras Hindu University, Varanasi 221005, India
| | - Sachchida Nand Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ashish Kumar
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India
| | - Veer Singh
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| |
Collapse
|
9
|
Hou J, Wei H, Liu B. iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network. PLoS Comput Biol 2023; 19:e1011242. [PMID: 37339125 DOI: 10.1371/journal.pcbi.1011242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
Accurately identifying potential piRNA-disease associations is of great importance in uncovering the pathogenesis of diseases. Recently, several machine-learning-based methods have been proposed for piRNA-disease association detection. However, they are suffering from the high sparsity of piRNA-disease association network and the Boolean representation of piRNA-disease associations ignoring the confidence coefficients. In this study, we propose a supplementarily weighted strategy to solve these disadvantages. Combined with Graph Convolutional Networks (GCNs), a novel predictor called iPiDA-SWGCN is proposed for piRNA-disease association prediction. There are three main contributions of iPiDA-SWGCN: (i) Potential piRNA-disease associations are preliminarily supplemented in the sparse piRNA-disease network by integrating various basic predictors to enrich network structure information. (ii) The original Boolean piRNA-disease associations are assigned with different relevance confidence to learn node representations from neighbour nodes in varying degrees. (iii) The experimental results show that iPiDA-SWGCN achieves the best performance compared with the other state-of-the-art methods, and can predict new piRNA-disease associations.
Collapse
Affiliation(s)
- Jialu Hou
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Hang Wei
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
| |
Collapse
|
10
|
Ogi DA, Jin S. Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine. Cells 2023; 12:1442. [PMID: 37408278 DOI: 10.3390/cells12101442] [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: 04/01/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 07/07/2023] Open
Abstract
Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing cellular differentiation based on promoting the expression of specific genes. It has also been utilized to determine the specific cell type. This review highlights RNAseq techniques, tools for RNAseq data interpretation, RNAseq data analytic methods and their utilities, and transcriptomics-enabled human stem cell differentiation. In addition, the review outlines the potential benefits of the transcriptomics-aided discovery of intrinsic factors influencing stem cell lineage commitment, transcriptomics applied to disease physiology studies using patients' induced pluripotent stem cell (iPSC)-derived cells for regenerative medicine, and the future outlook on the technology and its implementation.
Collapse
Affiliation(s)
- Derek A Ogi
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
- Center of Biomanufacturing for Regenerative Medicine, State University of New York at Binghamton, Binghamton, NY 13902, USA
| |
Collapse
|
11
|
LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
Collapse
Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| |
Collapse
|
12
|
Sugeno N, Hasegawa T. Unraveling the Complex Interplay between Alpha-Synuclein and Epigenetic Modification. Int J Mol Sci 2023; 24:ijms24076645. [PMID: 37047616 PMCID: PMC10094812 DOI: 10.3390/ijms24076645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Alpha-synuclein (αS) is a small, presynaptic neuronal protein encoded by the SNCA gene. Point mutations and gene multiplication of SNCA cause rare familial forms of Parkinson’s disease (PD). Misfolded αS is cytotoxic and is a component of Lewy bodies, which are a pathological hallmark of PD. Because SNCA multiplication is sufficient to cause full-blown PD, gene dosage likely has a strong impact on pathogenesis. In sporadic PD, increased SNCA expression resulting from a minor genetic background and various environmental factors may contribute to pathogenesis in a complementary manner. With respect to genetic background, several risk loci neighboring the SNCA gene have been identified, and epigenetic alterations, such as CpG methylation and regulatory histone marks, are considered important factors. These alterations synergistically upregulate αS expression and some post-translational modifications of αS facilitate its translocation to the nucleus. Nuclear αS interacts with DNA, histones, and their modifiers to alter epigenetic status; thereby, influencing the stability of neuronal function. Epigenetic changes do not affect the gene itself but can provide an appropriate transcriptional response for neuronal survival through DNA methylation or histone modifications. As a new approach, publicly available RNA sequencing datasets from human midbrain-like organoids may be used to compare transcriptional responses through epigenetic alterations. This informatic approach combined with the vast amount of transcriptomics data will lead to the discovery of novel pathways for the development of disease-modifying therapies for PD.
Collapse
Affiliation(s)
- Naoto Sugeno
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Takafumi Hasegawa
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| |
Collapse
|
13
|
Systems level analysis of sex-dependent gene expression changes in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:8. [PMID: 36681675 PMCID: PMC9867746 DOI: 10.1038/s41531-023-00446-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
Parkinson's disease (PD) is a heterogeneous disorder, and among the factors which influence the symptom profile, biological sex has been reported to play a significant role. While males have a higher age-adjusted disease incidence and are more frequently affected by muscle rigidity, females present more often with disabling tremors. The molecular mechanisms involved in these differences are still largely unknown, and an improved understanding of the relevant factors may open new avenues for pharmacological disease modification. To help address this challenge, we conducted a meta-analysis of disease-associated molecular sex differences in brain transcriptomics data from case/control studies. Both sex-specific (alteration in only one sex) and sex-dimorphic changes (changes in both sexes, but with opposite direction) were identified. Using further systems level pathway and network analyses, coordinated sex-related alterations were studied. These analyses revealed significant disease-associated sex differences in mitochondrial pathways and highlight specific regulatory factors whose activity changes can explain downstream network alterations, propagated through gene regulatory cascades. Single-cell expression data analyses confirmed the main pathway-level changes observed in bulk transcriptomics data. Overall, our analyses revealed significant sex disparities in PD-associated transcriptomic changes, resulting in coordinated modulations of molecular processes. Among the regulatory factors involved, NR4A2 has already been reported to harbor rare mutations in familial PD and its pharmacological activation confers neuroprotective effects in toxin-induced models of Parkinsonism. Our observations suggest that NR4A2 may warrant further research as a potential adjuvant therapeutic target to address a subset of pathological molecular features of PD that display sex-associated profiles.
Collapse
|
14
|
Ngum JA, Tatang FJ, Toumeni MH, Nguengo SN, Simo USF, Mezajou CF, Kameni C, Ngongang NN, Tchinda MF, Dongho Dongmo FF, Akami M, Ngane Ngono AR, Tamgue O. An overview of natural products that modulate the expression of non-coding RNAs involved in oxidative stress and inflammation-associated disorders. Front Pharmacol 2023; 14:1144836. [PMID: 37168992 PMCID: PMC10165025 DOI: 10.3389/fphar.2023.1144836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Oxidative stress is a state in which oxidants are produced in excess in the body's tissues and cells, resulting in a biological imbalance amid the generation of reactive oxygen and nitrogen species (RONS) from redox reactions. In case of insufficient antioxidants to balance, the immune system triggers signaling cascades to mount inflammatory responses. Oxidative stress can have deleterious effects on major macromolecules such as lipids, proteins, and nucleic acids, hence, Oxidative stress and inflammation are among the multiple factors contributing to the etiology of several disorders such as diabetes, cancers, and cardiovascular diseases. Non-coding RNAs (ncRNAs) which were once referred to as dark matter have been found to function as key regulators of gene expression through different mechanisms. They have dynamic roles in the onset and development of inflammatory and oxidative stress-related diseases, therefore, are potential targets for the control of those diseases. One way of controlling those diseases is through the use of natural products, a rich source of antioxidants that have drawn attention with several studies showing their involvement in combating chronic diseases given their enormous gains, low side effects, and toxicity. In this review, we highlighted the natural products that have been reported to target ncRNAs as mediators of their biological effects on oxidative stress and several inflammation-associated disorders. Those natural products include Baicalein, Tanshinone IIA, Geniposide, Carvacrol/Thymol, Triptolide, Oleacein, Curcumin, Resveratrol, Solarmargine, Allicin, aqueous extract or pulp of Açai, Quercetin, and Genistein. We also draw attention to some other compounds including Zanthoxylum bungeanum, Canna genus rhizome, Fuzi-ganjiang herb pair, Aronia melanocarpa, Peppermint, and Gingerol that are effective against oxidative stress and inflammation-related disorders, however, have no known effect on ncRNAs. Lastly, we touched on the many ncRNAs that were found to play a role in oxidative stress and inflammation-related disorders but have not yet been investigated as targets of a natural product. Shedding more light into these two last points of shadow will be of great interest in the valorization of natural compounds in the control and therapy of oxidative stress- and inflammation-associated disorders.
Collapse
|
15
|
Zhu Q, Jiang F, Song Y, Lu L, He F, Huang S, Huang Z, Yao J, Lei N, Huang J, Lu S. Small noncoding RNA dysregulation is implicated in manganism in a rat model of methylcyclopentadienyl manganese tricarbonyl-induced unrepaired striatum damage. J Toxicol Sci 2023; 48:535-546. [PMID: 37778982 DOI: 10.2131/jts.48.535] [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] [Indexed: 10/03/2023]
Abstract
The accumulation of excessively high manganese levels within the brain can contribute to a series of Parkinsonian symptoms referred to as manganism. The gasoline antiknock additive Methylcyclopentadienyl Manganese Tricarbonyl (MMT) is an environmental source of manganese exposure and can induce manganism in rats. While some prior reports have demonstrated the differential expression of small noncoding RNAs (sncRNAs) in patients with Parkinson's disease (PD), the degree of sncRNA dysfunction in manganism has yet to be clearly documented. As sncRNAs such as transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) exhibit high levels of modifications such as 3' terminal 3'-phosphate and 2',3'-cyclic phosphate modifications that disrupt the process of adapter ligation and m1A, m3C, m1G, and m22G RNA methylation, these transcripts are not detected in traditional small RNA-sequencing studies. Here, differential sncRNA expression was analyzed by comparing a rat model of MMT-induced unrepaired striatum damage to appropriate control samples via PANDORA-Seq, which can detect highly modified sncRNAs. Following the removal of sncRNA modifications, this approach identified 599 sncRNAs that were differentially expressed in the striatum of MMT-exposed rats relative to controls, as well as 1155 sncRNAs that were differentially expressed in Mn-treated and control rats. Additional functional analyses were performed to predict the putative targets of these sncRNAs, implicating a role for such sncRNA dysregulation in the pathogenesis of manganism in this rat model system.
Collapse
Affiliation(s)
- Qifeng Zhu
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fan Jiang
- Department of Rehabilitation medicine, the First Institute of Clinical Medicine Guangxi Medical University, China
| | - Yuanbo Song
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Lili Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fajian He
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Shuqi Huang
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Zhaoying Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jing Yao
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Ningning Lei
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jianmin Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Shijin Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| |
Collapse
|
16
|
PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences. Curr Environ Health Rep 2022; 9:650-660. [PMID: 35917009 DOI: 10.1007/s40572-022-00372-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW: The epigenome modulates gene expression in response to environmental stimuli. Modifications to the epigenome are potentially reversible, making them a promising therapeutic approach to mitigate environmental exposure effects on human health. This review details currently available genome and epigenome editing technologies and highlights ncRNA, including piRNA, as potential tools for targeted epigenome editing. RECENT FINDINGS: Zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) associated nuclease (CRISPR/Cas) research has significantly advanced genome editing technology, with broad promise in genetic research and targeted therapies. Initial epigenome-directed therapies relied on global modification and suffered from limited specificity. Adapted from current genome editing tools, zinc finger protein (ZFP), TALE, and CRISPR/nuclease-deactivated Cas (dCas) systems now confer locus-specific epigenome editing, with promising applicability in the field of environmental health sciences. However, high incidence of off-target effects and time taken for screening limit their use. FUTURE DEVELOPMENT: ncRNA serve as a versatile biomarker with well-characterized regulatory mechanisms that can easily be adapted to edit the epigenome. For instance, the transposon silencing mechanism of germline PIWI-interacting RNAs (piRNA) could be engineered to specifically methylate a given gene, overcoming pitfalls of current global modifiers. Future developments in epigenome editing technologies will inform risk assessment through mechanistic investigation and serve as potential modes of intervention to mitigate environmentally induced adverse health outcomes later in life.
Collapse
|
17
|
Garg P, Jamal F, Srivastava P. Deciphering the role of precursor miR-12136 and miR-8485 in the progression of intellectual disability (ID). IBRO Neurosci Rep 2022; 13:393-401. [DOI: 10.1016/j.ibneur.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
|
18
|
Dobricic V, Schilling M, Farkas I, Gveric DO, Ohlei O, Schulz J, Middleton L, Gentleman SM, Parkkinen L, Bertram L, Lill CM. Common signatures of differential microRNA expression in Parkinson's and Alzheimer's disease brains. Brain Commun 2022; 4:fcac274. [PMID: 36382223 PMCID: PMC9645562 DOI: 10.1093/braincomms/fcac274] [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: 04/07/2022] [Revised: 06/22/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
Dysregulation of microRNA gene expression has been implicated in many neurodegenerative diseases, including Parkinson's disease. However, the individual dysregulated microRNAs remain largely unknown. Previous meta-analyses have highlighted several microRNAs being differentially expressed in post-mortem Parkinson's disease and Alzheimer's disease brains versus controls, but they were based on small sample sizes. In this study, we quantified the expression of the most compelling Parkinson's and Alzheimer's disease microRNAs from these meta-analyses ('candidate miRNAs') in one of the largest Parkinson's/Alzheimer's disease case-control post-mortem brain collections available (n = 451), thereby quadruplicating previously investigated sample sizes. Parkinson's disease candidate microRNA hsa-miR-132-3p was differentially expressed in our Parkinson's (P = 4.89E-06) and Alzheimer's disease samples (P = 3.20E-24) compared with controls. Alzheimer's disease candidate microRNAs hsa-miR-132-5p (P = 4.52E-06) and hsa-miR-129-5p (P = 0.0379) were differentially expressed in our Parkinson's disease samples. Combining these novel data with previously published data substantially improved the statistical support (α = 3.85E-03) of the corresponding meta-analyses, clearly implicating these microRNAs in both Parkinson's and Alzheimer's disease. Furthermore, hsa-miR-132-3p/-5p (but not hsa-miR-129-5p) showed association with α-synuclein neuropathological Braak staging (P = 3.51E-03/P = 0.0117), suggesting that hsa-miR-132-3p/-5p play a role in α-synuclein aggregation beyond the early disease phase. Our study represents the largest independent assessment of recently highlighted candidate microRNAs in Parkinson's and Alzheimer's disease brains, to date. Our results implicate hsa-miR-132-3p/-5p and hsa-miR-129-5p to be differentially expressed in both Parkinson's and Alzheimer's disease, pinpointing shared pathogenic mechanisms across these neurodegenerative diseases. Intriguingly, based on publicly available high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation data, hsa-miR-132 may interact with SNCA messenger RNA in the human brain, possibly pinpointing novel therapeutic approaches in fighting Parkinson's disease.
Collapse
Affiliation(s)
- Valerija Dobricic
- Correspondence to: Prof Dr Christina M. Lill, MD, MSc Ageing Epidemiology Unit, School of Public Health Imperial College London, London, UK E-mail: ; Dr. Valerija Dobricic, Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany, E-mail:
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Ildiko Farkas
- Multiple Sclerosis and Parkinson’s Tissue Bank, Imperial College London, London W12 0NN, UK
| | - Djordje O Gveric
- Multiple Sclerosis and Parkinson’s Tissue Bank, Imperial College London, London W12 0NN, UK
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Jessica Schulz
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Lefkos Middleton
- Ageing and Epidemiology Unit (AGE), School of Public Health, Imperial College London, London W6 8RF, UK,Public Health Directorate, Imperial College NHS Healthcare Trust, London W6 8RF, UK
| | - Steve M Gentleman
- Department of Brain Sciences, Hammersmith Hospital campus, Imperial College London, London W12 0HS, UK
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany,Department of Psychology, University of Oslo, 0373 Oslo, Norway
| | - Christina M Lill
- Correspondence to: Prof Dr Christina M. Lill, MD, MSc Ageing Epidemiology Unit, School of Public Health Imperial College London, London, UK E-mail: ; Dr. Valerija Dobricic, Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany, E-mail:
| |
Collapse
|
19
|
iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network. PLoS Comput Biol 2022; 18:e1010671. [DOI: 10.1371/journal.pcbi.1010671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/14/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
Motivation
Piwi-interacting RNAs (piRNAs) play a critical role in the progression of various diseases. Accurately identifying the associations between piRNAs and diseases is important for diagnosing and prognosticating diseases. Although some computational methods have been proposed to detect piRNA-disease associations, it is challenging for these methods to effectively capture nonlinear and complex relationships between piRNAs and diseases because of the limited training data and insufficient association representation.
Results
With the growth of piRNA-disease association data, it is possible to design a more complex machine learning method to solve this problem. In this study, we propose a computational method called iPiDA-GCN for piRNA-disease association identification based on graph convolutional networks (GCNs). The iPiDA-GCN predictor constructs the graphs based on piRNA sequence information, disease semantic information and known piRNA-disease associations. Two GCNs (Asso-GCN and Sim-GCN) are used to extract the features of both piRNAs and diseases by capturing the association patterns from piRNA-disease interaction network and two similarity networks. GCNs can capture complex network structure information from these networks, and learn discriminative features. Finally, the full connection networks and inner production are utilized as the output module to predict piRNA-disease association scores. Experimental results demonstrate that iPiDA-GCN achieves better performance than the other state-of-the-art methods, benefitted from the discriminative features extracted by Asso-GCN and Sim-GCN. The iPiDA-GCN predictor is able to detect new piRNA-disease associations to reveal the potential pathogenesis at the RNA level. The data and source code are available at http://bliulab.net/iPiDA-GCN/.
Collapse
|
20
|
Seliger C, Meyer AL, Leidgens V, Rauer L, Moeckel S, Jachnik B, Proske J, Dettmer K, Rothhammer-Hampl T, Kaulen LD, Riemenschneider MJ, Oefner PJ, Kreutz M, Schmidt NO, Merrill M, Uhl M, Renner K, Vollmann-Zwerenz A, Proescholdt M, Hau P. Metabolic Heterogeneity of Brain Tumor Cells of Proneural and Mesenchymal Origin. Int J Mol Sci 2022; 23:ijms231911629. [PMID: 36232951 PMCID: PMC9569970 DOI: 10.3390/ijms231911629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Brain-tumor-initiating cells (BTICs) of proneural and mesenchymal origin contribute to the highly malignant phenotype of glioblastoma (GB) and resistance to current therapies. BTICs of different subtypes were challenged with oxidative phosphorylation (OXPHOS) inhibition with metformin to assess the differential effects of metabolic intervention on key resistance features. Whereas mesenchymal BTICs varied according to their invasiveness, they were in general more glycolytic and less responsive to metformin. Proneural BTICs were less invasive, catabolized glucose more via the pentose phosphate pathway, and responded better to metformin. Targeting glycolysis may be a promising approach to inhibit tumor cells of mesenchymal origin, whereas proneural cells are more responsive to OXPHOS inhibition. Future clinical trials exploring metabolic interventions should account for metabolic heterogeneity of brain tumors.
Collapse
Affiliation(s)
- Corinna Seliger
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
- Department of Neurology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-56-7507
| | - Anne-Louise Meyer
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center Freiburg, 79104 Freiburg, Germany
| | - Verena Leidgens
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Lisa Rauer
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Sylvia Moeckel
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Birgit Jachnik
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Judith Proske
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | | | - Leon D. Kaulen
- Department of Neurology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Marina Kreutz
- Department of Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Nils-Ole Schmidt
- Department of Neurosurgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Marsha Merrill
- Surgical Neurology Branch, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA
| | - Martin Uhl
- Department of Neurology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Kathrin Renner
- Department of Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Arabel Vollmann-Zwerenz
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Martin Proescholdt
- Department of Neurosurgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Peter Hau
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
21
|
Noronha O, Mesarosovo L, Anink JJ, Iyer A, Aronica E, Mills JD. Differentially Expressed miRNAs in Age-Related Neurodegenerative Diseases: A Meta-Analysis. Genes (Basel) 2022; 13:genes13061034. [PMID: 35741796 PMCID: PMC9222420 DOI: 10.3390/genes13061034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/05/2023] Open
Abstract
To date, no neurodegenerative diseases (NDDs) have cures, and the underlying mechanism of their pathogenesis is undetermined. As miRNAs extensively regulate all biological processes and are crucial regulators of healthy brain function, miRNAs differentially expressed in NDDs may provide insight into the factors that contribute to the emergence of protein inclusions and the propagation of deleterious cellular environments. A meta-analysis of miRNAs dysregulated in Alzheimer’s disease, Parkinson’s disease, multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration, dementia with Lewy bodies and frontotemporal lobar degeneration (TDP43 variant) was performed to determine if diseases within a proteinopathy have distinct or shared mechanisms of action leading to neuronal death, and if proteinopathies can be classified on the basis of their miRNA profiles. Our results identified both miRNAs distinct to the anatomy, disease type and pathology, and miRNAs consistently dysregulated within single proteinopathies and across neurodegeneration in general. Our results also highlight the necessity to minimize the variability between studies. These findings showcase the need for more transcriptomic research on infrequently occurring NDDs, and the need for the standardization of research techniques and platforms utilized across labs and diseases.
Collapse
Affiliation(s)
- Ocana Noronha
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Saitama 351-0106, Japan
| | - Lucia Mesarosovo
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - Jasper J. Anink
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - Anand Iyer
- Department of Internal Medicine, Erasmus Medicine Center, 3015 GD Rotterdam, The Netherlands;
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
| | - James D. Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands; (O.N.); (L.M.); (J.J.A.); (E.A.)
- Department of Clinical and Experimental Epilepsy, University College London, London WC1E 6BT, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, Gerrards Cross SL9 0RJ, UK
- Correspondence:
| |
Collapse
|
22
|
Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
Collapse
Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| |
Collapse
|
23
|
Dysregulated miRNAs as Biomarkers and Therapeutical Targets in Neurodegenerative Diseases. J Pers Med 2022; 12:jpm12050770. [PMID: 35629192 PMCID: PMC9143965 DOI: 10.3390/jpm12050770] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 12/20/2022] Open
Abstract
Alzheimer’s disease (AD), Parkinson’s disease (PD), and Amyotrophic Lateral Sclerosis (ALS) are representative neurodegenerative diseases (NDs) characterized by degeneration of selective neurons, as well as the lack of effective biomarkers and therapeutic treatments. In the last decade, microRNAs (miRNAs) have gained considerable interest in diagnostics and therapy of NDs, owing to their aberrant expression and their ability to target multiple molecules and pathways. Here, we provide an overview of dysregulated miRNAs in fluids (blood or cerebrospinal fluid) and nervous tissue of AD, PD, and ALS patients. By emphasizing those that are commonly dysregulated in these NDs, we highlight their potential role as biomarkers or therapeutical targets and describe the use of antisense oligonucleotides as miRNA therapies.
Collapse
|
24
|
Xie S, Yang J, Huang S, Fan Y, Xu T, He J, Guo J, Ji X, Wang Z, Li P, Chen J, Zhang Y. Disrupted myelination network in the cingulate cortex of Parkinson's disease. IET Syst Biol 2022; 16:98-119. [PMID: 35394697 PMCID: PMC9290774 DOI: 10.1049/syb2.12043] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
The cingulate cortex is part of the conserved limbic system, which is considered as a hub of emotional and cognitive control. Accumulating evidence suggested that involvement of the cingulate cortex is significant for cognitive impairment of Parkinson's disease (PD). However, mechanistic studies of the cingulate cortex in PD pathogenesis are limited. Here, transcriptomic and regulatory network analyses were conducted for the cingulate cortex in PD. Enrichment and clustering analyses showed that genes involved in regulation of membrane potential and glutamate receptor signalling pathway were upregulated. Importantly, myelin genes and the oligodendrocyte development pathways were markedly downregulated, indicating disrupted myelination in PD cingulate cortex. Cell‐type‐specific signatures revealed that myelinating oligodendrocytes were the major cell type damaged in the PD cingulate cortex. Furthermore, downregulation of myelination pathways in the cingulate cortex were shared and validated in another independent RNAseq cohort of dementia with Lewy bodies (DLB). In combination with ATACseq data, gene regulatory networks (GRNs) were further constructed for 32 transcription factors (TFs) and 466 target genes among differentially expressed genes (DEGs) using a tree‐based machine learning algorithm. Several transcription factors, including Olig2, Sox8, Sox10, E2F1, and NKX6‐2, were highlighted as key nodes in a sub‐network, which control many overlapping downstream targets associated with myelin formation and gliogenesis. In addition, the authors have validated a subset of DEGs by qPCRs in two PD mouse models. Notably, seven of these genes,TOX3, NECAB2 NOS1, CAPN3, NR4A2, E2F1 and FOXP2, have been implicated previously in PD or neurodegeneration and are worthy of further studies as novel candidate genes. Together, our findings provide new insights into the role of remyelination as a promising new approach to treat PD after demyelination.
Collapse
Affiliation(s)
- Song Xie
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiajun Yang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shenghui Huang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yuanlan Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tao Xu
- Molecular Neuropharmacology Lab, School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China
| | - Jiangshuang He
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiahao Guo
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, Louisiana, USA
| | - Zhibo Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Peijun Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiangfan Chen
- Molecular Neuropharmacology Lab, School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China.,Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| |
Collapse
|
25
|
Ali SD, Tayara H, Chong KT. Identification of piRNA disease associations using deep learning. Comput Struct Biotechnol J 2022; 20:1208-1217. [PMID: 35317234 PMCID: PMC8908038 DOI: 10.1016/j.csbj.2022.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/09/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a pivotal role in maintaining genome integrity by repression of transposable elements, gene stability, and association with various disease progressions. Cost-efficient computational methods for the identification of piRNA disease associations promote the efficacy of disease-specific drug development. In this regard, we developed a simple, robust, and efficient deep learning method for identifying the piRNA disease associations known as piRDA. The proposed architecture extracts the most significant and abstract information from raw sequences represented in a simplicated piRNA disease pair without any involvement of features engineering. Two-step positive unlabeled learning and bootstrapping technique are utilized to abstain from the false-negative and biased predictions dealing with positive unlabeled data. The performance of proposed method piRDA is evaluated using k-fold cross-validation. The piRDA is significantly improved in all the performance evaluation measures for the identification of piRNA disease associations in comparison to state-of-the-art method. Moreover, it is thus projected conclusively that the proposed computational method could play a significant role as a supportive and practical tool for primitive disease mechanisms and pharmaceutical research such as in academia and drug design. Eventually, the proposed model can be accessed using publicly available and user-friendly web tool athttp://nsclbio.jbnu.ac.kr/tools/piRDA/.
Collapse
Affiliation(s)
- Syed Danish Ali
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
| |
Collapse
|
26
|
Termine A, Fabrizio C, Strafella C, Caputo V, Petrosini L, Caltagirone C, Cascella R, Giardina E. A Hybrid Machine Learning and Network Analysis Approach Reveals Two Parkinson's Disease Subtypes from 115 RNA-Seq Post-Mortem Brain Samples. Int J Mol Sci 2022; 23:ijms23052557. [PMID: 35269707 PMCID: PMC8910747 DOI: 10.3390/ijms23052557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 12/26/2022] Open
Abstract
Precision medicine emphasizes fine-grained diagnostics, taking individual variability into account to enhance treatment effectiveness. Parkinson’s disease (PD) heterogeneity among individuals proves the existence of disease subtypes, so subgrouping patients is vital for better understanding disease mechanisms and designing precise treatment. The purpose of this study was to identify PD subtypes using RNA-Seq data in a combined pipeline including unsupervised machine learning, bioinformatics, and network analysis. Two hundred and ten post mortem brain RNA-Seq samples from PD (n = 115) and normal controls (NCs, n = 95) were obtained with systematic data retrieval following PRISMA statements and a fully data-driven clustering pipeline was performed to identify PD subtypes. Bioinformatics and network analyses were performed to characterize the disease mechanisms of the identified PD subtypes and to identify target genes for drug repurposing. Two PD clusters were identified and 42 DEGs were found (p adjusted ≤ 0.01). PD clusters had significantly different gene network structures (p < 0.0001) and phenotype-specific disease mechanisms, highlighting the differential involvement of the Wnt/β-catenin pathway regulating adult neurogenesis. NEUROD1 was identified as a key regulator of gene networks and ISX9 and PD98059 were identified as NEUROD1-interacting compounds with disease-modifying potential, reducing the effects of dopaminergic neurodegeneration. This hybrid data analysis approach could enable precision medicine applications by providing insights for the identification and characterization of pathological subtypes. This workflow has proven useful on PD brain RNA-Seq, but its application to other neurodegenerative diseases is encouraged.
Collapse
Affiliation(s)
- Andrea Termine
- Data Science Unit, IRCCS Santa Lucia Foundation c/o CERC, 00143 Rome, Italy; (A.T.); (C.F.)
| | - Carlo Fabrizio
- Data Science Unit, IRCCS Santa Lucia Foundation c/o CERC, 00143 Rome, Italy; (A.T.); (C.F.)
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy; (C.S.); (V.C.)
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy; (C.S.); (V.C.)
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy;
| | - Laura Petrosini
- Experimental and Behavioral Neurophysiology, IRCCS Santa Lucia Foundation c/o CERC, 00143 Rome, Italy;
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, 00179 Rome, Italy;
| | - Raffaella Cascella
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy;
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, 1000 Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy; (C.S.); (V.C.)
- UILDM Lazio ONLUS Foundation, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
- Correspondence:
| |
Collapse
|
27
|
Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages. Int J Mol Sci 2022; 23:ijms23052469. [PMID: 35269612 PMCID: PMC8910154 DOI: 10.3390/ijms23052469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Piwi interacting RNAs (piRNAs) are small non-coding single-stranded RNA species 20–31 nucleotides in size generated from distinct loci. In germline tissues, piRNAs are amplified via a “ping-pong cycle” to produce secondary piRNAs, which act in transposon silencing. In contrast, the role of somatic-derived piRNAs remains obscure. Here, we investigated the identity and distribution of piRNAs in human somatic tissues to determine their function and potential role in Parkinson’s disease (PD). Human datasets were curated from the Gene Expression Omnibus (GEO) database and a workflow was developed to identify piRNAs, which revealed 902 somatic piRNAs of which 527 were expressed in the brain. These were mainly derived from chromosomes 1, 11, and 19 compared to the germline tissues, which were from 15 and 19. Approximately 20% of somatic piRNAs mapped to transposon 3′ untranslated regions (UTRs), but a large proportion were sensed to the transcript in contrast to germline piRNAs. Gene set enrichment analysis suggested that somatic piRNAs function in neurodegenerative disease. piRNAs undergo dysregulation in different PD subtypes (PD and Parkinson’s disease dementia (PDD)) and stages (premotor and motor). piR-has-92056, piR-hsa-150797, piR-hsa-347751, piR-hsa-1909905, piR-hsa-2476630, and piR-hsa-2834636 from blood small extracellular vesicles were identified as novel biomarkers for PD diagnosis using a sparse partial least square discriminant analysis (sPLS-DA) (accuracy: 92%, AUC = 0.89). This study highlights a role for piRNAs in PD and provides tools for novel biomarker development.
Collapse
|
28
|
Singh G, Mallick B. Predicting sequence and structural features of effective piRNA target binding sites. J Mol Recognit 2022; 35:e2949. [PMID: 34979054 DOI: 10.1002/jmr.2949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022]
Abstract
Piwi-interacting RNA (piRNA) targets are usually identified through base pairing between the piRNA seed region and complementary bases on the target mRNAs, which often results in false predictions. Crosslinking immunoprecipitation (CLIP) study emerges as a promising method that enables accurate identification of PIWI-clade-based targets containing RNA-binding sites. In the present study, we have analyzed the piRNA-target CLIP-seq datasets to uncover the additional characteristic features of piRNA targets. We studied important sequence and structural features using IP+ and IP- set targets that might enhance the accuracy of target site predictions. Analysis has revealed substantial enrichment of AU in target sites as well as in and around the 30 nts upstream and downstream of target sites in IP+ set relative to IP- set that might be contributing to lowering the minimal folding energy of target sites of IP+ + set that might be easing the base pairing between piRNA and their targets. We have also found a lower MFE threshold (en) and higher miRanda score for piRNA targets. Interestingly, we have found that majority of the target sites are residing within 3'UTR, suggesting 3'UTR as a preferential target site like that of miRNA targets. Thus, we hypothesize that our findings on additional key features of piRNA target sites might be valuable in identifying the potential targets of piRNA accurately, which will aid in decrypting their functional importance. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Garima Singh
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| |
Collapse
|
29
|
Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021; 163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-Wide Association Studies (GWAS) have elucidated the genetic components of Parkinson's Disease (PD). However, because the vast majority of GWAS association signals fall within non-coding regions, translating these results into an interpretable, mechanistic understanding of the disease etiology remains a major challenge in the field. In this review, we provide an overview of the approaches to prioritize putative causal variants and genes as well as summarise the primary findings of previous studies. We then discuss recent efforts to integrate multi-omics data to identify likely pathogenic cell types and biological pathways implicated in PD pathogenesis. We have compiled full summary statistics of cell-type, tissue, and phentoype enrichment analyses from multiple studies of PD GWAS and provided them in a standardized format as a resource for the research community (https://github.com/RajLabMSSM/PD_omics_review). Finally, we discuss the experimental, computational, and conceptual advances that will be necessary to fully elucidate the effects of functional variants and genes on cellular dysregulation and disease risk.
Collapse
Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; UK Dementia Research Institute at Imperial College London, London, United Kingdom.
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Sección Departamental de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| |
Collapse
|
30
|
Rey F, Pandini C, Messa L, Launi R, Barzaghini B, Zangaglia R, Raimondi MT, Gagliardi S, Cereda C, Zuccotti GV, Carelli S. α-Synuclein antisense transcript SNCA-AS1 regulates synapses- and aging-related genes suggesting its implication in Parkinson's disease. Aging Cell 2021; 20:e13504. [PMID: 34799977 PMCID: PMC8672788 DOI: 10.1111/acel.13504] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/26/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022] Open
Abstract
SNCA protein product, α‐synuclein, is widely renowned for its role in synaptogenesis and implication in both aging and Parkinson's disease (PD), but research efforts are still needed to elucidate its physiological functions and mechanisms of regulation. In this work, we aim to characterize SNCA‐AS1, antisense transcript to the SNCA gene, and its implications in cellular processes. The overexpression of SNCA‐AS1 upregulates both SNCA and α‐synuclein and, through RNA‐sequencing analysis, we investigated the transcriptomic changes of which both genes are responsible. We highlight how they impact neurites' extension and synapses' biology, through specific molecular signatures. We report a reduced expression of markers associated with synaptic plasticity, and we specifically focus on GABAergic and dopaminergic synapses, for their relevance in aging processes and PD, respectively. A reduction in SNCA‐AS1 expression leads to the opposite effect. As part of this signature is co‐regulated by the two genes, we discriminate between functions elicited by genes specifically altered by SNCA‐AS1 or SNCA's overexpression, observing a relevant role for SNCA‐AS1 in synaptogenesis through a shared molecular signature with SNCA. We also highlight how numerous deregulated pathways are implicated in aging‐related processes, suggesting that SNCA‐AS1 could be a key player in cellular senescence, with implications for aging‐related diseases. Indeed, the upregulation of SNCA‐AS1 leads to alterations in numerous PD‐specific genes, with an impact highly comparable to that of SNCA's upregulation. Our results show that SNCA‐AS1 elicits its cellular functions through the regulation of SNCA, with a specific modulation of synaptogenesis and senescence, presenting implications in PD.
Collapse
Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco" University of Milan Milan Italy
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi” University of Milan Milan Italy
| | - Cecilia Pandini
- Genomic and post‐Genomic Center IRCCS Mondino Foundation Pavia Italy
- Department of Biology and Biotechnology “L. Spallanzani” University of Pavia Pavia Italy
| | - Letizia Messa
- Department of Chemistry, Materials and Chemical Engineering Politecnico di Milano Milan Italy
| | - Rossella Launi
- Department of Biomedical and Clinical Sciences "L. Sacco" University of Milan Milan Italy
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi” University of Milan Milan Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering Politecnico di Milano Milan Italy
| | - Roberta Zangaglia
- Parkinson's Disease and Movement Disorders Unit IRCCS Mondino Foundation Pavia Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering Politecnico di Milano Milan Italy
| | - Stella Gagliardi
- Genomic and post‐Genomic Center IRCCS Mondino Foundation Pavia Italy
| | - Cristina Cereda
- Genomic and post‐Genomic Center IRCCS Mondino Foundation Pavia Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco" University of Milan Milan Italy
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi” University of Milan Milan Italy
- Department of Pediatrics Children's Hospital "V. Buzzi" Milan Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco" University of Milan Milan Italy
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi” University of Milan Milan Italy
| |
Collapse
|
31
|
Kuo MC, Liu SCH, Hsu YF, Wu RM. The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways. J Biomed Sci 2021; 28:78. [PMID: 34794432 PMCID: PMC8603508 DOI: 10.1186/s12929-021-00775-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.
Collapse
Affiliation(s)
- Ming-Che Kuo
- Department of Medicine, Section of Neurology, Cancer Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sam Chi-Hao Liu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
32
|
Fonseca Cabral G, Schaan AP, Cavalcante GC, Sena-dos-Santos C, de Souza TP, Souza Port’s NM, dos Santos Pinheiro JA, Ribeiro-dos-Santos Â, Vidal AF. Nuclear and Mitochondrial Genome, Epigenome and Gut Microbiome: Emerging Molecular Biomarkers for Parkinson's Disease. Int J Mol Sci 2021; 22:9839. [PMID: 34576000 PMCID: PMC8471599 DOI: 10.3390/ijms22189839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is currently the second most common neurodegenerative disorder, burdening about 10 million elderly individuals worldwide. The multifactorial nature of PD poses a difficult obstacle for understanding the mechanisms involved in its onset and progression. Currently, diagnosis depends on the appearance of clinical signs, some of which are shared among various neurologic disorders, hindering early diagnosis. There are no effective tools to prevent PD onset, detect the disease in early stages or accurately report the risk of disease progression. Hence, there is an increasing demand for biomarkers that may identify disease onset and progression, as treatment-based medicine may not be the best approach for PD. Over the last few decades, the search for molecular markers to predict susceptibility, aid in accurate diagnosis and evaluate the progress of PD have intensified, but strategies aimed to improve individualized patient care have not yet been established. CONCLUSIONS Genomic variation, regulation by epigenomic mechanisms, as well as the influence of the host gut microbiome seem to have a crucial role in the onset and progress of PD, thus are considered potential biomarkers. As such, the human nuclear and mitochondrial genome, epigenome, and the host gut microbiome might be the key elements to the rise of personalized medicine for PD patients.
Collapse
Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ana Paula Schaan
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Giovanna C. Cavalcante
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Natacha M. Souza Port’s
- Laboratório de Neurofarmacologia Molecular, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará–R. dos Mundurucus, Belém 66073-000, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
| | - Amanda F. Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
- ITVDS—Instituto Tecnológico Vale Desenvolvimento Sustentável–R. Boaventura da Silva, Belém 66055-090, Brazil
| |
Collapse
|
33
|
Chen Z, Rasheed M, Deng Y. The epigenetic mechanisms involved in mitochondrial dysfunction: Implication for Parkinson's disease. Brain Pathol 2021; 32:e13012. [PMID: 34414627 PMCID: PMC9048811 DOI: 10.1111/bpa.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is one of the crucial factors involved in PD’s pathogenicity, which emerges from a combination of genetic and environmental factors. These factors cause differential molecular expression in neurons, such as varied transcriptional regulation of genes, elevated oxidative stress, α‐synuclein aggregation and endogenous neurotoxins release, which induces epigenetic modifications and triggers energy crisis by damaging mitochondria of the dopaminergic neurons (DN). So far, these events establish a complicated relationship with underlying mechanisms of mitochondrial anomalies in PD, which has remained unclear for years and made PD diagnosis and treatment extremely difficult. Therefore, in this review, we endeavored to discuss the complex association of epigenetic modifications and other associated vital factors in mitochondrial dysfunction. We propose a hypothesis that describes a vicious cycle in which mitochondrial dysfunction and oxidative stress act as a hub for regulating DA neuron's fate in PD. Oxidative stress triggers the release of endogenous neurotoxins (CTIQs) that lead to mitochondrial dysfunction along with abnormal α‐synuclein aggregation and epigenetic modifications. These disturbances further intensify oxidative stress and mitochondrial damage, amplifying the synthesis of CTIQs and works vice versa. This vicious cycle may result in the degeneration of DN to hallmark Parkinsonism. Furthermore, we have also highlighted various endogenous compounds and epigenetic marks (neurotoxic and neuroprotective), which may help for devising future diagnostic biomarkers and target specific drugs using novel PD management strategies.
Collapse
Affiliation(s)
- Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Madiha Rasheed
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, China
| |
Collapse
|
34
|
Trudler D, Ghatak S, Lipton SA. Emerging hiPSC Models for Drug Discovery in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:8196. [PMID: 34360966 PMCID: PMC8347370 DOI: 10.3390/ijms22158196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases affect millions of people worldwide and are characterized by the chronic and progressive deterioration of neural function. Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and Huntington's disease (HD), represent a huge social and economic burden due to increasing prevalence in our aging society, severity of symptoms, and lack of effective disease-modifying therapies. This lack of effective treatments is partly due to a lack of reliable models. Modeling neurodegenerative diseases is difficult because of poor access to human samples (restricted in general to postmortem tissue) and limited knowledge of disease mechanisms in a human context. Animal models play an instrumental role in understanding these diseases but fail to comprehensively represent the full extent of disease due to critical differences between humans and other mammals. The advent of human-induced pluripotent stem cell (hiPSC) technology presents an advantageous system that complements animal models of neurodegenerative diseases. Coupled with advances in gene-editing technologies, hiPSC-derived neural cells from patients and healthy donors now allow disease modeling using human samples that can be used for drug discovery.
Collapse
Affiliation(s)
- Dorit Trudler
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (D.T.); (S.G.)
| | - Swagata Ghatak
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (D.T.); (S.G.)
| | - Stuart A. Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (D.T.); (S.G.)
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| |
Collapse
|
35
|
Renner H, Becker KJ, Kagermeier TE, Grabos M, Eliat F, Günther P, Schöler HR, Bruder JM. Cell-Type-Specific High Throughput Toxicity Testing in Human Midbrain Organoids. Front Mol Neurosci 2021; 14:715054. [PMID: 34335182 PMCID: PMC8321240 DOI: 10.3389/fnmol.2021.715054] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Toxicity testing is a crucial step in the development and approval of chemical compounds for human contact and consumption. However, existing model systems often fall short in their prediction of human toxicity in vivo because they may not sufficiently recapitulate human physiology. The complexity of three-dimensional (3D) human organ-like cell culture systems ("organoids") can generate potentially more relevant models of human physiology and disease, including toxicity predictions. However, so far, the inherent biological heterogeneity and cumbersome generation and analysis of organoids has rendered efficient, unbiased, high throughput evaluation of toxic effects in these systems challenging. Recent advances in both standardization and quantitative fluorescent imaging enabled us to dissect the toxicities of compound exposure to separate cellular subpopulations within human organoids at the single-cell level in a framework that is compatible with high throughput approaches. Screening a library of 84 compounds in standardized human automated midbrain organoids (AMOs) generated from two independent cell lines correctly recognized known nigrostriatal toxicants. This approach further identified the flame retardant 3,3',5,5'-tetrabromobisphenol A (TBBPA) as a selective toxicant for dopaminergic neurons in the context of human midbrain-like tissues for the first time. Results were verified with high reproducibility in more detailed dose-response experiments. Further, we demonstrate higher sensitivity in 3D AMOs than in 2D cultures to the known neurotoxic effects of the pesticide lindane. Overall, the automated nature of our workflow is freely scalable and demonstrates the feasibility of quantitatively assessing cell-type-specific toxicity in human organoids in vitro.
Collapse
Affiliation(s)
- Henrik Renner
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Katharina J Becker
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Theresa E Kagermeier
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Martha Grabos
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Farsam Eliat
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Patrick Günther
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hans R Schöler
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jan M Bruder
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| |
Collapse
|
36
|
Chavda V, Madhwani K, Chaurasia B. PiWi RNA in Neurodevelopment and Neurodegenerative disorders. Curr Mol Pharmacol 2021; 15:517-531. [PMID: 34212832 DOI: 10.2174/1874467214666210629164535] [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: 01/21/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 11/22/2022]
Abstract
Shedding light on the mysterious dark matter of the genome gears up the knowledge of modern biology. Beyond the genome, epigenome layers an untraveled path of fundamental biological and functional roles of gene regulation. Extraordinary character- P element wimpy testis-induced (PiWi)-interacting RNA (piRNA) is a type of small non-coding RNA that serves as a defender that imposes genomic and cellular defense by silencing nucleic and structural invaders. PIWI proteins and piRNAs appear in both reproductive and somatic cells, though germ line richness is partially unraveled more as it was originally discovered. The foremost function is to suppress invasive DNA sequences, which move within genomic DNA referred to as transposon elements (TEs) and downstream target genes via Transcriptional gene silencing (TGS) and Post-translational gene silencing (PTGS). Germline piRNAs maintain genomic integrity, stability, sternness, and impact imprinting expression. Somatic tissue-specific piRNAs have been surprised by their novel roles. piRNA regulates neurodevelopmental processes in metazoans, including humans. Neural heterogeneity, neurogenesis, neural plasticity, and transgenerational inheritance of adaptive and long-term memory are governed by the PIWI pathway. Neuro-developmental, neurodegenerative or psychiatric illness are the outcome of dysregulated piRNA. Aberrant piRNA signature causes inappropriate switching on or off genes by activation of TEs, incorrect epigenetic tags on DNA, and or histones. Defective piRNA regulation leads to abnormal brain development and neurodegenerative etiology, promoting life-threatening disorders. Exemplification of exciting roles of piRNA is in infancy, so future investigation may expand on these observations using innovative techniques and launch them as impending biomarkers for diagnostics and therapeutics. In this current review, we have summarized the possible gene molecular role of piRNAs regulating neurobiology and contributing as uncharted biomarkers and therapeutic targets for life-threatening diseases.
Collapse
Affiliation(s)
- Vishal Chavda
- Department of Pharmacology, Nirma University, Ahmadabad, Gujarat, India
| | - Kajal Madhwani
- Department of Microbiology, Nirma University, Ahmadabad, Gujarat, India
| | | |
Collapse
|
37
|
Suster I, Feng Y. Multifaceted Regulation of MicroRNA Biogenesis: Essential Roles and Functional Integration in Neuronal and Glial Development. Int J Mol Sci 2021; 22:ijms22136765. [PMID: 34201807 PMCID: PMC8269442 DOI: 10.3390/ijms22136765] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that function as endogenous gene silencers. Soon after the discovery of miRNAs, a subset of brain-enriched and brain-specific miRNAs were identified and significant advancements were made in delineating miRNA function in brain development. However, understanding the molecular mechanisms that regulate miRNA biogenesis in normal and diseased brains has become a prevailing challenge. Besides transcriptional regulation of miRNA host genes, miRNA processing intermediates are subjected to multifaceted regulation by canonical miRNA processing enzymes, RNA binding proteins (RBPs) and epitranscriptomic modifications. Further still, miRNA activity can be regulated by the sponging activity of other non-coding RNA classes, namely circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs). Differential abundance of these factors in neuronal and glial lineages partly underlies the spatiotemporal expression and function of lineage-specific miRNAs. Here, we review the continuously evolving understanding of the regulation of neuronal and glial miRNA biogenesis at the transcriptional and posttranscriptional levels and the cooperativity of miRNA species in targeting key mRNAs to drive lineage-specific development. In addition, we review dysregulation of neuronal and glial miRNAs and the detrimental impacts which contribute to developmental brain disorders.
Collapse
Affiliation(s)
| | - Yue Feng
- Correspondence: ; Tel.: +1-404-727-0351
| |
Collapse
|
38
|
Strafella C, Caputo V, Termine A, Assogna F, Pellicano C, Pontieri FE, Macchiusi L, Minozzi G, Gambardella S, Centonze D, Bossù P, Spalletta G, Caltagirone C, Giardina E, Cascella R. Immune System and Neuroinflammation in Idiopathic Parkinson's Disease: Association Analysis of Genetic Variants and miRNAs Interactions. Front Genet 2021; 12:651971. [PMID: 34149802 PMCID: PMC8209518 DOI: 10.3389/fgene.2021.651971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
The present study investigated the association of SNPs involved in the regulation of immune response, cellular degenerative and neuroinflammatory pathways with the susceptibility and progression of idiopathic Parkinson's Disease (PD). In particular, 342 PD patients were subjected to a genotyping analysis of a panel of 120 SNPs by Open Array Technology. As control group, 503 samples representative of the European general population were utilized. The genetic analysis identified 26 SNPs associated with PD susceptibility. Of them, 12 SNPs were described as significant expression Quantitative Loci (eQTL) variants in different brain regions associated with motor and non-motor PD phenomenology. Moreover, the study highlighted 11 novel susceptibility genes for PD, which may alter multiple signaling pathways critically involved in peripheral immune response, neuroinflammation, neurodegeneration and dopaminergic neurons wiring. The study of miRNA-target genes highlighted a possible role of miR-499a, miR-196a2, and miR-29a in the modulation of multiple neuroinflammatory and neurodegenerative mechanisms underlying PD physiopathology. The study described a network of interconnected genes (APOE, CLU, IL6, IL7R, IL12B, INPP5D, MAPK1, MEF2C, MIF, and TNFSF14), which may act as upstream regulators in the modulation of biological pathways relevant to PD. Intriguingly, IL6 stands out as a master gene regulator since it may indirectly regulate the network of interconnected genes. The study highlighted different genes and miRNAs interactions potentially involved in PD physiopathology, which are worth to be further explored to improve the knowledge of disease and the research of novel treatments strategies.
Collapse
Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Andrea Termine
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Francesca Assogna
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Clelia Pellicano
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Francesco E. Pontieri
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Neuroscience, Mental Health and Sensory Organs, “Sapienza” Università di Roma, Rome, Italy
| | - Lucia Macchiusi
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulietta Minozzi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Stefano Gambardella
- Neuromed Institute IRCCS, Pozzilli, Italy
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino, Italy
| | | | - Paola Bossù
- Laboratory of Experimental Neuropsychobiology, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| |
Collapse
|
39
|
Rasheed M, Liang J, Wang C, Deng Y, Chen Z. Epigenetic Regulation of Neuroinflammation in Parkinson's Disease. Int J Mol Sci 2021; 22:4956. [PMID: 34066949 PMCID: PMC8125491 DOI: 10.3390/ijms22094956] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Neuroinflammation is one of the most significant factors involved in the initiation and progression of Parkinson's disease. PD is a neurodegenerative disorder with a motor disability linked with various complex and diversified risk factors. These factors trigger myriads of cellular and molecular processes, such as misfolding defective proteins, oxidative stress, mitochondrial dysfunction, and neurotoxic substances that induce selective neurodegeneration of dopamine neurons. This neuronal damage activates the neuronal immune system, including glial cells and inflammatory cytokines, to trigger neuroinflammation. The transition of acute to chronic neuroinflammation enhances the susceptibility of inflammation-induced dopaminergic neuron damage, forming a vicious cycle and prompting an individual to PD development. Epigenetic mechanisms recently have been at the forefront of the regulation of neuroinflammatory factors in PD, proposing a new dawn for breaking this vicious cycle. This review examined the core epigenetic mechanisms involved in the activation and phenotypic transformation of glial cells mediated neuroinflammation in PD. We found that epigenetic mechanisms do not work independently, despite being coordinated with each other to activate neuroinflammatory pathways. In this regard, we attempted to find the synergic correlation and contribution of these epigenetic modifications with various neuroinflammatory pathways to broaden the canvas of underlying pathological mechanisms involved in PD development. Moreover, this study highlighted the dual characteristics (neuroprotective/neurotoxic) of these epigenetic marks, which may counteract PD pathogenesis and make them potential candidates for devising future PD diagnosis and treatment.
Collapse
Affiliation(s)
| | | | | | | | - Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (J.L.); (C.W.); (Y.D.)
| |
Collapse
|
40
|
Huang X, Wong G. An old weapon with a new function: PIWI-interacting RNAs in neurodegenerative diseases. Transl Neurodegener 2021; 10:9. [PMID: 33685517 PMCID: PMC7938595 DOI: 10.1186/s40035-021-00233-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding transcripts that are highly conserved across species and regulate gene expression through pre- and post-transcriptional processes. piRNAs were originally discovered in germline cells and protect against transposable element expression to promote and maintain genome stability. In the recent decade, emerging roles of piRNAs have been revealed, including the roles in sterility, tumorigenesis, metabolic homeostasis, neurodevelopment, and neurodegenerative diseases. In this review, we summarize piRNA biogenesis in C. elegans, Drosophila, and mice, and further elaborate upon how piRNAs mitigate the harmful effects of transposons. Lastly, the most recent findings on piRNA participation in neurological diseases are highlighted. We speculate on the mechanisms of piRNA action in the development and progression of neurodegenerative diseases. Understanding the roles of piRNAs in neurological diseases may facilitate their applications in diagnostic and therapeutic practice.
Collapse
Affiliation(s)
- Xiaobing Huang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China
| | - Garry Wong
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China.
| |
Collapse
|
41
|
Shen L, Wang C, Chen L, Wong G. Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson's Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1. Front Neurosci 2021; 15:600462. [PMID: 33762903 PMCID: PMC7982545 DOI: 10.3389/fnins.2021.600462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) regulate gene expression and biological processes through specific genetic and epigenetic mechanisms. Recent studies have described a dysregulation of small non-coding RNAs in Parkinson’s disease (PD) tissues but have been limited in scope. Here, we extend these studies by comparing the dysregulation of both miRNAs and piRNAs from transgenic Caenorhabditis elegans (C. elegans) nematodes overexpressing pan-neuronally human α-synuclein wild-type (WT) (HASNWT OX) or mutant (HASNA53T OX). We observed 32 miRNAs and 112 piRNAs dysregulated in HASNA53T OX compared with WT. Genetic crosses of HASNA53T OX PD animal models with tdp-1 null mutants, the C. elegans ortholog of TDP-43, an RNA-binding protein aggregated in frontal temporal lobar degeneration, improved their behavioral deficits and changed the number of dysregulated miRNAs to 11 and piRNAs to none. Neuronal function-related genes T28F4.5, C34F6.1, C05C10.3, camt-1, and F54D10.3 were predicted to be targeted by cel-miR-1018, cel-miR-355-5p (C34F6.1 and C05C10.3), cel-miR-800-3p, and 21ur-1581 accordingly. This study provides a molecular landscape of small non-coding RNA dysregulation in an animal model that provides insight into the epigenetic changes, molecular processes, and interactions that occur during PD-associated neurodegenerative disorders.
Collapse
Affiliation(s)
- Linjing Shen
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Changliang Wang
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, China.,Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University, Shantou, China
| | - Garry Wong
- Centre for Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| |
Collapse
|
42
|
Dubois C, Kong G, Tran H, Li S, Pang TY, Hannan AJ, Renoir T. Small Non-coding RNAs Are Dysregulated in Huntington's Disease Transgenic Mice Independently of the Therapeutic Effects of an Environmental Intervention. Mol Neurobiol 2021; 58:3308-3318. [PMID: 33675499 DOI: 10.1007/s12035-021-02342-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide repeat expansion in the huntingtin gene. Transcriptomic dysregulations are well-documented in HD and alterations in small non-coding RNAs (sncRNAs), particularly microRNAs (miRNAs), could underpin that phenomenon. Additionally, environmental enrichment (EE), which is used to model a stimulating lifestyle in pre-clinical research, has been shown to ameliorate HD-related symptoms. However, the mechanisms mediating the therapeutic effects of EE remain largely unknown. This study assessed the effect of EE on sncRNA expression in the striatum of female R6/1 transgenic HD mice at 12 weeks (prior to over motor deficits) and 20 weeks (fully symptomatic) of age. When comparing wild-type and R6/1 mice in the standard housing condition, we found 6 and 64 miRNAs that were differentially expressed at 12 and 20 weeks of age, respectively. The 6 miRNAs (miR-132, miR-212, miR-222, miR-1a, miR-467a, and miR-669c) were commonly dysregulated at both time points. Additionally, genotype had minor effects on the levels of other sncRNAs, in particular, 1 piRNA was dysregulated at 12 weeks of age, and at 20 weeks of age 11 piRNAs, 1 tRNA- and 2 snoRNA-derived fragments were altered in HD mice. No difference in the abundance of other sncRNA subtypes, including rRNA- and snRNA- derived fragments, were observed. While EE improved locomotor symptoms in HD, we found no effect of the housing condition on any of the sncRNA populations examined. Our findings show that HD mainly affects miRNAs and has a minor effect on other sncRNA populations. Furthermore, the therapeutic effects of EE are not associated with the rescue of these dysregulated sncRNAs and may therefore exert these experience-dependent effects via other molecular mechanisms.
Collapse
Affiliation(s)
- Celine Dubois
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia
| | - Geraldine Kong
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia
| | - Harvey Tran
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia
| | - Shanshan Li
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia
| | - Terence Y Pang
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia.
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Thibault Renoir
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne Brain Centre, Parkville, VIC, 3010, Australia.
| |
Collapse
|
43
|
Ning L, Cui T, Zheng B, Wang N, Luo J, Yang B, Du M, Cheng J, Dou Y, Wang D. MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. Nucleic Acids Res 2021; 49:D160-D164. [PMID: 32833025 PMCID: PMC7779040 DOI: 10.1093/nar/gkaa707] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA-disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA-disease resources has become essential. Here, we have updated the mammal ncRNA-disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA-disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA-disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA-disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
Collapse
Affiliation(s)
- Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Boyang Zheng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Nuo Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Beilei Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Mengze Du
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guangdong Province, People's Republic of China
| | - Jun Cheng
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital)
| | - Yiying Dou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| |
Collapse
|
44
|
Logotheti S, Marquardt S, Richter C, Sophie Hain R, Murr N, Takan I, Pavlopoulou A, Pützer BM. Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. Cancers (Basel) 2020; 12:cancers12123789. [PMID: 33339112 PMCID: PMC7765507 DOI: 10.3390/cancers12123789] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Cancer is initiated by alterations in specific genes. However, at late stages, cancer cells become metastatic not necessarily through continuous accumulation of additional mutations, but by hijacking programs of normal embryonic development and reactivating them in an unusual place, at the wrong time. Here, we applied computational and experimental approaches to show that these malignant reactivations include genes that are crucial for the development and function of the nervous system. We use the paradigm of melanoma transition from less invasive to highly aggressive stages in order to show that major players of metastasis, such as TP73 gene products, are implicated in this process. This work provides evidence for interactions between cancer cells and the neuronal system, which may have important future implications for metastasis prevention and cancer management. Abstract Mechanisms governing tumor progression differ from those of initiation. One enigmatic prometastatic process is the recapitulation of pathways of neural plasticity in aggressive stages. Cancer and neuronal cells develop reciprocal interactions via mutual production and secretion of neuronal growth factors, neurothrophins and/or axon guidance molecules in the tumor microenvironment. Understanding cancer types where this process is active, as well as the drivers, markers and underlying mechanisms, has great significance for blocking tumor progression and improving patient survival. By applying computational and systemic approaches, in combination with experimental validations, we provide compelling evidence that genes involved in neuronal development, differentiation and function are reactivated in tumors and predict poor patient outcomes across various cancers. Across cancers, they co-opt genes essential for the development of distinct anatomical parts of the nervous system, with a frequent preference for cerebral cortex and neural crest-derived enteric nerves. Additionally, we show that p73, a transcription factor with a dual role in neuronal development and cancer, simultaneously induces neurodifferentiation and stemness markers during melanoma progression. Our data yield the basis for elucidating driving forces of the nerve–tumor cell crosstalk and highlight p73 as a promising regulator of cancer neurobiology.
Collapse
Affiliation(s)
- Stella Logotheti
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
- Correspondence: (S.L.); (B.M.P.); Tel.: +49-381-494-5066/68 (B.M.P.)
| | - Stephan Marquardt
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
| | - Christin Richter
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
| | - Renée Sophie Hain
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
| | - Nico Murr
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
| | - Işıl Takan
- Izmir Biomedicine and Genome Center (IBG), 35340 Balcova, Izmir, Turkey; (I.T.); (A.P.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balcova, Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center (IBG), 35340 Balcova, Izmir, Turkey; (I.T.); (A.P.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balcova, Izmir, Turkey
| | - Brigitte M. Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany; (S.M.); (C.R.); (R.S.H.); (N.M.)
- Department Life, Light & Matter, University of Rostock, 18059 Rostock, Germany
- Correspondence: (S.L.); (B.M.P.); Tel.: +49-381-494-5066/68 (B.M.P.)
| |
Collapse
|
45
|
Tafani X, Pascale E, Fattapposta F, Pucci M, D'Addario C, Adriani W. Cross-correlations between motifs in the 5'-UTR of DAT1 gene: Findings from Parkinson's disease. Adv Biol Regul 2020; 78:100753. [PMID: 33022465 DOI: 10.1016/j.jbior.2020.100753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Parkinson's disease (PD) is a neuro-degenerative disorder affecting the striatal motor system, caused by the loss of neuronal cells in the mid-brain, where reduced amounts of dopamine do cause involuntary movements and others symptoms. Alterations of methylome have been reported in PD epigenomic studies, and also human dopamine transporter gene (DAT1, SLC6A3) is considered as a candidate risk factor for PD. Since the DNA methylation on DAT promoter may well have a role in the development of this disease, we aimed to further assess the epigenetic control, by focusing on specific CpG sites located in the 5'-untranslated region (5'-UTR) of the DAT1 gene. Significant changes in DAT 5'-UTR methylation were already found in peripheral blood mononuclear cells (PBMCs) of PD subjects (Rubino et al., 2020). Of note, methylation values at the CpG 5 were increased. We run on same data a novel statistical approach: cross-correlation between pairs of loci. CpG 5 was the only always-differing variable but, alternatively, CpGs 2 and 6 or CpGs 1 and 3 were also significantly correlated with CpG 5. Interestingly, this picture emerged for those patients whose M2xM6 index was above-median; loci were rather independent for below-median patients. Present data may shed light into dynamics occurring at 5'-UTR of DAT1, a gene involved in PD but also in many psycho-physiological pathologies.
Collapse
Affiliation(s)
- Xhensina Tafani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Esterina Pascale
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
| | | | - Mariangela Pucci
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Claudio D'Addario
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Walter Adriani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy; Reference Center for Behavioral Science and Mental Health - Istituto Superiore di Sanità, Rome, Italy.
| |
Collapse
|
46
|
Low Levels of LRRK2 Gene Expression are Associated with LRRK2 SNPs and Contribute to Parkinson's Disease Progression. Neuromolecular Med 2020; 23:292-304. [PMID: 33015738 DOI: 10.1007/s12017-020-08619-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
Parkinson's disease (PD) is a chronic neurodegenerative disease that has relatively slow progression with motor symptoms. Leucine-rich repeat kinase 2 (LRRK2) gene mutations and polymorphisms are suggested to be associated with PD. In this study, we aimed to investigate the association between single-nucleotide polymorphisms (SNPs) of the LRRK2 gene, namely, rs11176013, rs10878371, rs11835105, and PD. Genotypes of 132 PD cases and 133 healthy individuals were determined by qRT-PCR. Haplotype analysis was performed. Additionally, LRRK2 mRNA expression levels were determined in 83 PD cases and 55 healthy subjects. The relationship between LRRK2 mRNA levels, the target SNPs, and clinical data was also investigated. Our results indicated that the "GG" genotype and "G" allele of rs11176013 and the "CC" genotype and "C" allele of rs10878371 were more frequent in cases. The "GCG" haplotype was significantly more frequent in cases. LRRK2 mRNA expression levels in patients were significantly lower than those in healthy individuals. The patients with the "CC" genotype for rs10878371 and the "GG" genotype for rs11176013 had decreased LRRK2 mRNA levels. We found that the rs11176013 "GG" genotype and the rs10878371 "CC" genotype were less frequently seen in cases with akinetic rigid or combined akinetic rigid and tremor-dominant initial symptoms. Consequently, our results demonstrate that the rs11176013 and rs10878371 polymorphisms are associated with PD in a Turkish cohort, and moreover, these results suggest that these polymorphisms may affect the expression of the LRRK2 gene and disease progression and thus play a role in the pathogenesis of PD.
Collapse
|
47
|
Piwi-interacting RNAs (piRNAs) as potential biomarkers and therapeutic targets for cardiovascular diseases. Angiogenesis 2020; 24:19-34. [PMID: 33011960 DOI: 10.1007/s10456-020-09750-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/09/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading causes of death worldwide. Increasing reports demonstrated that non-coding RNAs (ncRNAs) have been crucially involved in the development of CVDs. Piwi-interacting RNAs (piRNAs) are a novel cluster of small non-coding RNAs with strong uracil bias at the 5' end and 2'-O-methylation at the 3' end that are mainly present in the mammalian reproductive system and stem cells and serve as potential modulators of developmental and pathophysiological processes. Recently, piRNAs have been reported to be widely expressed in human tissues and can potentially regulate various diseases. Specifically, concomitant with the development of next-generation sequencing techniques, piRNAs have been found to be differentially expressed in CVDs, indicating their potential involvement in the occurrence and progression of heart diseases. However, the molecular mechanisms and signaling pathways involved with piRNA function have not been fully elucidated. In this review, we present the current understanding of the piRNAs from the perspectives of biogenesis, characteristics, biological function, and regulatory mechanisms, and highlight their potential roles and underlying mechanisms in CVDs, which will provide new insights into the potential applications of piRNAs in the clinical diagnosis, prognosis, and therapeutic strategies for heart diseases.
Collapse
|
48
|
Kelm-Nelson CA, Gammie S. Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats. BMC Genomics 2020; 21:625. [PMID: 32942992 PMCID: PMC7495669 DOI: 10.1186/s12864-020-07037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and quality of life issues and are present in 90% of PD patients; yet the underlying pathology mediating these significant voice deficits is unknown. The Pink1−/− rat is a valid model of early-onset PD that presents with analogous vocal communication deficits. Previous work shows abnormal α-synuclein protein aggregation in the periaqueductal gray (PAG), a brain region critical and necessary to the modulation of mammalian vocal behavior. In this study, we used high-throughput RNA sequencing to examine gene expression within the PAG of both male and female Pink1−/− rats as compared to age-matched wildtype controls. We used a bioinformatic approach to (1) test the hypothesis that loss of Pink1 in the PAG will influence the differential expression of genes that interact with Pink1, (2) highlight other key genes that relate to this type of Mendelian PD, and (3) catalog molecular targets that may be important for the production of rat vocalizations. Results Knockout of the Pink1 gene resulted in differentially expressed genes for both male and female rats that also mapped to human PD datasets. Pathway analysis highlighted several significant metabolic pathways. Weighted gene co-expression network analysis (WGCNA) was used to identify gene nodes and their interactions in (A) males, (B) females, and (C) combined-sexes datasets. For each analysis, within the module containing the Pink1 gene, Pink1 itself was the central node with the highest number of interactions with other genes including solute carriers, glutamate metabotropic receptors, and genes associated with protein localization. Strong connections between Pink1 and Krt2 and Hfe were found in both males and female datasets. In females a number of modules were significantly correlated with vocalization traits. Conclusions Overall, this work supports the premise that gene expression changes in the PAG may contribute to the vocal deficits observed in this PD rat model. Additionally, this dataset identifies genes that represent new therapeutic targets for PD voice disorders.
Collapse
Affiliation(s)
- Cynthia A Kelm-Nelson
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of Wisconsin-Madison, 1300 University Avenue, 483 Medical Sciences Center, Madison, WI, 53706, USA.
| | - Stephen Gammie
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
49
|
Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen‐Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. EMBO Mol Med 2020; 12:e11942. [PMID: 32715657 PMCID: PMC7507321 DOI: 10.15252/emmm.201911942] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are brain-abundant RNAs of mostly unknown functions. To seek their roles in Parkinson's disease (PD), we generated an RNA sequencing resource of several brain region tissues from dozens of PD and control donors. In the healthy substantia nigra (SN), circRNAs accumulate in an age-dependent manner, but in the PD SN this correlation is lost and the total number of circRNAs reduced. In contrast, the levels of circRNAs are increased in the other studied brain regions of PD patients. We also found circSLC8A1 to increase in the SN of PD individuals. CircSLC8A1 carries 7 binding sites for miR-128 and is strongly bound to the microRNA effector protein Ago2. Indeed, RNA targets of miR-128 are also increased in PD individuals, suggesting that circSLC8A1 regulates miR-128 function and/or activity. CircSLC8A1 levels also increased in cultured cells exposed to the oxidative stress-inducing agent paraquat but were decreased in cells treated with the neuroprotective antioxidant regulator drug Simvastatin. Together, our work links circSLC8A1 to oxidative stress-related Parkinsonism and suggests further exploration of its molecular function in PD.
Collapse
Affiliation(s)
- Mor Hanan
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Alon Simchovitz
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Nadav Yayon
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Shani Vaknine
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Roni Cohen‐Fultheim
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Miriam Karmon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Nimrod Madrer
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Talia Miriam Rohrlich
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Moria Maman
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Estelle R Bennett
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - David S Greenberg
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Hermona Soreq
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Sebastian Kadener
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Biology DepartmentBrandeis UniversityWalthamMAUSA
| |
Collapse
|
50
|
Acharya S, Salgado-Somoza A, Stefanizzi FM, Lumley AI, Zhang L, Glaab E, May P, Devaux Y. Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease. Int J Mol Sci 2020; 21:E6513. [PMID: 32899928 PMCID: PMC7555192 DOI: 10.3390/ijms21186513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD) is a complex and heterogeneous disorder involving multiple genetic and environmental influences. Although a wide range of PD risk factors and clinical markers for the symptomatic motor stage of the disease have been identified, there are still no reliable biomarkers available for the early pre-motor phase of PD and for predicting disease progression. High-throughput RNA-based biomarker profiling and modeling may provide a means to exploit the joint information content from a multitude of markers to derive diagnostic and prognostic signatures. In the field of PD biomarker research, currently, no clinically validated RNA-based biomarker models are available, but previous studies reported several significantly disease-associated changes in RNA abundances and activities in multiple human tissues and body fluids. Here, we review the current knowledge of the regulation and function of non-coding RNAs in PD, focusing on microRNAs, long non-coding RNAs, and circular RNAs. Since there is growing evidence for functional interactions between the heart and the brain, we discuss the benefits of studying the role of non-coding RNAs in organ interactions when deciphering the complex regulatory networks involved in PD progression. We finally review important concepts of harmonization and curation of high throughput datasets, and we discuss the potential of systems biomedicine to derive and evaluate RNA biomarker signatures from high-throughput expression data.
Collapse
Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Andrew I. Lumley
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| |
Collapse
|