Comparative peptidomic profile between human hypertrophic scar tissue and matched normal skin for identification of endogenous peptides involved in scar pathology

Peptidomic analysis reveals novel peptide PDLC promotes cell proliferation in hepatocellular carcinoma via Ras/Raf/MEK/ERK pathway

Hepatocellular carcinoma (HCC) still presents poor prognosis with low overall survival rates and limited therapeutic options available. Recently, attention has been drawn to peptidomic analysis, an emerging field of proteomics for the exploration of new potential peptide drugs for the treatment of various diseases. However, research on the potential function of HCC peptides is lacking. Here, we analyzed the peptide spectrum in HCC tissues using peptidomic techniques and explored the potentially beneficial peptides involved in HCC. Changes in peptide profiles in HCC were examined using liquid chromatography-mass spectrometry (LC-MS/MS). Analyze the physicochemical properties and function of differently expressed peptides using bioinformatics. The effect of candidate functional peptides on HCC cell growth and migration was evaluated using the CCK-8, colony formation, and transwell assays. Transcriptome sequencing analysis and western blot were employed to delve into the mode of action of potential peptide on HCC. Peptidomic analysis of HCC tissue yielded a total of 8683 peptides, of which 452 exhibited up-regulation and 362 showed down-regulation. The peptides that were differentially expressed, according to bioinformatic analysis, were closely linked to carbon metabolism and the mitochondrial inner membrane. The peptide functional validation identified a novel peptide, PDLC (peptide derived from liver cancer), which was found to dramatically boost HCC cell proliferation through the Ras/Raf/MEK/ERK signaling cascade. Our research defined the peptide's properties and pattern of expression in HCC and identified a novel peptide, PDLC, with a function in encouraging HCC progression, offering an entirely new potential therapeutic target the disease.

Integrative Analysis of Lactylome and Proteome of Hypertrophic Scar To Identify Pathways or Proteins Associated with Disease Development

Lactylation (Kla), a recently discovered post-translational modification derived from lactate, plays crucial roles in various cellular processes. However, the specific influence of lactylation on the biological processes underlying hypertrophic scar formation remains unclear. In this study, we present a comprehensive profiling of the lactylome and proteome in both hypertrophic scars and adjacent normal skin tissues. A total of 1023 Kla sites originating from 338 nonhistone proteins were identified based on lactylome analysis. Proteome analysis in hypertrophic scar and adjacent skin samples revealed the identification of 2008 proteins. It is worth noting that Kla exhibits a preference for genes associated with ribosome function as well as glycolysis/gluconeogenesis in both normal skin and hypertrophic scar tissues. Furthermore, the functional enrichment analysis demonstrated that differentially lactyled proteins are primarily involved in proteoglycans, HIF-1, and AMPK signaling pathways. The combined analysis of the lactylome and proteome data highlighted a significant upregulation of 14 lactylation sites in hypertrophic scar tissues. Overall, our investigation unveiled the significant involvement of protein lactylation in the regulation of ribosome function as well as glycolysis/gluconeogenesis, potentially contributing to the formation of hypertrophic scars.

The adipose-derived stem cell peptide ADSCP2 alleviates hypertrophic scar fibrosis via binding with pyruvate carboxylase and remodeling the metabolic landscape

AIM

The purpose of this study was to investigate the function and mechanism of a novel peptide derived from adipose-derived stem cell-conditioned medium (ADSC-CM).

METHODS

Mass spectrometry was applied to identify expressed peptides in ADSC-CM obtained at different time points. The cell counting kit-8 assay and quantitative reverse transcription polymerase chain reactions were performed to screen the functional peptides contained within ADSC-CM. RNA-seq, western blot, a back skin excisional model of BALB/c mice, the peptide pull-down assay, rescue experiments, untargeted metabolomics, and mixOmics analysis were performed to thoroughly understand the functional mechanism of selected peptide.

RESULTS

A total of 93, 827, 1108, and 631 peptides were identified in ADSC-CM at 0, 24, 48, and 72 h of conditioning, respectively. A peptide named ADSCP2 (DENREKVNDQAKL) derived from ADSC-CM inhibited collagen and ACTA2 mRNAs in hypertrophic scar fibroblasts. Moreover, ADSCP2 facilitated wound healing and attenuated collagen deposition in a mouse model. ADSCP2 bound with the pyruvate carboxylase (PC) protein and inhibited PC protein expression. Overexpressing PC rescued the reduction in collagen and ACTA2 mRNAs caused by ADSCP2. Untargeted metabolomics identified 258 and 447 differential metabolites in the negative and positive mode, respectively, in the ADSCP2-treated group. The mixOmics analysis, which integrated RNA-seq and untargeted metabolomics data, provided a more holistic view of the functions of ADSCP2.

CONCLUSION

Overall, a novel peptide derived from ADSC-CM, named ADSCP2, attenuated hypertrophic scar fibrosis in vitro and in vivo, and the novel peptide ADSCP2 might be a promising drug candidate for clinical scar therapy.

Peptide deregulated in hypertrophic scar-1 alleviates hypertrophic scar fibrosis by targeting focal adhesion kinase and pyruvate kinase M2 and remodeling the metabolic landscape

Hypertrophic scarring is a fibrotic skin disease characterized by excessive deposition of collagens. Emerging evidence has suggested important roles for peptides in fibrosis-related diseases. Here, we demonstrate that a skin-derived endogenous peptide, peptide deregulated in hypertrophic scar-1 (PDHS1), with the sequence IATTTASAATAAAIGATPRAK, inhibits cell proliferation, promotes apoptosis, decreases the proportion of cells in S phase, and decreases collagen synthesis in hypertrophic scar fibroblasts. Additionally, treatment with PDHPS1 alleviates hypertrophic scarring in a rabbit ear model. PDHPS1 was found to bind to focal adhesion kinase (FAK) and to decrease its activity. PDHPS1 was also shown to bind to pyruvate kinase M2 (PKM2) and to decreased its expression. Smad2 phosphorylation is also inhibited by treatment with PDHPS1. Overexpression of FAK rescues the decreased expression of COL3A1 induced by PDHPS1 treatment. Targeted metabolomics revealed that PDHPS1 reprogramed metabolism that related to amino acid synthesis, leading to decreases of the key glycolysis intermediates glucose-6-phosphate and fructose-6-phosphate. These results demonstrated that the endogenous peptide PDHPS1 alleviates hypertrophic scar fibrosis in vitro and in vivo by targeting FAK and PKM2 and remodeling the metabolic landscape. Overall, treatment with PDHPS1 is a potential therapeutic strategy for hypertrophic scarring.

Epidermal Potentiation of Dermal Fibrosis: Lessons from Occlusion and Mucosal Healing

Fibrotic skin conditions, such as hypertrophic and keloid scars, frequently result from injury to the skin and as sequelae to surgical procedures. The development of skin fibrosis may lead to patient discomfort, limitation in range of motion, and cosmetic disfigurement. Despite the frequency of skin fibrosis, treatments that seek to address the root causes of fibrosis are lacking. Much research into fibrotic pathophysiology has focused on dermal pathology, but less research has been performed to understand aberrations in fibrotic epidermis, leading to an incomplete understanding of dermal fibrosis. The literature on occlusion, a treatment modality known to reduce dermal fibrosis, in part through accelerating wound healing and regulating aberrant epidermal inflammation that otherwise drives fibrosis in the dermis, is reviewed. There is a focus on epidermal-dermal crosstalk, which contributes to the development and maintenance of dermal fibrosis, an underemphasized interplay that may yield novel strategies for treatment if understood in more detail.

Keloid Patient Plasma-Derived Exosomal hsa_circ_0020792 Promotes Normal Skin Fibroblasts Proliferation, Migration, and Fibrogenesis via Modulating miR-193a-5p and Activating TGF-β1/Smad2/3 Signaling

Background

Keloids are fibroproliferative disorders, which seriously affect the quality of life of patients with keloids. Additionally, circRNAs are enriched within exosomes derived from human blood samples, whereas their relationship with keloids remains largely unknown. It has been reported that hsa_circ_0020792 was abnormally upregulated in keloid tissues. However, the role of keloid patient plasma-derived exosomal hsa_circ_0020792 in the formation and development of keloids is not well understood.

Methods

Exosomes were isolated from the peripheral blood plasma of the patients with keloids (keloid patient-Exo) and healthy controls (Healthy control-Exo). The hsa_circ_0020792 and miR-193a-5p levels in keloid patient-Exo and healthy control-Exo, as well as in keloid fibroblasts and normal skin fibroblasts (NFs) were evaluated by RT-qPCR.

Results

The level of hsa_circ_0020792 was remarkably increased in keloid patient-Exo and keloid fibroblasts compared with that in Healthy control-Exo and NFs, respectively. In addition, keloid patient-Exo obviously enhanced the viability, migration, and extracellular matrix (ECM) synthesis, but reduced the apoptosis of NFs. Moreover, keloid patient-Exo notably promoted the fibrogenesis of NFs, as characterized by enhanced TGF-β signaling, increased expressions of phosphorylated Smad2/3. However, downregulation of hsa_circ_0020792 markedly reversed the promoting effects of keloid patient-Exo on cell growth, migration, and myofibroblast activation and fibrogenesis. Furthermore, downregulation of hsa_circ_0020792 significantly reduced the viability, migration, and fibrogenesis in NFs, whereas these phenomena were reversed by miR-193a-5p inhibitor.

Conclusion

Collectively, keloid patient plasma-derived exosomal hsa_circ_0020792 could promote the proliferation, migration, and fibrogenesis of NFs via modulating miR-193a-5p and activating TGF-β1/Smad2/3 signaling.

TMT-Based Comparative Peptidomics Analysis of Rice Seedlings under Salt Stress: An Accessible Method to Explore Plant Stress-Tolerance Processing

Rice (Oryza sativa L.) is an important staple crop, particularly in Asia, and abiotic stress conditions easily reduce its yields. Salt stress is one of the critical factors affecting rice growth and yield. In this study, a tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for peptidomics analysis. A total of 911 and 1263 nonredundant peptides were identified in two pooled shoot tissue samples, while there were 770 and 672 nonredundant peptides in two pooled root tissue samples, respectively. Compared with the control groups, dozens to hundreds of differentially expressed peptides (DEPs) were characterized in all treatment groups. To explore the potential functions of these DEPs, we analyzed the basic characteristics of DEPs and further analyzed the annotated Gene Ontology terms according to their precursor proteins. Several DEP precursor proteins were closely related to the response to salt stress, and some were derived from the functional domains of their corresponding precursors. The germination rate and cotyledon greening rate of transgenic Arabidopsis expressing two DEPs, OsSTPE2 and OsSTPE3, were significantly enhanced under salt stress. The described workflow enables the discovery of a functional pipeline for the characterization of the plant peptidome and reveals two new plant peptides that confer salinity tolerance to plants. Data are available via ProteomeXchange with identifier PXD037574.

OMICS Approaches Evaluating Keloid and Hypertrophic Scars

Abnormal scar formation during wound healing can result in keloid and hypertrophic scars, which is a major global health challenge. Such abnormal scars can cause significant physiological pain and psychological distress and become a financial burden. Due to the biological complexity of scar formation, the pathogenesis of such scars and how to prevent them from forming remains elusive. In this review paper, we delve into the world of "omics" approaches to study abnormal scars and provide examples of genomics, transcriptomics, proteomics, epigenomics, and metabolomics. The benefits of "omics" approaches are that they allow for high-throughput studies and the analysis of 100s to 1000s of genes and proteins with the accumulation of large quantities of data. Currently in the field, there is a lack of "omics" review articles describing pathological scars. In this review, we summarize genome-wide linkage analysis, genome-wide association studies, and microarray data to name a few omics technologies. Such data can provide novel insights into different molecular pathways and identify novel factors which may not be captured through small-scale laboratory techniques.

Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides

Wound infection is a common and serious medical condition with an unmet need for improved diagnostic tools. A peptidomic approach, aided by mass spectrometry and bioinformatics, could provide novel means of identifying new peptide biomarkers for wound healing and infection assessment. Wound fluid is suitable for peptidomic analysis since it is both intimately tied to the wound environment and is readily available. In this study we investigate the peptidomes of wound fluids derived from surgical drainages following mastectomy and from wound dressings following facial skin grafting. By applying sorting algorithms and open source third party software to peptidomic label free tandem mass spectrometry data we provide an unbiased general methodology for analyzing and differentiating between peptidomes. We show that the wound fluid peptidomes of patients are highly individualized. However, differences emerge when grouping the patients depending on wound type. Furthermore, the abundance of peptides originating from documented antimicrobial regions of hemoglobin in infected wounds may contribute to an antimicrobial wound environment, as determined by in silico analysis. We validate our findings by compiling literature on peptide biomarkers and peptides of physiological significance and cross checking the results against our dataset, demonstrating that well-documented peptides of immunological significance are abundant in infected wounds, and originate from certain distinct regions in proteins such as hemoglobin and fibrinogen. Ultimately, we have demonstrated the power using sorting algorithms and open source software to help yield insights and visualize peptidomic data.

Comparative peptidome profiling reveals critical roles for peptides in the pathology of pancreatic cancer

BACKGROUNDS/AIMS

Pancreatic cancer is a digestive system tumour disease with a notably poor prognosis and a 5-year survival rate of less than 10 %. In recent years, peptide drugs have shown great clinical value in antitumour applications. We aim to identify differentially expressed peptides by using peptidomics techniques to explore the mechanisms involved in the development and pathology of pancreatic cancer.

METHODS

We performed peptidomic analysis of pancreatic cancer and paired paracancerous tissues by using ITRAQ labelling technology and conducted in-depth bioinformatics analysis and functional studies on differentially expressed peptides.

RESULTS

A total of 2,881 peptides were identified, of which 133 were differentially expressed (116 were upregulated and 17 were downregulated). By using GO analysis, the differentially expressed peptides were found to be closely related to the tumour microenvironment and extracellular matrix. KEGG enrichment analysis revealed that precursor proteins were closely related to the T2DM and RAS signalling pathways. The endogenous peptide P1DG can significantly inhibit the proliferation, migration and invasion of pancreatic cancer cells.

CONCLUSION

P1DG and its precursor GAPDH may be closely related to the proliferation, migration and invasion of pancreatic cancer. Peptidomics can aid in understanding the pathogenesis of pancreatic cancer more comprehensively.

Emerging evidence for the roles of peptide in hypertrophic scar

Hypertrophic scar is a dermal fibroproliferative disorder characterized by excess collagen deposition. There are many existing treatment modalities, but none works perfectly in all individuals. Recently, evidence is increasing that peptides can play crucial roles in the prevention or treatment of hypertrophic scar. The peptides may be derived from growth factors, hormones, and intracellular products of proteolysis. In vitro and in vivo studies have revealed that a number of peptides, usually topically applied, have beneficial effects on fibroblasts in rat, mouse, hamster, pig and rabbit scar models. The length of such peptides typically ranges between 10 and 15 amino acids (aa). Peptides may reduce scar progenitors, prevent excessive scarring, decrease scar growth, speed re-epithelialization and promote scar maturation through multiple mechanisms. They may target TGF-β signaling, fibroblast function or collagen modulation, inflammation, renin angiotensin system, gap junction and other pathways. However, there is a paucity of evidence regarding specific binding sites for these peptides in scar models. Here, we review current research progress on the roles of peptides and underlying mechanisms in hypertrophic scar. We also discuss the clinical potential of peptides as therapeutic agents in scarring. Finally, the functions of several peptide-related compounds in hypertrophic scar are summarized.

Mass spectrometry-based peptidome profiling of human serous ovarian cancer tissues

BACKGROUND

Bioactive peptides existing in vivo have been considered as an important class of natural medicines for the treatment of diseases. Peptidome analysis of tissues and biofluids had provided important information about the differentially expressed bioactive peptides in vivo.

METHODS

Here, we analyzed the peptidome of serous ovarian cancer tissue samples and normal ovarian epithelial tissue samples by mass spectrometry and further investigated the possible bioactive peptides that were differentially expressed.

RESULTS

We identified 634 differentially expressed peptides, 508 of these peptides were highly abundant in serous ovarian cancer tissues, a result consistent with higher protease activity in ovarian cancer patients. The difference in preferred cleavage sites between the serous ovarian cancer tissues and normal ovarian epithelium indicated the characteristic peptidome of ovarian cancer and the nature of cancer-associated protease activity. Interestingly, KEGG pathway analysis of the peptide precursors indicated that the differentially regulated pathways in ovarian cancer are highly consistent with the pathways discovered in other cancers. Besides, we found that a proportion of the differentially expressed peptides are similar to the known immune-regulatory peptides and anti-bacterial peptides. Then we further investigated the function of the two down-regulated peptides in ovarian cancer cells and found that peptide P1DS significantly inhibited the invasion and migration of OVCAR3 and SKOV3 ovarian cancer cells.

CONCLUSIONS

Our results are the first to identify the differentially expressed peptides between the serous ovarian cancer tissue and the normal ovarian epithelium. Our results indicate that bioactive peptides involved in tumorigenesis are existed in vivo.