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TMT-based proteomics of BMDMs following virus infection

ABSTRACT: To identify potential regulators involved in virus-triggered innate immune response, we used tandem mass tagging (TMT)-based shotgun proteomic analysis of murine bone marrow-derived macrophages (BMDMs) following sendai virus (SeV) infection. This approach facilitated the identification and relative quantification of up- or down-regulated proteins, as evaluated by replicates. Kyoto encyclopedia of genes and genomes (KEGG) analysis indicated that proteins involved in innate immune and inflammatory responses significantly increased following SeV infection. Surprisingly, we also observed a series of proteins involved in the regulation of cell cycle and DNA damage repair process were greatly impaired after SeV infection.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Bone Marrow, Macrophage

SUBMITTER: Caoqi Lei

LAB HEAD: Caoqi Lei

PROVIDER: PXD051098 | Pride | 2025-04-03

REPOSITORIES: Pride

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			Action	DRS
	O20210810yuel_LCQ_tmt16plex_60min_.msf	Msf
	O20210810yuel_LCQ_tmt16plex_60min_1.raw	Raw
	O20210810yuel_LCQ_tmt16plex_60min_10.raw	Raw
	O20210810yuel_LCQ_tmt16plex_60min_11.raw	Raw
	O20210810yuel_LCQ_tmt16plex_60min_12.raw	Raw

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Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.

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TMT-based proteomics of BMDMs following virus infection

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