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A porcine spectral assay library to quantify brain proteome by DIA-MS

ABSTRACT: The peptide-centric analysis requires spectral assay libraries that allow for the extraction of quantitative data in mass spectrometry-based methods, including data-independent acquisition (DIA), parallel reaction monitoring (PRM), or selected reaction monitoring (SRM). Such spectral libraries have been generated for humans (pan-human, T-cells, HLA subtypes) and other organisms such as mouse, E. coli, zebrafish, S. aureus, M. tuberculosis, etc. Here, we focused on the pig (Sus scrofa), a biomedical model capable of recapitulating the complexity of human pathology. We analyzed brain tissues and cerebrospinal fluids from a transgenic minipig model of Huntington's disease subjected to multiple extraction and fractionation steps. We generated a porcine spectral library for 8,321 proteins and demonstrated that this library provides a valuable resource to confidently and reproducibly quantify porcine proteins at the proteome-wide level. Via targeted assays, it enables the quantification of selected proteins with a key role not only in neuroscience.

INSTRUMENT(S):

ORGANISM(S): Sus Scrofa Domesticus (domestic Pig)

TISSUE(S): Brain, Cerebrospinal Fluid

DISEASE(S): Huntington Disease

SUBMITTER: Jakub Cervenka

LAB HEAD: Petr Vodicka

PROVIDER: PXD074603 | Pride | 2026-05-18

REPOSITORIES: pride

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Project description:The major inducible 70 kDa heat shock protein (hsp70) is host protective in a mouse model of measles virus (MeV) brain infection. Transgenic constitutive expression of hsp70 in neurons, the primary target of MeV infection, abrogates neurovirulence in neonatal H-2d congenic C57BL/6 mice. A significant level of protection is retained after depletion of T lymphocytes, implicating innate immune mechanisms. Focus of the present work was to elucidate the basis for hsp70-dependent innate immunity using this model. Transcriptome analysis of brains from transgenic (TG) and non-transgenic (NT) mice 5 days after infection identified type 1 interferon (IFN) signaling and macrophage activation/antigen presentation as the main differences linked to survival. The pivotal role for type 1 IFN in hsp70-mediated protection was demonstrated in mice with a genetically disrupted type 1 IFN receptor (IFNAR-/-), where IFNAR-/- eliminated the difference in survival between TG and NT mice. Brain macrophages, not neurons, are the predominant source of type 1 IFN in the virus-infected brain, and in vitro studies provided a mechanistic basis by which MeV-infected neurons can induce IFN-β in uninfected microglia in an hsp70-dependent manner. MeV infection induced extracellular release of hsp70 from mouse neuronal cells that constitutively express hsp70, and extracellular hsp70 induced IFN-β transcription in mouse microglial cells through Toll-like receptors 2 and 4. Collectively, results support a novel axis of type 1 IFN-dependent antiviral immunity in the virus-infected brain that is driven by hsp70. Hsp70 expression in mice enhances gene expression related to antiviral immune response against MeV neurovirulence. We performed microarrays on whole brain tissues in mice to obtain an unbiased picture of how hsp70 alters host innate responses to viral infection. Hsp70-overexpressing transgenic (TG) and non-transgenic (NT) mice were infected with MeV intracranially, and total brain mRNA harvested at 5 and 10 days post infection (d.p.i.) was analyzed, sampling the hemisphere opposite the side of viral inoculation. Analysis includes 6 groups: infected TG at 5 d.p.i. (n=4), infected TG at 10 d.p.i. (n=5), infected NT at 5 d.p.i. (n=4), infected NT at 10 d.p.i. (n=5), uninfected TG at 5 d.p.i. (n=4), and uninfected NT at 5 d.p.i. (n=4).

Project description:Directing differentiation of human embryonic stem cells (hESC) into specific cell types using an easy and reproducible protocol is a perquisite for the clinical use of hESC in regenerative medicine protocols. Here, we report the generation of mesodermal cells with differentiation potential to myocytes, osteoblasts, chondrocytes and adipocytes. We demonstrate that during hESC differentiation as embryoid bodies (EB), inhibition of TGF-b/Activin/Nodal signaling using SB-431542 (SB) markedly up-regulated paraxial mesodermal markers (TBX6, TBX5), early myogenic transcriptional factors (Myf5, Pax7) as well as myocyte committed markers (NCAM, CD34, Desmin, MHC (fast), alpha-smooth muscle actin, Nkx2.5, cTNT). Establishing EB outgrowth cultures (SB-OG) in the presence of SB (1 uM) led to further enrichment of cells expressing markers for myocyte progenitor cell: CD34+ (33%), NCAM+ (CD56) (73%), PAX7 (25%) and mature myocyte proteins (MYOD1, tropomyocin, fast MHC an; d SERCA1). Further analysis using DNA microarray revealed differential up-regulation of 117 genes (>2-fold compared to control cells) annotated to myogenic development and function. During ex vivo culture, contracting myocytes were observed (80% of the population) and the cells formed myofibres when implanted intramuscularly in vivo. Furthermore, in the presence of fetal bovine serum (10% FBS), SB-OG cells developed morphologically and phenotypically into a homogeneous stromal (mesenchymal) stem cell (MSC)-like population expressing characteristic MSC CD markers: CD44 (100%), CD73 (98%), CD146 (96%) and CD166 (88%). They were karyotypically normal and were able to differentiate ex vivo and in vivo into osteoblasts, adipocytes and chondrocytes. Experiment Overall Design: Human ESCs were differentiated as EBs for 10 days, where after EBs were plated onto fibronectin coated petri dishes. At confluency the outgrowth culture was passaged, at passage 5 3 samples were taken from both control-OG and SB-OG. the samples were mixed and frozen.

			Action	DRS
	Abundances.zip	Other
	DIALibQC.zip	Other
	Export_schemes.zip	Other
	Files_overview.xlsx	Xlsx
	Gene_ontology_annotation.tsv	Tabular

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A porcine spectral assay library to quantify brain proteome by DIA-MS

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