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Proteomic analysis of SIRT1-interacting proteins in rat nucleus pulposus cells

ABSTRACT: This study identifies proteins interacting with SIRT1 in nucleus pulposus cells. We performed a pulldown assay using anti-SIRT1 antibodies. The analysis identified 540 unique SIRT1-binding partners.

INSTRUMENT(S):

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Nucleus Pulposus Cell Of Intervertebral Disc, Nucleus Pulposus

DISEASE(S): Degenerative Disc Disease

SUBMITTER: QIQI XIE

LAB HEAD: Haihong Zhang

PROVIDER: PXD073166 | Pride | 2026-04-27

REPOSITORIES: Pride

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			Action	DRS
	8772_IgG.raw	Raw
	8772_WZL.raw	Raw
	8772_ZRS.raw	Raw
	GP_20240717_8772_PD.xlsx	Xlsx
	checksum.txt	Txt

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Publications

FGF21-Mediated Upregulation of SIRT1 Delays Intervertebral Disc Degeneration by Promoting PINK1/Parkin Dependent Mitophagy Through Deacetylation of FOXO3.

Wu Zuo-Long ZL Ran Rui R Xie Qi-Qi QQ Zhang Cong C Chen Ya-Jun YJ Cheng Peng P Wang Ke-Ping KP Zhang Hai-Hong HH

Aging cell 20260401 4

Intervertebral Disc Degeneration (IDD) is a common degenerative spinal disease and a leading cause of low back pain and disability. The senescence of nucleus pulposus cells (NPCs) is a central mechanism driving the pathological progression of IDD, though its regulatory mechanisms remain unclear. Bioinformatic analysis identified FGF21 as a key gene regulating NPCs senescence. In both human and rat degenerated intervertebral discs, FGF21 expression was significantly downregulated and closely asso ...[more]

PMID: 41860561

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Expression data from synovium, bone marrow and nucleus pulposus

Project description:Synovial and bone marrow mesenchymal stem cells after intradiscally injection show regenerative effects of nucleus pulposus. Microarray analyses of rats were performed to investigate the closeness of the gene profiles between the nucleus pulposus cells and the synovial or bone marrow mesenchymal stem cells. To investigate interaction between synovial mesenchymal stem cells and nucleus pulposus cells, human synovial mesenchymal stem cells and rat nucleus pulposus cells were co-cultured, and species specific microarray were performed. Synovium of knee joints, bone marrow and nucleus pulposus were harvested from rat or human, and cells were isolated for RNA extraction and hybridization on Affymetrix microarrays. To compare the gene profiles each other, isolated cells were mono-cultured respectively, and human synovial mesenchymal stem cells and rat nucleus pulposus cells were co-cultured.

2010-10-11 | E-GEOD-24612 | biostudies-arrayexpress

MicroRNAs expression profiling of human nucleus pulposus cells: control vs. degeneration

Project description:MicroRNAs expression profiling of human nucleus pulposus cells derived from patients with disc degeneration in comparison with those derived from patients with scoliosis as control. Two-condition experiment: control nucleus pulposus cells vs. degenerative nucleus pulposus cells. Biological replicates: 3 control, 3 degenerated, independently harvested. Four replicates per array. The supplementary file 'GSE19943_fold_pvalue.txt' contains fold-changes and p-values.

2012-01-01 | E-GEOD-19943 | biostudies-arrayexpress

Lactylation of nucleus pulposus cells

Project description:Nucleus pulposus (NP) resides in hypoxic microenvironment due to the avascular structure of intervertebral disc (IVD). Intracellular lactate drives lysine lactylation (Kla) as a newly epigenetic modification. However, the impact of Kla on NPCs remains unknown. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we showed a global lactylome profiling on NPCs cultured in normoxia and hypoxia environment and found that 3510 lactylation sites on 1052 proteins in NPCs on non-histone proteins. Moreover, there are 18 proteins with 129 Kla sites exclusively detected in the normoxia group, and 117 Kla sites in 27 proteins were specific in hypoxia group. Together, our dates reveals that Kla plays an important role in regulating cellular metabolism and may contribute to IDD progression.

2025-05-06 | PXD048244 | Pride

SIRT1/SIRT3 are robust lysine delactylases and SIRT1-mediated delactylation regulates glycolysis

Project description:Lysine lactylation (Kla), a newly identified epigenetic mark triggered by lactate during glycolysis, including the Warburg effect, marks a pivotal juncture between metabolic pathways and gene regulation. The discovery of enzymes such as p300 and HDAC1/3 has been pivotal in deciphering the regulatory dynamics of Kla, though questions about additional regulatory enzymes, their specific Kla substrates, and the underlying functional mechanisms persist. Our investigation bridges these knowledge gaps by identifying SIRT1 and SIRT3 as key "erasers" of Kla, providing insights into their selective regulatory impact on both histone and non-histone proteins. Through a quantitative proteomic analysis in wildtype, SIRT1 knockout, and SIRT3 knockout HepG2 cells, we delineated a comprehensive landscape of Kla and lysine acetylation (Kac) sites. The results demonstrate a distinct specificity in the substrates modified by SIRT1 and SIRT3, underscoring their differentiated roles in cellular signaling pathways. Particularly, we highlight the role of specific Kla modifications, such as those on the M2 splice isoform of pyruvate kinase (PKM2), in modulating metabolic pathways and cell proliferation, thereby expanding the recognized implications of Kla beyond its epigenetic roles. Therefore, this study paves the way for deeper understanding of the functional phenotypes and mechanisms of Kla, offering new insights into its broader biological significance.

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Phosphorylation level of SIRT1 in proliferating and senescent IMR90 cells

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2020-09-29 | PXD020081 | Pride

Gene expression in FIH-1 silenced human nucleus pulposus cells

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Effects of Sirt1 manipulation on gene expression in human Caco-2 cell line

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2012-07-04 | E-GEOD-30486 | biostudies-arrayexpress

Whole-protein lactylation proteome analysis of rat nucleus pulposus tissues

Project description:Lactate accumulation is a hallmark and contributing factor of intervertebral disc degeneration (IVDD). Lactate accumulation facilitates protein lactylation, while the role and mechanism of protein lactylation in IVDD remain unclear. In this study, we performed sequencing of the lactylation sites of whole protein in nucleus pulposus tissues of 3 normal and 3 acupuncture induced intervertebral disc degeneration rats to explore the function of different lactylation sites and their effects on intervertebral disc degeneration.

2026-04-13 | PXD072520 | Pride

SIRT1 affects DNA methylation of polycomb group protein target genes (PGCTs), a hotspot of the epigenetic shift observed in ageing.

Project description:Beneficial effects of SIRT1 on healthspan are likely to be pleiotropic and may include effects on DNA methylation. We demonstrated recently that manipulating SIRT1 in human cells affected DNA methylation of a panel of test genes, and that genes with expression modified by dietary restriction corresponded with genes that underwent changes in DNA methylation during ageing. Here we tested the hypothesis that genes particularly susceptible to SIRT1-induced effects on DNA methylation across the genome map to genes for which DNA methylation changes during ageing. We increased or reduced SIRT1 expression in human intestinal (Caco-2) and vascular endothelial (HuVEC) cells by transient transfection with an expression construct or with siRNA respectively. Effects on DNA methylation were measured by enriching for the methylated faction then either sequencing (HuVEC) or hybridising to a human promoter microarray (Caco-2). Effects using these two different cell lines and techniques for analysis were remarkably consistent. Genes with a DNA methylation status affected by SIRT1 manipulation were enriched for those that undergo age-dependent changes in DNA methylation, thus supporting our hypothesis. Polycomb group protein target genes (PCGTs), which are suppressed by epigenetic mechanisms in stem cells and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation, were over-represented within the set of genes showing altered DNA methylation in response to SIRT1 manipulation in both cell lines. We thus propose that effects of SIRT1 to extend healthspan include influences on the DNA methylation status of genes affected during ageing, in particular PCGTs. MBD-Sequencing to ascertain effects of SIRT1 over & under expression on methylation, in presence and absence of TNF-alpha. One sample per condition.

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