Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models
Niemann–Pick disease type C (NPC) is an autosomal recessive disorder with progressive neurodegeneration. Although the causative genes were previously identified, NPC has unclear pathophysiological aspects, and patients with NPC present various symptoms and onset ages. However, various novel biomarke...
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MDPI AG
2023-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/21/15642 |
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| author | Keitaro Miyoshi Eiji Hishinuma Naomi Matsukawa Yoshitaka Shirasago Masahiro Watanabe Toshihiro Sato Yu Sato Masaki Kumondai Masafumi Kikuchi Seizo Koshiba Masayoshi Fukasawa Masamitsu Maekawa Nariyasu Mano |
| author_facet | Keitaro Miyoshi Eiji Hishinuma Naomi Matsukawa Yoshitaka Shirasago Masahiro Watanabe Toshihiro Sato Yu Sato Masaki Kumondai Masafumi Kikuchi Seizo Koshiba Masayoshi Fukasawa Masamitsu Maekawa Nariyasu Mano |
| author_sort | Keitaro Miyoshi |
| collection | DOAJ |
| description | Niemann–Pick disease type C (NPC) is an autosomal recessive disorder with progressive neurodegeneration. Although the causative genes were previously identified, NPC has unclear pathophysiological aspects, and patients with NPC present various symptoms and onset ages. However, various novel biomarkers and metabolic alterations have been investigated; at present, few comprehensive proteomic alterations have been reported in relation to NPC. In this study, we aimed to elucidate proteomic alterations in NPC and perform a global proteomics analysis for NPC model cells. First, we developed two NPC cell models by knocking out <i>NPC1</i> using CRISPR/Cas9 (KO1 and KO2). Second, we performed a label-free (LF) global proteomics analysis. Using the LF approach, more than 300 proteins, defined as differentially expressed proteins (DEPs), changed in the KO1 and/or KO2 cells, while the two models shared 35 DEPs. As a bioinformatics analysis, the construction of a protein–protein interaction (PPI) network and an enrichment analysis showed that common characteristic pathways such as ferroptosis and mitophagy were identified in the two model cells. There are few reports of the involvement of NPC in ferroptosis, and this study presents ferroptosis as an altered pathway in NPC. On the other hand, many other pathways and DEPs were previously suggested to be associated with NPC, supporting the link between the proteome analyzed here and NPC. Therapeutic research based on these results is expected in the future. |
| first_indexed | 2024-03-11T11:28:49Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T11:28:49Z |
| publishDate | 2023-10-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-88935e7d5eeb4ebf83154f9f1db2c8122023-11-10T15:04:44ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-10-0124211564210.3390/ijms242115642Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell ModelsKeitaro Miyoshi0Eiji Hishinuma1Naomi Matsukawa2Yoshitaka Shirasago3Masahiro Watanabe4Toshihiro Sato5Yu Sato6Masaki Kumondai7Masafumi Kikuchi8Seizo Koshiba9Masayoshi Fukasawa10Masamitsu Maekawa11Nariyasu Mano12Faculty of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanAdvanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai 980-8573, JapanTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai 980-8573, JapanDepartment of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, JapanGraduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanDepartment of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanDepartment of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanDepartment of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanFaculty of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanAdvanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai 980-8573, JapanDepartment of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, JapanFaculty of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanFaculty of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-Ku, Sendai 980-8574, JapanNiemann–Pick disease type C (NPC) is an autosomal recessive disorder with progressive neurodegeneration. Although the causative genes were previously identified, NPC has unclear pathophysiological aspects, and patients with NPC present various symptoms and onset ages. However, various novel biomarkers and metabolic alterations have been investigated; at present, few comprehensive proteomic alterations have been reported in relation to NPC. In this study, we aimed to elucidate proteomic alterations in NPC and perform a global proteomics analysis for NPC model cells. First, we developed two NPC cell models by knocking out <i>NPC1</i> using CRISPR/Cas9 (KO1 and KO2). Second, we performed a label-free (LF) global proteomics analysis. Using the LF approach, more than 300 proteins, defined as differentially expressed proteins (DEPs), changed in the KO1 and/or KO2 cells, while the two models shared 35 DEPs. As a bioinformatics analysis, the construction of a protein–protein interaction (PPI) network and an enrichment analysis showed that common characteristic pathways such as ferroptosis and mitophagy were identified in the two model cells. There are few reports of the involvement of NPC in ferroptosis, and this study presents ferroptosis as an altered pathway in NPC. On the other hand, many other pathways and DEPs were previously suggested to be associated with NPC, supporting the link between the proteome analyzed here and NPC. Therapeutic research based on these results is expected in the future.https://www.mdpi.com/1422-0067/24/21/15642Niemann–Pick disease type Cglobal proteomicsliquid chromatography–electrospray ionization tandem mass spectrometrymodel cellknock outenrichment pathway analysis |
| spellingShingle | Keitaro Miyoshi Eiji Hishinuma Naomi Matsukawa Yoshitaka Shirasago Masahiro Watanabe Toshihiro Sato Yu Sato Masaki Kumondai Masafumi Kikuchi Seizo Koshiba Masayoshi Fukasawa Masamitsu Maekawa Nariyasu Mano Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models International Journal of Molecular Sciences Niemann–Pick disease type C global proteomics liquid chromatography–electrospray ionization tandem mass spectrometry model cell knock out enrichment pathway analysis |
| title | Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models |
| title_full | Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models |
| title_fullStr | Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models |
| title_full_unstemmed | Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models |
| title_short | Global Proteomics for Identifying the Alteration Pathway of Niemann–Pick Disease Type C Using Hepatic Cell Models |
| title_sort | global proteomics for identifying the alteration pathway of niemann pick disease type c using hepatic cell models |
| topic | Niemann–Pick disease type C global proteomics liquid chromatography–electrospray ionization tandem mass spectrometry model cell knock out enrichment pathway analysis |
| url | https://www.mdpi.com/1422-0067/24/21/15642 |
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