Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study
Huntington’s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (<i>HTT</i>) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-09-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/9/1801 |
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| author | Nela Pragathi Sneha S. Akila Parvathy Dharshini Y.-h. Taguchi M. Michael Gromiha |
| author_facet | Nela Pragathi Sneha S. Akila Parvathy Dharshini Y.-h. Taguchi M. Michael Gromiha |
| author_sort | Nela Pragathi Sneha |
| collection | DOAJ |
| description | Huntington’s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (<i>HTT</i>) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD. |
| first_indexed | 2024-03-10T22:43:54Z |
| format | Article |
| id | doaj.art-f83d877ce28744cca020e77975dc0104 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T22:43:54Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-f83d877ce28744cca020e77975dc01042023-11-19T10:53:53ZengMDPI AGGenes2073-44252023-09-01149180110.3390/genes14091801Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome StudyNela Pragathi Sneha0S. Akila Parvathy Dharshini1Y.-h. Taguchi2M. Michael Gromiha3Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, IndiaDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, IndiaDepartment of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, JapanDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, IndiaHuntington’s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (<i>HTT</i>) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.https://www.mdpi.com/2073-4425/14/9/1801Huntington’s diseaseBrodmann area 4tissue-specific network analysisvariant effectfunction interaction network |
| spellingShingle | Nela Pragathi Sneha S. Akila Parvathy Dharshini Y.-h. Taguchi M. Michael Gromiha Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study Genes Huntington’s disease Brodmann area 4 tissue-specific network analysis variant effect function interaction network |
| title | Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study |
| title_full | Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study |
| title_fullStr | Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study |
| title_full_unstemmed | Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study |
| title_short | Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study |
| title_sort | investigating neuron degeneration in huntington s disease using rna seq based transcriptome study |
| topic | Huntington’s disease Brodmann area 4 tissue-specific network analysis variant effect function interaction network |
| url | https://www.mdpi.com/2073-4425/14/9/1801 |
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