| Experiment Id | GSE190879 | Name | Dissecting molecular pathways of neuropathology of PHTS by transcriptomics and proteomics |
| Experiment Type | RNA-Seq | Study Type | WT vs. Mutant |
| Source | GEO | Curation Date | 2024-08-06 |
| description | PTEN Harmatoma Tumor Syndrome is a collection of clinical diagnosis with patients harbouring germline mutation in the PTEN gene. Most affected individuals have extreme macrocephaly and autism spectrum disorders were diagnosed in ~10% of the patients. However, the underpinning molecular mechanisms are not fully defined. The aim of this study is to compare the transcriptomic profiles of somatosensory cortices from Pten+/- and wild-type littermates (C57Bl6/J) of female and male at P30 and P42, primary neural cells, neuroprogenitor cells (NPCs), cortical astrocytes (PCA) and cortical neurons (PCN) from C57Bl6/J mice, with wild-type (WT as control for Pten+/- or CTRL as control for Nes-KO), heterozygous (Pten+/-)and complete knockout of Pten (Nes-KO). The study included performing RNA sequencing of these tissues and neural cells and integrating the data with human autism candidate genes (SFARI), and enrichment with GWAS genes for neurological diseases and traits. Methods: RNA sequencing of the somatosensory cortices and primary neural cells: Somatosensory cortices are cut from female and male mice at P30 and P42. NPCs are from E12.5 embryos. PCNs are from E15.5 embryos. PCAs are from P0 or P2 pups. Samples were lysed in TRIzol and RNA was extracted with chloroform/isopropanol and ethanol. Poly-A eniched RNA was used for library contruction. Results: We identified widespread signature genes in different samples, with enhanced immune response and oligodendrocyte development in somatosensory cortex, suppressed immediate early response genes in Pten+/- neurons, upregulated cilium components in astrocyte and downregulated inhibitory neurons in Pten knockout neural cells through RNA sequencing, which further enriched in GWAS genes of schizophrenia. Conclusion: Our study represents the first detailed comprehensive RNA-sequencing of somatosensory cortex and individual types of neural cells of transgenic mice with Pten heterozygous and homozygous knockout. The result suggested Pten effects on dysregulated immune response, immediately early response, cilium function and interneurons development which would direct further molecular studies on neuropathologenic mechanisms for PHTS. All individual groups of somatosensory cortex and cell types with their control were from littermates, each genotype has 3 biological replicates, except Pten+/- group of P30M (which has 2 samples). P30F (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample. P30M (WT vs Pten+/-): 3x WT and 2x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample. P42F (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample. P42M (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample. NPC (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq2500 platform with single read at 50bp and 20M bp reads per sample. PCA (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq4000 platform with paired-end read at 150bp and 20M bp reads per sample. PCN at DIV14 (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq4000 platform with paired-end read at 150bp and 20M bp reads per sample. NPC (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq4000 platform with paired-end read at 150bp and 13.3M bp reads per sample. PCA (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq2500 platform with paired-end read at 150bp and 20M bp reads per sample. PCN at DIV14 (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq2500 platform with paired-end read at 150bp and 20M bp reads per sample. |
