Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts

Role of a small GTPase Cdc42 in aging and age-related diseases

A small GTPase, Cdc42 is evolutionarily one of the most ancient members of the Rho family, which is ubiquitously expressed and involved in a wide range of fundamental cellular functions. The crucial role of Cdc42 includes regulation of the actin cytoskeleton, cell polarity, morphology and migration, endocytosis and exocytosis, cell cycle, and proliferation in many different cell types. Many studies have provided compelling yet contradicting evidence that Cdc42 dysregulation plays an important role in cellular and tissue aging. Furthermore, Cdc42 is a critical factor in the development and progression of aging-related pathologies, such as neurodegenerative and cardiovascular disorders, diabetes type 2, and aging-related disorders of the joints and bones, and the inhibition of the Cdc42 demonstrates potentially significant therapeutic and anti-aging effects in animal models of aging and disease. However, regulation of Cdc42 expression and activity is very complex and depends on many factors, such as the origin and complexity of the tissues, hormonal status, etc. Therefore, this review is focused on current advances in understanding the underlying cellular and molecular mechanisms associated with Cdc42 activity and regulation of senescence in different cell types since they may provide a foundation for novel therapeutic strategies and targeted drugs to reverse the aging process and treat aging-associated disorders.

Oxidative stress response in regulatory and conventional T cells: a comparison between patients with chronic coronary syndrome and healthy subjects

Background

Inflammation and oxidative stress form a vicious circle in atherosclerosis. Oxidative stress can have detrimental effects on T cells. A unique subset of CD4⁺ T cells, known as regulatory T (T_reg) cells, has been associated with atheroprotective effects. Reduced numbers of T_reg cells is a consistent finding in patients with chronic coronary syndrome (CCS). However, it is unclear to what extent these cells are sensitive to oxidative stress. In this pilot study, we tested the hypothesis that oxidative stress might be a potential contributor to the T_reg cell deficit in CCS patients.

Methods

Thirty patients with CCS and 24 healthy controls were included. T_reg (CD4⁺CD25⁺CD127⁻) and conventional T (CD4⁺CD25⁻, T_conv) cells were isolated and treated with increasing doses of H₂O₂. Intracellular ROS levels and cell death were measured after 2 and 18 h, respectively. The expression of antioxidant genes was measured in freshly isolated T_reg and T_conv cells. Also, total antioxidant capacity (TAC) was measured in fresh peripheral blood mononuclear cells, and oxidized (ox) LDL/LDL ratios were determined in plasma.

Results

At all doses of H₂O_2, T_reg cells accumulated more ROS and exhibited higher rates of death than their T_conv counterparts, p < 0.0001. T_reg cells also expressed higher levels of antioxidant genes, including thioredoxin and thioredoxin reductase-1 (p < 0.0001), though without any differences between CCS patients and controls. T_conv cells from CCS patients were, on the other hand, more sensitive to oxidative stress ex vivo and expressed more thioredoxin reductase-1 than T_conv cells from controls, p < 0.05. Also, TAC levels were lower in patients, 0.97 vs 1.53 UAE/100 µg, p = 0.001, while oxLDL/LDL ratios were higher, 29 vs 22, p = 0.006.

Conclusion

T_reg cells isolated from either CCS patients or healthy controls were all highly sensitive to oxidative stress ex vivo. There were signs of oxidant-antioxidant imbalance in CCS patients and we thus assume that oxidative stress may play a role in the reduction of T_reg cells in vivo.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02906-2.

The proteomic study of serially passaged human skin fibroblast cells uncovers down-regulation of the chromosome condensin complex proteins involved in replicative senescence

Dermal fibroblast is one of the major constitutive cells of skin and plays a central role in skin senescence. The replicative senescence of fibroblasts may cause skin aging, bad wound healing, skin diseases and even cancer. In this study, a label-free quantitative proteomic approach was employed to analyzing the serial passaged human skin fibroblast (CCD-1079Sk) cells, resulting in 3371 proteins identified. Of which, 280 proteins were significantly changed in early passage (6 passages, P6), middle passage (12 passages, P12) and late passage (21 passages, P21), with a time-dependent decrease or increase tendency. Bioinformatic analysis demonstrated that the chromosome condensin complex, including structural maintenance of chromosomes protein 2 (SMC2) and structural maintenance of chromosomes protein 4 (SMC4), were down-regulated in the serially passaged fibroblast cells. The qRT-PCR and Western Blot experiments confirmed that the expression of these two proteins were significantly down-regulated in a time-dependent manner in the subculture of human skin fibroblasts (HSFb cells). In summary, we used serially passaged human skin fibroblast cells coupled with quantitative proteomic approach to profile the protein expression pattern in the temporal progress of replicative senescence in HSFb cells and revealed that the down-regulation of the chromosome condensin complex subunits, such as SMC2 and SMC4, may play an important role in the fibroblast senescence.

Oxidative stress in aging: advances in proteomic approaches

Aging is a gradual, complex process in which cells, tissues, organs, and the whole organism itself deteriorate in a progressive and irreversible manner that, in the majority of cases, implies pathological conditions that affect the individual's Quality of Life (QOL). Although extensive research efforts in recent years have been made, the anticipation of aging and prophylactic or treatment strategies continue to experience major limitations. In this review, the focus is essentially on the compilation of the advances generated by cellular expression profile analysis through proteomics studies (two-dimensional [2D] electrophoresis and mass spectrometry [MS]), which are currently used as an integral approach to study the aging process. Additionally, the relevance of the oxidative stress factors is discussed. Emphasis is placed on postmitotic tissues, such as neuronal, muscular, and red blood cells, which appear to be those most frequently studied with respect to aging. Additionally, models for the study of aging are discussed in a number of organisms, such as Caenorhabditis elegans, senescence-accelerated probe-8 mice (SAMP8), naked mole-rat (Heterocephalus glaber), and the beagle canine. Proteomic studies in specific tissues and organisms have revealed the extensive involvement of reactive oxygen species (ROS) and oxidative stress in aging.

An integrated proteomics analysis of bone tissues in response to mechanical stimulation

Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. However, it is still poorly understood how genes and proteins in bone cells are orchestrated to respond to mechanical stimulations. In this research, we applied integrated proteomics, statistical, and network biology techniques to study proteome-level changes to bone tissue cells in response to two different conditions, normal loading and fatigue loading. We harvested ulna midshafts and isolated proteins from the control, loaded, and fatigue loaded Rats. Using a label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) experimental proteomics technique, we derived a comprehensive list of 1,058 proteins that are differentially expressed among normal loading, fatigue loading, and controls. By carefully developing protein selection filters and statistical models, we were able to identify 42 proteins representing 21 Rat genes that were significantly associated with bone cells' response to quantitative changes between normal loading and fatigue loading conditions. We further applied network biology techniques by building a fatigue loading activated protein-protein interaction subnetwork involving 9 of the human-homolog counterpart of the 21 rat genes in a large connected network component. Our study shows that the combination of decreased anti-apoptotic factor, Raf1, and increased pro-apoptotic factor, PDCD8, results in significant increase in the number of apoptotic osteocytes following fatigue loading. We believe controlling osteoblast differentiation/proliferation and osteocyte apoptosis could be promising directions for developing future therapeutic solutions for related bone diseases.

Hydrogen peroxide fuels aging, inflammation, cancer metabolism and metastasis: the seed and soil also needs "fertilizer"

In 1889, Dr. Stephen Paget proposed the "seed and soil" hypothesis, which states that cancer cells (the seeds) need the proper microenvironment (the soil) for them to grow, spread and metastasize systemically. In this hypothesis, Dr. Paget rightfully recognized that the tumor microenvironment has an important role to play in cancer progression and metastasis. In this regard, a series of recent studies have elegantly shown that the production of hydrogen peroxide, by both cancer cells and cancer-associated fibroblasts, may provide the necessary "fertilizer," by driving accelerated aging, DNA damage, inflammation and cancer metabolism, in the tumor microenvironment. By secreting hydrogen peroxide, cancer cells and fibroblasts are mimicking the behavior of immune cells (macrophages/neutrophils), driving local and systemic inflammation, via the innate immune response (NFκB). Thus, we should consider using various therapeutic strategies (such as catalase and/or other anti-oxidants) to neutralize the production of cancer-associated hydrogen peroxide, thereby preventing tumor-stroma co-evolution and metastasis. The implications of these findings for overcoming chemo-resistance in cancer cells are also discussed in the context of hydrogen peroxide production and cancer metabolism.

The role of intracellular glutathione in the progression of Chlamydia trachomatis infection

The productive internalization in the host cell of Chlamydia trachomatis elementary bodies and their infectivity depends on the degree of reduction of disulfide bonds in the outer envelope of the elementary body. We have hypothesized that the reducing agent may be intracellular glutathione (GSH). Three approaches were used to modulate the intracellular GSH concentration: (1) treatment of cells with buthionine sulfoximine, which causes irreversible inhibition of GSH biosynthesis; (2) hydrogen peroxide-induced oxidation of GSH by intracellular glutathione peroxidases; and (3) treatment of cells with N-acetyl-l-cysteine (NAC), a precursor of glutathione. In the first two cases, we observed a four- to sixfold inhibition of C. trachomatis infection, whereas in NAC-treated cells we detected an increase in the size of chlamydial inclusions. Using a proteomics approach, we showed that the inhibition of chlamydial infection does not combine with alterations in protein expression patterns after cell treatment. These results suggest that GSH plays a key role in the reduction of disulfide bonds in the C. trachomatis outer envelope at an initial stage of the infection.

Study of gene expression profiles in TK6 human cells exposed to DNA-oxidizing agents

During the last decade, there has been clear progress in using threshold in risk assessment but its acceptance by scientists is still under debate. Contrary to indirect DNA-damaging agents, DNA-reactive agents have been assumed to have a non-threshold mode of action, as they directly induce DNA lesions that potentially can be converted into mutations. However, in recent years there is a growing number of data establishing threshold doses even for these DNA-reactive compounds. Indeed, there are several defence and repair mechanisms that provide protection and that may be responsible for genotoxic thresholds. In this context, we recently showed that DNA-oxidizing agents exhibit a thresholded dose-response in vitro with respect to chromosomal alterations. We have hypothesized the involvement of different cellular responses whose nature and efficiency depend on the stress level. The aim of this study was to develop a more complete understanding of these underlying mechanisms. We investigated global gene expression profiles of human lymphoblastoid TK6 cells after exposure to potassium bromate and hydrogen peroxide (via glucose oxidase). Cells were treated for 1h and mRNAs were isolated either immediately at the end of the treatment or after a 23-h recovery period. Our results showed that cells have developed elaborate cellular responses to oxidative stress in order to maintain genomic integrity. Many of altered genes were redox-sensitive transcription factors such as p53, NF-kappaB, AP-1 and Nrf2. Their downstream target genes and signalling pathways were subsequently activated leading mainly to the induction of antioxidant defenses, inflammation, cell cycle arrest, DNA repair and cell death. Overall, our study allowed the identification of key events involved in the thresholded response observed after DNA-oxidizing agents exposure and shows the usefulness of the combination of standard in vitro genotoxicity assays with gene expression profiling technology to determine modes of action, particularly for critical risk assessment.

Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers

BACKGROUND

Although prior studies have demonstrated a smoking-induced field of molecular injury throughout the lung and airway, the impact of smoking on the airway epithelial proteome and its relationship to smoking-related changes in the airway transcriptome are unclear.

METHODOLOGY/PRINCIPAL FINDINGS

Airway epithelial cells were obtained from never (n = 5) and current (n = 5) smokers by brushing the mainstem bronchus. Proteins were separated by one dimensional polyacrylamide gel electrophoresis (1D-PAGE). After in-gel digestion, tryptic peptides were processed via liquid chromatography/ tandem mass spectrometry (LC-MS/MS) and proteins identified. RNA from the same samples was hybridized to HG-U133A microarrays. Protein detection was compared to RNA expression in the current study and a previously published airway dataset. The functional properties of many of the 197 proteins detected in a majority of never smokers were similar to those observed in the never smoker airway transcriptome. LC-MS/MS identified 23 proteins that differed between never and current smokers. Western blotting confirmed the smoking-related changes of PLUNC, P4HB1, and uteroglobin protein levels. Many of the proteins differentially detected between never and current smokers were also altered at the level of gene expression in this cohort and the prior airway transcriptome study. There was a strong association between protein detection and expression of its corresponding transcript within the same sample, with 86% of the proteins detected by LC-MS/MS having a detectable corresponding probeset by microarray in the same sample. Forty-one proteins identified by LC-MS/MS lacked detectable expression of a corresponding transcript and were detected in

CONCLUSIONS/SIGNIFICANCE

1D-PAGE coupled with LC-MS/MS effectively profiled the airway epithelium proteome and identified proteins expressed at different levels as a result of cigarette smoke exposure. While there was a strong correlation between protein and transcript detection within the same sample, we also identified proteins whose corresponding transcripts were not detected by microarray. This noninvasive approach to proteomic profiling of airway epithelium may provide additional insights into the field of injury induced by tobacco exposure.

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MESH Headings

• Adult
• Blotting, Western
• Bronchi/cytology
• Bronchi/drug effects
• Bronchi/metabolism
• Chromatography, Liquid/methods
• Electrophoresis, Polyacrylamide Gel/methods
• Epithelial Cells/cytology
• Epithelial Cells/drug effects
• Epithelial Cells/physiology
• Female
• Gene Expression Profiling
• Glycoproteins/metabolism
• Humans
• Male
• Microarray Analysis
• Middle Aged
• Molecular Sequence Data
• Phosphoproteins/metabolism
• Procollagen-Proline Dioxygenase/metabolism
• Protein Disulfide-Isomerases/metabolism
• Proteome/analysis
• Respiratory Mucosa/cytology
• Respiratory Mucosa/drug effects
• Smoking/adverse effects
• Tandem Mass Spectrometry/methods
• Uteroglobin/metabolism
• Young Adult
• Tobacco Products

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Grants

• R01 CA124640 NCI NIH HHS
• U01 ES016035 NIEHS NIH HHS
• R01CA124640 NCI NIH HHS
• U01ES016035 NIEHS NIH HHS

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Affiliation(s)

Katrina Steiling The Pulmonary Center, Boston University Medical Center, Boston, Massachusetts, United States of America.
Aran Y Kadar
Agnes Bergerat
James Flanigon
Sriram Sridhar
Vishal Shah
Q Rushdy Ahmad
Jerome S Brody
Marc E Lenburg
Martin Steffen
Avrum Spira

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Collaborators Collapse