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MNK3 cells with CRISPR interference or activation at the CLN3 gene

ABSTRACT: This RNA-seq data in MNK3 cells with CRISPRi/a at CLN3 accompanies the manuscript: "High resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn's Disease aetiology".

ORGANISM(S): Mus musculus

PROVIDER: GSE313942 | GEO | 2026/01/28

REPOSITORIES: GEO

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	GSE313942_CRISPRia_CLN3_raw_counts.txt.gz	Txt

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CLN3 patients with differing progression of the disease

2011-06-08 | GSE22225 | GEO

Loss of CLN3 in HEK cells

Project description:To understand the consequences of CLN3 loss, we performed RNAseq in HEK cells with CRISPR-Cas9-mediated KO of CLN3 (CLN3-KO) or parental HEK WT cells.

2024-12-23 | GSE265831 | GEO

CLN3 patients with differing progression of the disease

Project description:Mutations in the CLN3 gene lead to juvenile neuronal ceroid lipofuscinosis, a pediatric neurodegenerative disorder characterized by visual loss, epilepsy and psychomotor deterioration. Although most CLN3 patients carry the same 1 kb deletion in the CLN3 gene, their disease phenotype can be variable. The aims of this study were (1) to identify genes that are dysregulated in CLN3 disease regardless of the clinical course that could be useful as biomarkers, and (2) to find modifier genes that affect the progression rate of the disease. Genome-wide expression profiling was performed in 8 CLN3 patients, homozygous for the 1 kb deletion, with different disease progression and compared to seven age and gender matched controls. Lymphocytes from eight patients diagnosed with CLN3 disease,all homozygous for the 1 kb deletion in the CLN3 gene and classified as having rapid (n = 2), average (n=4), and slow disease progression (n = 2), were used. These eight patients did not receive anticonvulsive medication. In addition, lymphocytes of seven age and gender matched controls were included in the study. Lymphocytes were prepared from fresh patient blood samples by Ficoll-gradient centrifugation (BiocollM-BM-., Biochrom AG, Berlin, Germany) according to the manufacturerM-bM-^@M-^Ys protocol and used for RNA isolation (RNeasyM-BM-. Micro Kit, Qiagen, Hilden, Germany).

2011-06-08 | E-GEOD-22225 | biostudies-arrayexpress

Promoter Capture Hi-C performed on human Type 3 Innate Lymphoid Cells (ILC3s)

Project description:This promoter capture Hi-C data in tonsil-derived ILC3 cells accompanies the manuscript: "High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk"

2026-01-28 | GSE216267 | GEO

Transcription profiling of cln3-delta bck2-delta G1 arrested yeast cells 0 to 80 minutes after overexpression of CLN3

Project description:Time course experiment to study the expression profile of cln3-delta bck2-delta G1 arrested yeast cells upon overexpression of CLN3

2010-06-14 | E-TABM-764 | biostudies-arrayexpress

Loss of CLN3 in HEK cells

Project description:Loss of CLN3 in HEK cells

| PRJNA1104285 | ENA

Proteomics of CLN3-deficient murine microglia identifies a disease associated phenotype with lysosomal alterations

Project description:Loss-of-function mutations in CLN3 cause juvenile Batten disease, featuring neurodegeneration and early-stage neuroinflammation. How loss of CLN3 function leads to early neuroinflammation is not yet understood. Here, we have comprehensively studied microglia from Cln3∆ex7/8 mice, a genetically accurate disease model. Loss of CLN3 function in microglia leads to lysosomal storage material accumulation and abnormal morphology of subcellular organelles. We also discovered pathological proteomic signatures consistent with defects in lysosomal function and indicative of abnormal lipid metabolism. CLN3-deficient microglia were unable to efficiently turnover myelin and metabolize the associated lipids, showing defects in lipid droplet formation and cholesterol accumulation.

2024-10-23 | PXD048550 | Pride

LOSS OF THE BATTEN DISEASE PROTEIN CLN3 LEADS TO MIS-TRAFFICKING OF M6PR AND DEFECTIVE AUTOPHAGIC-LYSOSOMAL REFORMATION

Project description:Batten disease, one of the most devastating types of neurodegenerative lysosomal storage disorders, is caused by mutations in CLN3. Here, we show that CLN3 is a vesicular trafficking hub connecting the Golgi and lysosome compartments. Proteomic analysis reveals that CLN3 interacts with several endo-lysosomal trafficking proteins, including the cation-independent mannose 6 phosphate receptor (CI-M6PR), which coordinates the targeting of lysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking of CI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lysosomal reformation. Conversely, CLN3 overexpression promotes the formation of multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent, generating newly formed proto-lysosomes. Together, our findings reveal that CLN3 functions as a link between the M6P-dependent trafficking of lysosomal enzymes and lysosomal reformation pathway, explaining the global impairment of lysosomal function in Batten disease.

2023-06-20 | PXD031582 | Pride

The Batten disease gene product CLN3 is required for the efflux of glycerophosphodiesters from lysosomes

Project description:The lysosome has many cellular roles, including degrading and recycling macromolecules and signaling to the mTORC1 growth regulator. Lysosomal dysfunction occurs in various human diseases, including common neurodegenerative diseases as well as monogenic lysosomal storage disorders (LSDs). For most LSDs the causal genes have been identified, but in many cases the function of the implicated gene is unknown. Here, we develop the LysoTag mouse line for the tissue-specific isolation of intact lysosomes that are compatible with the multimodal profiling of their contents. We apply it to the study of CLN3, a lysosomal transmembrane protein of unclear function whose loss causes juvenile neuronal ceroid lipofuscinosis (Batten disease), a lethal neurodegenerative LSD. Untargeted metabolite profiling of lysosomes from the brains of mice lacking CLN3 revealed a massive accumulation of glycerophosphodiesters (GPDs), the end products of glycerophospholipid catabolism. GPDs also accumulate in the lysosomes of CLN3-deficient cultured cells and stable isotope tracing experiments show that CLN3 is required for their lysosomal egress. Loss of CLN3 also alters upstream glycerophospholipid catabolism in the lysosome. Our results suggest that CLN3 is a lysosomal effluxer of GPDs and reveal Batten disease as the first, to our knowledge, neurodegenerative LSD with a primary defect in glycerophospholipid metabolism.

2022-07-11 | PXD018624 | Pride

Gene expression analyses in male and female Cln3Δex7/8 mouse brains following oral administration of flupirtine for 14 weeks

Project description:The Neuronal Ceroid Lipofuscinoses, one of the most common fatal neurodegenerative diseases of childhood, is caused by mutations of the CLN3 gene. Treatment regimens are symptomatic, highlighting the importance of disease-modifying drugs. Flupirtine confers neuroprotective effects in CLN3-deficient cells as well as in Cln3Δex7/8 mice. The purpose of the present study is to discern global expression programs embodying therapeutic targeting of CLN3 disease. Differential gene expression in the brains of 18-week-old Cln3Δex7/8 mice, a knock-in mouse model, was determined after daily oral supplementation of vehicle or flupirtine (30 mg/kg BW), for a period of 14 weeks, using GeneChip Mouse Genome 430 2.0 array platform from Affymetrix and quantitative real-time PCR. This manuscript sheds light on global expression programs that are associated with therapeutic treatment of CLN3 disease by flupirtine in male and female mice separately. Understanding the molecular effects of flupirtine treatment herein would pave the way for new personalized and sex-specific strategies for treatment of this debilitating genetic disease.

2021-05-01 | E-MTAB-9812 | biostudies-arrayexpress

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