Quantitative proteomic analysis of global effect of LLL12 on U87 cell's proteome: An insight into the molecular mechanism of LLL12

Potential of Natural Products in the Treatment of Glioma: Focus on Molecular Mechanisms

Despite the waning of traditional treatments for glioma due to possible long-term issues, the healing possibilities of substances derived from nature have been reignited in the scientific community. These natural substances, commonly found in fruits and vegetables, are considered potential alternatives to pharmaceuticals, as they have been shown in prior research to impact pathways surrounding cancer progression, metastases, invasion, and resistance. This review will explore the supposed molecular mechanisms of different natural components, such as berberine, curcumin, coffee, resveratrol, epigallocatechin-3-gallate, quercetin, tanshinone, silymarin, coumarin, and lycopene, concerning glioma treatment. While the benefits of a balanced diet containing these compounds are widely recognized, there is considerable scope for investigating the efficacy of these natural products in treating glioma.

Multifaceted Pharmacological Potentials of Curcumin, Genistein, and Tanshinone IIA through Proteomic Approaches: An In-Depth Review

Phytochemicals possess various intriguing pharmacological properties against diverse pathological conditions. Extensive studies are on-going to understand the structural/functional properties of phytochemicals as well as the molecular mechanisms of their therapeutic function against various disease conditions. Phytochemicals such as curcumin (Cur), genistein (Gen), and tanshinone-IIA (Tan IIA) have multifaceted therapeutic potentials and various efforts are in progress to understand the molecular dynamics of their function with different tools and technologies. Cur is an active lipophilic polyphenol with pleiotropic function, and it has been shown to possess various intriguing properties including antioxidant, anti-inflammatory, anti-microbial, anticancer, and anti-genotoxic properties besides others beneficial properties. Similarly, Gen (an isoflavone) exhibits a wide range of vital functions including antioxidant, anti-inflammatory, pro-apoptotic, anti-proliferative, anti-angiogenic activities etc. In addition, Tan IIA, a lipophilic compound, possesses antioxidant, anti-angiogenic, anti-inflammatory, anticancer activities, and so on. Over the last few decades, the field of proteomics has garnered great momentum mainly attributed to the recent advancement in mass spectrometry (MS) techniques. It is envisaged that the proteomics technology has considerably contributed to the biomedical research endeavors lately. Interestingly, they have also been explored as a reliable approach to understand the molecular intricacies related to phytochemical-based therapeutic interventions. The present review provides an overview of the proteomics studies performed to unravel the underlying molecular intricacies of various phytochemicals such as Cur, Gen, and Tan IIA. This in-depth study will help the researchers in better understanding of the pharmacological potential of the phytochemicals at the proteomics level. Certainly, this review will be highly instrumental in catalyzing the translational shift from phytochemical-based biomedical research to clinical practice in the near future.

The development and clinical applications of proteomics: an Indian perspective

INTRODUCTION

Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic.

AREAS COVERED

This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed.

EXPERT OPINION

The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.

Identification and Analysis of Glioblastoma Biomarkers Based on Single Cell Sequencing

Glioblastoma (GBM) is one of the most common and aggressive primary adult brain tumors. Tumor heterogeneity poses a great challenge to the treatment of GBM, which is determined by both heterogeneous GBM cells and a complex tumor microenvironment. Single-cell RNA sequencing (scRNA-seq) enables the transcriptomes of great deal of individual cells to be assayed in an unbiased manner and has been applied in head and neck cancer, breast cancer, blood disease, and so on. In this study, based on the scRNA-seq results of infiltrating neoplastic cells in GBM, computational methods were applied to screen core biomarkers that can distinguish the discrepancy between GBM tumor and pericarcinomatous environment. The gene expression profiles of GBM from 2343 tumor cells and 1246 periphery cells were analyzed by maximum relevance minimum redundancy (mRMR). Upon further analysis of the feature lists yielded by the mRMR method, 31 important genes were extracted that may be essential biomarkers for GBM tumor cells. Besides, an optimal classification model using a support vector machine (SVM) algorithm as the classifier was also built. Our results provided insights of GBM mechanisms and may be useful for GBM diagnosis and therapy.

Overview of the STAT-3 signaling pathway in cancer and the development of specific inhibitors

Signal transducer and activator of transcription (STAT) proteins represent novel therapeutic targets for the treatment of cancer. In particular, STAT-3 serves critical roles in several cellular processes, including the cell cycle, cell proliferation, cellular apoptosis and tumorigenesis. Persistent activation of STAT-3 has been reported in a variety of cancer types, and a poor prognosis of cancer may be associated with the phosphorylation level of STAT-3. Furthermore, elevated STAT-3 activity has been demonstrated in a variety of mammalian cancers, both in vitro and in vivo. This indicates that STAT-3 serves an important role in the progression of numerous cancer types. A significant obstacle in developing STAT-3 inhibitors is the demonstration of the antitumor efficacy in in vivo systems and the lack of animal models for human tumors. Therefore, it is crucial to determine whether available STAT-3 inhibitors are suitable for clinical trials. Moreover, further preclinical studies are necessary to focus on the impact of STAT-3 inhibitors on tumor cells. When considering STAT-3 hyper-activation in human cancer, selective targeting to these proteins holds promise for significant advancement in cancer treatment. In the present study, advances in our knowledge of the structure of STAT-3 protein and its regulatory mechanisms are summarized. Moreover, the STAT-3 signaling pathway and its critical role in malignancy are discussed, in addition to the development of STAT-3 inhibitors in various cancer types.

ACT001 modulates the NF-κB/MnSOD/ROS axis by targeting IKKβ to inhibit glioblastoma cell growth

Glioblastomas are high-grade brain tumors with poor prognoses, and new therapeutic approaches for these tumors are critically needed. This study revealed the underlying mechanisms of a new orphan drug, ACT001, that is currently in clinical trials for the treatment of advanced glioblastoma in Australia and China. ACT001 significantly suppressed glioma cell proliferation and induced apoptosis and cell cycle arrest in vitro, as determined by Cell Counting Kit-8 assays and flow cytometry. In addition, U-118 MG cells with high expression of p-IKKβ were sensitive to ACT001. Changes in the oxidative stress pathway in U-118 MG cells were detected with the isobaric tags for relative and absolute quantitation (iTRAQ) method. We further verified that ACT001 elevated the levels of reactive oxygen species (ROS) by regulating NF-κB-targeted MnSOD. ACT001 markedly inhibited NF-κB activation by directly binding IKKβ and inhibiting its phosphorylation. Overexpression of IKKβ markedly attenuated the changes in MnSOD and NOX1, indicating that ACT001 increased the levels of ROS by reducing the protein expression of p-IKKβ. Furthermore, ACT001 reduced cyclin B1/CDC2 expression and triggered G₂/M phase arrest by increasing ROS production. ACT001 also upregulated the expression of Bax and Bim and induced apoptosis in a ROS-dependent manner. ACT001 effectively suppressed the growth of U-118 MG tumors in BALB/c nude mice and GL-261-luciferase tumors in C57BL/6 J mice. Finally, ACT001 downregulated the expression of p-p65, MnSOD, cyclin B1, CDC2, and Ki67 in U-118 MG tumor tissues. Patients with activated NF-κB signaling should thus be given priority for enrollment in future phase II clinical trials. KEY MESSAGES: ACT001 directly bind to IKKβ and inhibited its phosphorylation. The inhibition of p-IKKβ induced the generation of ROS. ACT001 promoted the generation of ROS by regulating MnSOD expression to induce G₂/M phase arrest.

Phosphoglycerate Mutase 1 Promotes Cell Proliferation and Neuroblast Differentiation in the Dentate Gyrus by Facilitating the Phosphorylation of cAMP Response Element-Binding Protein

In a previous study, we observed a significant increase in phosphoglycerate mutase 1 (PGAM1) levels after pyridoxine treatment. In the present study, we investigated the effects of PGAM1 on novel object recognition, cell proliferation, and neuroblast differentiation in the dentate gyrus. We generated a Tat-PGAM1 fusion protein to cross the blood-brain barrier and neuronal plasma membrane. We administered the Tat peptide, control-PGAM1, or Tat-PGAM1 fusion protein to 8-week-old mice once a day for 3 weeks and tested novel object recognition memory. The mice were then euthanized to conduct western blot analysis for polyhistidine expression and immunohistochemical analysis for Ki67, doublecortin, and phosphorylated cAMP response element-binding protein. Mice treated with Tat peptide showed similar exploration times for familiar and new objects and the discrimination index was significantly lower in this group than in the control group. Tat-PGAM1 moderately increased the exploration time of new objects when compared to familiar objects, while the discrimination index was significantly higher in the Tat-PGAM1-treated group, but not in the control-PGAM1-treated group, when compared with the control group. Higher PGAM1 protein expression was observed in the hippocampus of Tat-PGAM1-treated mice when compared with the hippocampi of control, Tat peptide-, and control-PGAM1-treated mice, using western blot analysis. In addition, the numbers of proliferating cells and differentiated neuroblasts were significantly lower in the Tat peptide-treated group than in the control group. In contrast, the numbers of proliferating cells and differentiated neuroblasts in the dentate gyrus were higher in the Tat-PGAM1-treated group than in the control group. Administration of Tat-PGAM1 significantly facilitated the phosphorylation of cAMP response element-binding protein in the dentate gyrus. Administration of control-PGAM1 did not show any significant effects on novel object recognition, cell proliferation, and neuroblast differentiation in the dentate gyrus. These results suggest that PGAM1 plays a role in cell proliferation and neuroblast differentiation in the dentate gyrus via the phosphorylation of cAMP response element-binding protein in the hippocampus.

Expression and clinical significance of basic transcription factor 3 in nasopharyngeal carcinoma

Basic transcription factor 3 (BTF3), a transcription factor and modulator of apoptosis, is differentially expressed in carcinoma. To acquire further understanding of the involvement of BTF3 in carcinoma, the present study analyzed the expression of BTF3, as well as its role in cell function in nasopharyngeal carcinoma (NPC). BTF3 transcription rates in human NPC samples (n=46) and adjacent normal tissue samples (n=46) were analyzed using reverse transcription-quantitative polymerase chain reaction and immunohistochemistry. BTF3-silencing in NPC cells was performed via specific small interfering RNA molecules. The function of BTF3 was analyzed by proliferation assays and colony forming assays using a Cellomic assay system. The positive expression rates of BTF3 were significantly increased in cancerous tissues compared with those in adjacent tissues (P<0.05). In addition, BTF3-silencing decreased cell proliferation and colony formation (P<0.01) in TCA-8113 and 5–8F cells. BTF3 is overexpressed in NPC, and its silencing is associated with decreased cell proliferation and colony formation, enhanced apoptosis and cell cycle regulation of TCA-8113 and 5–8F cells.

Phosphoglycerate mutase 1 is highly expressed in C6 glioma cells and human astrocytoma

The aim of the present study was to examine the expression of phosphoglycerate mutase 1 (PGAM1) in astrocytomas, and to investigate its role in the progression of astrocytomas. The expression of PGAM1 mRNA in rat C6 glioma cells and normal astrocytes was determined using the reverse transcription-semi-quantitative polymerase chain reaction, and immunohistochemistry was used to detect the expression of PGAM1 protein in human astrocytomas and adjacent brain tissue. These data suggested that the expression of PGAM1 in rat C6 glioma cells was significantly increased compared with that of normal astrocytes (P<0.05), and the expression of PGAM1 protein in human astrocytoma tissue was significantly increased compared with that of the brain tissue surrounding the tumor (P<0.05). In addition, PGAM1 protein was more frequently expressed in high-grade astrocytomas compared with low-grade astrocytomas. These data indicate that the expression of PGAM1 is increased in C6 cells and human astrocytomas, and PGAM1 is probably involved in the tumorigenesis and progression of glioma, which may be a potential target for glioma treatment.

Differential proteomics research of Bacillus amyloliquefaciens and its genome-shuffled saltant for improving fengycin production

In the previous study, we used genome shuffling to improve fengycin production of the original strain Bacillus amyloliquefaciens ES-2-4. After two rounds of genome shuffling, a high-yield recombinant FMB72 strain that exhibited 8.30-fold increase in fengycin production was obtained. In this study, comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB72 strains was conducted to examine the differentially expressed proteins. In the shuffled strain FMB72, 50 differently expressed spots (p<0.05) were selected to be excised and analyzed using Matrix-Assisted Laser Desorption/Ionization Time of Flight/Time of Flight Mass Spectrometry, and finally 44 protein spots were confidently identified according to NCBI database. According to clusters of orthologous groups (COG) functional category analysis and related references, the differentially expressed proteins could be classified into several functional categories, including proteins involved in metabolism, energy generation and conversion, DNA replication, transcription, translation, ribosomal structure and biogenesis, cell motility and secretion, signal transduction mechanisms, general function prediction. Of the 44 identified proteins, signaling proteins ComA and Spo0A may positively regulate fengycin synthesis at transcriptional level. Taken together, the present study will be informative for exploring the exact roles of ComA and Spo0A in fengycin synthesis and explaining the molecular mechanism of fengycin synthesis.

Identification of Key Candidate Proteins and Pathways Associated with Temozolomide Resistance in Glioblastoma Based on Subcellular Proteomics and Bioinformatical Analysis

TMZ resistance remains one of the main reasons why treatment of glioblastoma (GBM) fails. In order to investigate the underlying proteins and pathways associated with TMZ resistance, we conducted a cytoplasmic proteome research of U87 cells treated with TMZ for 1 week, followed by differentially expressed proteins (DEPs) screening, KEGG pathway analysis, protein–protein interaction (PPI) network construction, and validation of key candidate proteins in TCGA dataset. A total of 161 DEPs including 65 upregulated proteins and 96 downregulated proteins were identified. Upregulated DEPs were mainly related to regulation in actin cytoskeleton, focal adhesion, and phagosome and PI3K-AKT signaling pathways which were consistent with our previous studies. Further, the most significant module consisted of 28 downregulated proteins that were filtered from the PPI network, and 9 proteins (DHX9, HNRNPR, RPL3, HNRNPA3, SF1, DDX5, EIF5B, BTF3, and RPL8) among them were identified as the key candidate proteins, which were significantly associated with prognosis of GBM patients and mainly involved in ribosome and spliceosome pathway. Taking the above into consideration, we firstly identified candidate proteins and pathways associated with TMZ resistance in GBM using proteomics and bioinformatic analysis, and these proteins could be potential biomarkers for prevention or prediction of TMZ resistance in the future.

Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast

Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy.

Proteomic level changes associated with S3I201 treated U87 glioma cells

Glioblastoma multiforme is Grade IV brain tumor associated with high mortality and limited therapeutics. Signal Transducer and Activator of Transcription 3 (STAT3) is persistently active in several cancers including gliomas, and plays a major role in disease progression and survival of glioma patients, thus being a potential therapeutic target for treatment. S3I201 and its analogs inhibit the transcriptional functions of STAT3 and reduce growth of tumor tissues. Here we have studied proteomic alteration associated with S3I201 treated U87 cells using 2-DE and Isobaric tags for relative and absolute quantitation coupled with mass spectrometry. This analysis revealed 136 differentially expressed proteins which were functionally classified with gene ontology analysis. Results showed metabolism, apoptosis, cytoskeletal behaviour, cell redox homeostasis and immune response as the most affected biological processes on S3I201 treatment. Apoptosis-inducing factor 1 mitochondrial, cyclophilin A and chloride intra-cellular channel protein 1 were found to be up-regulated which possibly contributes to its anti-tumorigenic function. Several glycolytic enzymes like phosphoglycerate mutase 1 were also found to be up-regulated and its expression was validated using immunoblot. Conclusively, our study shows the downstream effects of S3I201 in U87 glioma cells and suggests its therapeutic potential.

SIGNIFICANCE

Gliomas with constitutive expression can be treated with STAT3 inhibitors. S3I201, a STAT3 inhibitor, reduces the growth of glioma cells thus could be studied further for its application as anti-glioma agent. This study investigated proteomic alteration associated with S3I201 in U87 cells using complementary proteomic approaches, and our findings suggest that S3I201 influences central metabolism, apoptosis, cytoskeletal behaviour, cell redox homeostasis and immune response as the most affected biological processes which altogether contribute to its anti-tumorigenic activity. Several proteins were identified which may serve as prognostic or predictive markers in GBM. Apoptosis-inducing factor 1 mitochondrial and cyclophilin A were identified as potential therapeutic targets and further investigations on these candidates may facilitate therapeutic development and suggests that GBM therapy can be improved by targeting cellular metabolism and by using immunotherapy.

Increased intramuscular fat induced by reduced dietary protein in finishing pigs: effects on the longissimus lumborum muscle proteome

Reduced protein diets affects the amounts of proteins related to fibre type and structure and energy.

Feedback Activation of STAT3 as a Cancer Drug-Resistance Mechanism

Signal transducer and activator of transcription 3 (STAT3) plays crucial roles in several cellular processes such as cell proliferation and survival, and has been found to be aberrantly activated in many cancers. Much research has explored the leading mechanisms for regulating the STAT3 pathway and its role in promoting tumorigenesis. We focus here on recent evidence suggesting that feedback activation of STAT3 plays a prominent role in mediating drug resistance to a broad spectrum of targeted cancer therapies and chemotherapies. We highlight the potential of co-targeting STAT3 and its primary target to overcome drug resistance, and provide perspective on repurposing clinically approved drugs as STAT3 pathway inhibitors, in combination with the FDA-approved receptor tyrosine kinase (RTK) inhibitors, to improve clinical outcome of cancer treatment.

Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis

High resolution proteomics approaches have been successfully utilized for the comprehensive characterization of the cell proteome. However, in the case of quantitative proteomics an open question still remains, which quantification strategy is best suited for identification of biologically relevant changes, especially in clinical specimens. In this study, a thorough comparison of a label-free approach (intensity-based) and 8-plex iTRAQ was conducted as applied to the analysis of tumor tissue samples from non-muscle invasive and muscle-invasive bladder cancer. For the latter, two acquisition strategies were tested including analysis of unfractionated and fractioned iTRAQ-labeled peptides. To reduce variability, aliquots of the same protein extract were used as starting material, whereas to obtain representative results per method further sample processing and MS analysis were conducted according to routinely applied protocols. Considering only multiple-peptide identifications, LC-MS/MS analysis resulted in the identification of 910, 1092 and 332 proteins by label-free, fractionated and unfractionated iTRAQ, respectively. The label-free strategy provided higher protein sequence coverage compared to both iTRAQ experiments. Even though pre-fraction of the iTRAQ labeled peptides allowed for a higher number of identifications, this was not accompanied by a respective increase in the number of differentially expressed changes detected. Validity of the proteomics output related to protein identification and differential expression was determined by comparison to existing data in the field (Protein Atlas and published data on the disease). All methods predicted changes which to a large extent agreed with published data, with label-free providing a higher number of significant changes than iTRAQ. Conclusively, both label-free and iTRAQ (when combined to peptide fractionation) provide high proteome coverage and apparently valid predictions in terms of differential expression, nevertheless label-free provides higher sequence coverage and ultimately detects a higher number of differentially expressed proteins. The risk for receiving false associations still exists, particularly when analyzing highly heterogeneous biological samples, raising the need for the analysis of higher sample numbers and/or application of adjustment for multiple testing.

Elevated GAPDH expression is associated with the proliferation and invasion of lung and esophageal squamous cell carcinomas

Glyceraldehyde-3-phosphate dehydrogenase, is one of the most investigated housekeeping genes and widely used as an internal control in analysis of gene expression levels. The present study was designed to assess whether GAPDH is associated with cancer cell growth and progression and, therefore may not be a good internal control in cancer research. Our results from clinical tissue studies showed that the levels of GAPDH protein were significantly up-regulated in lung squamous cell carcinoma tissues, compared with the adjacent normal lung tissues, and this was confirmed by western blotting and immunohistochemistry. GAPDH knockdown by siRNA resulted in significant reductions in proliferation, migration, and invasion of lung squamous carcinoma cells in vitro. In a nude mouse cancer xenograft model, GAPDH knockdown significantly inhibited the cell proliferation and migration/invasion in vivo. In summary, GAPDH may not be an appropriate internal control for gene expression studies, especially in cancer research. The role of GAPDH in cancer development and progression should be further examined in pre-clinical and clinical studies.