Comprehensive analysis of lysine crotonylation modification in patients with chronic renal failure

Protein post-translational modification crotonylation of TXN and GLO1 in artery and vein grafts for coronary artery surgery

A key problem in coronary artery bypass grafting (CABG) is the lower long-term patency of the saphenous vein (SV) compared to internal thoracic artery (ITA). The potential strategies to improve the long-term patency of the vein graft include developing drugs to block unfavorable pathways in the vein and even to change the protein structure of the vein towards arterial structure. It is therefore important to understand the differences of the protein structure between arterial and venous grafts. Using post-translational modification (PTM) proteomics, we systematically investigated differences between ITA and SV with regard to a vascular stenosis-related PTM crotonylation. Crotonylome and PTM crotonylation in paired ITA and SV segments (n = 150) from patients undergoing CABG surgery were performed by proteomics analysis with further validation. To elucidate the underlying mechanisms, we focused on three crotonylated enzymatic proteins with anti-oxidative effects-thioredoxin (TXN), glyoxalase 1 (GLO1), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) - whose crotonylation patterns were systematically investigated. The functional validation was performed using both site-mutation experiments in HEK293 cells and pharmacological inhibitors in ex vivo cultured ITA/SV tissue specimens. Comprehensive crotonyl-proteomics demonstrated 3652 proteins are differentially-expressed and 411 proteins are differentially-crotonylated in ITA/SV segments. In the identified crotonylated proteins, SV demonstrated significantly higher levels compared to ITA. Notably, SV showed higher crotonylation levels on TXN-K3, GLO1-K157, and GAPDH-K61, which were associated with decreased enzymatic activity, elevated methylglyoxal (MGO) accumulation, and increased oxidative stress. Inhibition of CREB-binding protein (CBP) reversed oxidative stress in SV by suppressing crotonylation of the three enzymes. In Hek293 cells, both site-specific and comprehensive crotonylation decreased the activities of TXN/GLO1/GAPDH, which in turn triggered the accumulation of MGO. Overexpression of histone deacetylases HDAC1 and HDAC3 showed the opposite effect, restoring enzyme function. This study is the first to reveal significant differences in PTM crotonylation between human ITA and SV, shedding light on the biological mechanisms underlying the functional disparities between these grafts. These differences impact the enzymatic activity of key proteins involved in oxidative stress, providing insights into the molecular basis of graft performance. Importantly, these findings form a scientific basis for developing specific methods including new anti-oxidative drugs and gene therapy to target on crotonylation in the vein graft in order to improve the long-term graft patency.

Sodium Crotonate Alleviates Diabetic Kidney Disease Partially Via the Histone Crotonylation Pathway

Diabetic kidney disease (DKD) is a common microvascular complication of diabetes, inflammation and fibrosis play an important role in its progression. Histone lysine crotonylation (Kcr) was first identified as a new type of post-translational modification in 2011. In recent years, prominent progress has been made in the study of sodium crotonate (NaCr) and histone Kcr in kidney diseases. However, the effects of NaCr and NaCr-induced Kcr on DKD remain unclear. In this study, db/db mice and high glucose-induced human tubular epithelial cells (HK-2) were used respectively, and exogenous NaCr and crotonoyl-coenzyme A (Cr-CoA) as intervention reagents, histone Kcr and DKD-related indicators were detected. The results confirmed that NaCr had an antidiabetic effect and decreased blood glucose and serum lipid levels and alleviated renal function and DKD-related inflammatory and fibrotic damage. NaCr also induced histone Kcr and histone H3K18 crotonylation (H3K18cr). However, NaCr and Cr-CoA-induced histone Kcr and protective effects were reversed by inhibiting the activity of Acyl-CoA synthetase short-chain family member 2 (ACSS2) or histone acyltransferase P300 in vitro. In summary, our data reveal that NaCr may mitigate DKD via an antidiabetic effect as well as through ACSS2 and P300-induced histone Kcr, suggesting that Kcr may be the potential molecular mechanism and prevention target of DKD.

Application of crotonylation modification in pan-vascular diseases

Pan-vascular diseases, based on systems biology theory, explore the commonalities and individualities of important target organs such as cardiovascular, cerebrovascular and peripheral blood vessels, starting from the systemic and holistic aspects of vascular diseases. The purpose is to understand the interrelationships and results between them, achieve vascular health or sub-health, and comprehensively improve the physical and mental health of the entire population. Post-translational modification (PTM) is an important part of epigenetics, including phosphorylation, acetylation, ubiquitination, methylation, etc., playing a crucial role in the pan-vascular system. Crotonylation is a novel type of PTM that has made significant progress in the research of pan-vascular related diseases in recent years. Based on the review of previous studies, this article summarises the various regulatory factors of crotonylation, physiological functions and the mechanisms of histone and non-histone crotonylation in regulating pan-vascular related diseases to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment and the value of clinical translation.

Function and mechanism of lysine crotonylation in health and disease

Lysine crotonylation is a newly identified posttranslational modification that is different from the widely studied lysine acetylation in structure and function. In the last dozen years, great progress has been made in lysine crotonylation-related studies, and lysine crotonylation is involved in reproduction, development and disease. In this review, we highlight the similarities and differences between lysine crotonylation and lysine acetylation. We also summarize the methods and tools for the detection and prediction of lysine crotonylation. At the same time, we outline the recent advances in understanding the mechanisms of enzymatic and metabolic regulation of lysine crotonylation, as well as the regulating factors that selectively recognize this modification. Particularly, we discussed how dynamic changes in crotonylation status maintain physiological health and result in the development of disease. This review not only points out the new functions of lysine crotonylation but also provides new insights and exciting opportunities for managing various diseases.

Potential functions and mechanisms of lysine crotonylation modification (Kcr) in tumorigenesis and lymphatic metastasis of papillary thyroid cancer (PTC)

OBJECTIVES

To examine the putative functions and mechanisms of lysine crotonylation (Kcr) during the development and progression of papillary thyroid cancer (PTC).

METHODS

Samples of thyroid cancer tissues were collected and subjected to liquid chromatography-tandem mass spectrometry. Crotonylated differentially expressed proteins (DEPs) and differentially expressed Kcr sites (DEKSs) were analyzed by Motif, dynamic expression model analysis (Mfuzz), subcellular localization, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Go Ontology (GO) annotation, and protein-protein interaction analysis (PPI). Validation was performed by immunohistochemistry (IHC).

RESULTS

A total of 262 crotonylated DEPs and 702 DEKSs were quantitated. First, for the tumor/normal comparison, a dynamic expression model analysis (Mfuzz) of the DEKSs revealed that clusters 1, 3, and 4 increased with the progression of thyroid cancer; however, cluster 6 showed a dramatic increase during the transition from N0-tumor to N1-tumor. Furthermore, based on GO annotation, KEGG, and PPI, the crotonylated DEPs were primarily enriched in the PI3K-Akt signaling pathway, Cell cycle, and Hippo signaling pathway. Of note, crosstalk between the proteome and Kcr proteome suggested a differential changing trend, which was enriched in Thyroid hormone synthesis, Pyruvate metabolism, TCA cycle, Cell cycle, and Apoptosis pathways. Similarly, for the LNM comparison group, the DEKSs and related DEPs were primarily enriched in Hydrogen peroxide catabolic process and Tight junction pathway. Finally, according to The Cancer Genome Atlas Program (TCGA) database, the differential expression of Kcr DEPs were associated with the prognosis of thyroid cancer, indicating the prognostic significance of these proteins. Moreover, based on the clinical validation of 47 additional samples, Kcr was highly expressed in thyroid tumor tissues compared with normal tissue (t = 9.792, P < 0.001). In addition, a positive correlation was observed between Kcr and N-cadherin (r = 0.5710, P = 0.0015). Moreover, N-cadherin expression was higher in the relatively high Kcr expression group (χ2 = 18.966, P < 0.001).

CONCLUSIONS

Higher Kcr expression was correlated with thyroid tumorigenesis and lymphatic metastasis, which may regulate thyroid cancer progression by Pyruvate metabolism, TCA cycle, Cell cycle, and other pathways.

Protein crotonylation: Basic research and clinical diseases

Crotonylation is an importantly conserved post-translational modification, which is completely different from acetylation. In recent years, it has been confirmed that crotonylation occurs on histone and non-histone. Crotonylated Histone primarily affects gene expression through transcriptional regulation, while non-histone Crotonylation mainly regulates protein functions including protein activity, localization, and stability, as well as protein-protein interactions. The change in protein expression and function will affect the physiological process of cells and even cause disease. Reviewing previous studies, this article summarizes the mechanisms of histone and non-histone crotonylation in regulating diseases and cellular physiological processes to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment.

Lysine succinylation analysis reveals the effect of Sirt5 on synovial fibroblasts in rheumatoid arthritis patients

Rheumatoid arthritis (RA) is an autoimmune disease with complex etiology, and its pathological mechanism remains unclear. Our aim was to explore the effect of protein succinylation on RA by silencing Sirt5, sequencing succinylated proteins, and analyzing the sequencing results to identify potential biomarkers. We wanted to gain a clearer understanding of RA pathogenesis, quantitative assessment of succinylated proteins in Fibroblast-like synoviocytes (FLS) from RA patients using liquid chromatography- tandem mass spectrometry and enrichment analysis investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 679 proteins and 2,471 lysine succinylation sites were found in RA patients, and 436 differentially expressed proteins and 1,548 differentially expressed succinylation sites were identified. Among them, 48 succinylation sites were upregulated in 38 proteins and 144 succinylation sites were downregulated in 82 proteins. Bioinformatics showed that succinylated proteins were significantly enriched in amino and fatty acid metabolisms. Results indicated that Sirt5 can affect various biological processes involved in RA FLSs, and succinylation caused by silencing Sirt5 plays a major role in RA progression. This study provides further understanding of RA pathogenesis and may facilitate searching for potential RA biomarkers.

Functioning and mechanisms of PTMs in renal diseases

Post-translational modifications (PTMs) are crucial epigenetic mechanisms that regulate various cellular biological processes. The use of mass spectrometry (MS)-proteomics has led to the discovery of numerous novel types of protein PTMs, such as acetylation, crotonylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, protein propionylation and butyrylation, succinylation, malonylation, lactylation, and histone methylation. In this review, we specifically highlight the molecular mechanisms and roles of various histone and some non-histone PTMs in renal diseases, including diabetic kidney disease. PTMs exhibit diverse effects on renal diseases, which can be either protective or detrimental, depending on the specific type of protein PTMs and their respective targets. Different PTMs activate various signaling pathways in diverse renal pathological conditions, which could provide novel insights for studying epigenetic mechanisms and developing potential therapeutic strategies for renal diseases.

Crotonylation and disease: Current progress and future perspectives

Histone lysine crotonylation was first identified as a new type of post-translational modification in 2011. In recent years, prominent progress has been made in the study of histone and nonhistone crotonylation in reproduction, development, and disease. Although the regulatory enzyme systems and targets of crotonylation partially overlap with those of acetylation, the peculiar CC bond structure of crotonylation suggests that crotonylation may have specific biological functions. In this review, we summarize the latest research progress regarding crotonylation, especially its regulatory factors and relationship with diseases, which suggest further research directions for crotonylation and provide new ideas for developing disease intervention and treatment regimens.

Quantitative Crotonylome Analysis Reveals the Mechanism of Shenkang Injection on Diabetic Nephropathy

Shenkang injection (SKI) has been widely used in the clinical treatment of chronic kidney diseases in China because of its efficacy and safety. However, the underlying mechanism of SKI in diabetic nephropathy (DN) remains unclear. The present study aimed to investigate the renoprotective effects and possible mechanisms of SKI in diabetic db/db mice. We showed that SKI ameliorated hyperglycemia and abnormal renal biochemical parameters in db/db mice. Crotonylome and subsequent bioinformatics analyses indicated that the molecular functions of the significantly different crotonylated proteins regulated by SKI were closely related to oxidoreductase activity and oxidative phosphorylation might be one of the main pathways through which SKI functions in DN. Subsequent PRM validation of the selected crotonylated proteins confirmed these findings. In addition, we determined that SKI could regulate the expression of specific proteins in oxidative phosphorylation complexes and enhance antioxidant capacity. Taken together, our data suggest that SKI exerted the protective effect against DN potentially through reversing the abnormal crotonylation expression of oxidoreductase-related proteins.