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KAP240761

BioProject Title

Single-cell and spatial transcriptomic analysis to elucidate the molecular mechanisms underlying sporadic Parkinson's disease in South Korea

The heterogeneity in various aspects of Parkinson's disease (PD) is increasingly recognized as an important aspect in understanding the condition, with ethnicity and race being one of the major causes of heterogeneity that affects the risk and symptoms of PD onset. While there have been numerous reports related to PD in East Asia, there has been a lack of contribution from single-cell (or nucleus) transcriptome studies, which have been making significant contributions to understanding PD. In this study, we profiled nuclei extracted from the substantia nigra (SN) of confirmed pathological PD and control patients in South Korea, revealing 8 different cell types through cluster analysis. Monocle-based pseudotime analysis identified two disease-associated trajectories for each astrocyte and microglia and identified genes that differentiate them. Interestingly, we uncovered the inflammatory intervention in the early PD-associated transition in microglia and identified the molecular features of this intermediate state of microglia. In addition, gene regulatory networks (GRNs) based on TENET analysis revealed the detrimental effect of an HSPA5-led module in microglia and MSRB3- and HDAC8- led modules specifying the two different astrocyte trajectories. In SN neurons, we observed high heterogeneity and population changes, a decrease in dopaminergic and glutamatergic neurons and a proportional increase in GABAergic neurons. By deconvolution in spatial transcriptome obtained the PD sample, we confirmed spatiotemporal heterogeneity of neuronal subpopulations and PD-associated progressive gliosis specific to dopaminergic nuclei, SN and ventral tegmental areas (VTAs). In conclusion, our approach has enabled us to identify the genetic and spatial characterization of neurons and to demonstrate different glial fates in PD. These findings advance our molecular understanding of cell type-specific changes in Korean PD progression, providing an important foundation for predicting and validating interventions or drug effects for future treatments.

Common Fields

Common Fields - BioProject, Data Type, Submission date, Access, Release date, Runs
BioProject	KAP240761
Data Type	fastq
Submission date	2024-07-03
Access	Public
Release date	2025-12-22
Runs	14

Accession

Accession - Division, BIOSAMPLEs
Division	Run	Bytes	Download
Total	14	375,829,960,163 375,829,960,163	Metadata

BioProject * All samples * All experiments

Run Metadata

Primary

(14 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
Run ID	Experiment ID	BioSample ID	library name	filetype	file name	bytes (total)	Registration date	Release date	Access type	Protocol
KAR24064921	KAE24064921	KAS24091963	BB20-9-SN1	fastq	BB20-9-SN1_S1_L007_I1_001.fastq.gz \| BB20-9-SN1_S1_L007_I2_001.fastq.gz \| BB20-9-SN1_S1_L007_R1_001.fastq.gz \| BB20-9-SN1_S1_L007_R2_001.fastq.gz	33,905,335,658 33,905,335,658	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064922	KAE24064922	KAS24091964	BB19-14-SN2	fastq	BB19-14-SN2_S3_L001_I1_001.fastq.gz \| BB19-14-SN2_S3_L001_I2_001.fastq.gz \| BB19-14-SN2_S3_L001_R1_001.fastq.gz \| BB19-14-SN2_S3_L001_R2_001.fastq.gz	10,268,118,587 10,268,118,587	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064923	KAE24064923	KAS24091965	BB19-23-SN5	fastq	BB19-23-SN5_S2_L002_I1_001.fastq.gz \| BB19-23-SN5_S2_L002_I2_001.fastq.gz \| BB19-23-SN5_S2_L002_R1_001.fastq.gz \| BB19-23-SN5_S2_L002_R2_001.fastq.gz	11,740,817,643 11,740,817,643	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064924	KAE24064924	KAS24091966	BB20-13-SN8	fastq	BB20-13-SN8_S1_L005_I1_001.fastq.gz \| BB20-13-SN8_S1_L005_I2_001.fastq.gz \| BB20-13-SN8_S1_L005_R1_001.fastq.gz \| BB20-13-SN8_S1_L005_R2_001.fastq.gz	39,826,399,686 39,826,399,686	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064925	KAE24064925	KAS24091967	BB18-18-SN9	fastq	BB18-18-SN9_S1_L006_I1_001.fastq.gz \| BB18-18-SN9_S1_L006_I2_001.fastq.gz \| BB18-18-SN9_S1_L006_R1_001.fastq.gz \| BB18-18-SN9_S1_L006_R2_001.fastq.gz	36,687,253,322 36,687,253,322	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064926	KAE24064926	KAS24091968	BB18-17-SN10	fastq	BB18-17-SN10_S1_L002_I1_001.fastq.gz \| BB18-17-SN10_S1_L002_I2_001.fastq.gz \| BB18-17-SN10_S1_L002_R1_001.fastq.gz \| BB18-17-SN10_S1_L002_R2_001.fastq.gz	33,692,461,838 33,692,461,838	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064927	KAE24064927	KAS24091969	BB18-10-SN11	fastq	BB18-10-SN11_S1_L003_I1_001.fastq.gz \| BB18-10-SN11_S1_L003_I2_001.fastq.gz \| BB18-10-SN11_S1_L003_R1_001.fastq.gz \| BB18-10-SN11_S1_L003_R2_001.fastq.gz	32,953,453,219 32,953,453,219	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064928	KAE24064928	KAS24091970	BB19-05-SN12	fastq	BB19-05-SN12_S1_L004_I1_001.fastq.gz \| BB19-05-SN12_S1_L004_I2_001.fastq.gz \| BB19-05-SN12_S1_L004_R1_001.fastq.gz \| BB19-05-SN12_S1_L004_R2_001.fastq.gz	33,417,066,059 33,417,066,059	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064929	KAE24064929	KAS24091971	BB22-11-SN13-A1	fastq	BB22-11-SN13-A1_S1_L006_I1_001.fastq.gz \| BB22-11-SN13-A1_S1_L006_I2_001.fastq.gz \| BB22-11-SN13-A1_S1_L006_R1_001.fastq.gz \| BB22-11-SN13-A1_S1_L006_R2_001.fastq.gz	15,895,947,645 15,895,947,645	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24064930	KAE24064930	KAS24091971	BB22-11-SN13-D1	fastq	BB22-11-SN13-D1_S1_L006_I1_001.fastq.gz \| BB22-11-SN13-D1_S1_L006_I2_001.fastq.gz \| BB22-11-SN13-D1_S1_L006_R1_001.fastq.gz \| BB22-11-SN13-D1_S1_L006_R2_001.fastq.gz	16,286,304,500 16,286,304,500	2024-07-03	2025-12-22	PUBLIC	Protocol
KAR24093004	KAE24093004	KAS24117477	BB22-11-SN13-A	fastq	BB22-11_SN13-A_S1_L005_I1_001.fastq.gz \| BB22-11_SN13-A_S1_L005_I2_001.fastq.gz \| BB22-11_SN13-A_S1_L005_R1_001.fastq.gz \| BB22-11_SN13-A_S1_L005_R2_001.fastq.gz	29,594,509,286 29,594,509,286	2025-05-27	2025-12-22	PUBLIC	Protocol
KAR24093005	KAE24093005	KAS24117478	BB22-25-SN14-B	fastq	BB22-25_SN14-B_S2_L005_I1_001.fastq.gz \| BB22-25_SN14-B_S2_L005_I2_001.fastq.gz \| BB22-25_SN14-B_S2_L005_R1_001.fastq.gz \| BB22-25_SN14-B_S2_L005_R2_001.fastq.gz	28,153,330,720 28,153,330,720	2025-05-27	2025-12-22	PUBLIC	Protocol
KAR24093006	KAE24093006	KAS24117479	BB24-09-SN16-A	fastq	BB24-09-SN16-A_S1_L008_I1_001.fastq.gz \| BB24-09-SN16-A_S1_L008_I2_001.fastq.gz \| BB24-09-SN16-A_S1_L008_R1_001.fastq.gz \| BB24-09-SN16-A_S1_L008_R2_001.fastq.gz	28,722,593,185 28,722,593,185	2025-05-27	2025-12-22	PUBLIC	Protocol
KAR24093007	KAE24093007	KAS24117480	BB24-10-SN17-B	fastq	BB24-10-SN17-B_S2_L008_I1_001.fastq.gz \| BB24-10-SN17-B_S2_L008_I2_001.fastq.gz \| BB24-10-SN17-B_S2_L008_R1_001.fastq.gz \| BB24-10-SN17-B_S2_L008_R2_001.fastq.gz	24,686,368,815 24,686,368,815	2025-05-27	2025-12-22	PUBLIC	Protocol

Analysis

(6 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
Analysis ID	analysis type	analysis file	bytes(GB)	Release date	Processed method
KAZ00005848		CytAssist_BB22-11-SN13-A1.tif	6,420,044 6,420,044	2025-12-22	Processed method
KAZ00005849		CytAssist_BB22-11-SN13-D1.tif	7,277,882 7,277,882	2025-12-22	Processed method
KAZ00005847	ABUNDANCE_MEASUREMENT	CytAssist_BB22-11_SN13-A.tif	19,090,038 19,090,038	2025-12-22	Processed method
KAZ00005844	ABUNDANCE_MEASUREMENT	CytAssist_BB22-25_SN14-B.tif	14,481,162 14,481,162	2025-12-22	Processed method
KAZ00005845	ABUNDANCE_MEASUREMENT	CytAssist_BB24-09-SN16-A.tif	17,085,238 17,085,238	2025-12-22	Processed method
KAZ00005846	ABUNDANCE_MEASUREMENT	CytAssist_BB24-10-SN17-B.tif	15,380,224 15,380,224	2025-12-22	Processed method

Reference

(0 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
reference type	RefSeq accession ID	file name
No Run data.

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KRA Korea Sequence Read Archive