by Keyword: transcriptomics

Andres-Benito, P, Flores, A, Busquet-Areny, S, Carmona, M, Ausin, K, Cartas-Cejudo, P, Lachen-Montes, M, Del Rio, JA, Fernandez-Irigoyen, J, Santamaria, E, Ferrer, I, (2023). Deregulated Transcription and Proteostasis in Adult mapt Knockout Mouse International Journal Of Molecular Sciences 24, 6559

Transcriptomics and phosphoproteomics were carried out in the cerebral cortex of B6.Cg-Mapttm1(EGFP)Klt (tau knockout: tau-KO) and wild-type (WT) 12 month-old mice to learn about the effects of tau ablation. Compared with WT mice, tau-KO mice displayed reduced anxiety-like behavior and lower fear expression induced by aversive conditioning, whereas recognition memory remained unaltered. Cortical transcriptomic analysis revealed 69 downregulated and 105 upregulated genes in tau-KO mice, corresponding to synaptic structures, neuron cytoskeleton and transport, and extracellular matrix components. RT-qPCR validated increased mRNA levels of col6a4, gabrq, gad1, grm5, grip2, map2, rab8a, tubb3, wnt16, and an absence of map1a in tau-KO mice compared with WT mice. A few proteins were assessed with Western blotting to compare mRNA expression with corresponding protein levels. Map1a mRNA and protein levels decreased. However, β-tubulin III and GAD1 protein levels were reduced in tau-KO mice. Cortical phosphoproteomics revealed 121 hypophosphorylated and 98 hyperphosphorylated proteins in tau-KO mice. Deregulated phosphoproteins were categorized into cytoskeletal (n = 45) and membrane proteins, including proteins of the synapses and vesicles, myelin proteins, and proteins linked to membrane transport and ion channels (n = 84), proteins related to DNA and RNA metabolism (n = 36), proteins connected to the ubiquitin-proteasome system (UPS) (n = 7), proteins with kinase or phosphatase activity (n = 21), and 22 other proteins related to variegated pathways such as metabolic pathways, growth factors, or mitochondrial function or structure. The present observations reveal a complex altered brain transcriptome and phosphoproteome in tau-KO mice with only mild behavioral alterations.

JTD Keywords: computational platform, conformational-changes, cytoskeleton, disease, expression, isoforms, mechanisms, mice, phosphoproteomics, phosphorylation, synapse, tau-ko, tauopathies, transcriptomics, Tau-ko, Tau-protein, Transcriptomics

Villacampa, EG, Larsson, L, Mirzazadeh, R, Kvastad, L, Andersson, A, Mollbrink, A, Kokaraki, G, Monteil, V, Schultz, N, Appelberg, KS, Montserrat, N, Zhang, HB, Penninger, JM, Miesbach, W, Mirazimi, A, Carlson, J, Lundeberg, J, (2021). Genome-wide spatial expression profiling in formalin-fixed tissues Cell Genom 1, 100065

Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.© 2021 The Authors.

JTD Keywords: colonic transit, gut, intestinal motility, ld score regression, metaanalysis, nervous-system, neurotrophic factor, population, severity, Covid-19, Ffpe, Genome-wide, Irritable-bowel-syndrome, Mouse brain, Organoids, Ovarian carcinosarcoma, Pfa, Sars-cov-2, Spatial transcriptomics, Visium