Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data
Background: Fibrolamellar carcinoma (FLC) is a rare type of liver cancer that primarily affects adolescents and young adults without prior liver disease or viral infections. Patients with FLC generally have non-specific symptoms, are often diagnosed at a later stage, and experience a higher frequenc...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-08-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/14/9/1709 |
| _version_ | 1797579967213600768 |
|---|---|
| author | Janghyun Kim Young Kim Bora Lee |
| author_facet | Janghyun Kim Young Kim Bora Lee |
| author_sort | Janghyun Kim |
| collection | DOAJ |
| description | Background: Fibrolamellar carcinoma (FLC) is a rare type of liver cancer that primarily affects adolescents and young adults without prior liver disease or viral infections. Patients with FLC generally have non-specific symptoms, are often diagnosed at a later stage, and experience a higher frequency of metastases compared to patients with other liver cancers. A fusion transcript of DNAJB1 and PRKACA, which can lead to increased activity of PKA and cellular proliferation, has been identified in all FLC patients, but the exact mechanism through which FLC develops remains unclear. In this study, we investigated common lncRNA profiles in various FLC samples using bioinformatics analyses. Methods: We analyzed differentially expressed (DE) lncRNAs from three RNA sequencing datasets. Using lncRNAs and DE mRNAs, we predicted potential lncRNA target genes and performed Gene Ontology (GO) and KEGG analyses with the DE lncRNA target genes. Moreover, we screened for small-molecule compounds that could act as therapeutic targets for FLC. Results: We identified 308 DE lncRNAs from the RNA sequencing datasets. In addition, we performed a trans-target prediction analysis and identified 454 co-expressed pairs in FLC. The GO analysis showed that the lncRNA-related up-regulated mRNAs were enriched in the regulation of protein kinase C signaling and cAMP catabolic processes, while lncRNA-related down-regulated mRNAs were enriched in steroid, retinol, cholesterol, and xenobiotic metabolic processes. The analysis of small-molecule compounds for FLC treatment identified vitexin, chlorthalidone, triamterene, and amiloride, among other compounds. Conclusions: We identified potential therapeutic targets for FLC, including lncRNA target genes as well as small-molecule compounds that could potentially be used as treatments. Our findings could contribute to furthering our understanding of FLC and providing potential avenues for diagnosis and treatment. |
| first_indexed | 2024-03-10T22:43:39Z |
| format | Article |
| id | doaj.art-ab9275627d97491398c38a5b060d153b |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T22:43:39Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-ab9275627d97491398c38a5b060d153b2023-11-19T10:52:36ZengMDPI AGGenes2073-44252023-08-01149170910.3390/genes14091709Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing DataJanghyun Kim0Young Kim1Bora Lee2Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of KoreaDepartment of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of KoreaDepartment of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of KoreaBackground: Fibrolamellar carcinoma (FLC) is a rare type of liver cancer that primarily affects adolescents and young adults without prior liver disease or viral infections. Patients with FLC generally have non-specific symptoms, are often diagnosed at a later stage, and experience a higher frequency of metastases compared to patients with other liver cancers. A fusion transcript of DNAJB1 and PRKACA, which can lead to increased activity of PKA and cellular proliferation, has been identified in all FLC patients, but the exact mechanism through which FLC develops remains unclear. In this study, we investigated common lncRNA profiles in various FLC samples using bioinformatics analyses. Methods: We analyzed differentially expressed (DE) lncRNAs from three RNA sequencing datasets. Using lncRNAs and DE mRNAs, we predicted potential lncRNA target genes and performed Gene Ontology (GO) and KEGG analyses with the DE lncRNA target genes. Moreover, we screened for small-molecule compounds that could act as therapeutic targets for FLC. Results: We identified 308 DE lncRNAs from the RNA sequencing datasets. In addition, we performed a trans-target prediction analysis and identified 454 co-expressed pairs in FLC. The GO analysis showed that the lncRNA-related up-regulated mRNAs were enriched in the regulation of protein kinase C signaling and cAMP catabolic processes, while lncRNA-related down-regulated mRNAs were enriched in steroid, retinol, cholesterol, and xenobiotic metabolic processes. The analysis of small-molecule compounds for FLC treatment identified vitexin, chlorthalidone, triamterene, and amiloride, among other compounds. Conclusions: We identified potential therapeutic targets for FLC, including lncRNA target genes as well as small-molecule compounds that could potentially be used as treatments. Our findings could contribute to furthering our understanding of FLC and providing potential avenues for diagnosis and treatment.https://www.mdpi.com/2073-4425/14/9/1709fibrolamellar carcinoma (FLC)long non-coding RNA (lncRNA)therapeutic targets |
| spellingShingle | Janghyun Kim Young Kim Bora Lee Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data Genes fibrolamellar carcinoma (FLC) long non-coding RNA (lncRNA) therapeutic targets |
| title | Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data |
| title_full | Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data |
| title_fullStr | Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data |
| title_full_unstemmed | Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data |
| title_short | Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data |
| title_sort | identification of long non coding rna profiles and potential therapeutic agents for fibrolamellar carcinoma based on rna sequencing data |
| topic | fibrolamellar carcinoma (FLC) long non-coding RNA (lncRNA) therapeutic targets |
| url | https://www.mdpi.com/2073-4425/14/9/1709 |
| work_keys_str_mv | AT janghyunkim identificationoflongnoncodingrnaprofilesandpotentialtherapeuticagentsforfibrolamellarcarcinomabasedonrnasequencingdata AT youngkim identificationoflongnoncodingrnaprofilesandpotentialtherapeuticagentsforfibrolamellarcarcinomabasedonrnasequencingdata AT boralee identificationoflongnoncodingrnaprofilesandpotentialtherapeuticagentsforfibrolamellarcarcinomabasedonrnasequencingdata |