Research progress on post-translational modification of proteins and cardiovascular diseases

Regulation of autophagy: Insights into O-GlcNAc modification mechanisms

Autophagy is a "self-eating" biological process that degrades cytoplasmic contents to ensure cellular homeostasis. Its response to stimuli occurs in two stages: Within a few to several hours of exposure to a stress condition, autophagic flow rapidly increases, which is mediated by post-translational modification (PTM). Subsequently, the transcriptional program is activated and mediates the persistent autophagic response. O-linked β-N-acetylglucosamine (O-GlcNAc) modification is an inducible and dynamically cycling PTM; mounting evidence suggests that O-GlcNAc modification participates in the total autophagic process, including autophagy initiation, autophagosome formation, autophagosome-lysosome fusion, and transcriptional process. In this review, we summarize the current knowledge on the emerging role of O-GlcNAc modification in regulating autophagy-associated proteins and explain the different regulatory effects on autophagy exerted by O-GlcNAc modification.

Unravelling disease complexity: integrative analysis of multi-omic data in clinical research

INTRODUCTION

A holistic view on biological systems is today a reality with the application of multi-omic technologies. These technologies allow the profiling of genome, epigenome, transcriptome, proteome, metabolome as well as newly emerging 'omes.' While the multiple layers of data accumulate, their integration and reconciliation in a single system map is a cumbersome exercise that faces many challenges. Application to human health and disease requires large sample sizes, robust methodologies and high-quality standards.

AREAS COVERED

We review the different methods used to integrate multi-omics, as recent ones including artificial intelligence. With proteomics as an anchor technology, we then present selected applications of its data combination with other omics layers in clinical research, mainly covering literature from the last five years in the Scopus and/or PubMed databases.

EXPERT OPINION

Multi-omics is powerful to comprehensively type molecular layers and link them to phenotype. Yet, technologies and data are very diverse and still strategies and methodologies to properly integrate these modalities are needed.

Metabolites-mediated posttranslational modifications in cardiac metabolic remodeling: Implications for disease pathology and therapeutic potential

The nonenergy - producing functions of metabolism are attracting increasing attention, as metabolic changes are involved in discrete pathways modulating enzyme activity and gene expression. Substantial evidence suggests that myocardial metabolic remodeling occurring during diabetic cardiomyopathy, heart failure, and cardiac pathological stress (e.g., myocardial ischemia, pressure overload) contributes to the progression of pathology. Within the rewired metabolic network, metabolic intermediates and end-products can directly alter protein function and/or regulate epigenetic modifications by providing acyl groups for posttranslational modifications, thereby affecting the overall cardiac stress response and providing a direct link between cellular metabolism and cardiac pathology. This review provides a comprehensive overview of the functional diversity and mechanistic roles of several types of metabolite-mediated histone and nonhistone acylation, namely O-GlcNAcylation, lactylation, crotonylation, β-hydroxybutyrylation, and succinylation, as well as fatty acid-mediated modifications, in regulating physiological processes and contributing to the progression of heart disease. Furthermore, it explores the potential of these modifications as therapeutic targets for disease intervention.

Unraveling the metabolic‒epigenetic nexus: a new frontier in cardiovascular disease treatment

Cardiovascular diseases are the leading causes of death worldwide. However, there are still shortcomings in the currently employed treatment methods for these diseases. Therefore, exploring the molecular mechanisms underlying cardiovascular diseases is an important avenue for developing new treatment strategies. Previous studies have confirmed that metabolic and epigenetic alterations are often involved in cardiovascular diseases across patients. Moreover, metabolic and epigenetic factors interact with each other and affect the progression of cardiovascular diseases in a coordinated manner. Lactylation is a novel posttranslational modification (PTM) that links metabolism with epigenetics and affects disease progression. Therefore, analyzing the crosstalk between cellular metabolic and epigenetic factors in cardiovascular diseases is expected to provide insights for the development of new treatment strategies. The purpose of this review is to describe the relationship between metabolic and epigenetic factors in heart development and cardiovascular diseases such as heart failure, myocardial infarction, and atherosclerosis, with a focus on acylation and methylation, and to propose potential therapeutic measures.

Lactylation: a promising therapeutic target in ischemia-reperfusion injury management

Ischemia-reperfusion injury (IRI) is a critical condition that poses a significant threat to patient safety. The production of lactate increases during the process of IRI, and lactate serves as a crucial indicator for assessing the severity of such injury. Lactylation, a newly discovered post-translational modification in 2019, is induced by lactic acid and predominantly occurs on lysine residues of histone or nonhistone proteins. Extensive studies have demonstrated the pivotal role of lactylation in the pathogenesis and progression of various diseases, including melanoma, myocardial infarction, hepatocellular carcinoma, Alzheimer's disease, and nonalcoholic fatty liver disease. Additionally, a marked correlation between lactylation and inflammation has been observed. This article provides a comprehensive review of the mechanism underlying lactylation in IRI to establish a theoretical foundation for better understanding the interplay between lactylation and IRI.

The role of lactate metabolism and lactylation in pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a complex and progressive disease characterized by elevated pulmonary artery pressure and vascular remodeling. Recent studies have underscored the pivotal role of metabolic dysregulation and epigenetic modifications in the pathogenesis of PAH. Lactate, a byproduct of glycolysis, is now recognized as a key molecule that links cellular metabolism with activity regulation. Recent findings indicate that, in addition to altered glycolytic activity and dysregulated. Lactate homeostasis and lactylation-a novel epigenetic modification-also play a significant role in the development of PAH. This review synthesizes current knowledge regarding the relationship between altered glycolytic activity and PAH, with a particular focus on the cumulative effects of lactate in pulmonary vascular cells. Furthermore, lactylation, an emerging epigenetic modification, is discussed in the context of PAH. By elucidating the complex interplay between lactate metabolism and lactylation in PAH, this review aims to provide insights into potential therapeutic targets. Understanding these metabolic pathways may lead to innovative strategies for managing PAH and improving patient outcomes. Future research should focus on the underlying mechanisms through which lactylation influences the pathophysiology of PAH, thereby aiding in the development of targeted interventions.

Single Cell Proteomics Reveals Novel Cell Phenotypes in Marfan Mouse Aneurysm

Background

Single-cell omics technology is a powerful tool in biomedical research. However, single cell proteomics has lagged due to an inability to amplify peptides in a similar fashion to nucleotide strings. Single cell proteomics is important because proteins are the main functional unit in cells, and they often poorly correlate with mRNA quantities. In this paper we describe the first single cell proteomic analysis of complex tissue, comparing aneurysmal and normal mouse aorta from males and females. We also compare and integrate our single cell proteomic profiles with a matching single cell transcriptomics dataset.

Methods

We compared single cell proteomes between male and female, wild-type and Fbn1 C1041G/+ Marfan mice (N=3 per group). Individual cells from mouse aortic root single cell suspensions were deposited in 384 well plates and subjected to ultra-sensitive nanoflow liquid chromatography-ion mobility-time of flight-mass spectrometry. The data were analyzed with leiden clustering to identify cell types. Statistical analyses were performed to detect differential proteins within cell types and multi-omics analysis integrated single cell proteomics with published single cell RNA-seq.

Results

We identified all major aortic cell types including 7 distinct smooth muscle cell subtypes. The proportion of these cells varied based on sex and the Fbn1 C1041G/+ genotype. Differentially expressed proteins between male and female in addition to wild-type and Marfan samples uncovered enhanced endothelial to mesenchymal transition patterns in endothelial cells from male Marfan mice. Comparisons between single cell RNA and single cell proteomic profiles showed similarities in major subtypes but not smooth muscle cell subtypes. Multi-omics analysis of these two single cell platforms demonstrated a potential novel role for smooth muscle cell derived angiotensin signaling in the Marfan phenotype.

Conclusions

Single cell proteomics identified new subpopulations of vascular smooth muscles cells and novel cell type specific protein signatures related to sex differences and aneurysm formation.

Abbreviations

Next generation sequencing (NGS), Mass spectrometer (MS), Single cell proteomics by Mass Spectrometry (ScOPE-MS), Marfan's syndrome (MFS), Fibrillin 1 (FBN1), Transforming growth factor β (TGFβ), Smooth muscle cell (SMC), Single cell proteomic (scProteomic), Differentially expressed proteins (DEPs), Wild-type (WT), Hanks' balanced salt solution (HBSS), Fetal bovine serum (FBS), Dulbecco's Modified Eagle Medium (DMEM), Data-independent acquisition parallel accumulation-serial fragmentation (DIA-PASEF), Magnetic assisted cell sorted (MACS), Single Cell Analysis in Python (Scanpy), Kyoto Encyclopedia of Genes and Genomes (KEGG), Principal component analysis (PCA), Uniform manifold projection (UMAP), Single cell transcriptomic (scTranscriptomic), Smoothelin (Smtn), Transgelin (Tagln), Myosin heavy chain 11 (Myh11), Platelet endothelial cell adhesion molecule 1 (Pecam1), Dipeptidase 1 (Dpep1), Uncoupling protein 1 (Ucp1), Low-density lipoprotein receptor-related protein (Lrp1), DNA ligase 3 (Lig3), Capsaicin channel transient receptor potential vanilloid 1 (Trpv1), Endothelial to mesenchymal transition (endMT), Intercellular adhesion molecule 1 (Icam1), Intercellular adhesion molecule 2 (Icam2), Endothelial cell-selective adhesion molecule (Esam), Calponin 1 (Cnn1), Vimentin (Vim), Zinc finger E-box-binding homeobox 1 (Zeb1), Snail family transcriptional repressor 1 (Snai1), Tropomyosin alpha-4 chain (Tpm4), Angiotensin converting enzyme (Ace).

The role of myocardial energy metabolism perturbations in diabetic cardiomyopathy: from the perspective of novel protein post-translational modifications

Diabetic cardiomyopathy (DbCM), a significant chronic complication of diabetes, manifests as myocardial hypertrophy, fibrosis, and other pathological alterations that substantially impact cardiac function and elevate the risk of cardiovascular diseases and patient mortality. Myocardial energy metabolism disturbances in DbCM, encompassing glucose, fatty acid, ketone body and lactate metabolism, are crucial factors that contribute to the progression of DbCM. In recent years, novel protein post-translational modifications (PTMs) such as lactylation, β-hydroxybutyrylation, and succinylation have been demonstrated to be intimately associated with the myocardial energy metabolism process, and in conjunction with acetylation, they participate in the regulation of protein activity and gene expression activity in cardiomyocytes. This review examines the epigenetic pathogenesis of DbCM, primarily focusing on myocardial energy metabolism perturbations and novel PTMs associated with them. It provides a detailed analysis of the mechanisms of these novel PTMs in DbCM to enhance the understanding of DbCM pathophysiology and establish a theoretical foundation for the development of new treatment strategies for DbCM.

Rapid Characterization of the Potential Active of Sinomenine in Rats by Ultra-High-Performance Liquid Chromatography-Quadrupole-Exactive Orbitrap Mass Spectrometry and Molecular Docking

Sinomenium acutum (Thunb.) Rehd. et Wils is widely used in the treatment of rheumatoid arthritis, with its alkaloid compound sinomenine (SIN) being renowned for its significant anti-inflammatory properties. However, despite its widespread application, the in vivo anti-inflammatory mechanisms and metabolic pathways of SIN remain incompletely understood. This study established a rapid and reliable method based on an ultra-high-performance liquid chromatography method coupled with Quadrupole-Exactive Orbitrap mass spectrometry and molecular docking to identify and characterize SIN and 69 metabolites in rat plasma, urine, and feces, revealing primary metabolic pathways of hydroxylation, demethylation, sulfation, and glucuronidation. Molecular docking results revealed that phase I reactions, including dedimethylation, demethylation, dehydrogenation, and dihydroxylation, along with their composite reactions, were pivotal in influencing SIN's in vivo anti-inflammatory activity. M28, M36, and M59 are potentially the most anti-inflammatory active metabolites of SIN in vivo. This comprehensive analysis unveils SIN's metabolic pathways, offering insights into its biological processes and suggesting a novel approach for exploring active drug constituents. These findings pave the way for further understanding SIN's anti-inflammatory mechanisms, contributing significantly to the development of new therapeutic strategies.

Recent advances in serum response factor posttranslational modifications and their therapeutic potential in cardiovascular and neurological diseases

Serum Response Factor (SRF) is a key regulatory transcription factor present in various cell types throughout the body, playing essential roles in cellular functions under physiological conditions. Mutations and abnormal expression of SRF have been linked to the development of various diseases and disorders. Recent evidence highlights that post-translational modifications (PTMs) are critical for regulating SRF function in different cell types and contribute to disease pathogenesis. Targeting SRF-related PTMs is emerging as a promising therapeutic approach for treating SRF-associated diseases. In this review, we summarize recent advances in understanding SRF PTMs and their underlying regulatory mechanisms. We also explore the implications of SRF-PTM in related cardiovascular and neurological diseases and their potential for therapeutic intervention. This information underscores the significance of SRF PTMs in both physiological and pathological contexts, enhancing our understanding of disease mechanisms and paving the way for the development of novel therapeutic strategies.

The double whammy of ER-retention and dominant-negative effects in numerous autosomal dominant diseases: significance in disease mechanisms and therapy

The endoplasmic reticulum (ER) employs stringent quality control mechanisms to ensure the integrity of protein folding, allowing only properly folded, processed and assembled proteins to exit the ER and reach their functional destinations. Mutant proteins unable to attain their correct tertiary conformation or form complexes with their partners are retained in the ER and subsequently degraded through ER-associated protein degradation (ERAD) and associated mechanisms. ER retention contributes to a spectrum of monogenic diseases with diverse modes of inheritance and molecular mechanisms. In autosomal dominant diseases, when mutant proteins get retained in the ER, they can interact with their wild-type counterparts. This interaction may lead to the formation of mixed dimers or aberrant complexes, disrupting their normal trafficking and function in a dominant-negative manner. The combination of ER retention and dominant-negative effects has been frequently documented to cause a significant loss of functional proteins, thereby exacerbating disease severity. This review aims to examine existing literature and provide insights into the impact of dominant-negative effects exerted by mutant proteins retained in the ER in a range of autosomal dominant diseases including skeletal and connective tissue disorders, vascular disorders, neurological disorders, eye disorders and serpinopathies. Most crucially, we aim to emphasize the importance of this area of research, offering substantial potential for understanding the factors influencing phenotypic variability associated with genetic variants. Furthermore, we highlight current and prospective therapeutic approaches targeted at ameliorating the effects of mutations exhibiting dominant-negative effects. These approaches encompass experimental studies exploring treatments and their translation into clinical practice.

PTMs of PD-1/PD-L1 and PROTACs application for improving cancer immunotherapy

Immunotherapy has been developed, which harnesses and enhances the innate powers of the immune system to fight disease, particularly cancer. PD-1 (programmed death-1) and PD-L1 (programmed death ligand-1) are key components in the regulation of the immune system, particularly in the context of cancer immunotherapy. PD-1 and PD-L1 are regulated by PTMs, including phosphorylation, ubiquitination, deubiquitination, acetylation, palmitoylation and glycosylation. PROTACs (Proteolysis Targeting Chimeras) are a type of new drug design technology. They are specifically engineered molecules that target specific proteins within a cell for degradation. PROTACs have been designed and demonstrated their inhibitory activity against the PD-1/PD-L1 pathway, and showed their ability to degrade PD-1/PD-L1 proteins. In this review, we describe how PROTACs target PD-1 and PD-L1 proteins to improve the efficacy of immunotherapy. PROTACs could be a novel strategy to combine with radiotherapy, chemotherapy and immunotherapy for cancer patients.

The effects of glycosylation modifications on monocyte recruitment and foam cell formation in atherosclerosis

The monocyte recruitment and foam cell formation have been intensively investigated in atherosclerosis. Nevertheless, as the study progressed, it was obvious that crucial molecules participated in the monocyte recruitment and the membrane proteins in macrophages exhibited substantial glycosylation modifications. These modifications can exert a significant influence on protein functions and may even impact the overall progression of diseases. This article provides a review of the effects of glycosylation modifications on monocyte recruitment and foam cell formation. By elaborating on these effects, we aim to understand the underlying mechanisms of atherogenesis further and to provide new insights into the future treatment of atherosclerosis.

Ion channel trafficking implications in heart failure

Heart failure (HF) is recognized as an epidemic in the contemporary world, impacting around 1%-2% of the adult population and affecting around 6 million Americans. HF remains a major cause of mortality, morbidity, and poor quality of life. Several therapies are used to treat HF and improve the survival of patients; however, despite these substantial improvements in treating HF, the incidence of HF is increasing rapidly, posing a significant burden to human health. The total cost of care for HF is USD 69.8 billion in 2023, warranting a better understanding of the mechanisms involved in HF. Among the most serious manifestations associated with HF is arrhythmia due to the electrophysiological changes within the cardiomyocyte. Among these electrophysiological changes, disruptions in sodium and potassium currents' function and trafficking, as well as calcium handling, all of which impact arrhythmia in HF. The mechanisms responsible for the trafficking, anchoring, organization, and recycling of ion channels at the plasma membrane seem to be significant contributors to ion channels dysfunction in HF. Variants, microtubule alterations, or disturbances of anchoring proteins lead to ion channel trafficking defects and the alteration of the cardiomyocyte's electrophysiology. Understanding the mechanisms of ion channels trafficking could provide new therapeutic approaches for the treatment of HF. This review provides an overview of the recent advances in ion channel trafficking in HF.

The mechanisms, regulations, and functions of histone lysine crotonylation

Histone lysine crotonylation (Kcr) is a new acylation modification first discovered in 2011, which has important biological significance for gene expression, cell development, and disease treatment. In the past over ten years, numerous signs of progress have been made in the research on the biochemistry of Kcr modification, especially a series of Kcr modification-related "reader", "eraser", and "writer" enzyme systems are identified. The physiological function of crotonylation and its correlation with development, heredity, and spermatogenesis have been paid more and more attention. However, the development of disease is usually associated with abnormal Kcr modification. In this review, we summarized the identification of crotonylation modification, Kcr-related enzyme system, biological functions, and diseases caused by abnormal Kcr. This knowledge supplies a theoretical basis for further exploring the function of crotonylation in the future.