Analysis of human brain tissue derived from DBS surgery
Abstract Background Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic a...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Translational Neurodegeneration |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40035-022-00297-y |
| _version_ | 1828378810696859648 |
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| author | Salla M. Kangas Jaakko Teppo Maija J. Lahtinen Anu Suoranta Bishwa Ghimire Pirkko Mattila Johanna Uusimaa Markku Varjosalo Jani Katisko Reetta Hinttala |
| author_facet | Salla M. Kangas Jaakko Teppo Maija J. Lahtinen Anu Suoranta Bishwa Ghimire Pirkko Mattila Johanna Uusimaa Markku Varjosalo Jani Katisko Reetta Hinttala |
| author_sort | Salla M. Kangas |
| collection | DOAJ |
| description | Abstract Background Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic and proteomic profiles. Therefore, fresh brain tissue samples from living patients represent a valuable resource of metabolically intact tissue. Implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. Here, we describe an improved approach to collecting brain tissues from surgical instruments used in implantation of DBS device for transcriptomics and proteomics analyses. Methods Samples were extracted from guide tubes and recording electrodes used in routine DBS implantation procedure to treat patients with Parkinson’s disease, genetic dystonia and tremor. RNA sequencing was performed in tissues extracted from the recording microelectrodes and liquid chromatography-mass spectrometry (LC-MS) performed in tissues from guide tubes. To assess the performance of the current approach, the obtained datasets were compared with previously published datasets representing brain tissues. Results Altogether, 32,034 RNA transcripts representing the unique Ensembl gene identifiers were detected from eight samples representing both hemispheres of four patients. By using LC-MS, we identified 734 unique proteins from 31 samples collected from 14 patients. The datasets are available in the BioStudies database (accession number S-BSST667). Our results indicate that surgical instruments used in DBS installation retain brain material sufficient for protein and gene expression studies. Comparison with previously published datasets obtained with similar approach proved the robustness and reproducibility of the protocol. Conclusions The instruments used during routine DBS surgery are a useful source for obtaining fresh brain tissues from living patients. This approach overcomes the issues that arise from using postmortem tissues, such as the effect of postmortem interval on transcriptomic and proteomic landscape of the brain, and can be used for studying molecular aspects of DBS-treatable diseases. |
| first_indexed | 2024-12-10T03:29:41Z |
| format | Article |
| id | doaj.art-01bcf4d50e8f47fa87519123d6cba3ff |
| institution | Directory Open Access Journal |
| issn | 2047-9158 |
| language | English |
| last_indexed | 2024-12-10T03:29:41Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Translational Neurodegeneration |
| spelling | doaj.art-01bcf4d50e8f47fa87519123d6cba3ff2022-12-22T02:03:51ZengBMCTranslational Neurodegeneration2047-91582022-04-0111111610.1186/s40035-022-00297-yAnalysis of human brain tissue derived from DBS surgerySalla M. Kangas0Jaakko Teppo1Maija J. Lahtinen2Anu Suoranta3Bishwa Ghimire4Pirkko Mattila5Johanna Uusimaa6Markku Varjosalo7Jani Katisko8Reetta Hinttala9PEDEGO Research Unit, University of OuluInstitute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of HelsinkiMedical Research Center, Oulu University Hospital, University of OuluInstitute for Molecular Medicine Finland (FIMM), HiLIFE Helsinki Institute of Life Science, University of HelsinkiInstitute for Molecular Medicine Finland (FIMM), HiLIFE Helsinki Institute of Life Science, University of HelsinkiInstitute for Molecular Medicine Finland (FIMM), HiLIFE Helsinki Institute of Life Science, University of HelsinkiPEDEGO Research Unit, University of OuluInstitute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of HelsinkiMedical Research Center, Oulu University Hospital, University of OuluPEDEGO Research Unit, University of OuluAbstract Background Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic and proteomic profiles. Therefore, fresh brain tissue samples from living patients represent a valuable resource of metabolically intact tissue. Implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. Here, we describe an improved approach to collecting brain tissues from surgical instruments used in implantation of DBS device for transcriptomics and proteomics analyses. Methods Samples were extracted from guide tubes and recording electrodes used in routine DBS implantation procedure to treat patients with Parkinson’s disease, genetic dystonia and tremor. RNA sequencing was performed in tissues extracted from the recording microelectrodes and liquid chromatography-mass spectrometry (LC-MS) performed in tissues from guide tubes. To assess the performance of the current approach, the obtained datasets were compared with previously published datasets representing brain tissues. Results Altogether, 32,034 RNA transcripts representing the unique Ensembl gene identifiers were detected from eight samples representing both hemispheres of four patients. By using LC-MS, we identified 734 unique proteins from 31 samples collected from 14 patients. The datasets are available in the BioStudies database (accession number S-BSST667). Our results indicate that surgical instruments used in DBS installation retain brain material sufficient for protein and gene expression studies. Comparison with previously published datasets obtained with similar approach proved the robustness and reproducibility of the protocol. Conclusions The instruments used during routine DBS surgery are a useful source for obtaining fresh brain tissues from living patients. This approach overcomes the issues that arise from using postmortem tissues, such as the effect of postmortem interval on transcriptomic and proteomic landscape of the brain, and can be used for studying molecular aspects of DBS-treatable diseases.https://doi.org/10.1186/s40035-022-00297-yDeep brain stimulationMovement disordersBrainProteomicsTranscriptomicsRNA sequencing |
| spellingShingle | Salla M. Kangas Jaakko Teppo Maija J. Lahtinen Anu Suoranta Bishwa Ghimire Pirkko Mattila Johanna Uusimaa Markku Varjosalo Jani Katisko Reetta Hinttala Analysis of human brain tissue derived from DBS surgery Translational Neurodegeneration Deep brain stimulation Movement disorders Brain Proteomics Transcriptomics RNA sequencing |
| title | Analysis of human brain tissue derived from DBS surgery |
| title_full | Analysis of human brain tissue derived from DBS surgery |
| title_fullStr | Analysis of human brain tissue derived from DBS surgery |
| title_full_unstemmed | Analysis of human brain tissue derived from DBS surgery |
| title_short | Analysis of human brain tissue derived from DBS surgery |
| title_sort | analysis of human brain tissue derived from dbs surgery |
| topic | Deep brain stimulation Movement disorders Brain Proteomics Transcriptomics RNA sequencing |
| url | https://doi.org/10.1186/s40035-022-00297-y |
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