Membrane proteomic analysis comparing squamous cell lung cancer tissue and tumour-adjacent normal tissue

AFM-Based Poroelastic@Membrane Analysis of Cells and its Opportunities for Translational Medicine

Cell mechanics is an emerging field of research for translational medicine. Here, the cell is modeled as poroelastic cytoplasm wrapped by tensile membrane (poroelastic@membrane model) and is characterized by the atomic force microscopy (AFM). The parameters of cytoskeleton network modulus EC , cytoplasmic apparent viscosity ηC , and cytoplasmic diffusion coefficient DC are used to describe the mechanical behavior of cytoplasm, and membrane tension γ is used to evaluate the cell membrane. Poroelastic@membrane analysis of breast cells and urothelial cells show that non-cancer cells and cancer cells have different distribution regions and distribution trends in the four-dimensional space composed of EC , ηC . From non-cancer to cancer cells, there is often a trend of γ, EC , ηC decreases and DC increases. Patients with urothelial carcinoma at different malignant stages can be distinguished at high sensitivity and specificity by analyzing the urothelial cells from tissue or urine. However, sampling directly from tumor tissues is an invasive method, may lead to undesirable consequences. Thus, AFM-based poroelastic@membrane analysis of urothelial cells from urine may provide a non-invasive and no-bio-label method to detecting urothelial carcinoma.

Advances in the application of proteomics in lung cancer

Although the incidence and mortality of lung cancer have decreased significantly in the past decade, it is still one of the leading causes of death, which greatly impairs people’s life and health. Proteomics is an emerging technology that involves the application of techniques for identifying and quantifying the overall proteins in cells, tissues and organisms, and can be combined with genomics, transcriptomics to form a multi-omics research model. By comparing the content of proteins between normal and tumor tissues, proteomics can be applied to different clinical aspects like diagnosis, treatment, and prognosis, especially the exploration of disease biomarkers and therapeutic targets. The applications of proteomics have promoted the research on lung cancer. To figure out potential applications of proteomics associated with lung cancer, we summarized the role of proteomics in studies about tumorigenesis, diagnosis, prognosis, treatment and resistance of lung cancer in this review, which will provide guidance for more rational application of proteomics and potential therapeutic strategies of lung cancer.

Ubiquitination-mediated molecular pathway alterations in human lung squamous cell carcinomas identified by quantitative ubiquitinomics

Abnormal ubiquitination is extensively associated with cancers. To investigate human lung cancer ubiquitination and its potential functions, quantitative ubiquitinomics was carried out between human lung squamous cell carcinoma (LSCC) and control tissues, which characterized a total of 627 ubiquitin-modified proteins (UPs) and 1209 ubiquitinated lysine sites. Those UPs were mainly involved in cell adhesion, signal transduction, and regulations of ribosome complex and proteasome complex. Thirty three UPs whose genes were also found in TCGA database were significantly related to overall survival of LSCC. Six significant networks and 234 hub molecules were obtained from the protein-protein interaction (PPI) analysis of those 627 UPs. KEGG pathway analysis of those UPs revealed 47 statistically significant pathways, and most of which were tumor-associated pathways such as mTOR, HIF-1, PI3K-Akt, and Ras signaling pathways, and intracellular protein turnover-related pathways such as ribosome complex, ubiquitin-mediated proteolysis, ER protein processing, and proteasome complex pathways. Further, the relationship analysis of ubiquitination and differentially expressed proteins shows that ubiquitination regulates two aspects of protein turnover - synthesis and degradation. This study provided the first profile of UPs and molecular networks in LSCC tissue, which is the important resource to insight into new mechanisms, and to identify new biomarkers and therapeutic targets/drugs to treat LSCC.

Advances in sample preparation for membrane proteome quantification

Membrane proteins mediate various biological processes. Most drugs commercially available target proteins on the cell surface. Therefore, proteomics of plasma membrane proteins provides useful information for drug discovery. However, membrane proteins are one of the most difficult biological groups to quantify by proteomics because of their hydrophobicity and low protein content. To obtain unbiased quantitative membrane proteomics data, specific strategies should be followed during sample preparation. This review explores the most recent advances in sample preparation for the quantitative analysis of the membrane proteome, including enrichment by subcellular fractionation and trypsin digestion.

AFM Force Relaxation Curve Reveals That the Decrease of Membrane Tension Is the Essential Reason for the Softening of Cancer Cells

Differences in stiffness constitute an extremely important aspect of the mechanical differences between cancer cells and normal cells, and atomic force microscopy (AFM) is the most commonly used tool to characterize the difference in stiffness. However, the process of mechanical characterization using AFM has been controversial and the influence of the membrane tension on AFM measurement results was often ignored. Here, a physical model involving a simultaneous consideration of the effects of the cell membrane, cytoskeleton network and cytosol was proposed. We carried out a theoretical analysis of AFM force relaxation curves, and as a result solved many of the remaining controversial issues regarding AFM-based mechanical characterization of cells, and provided a quantitative solution for the membrane tension measured using AFM indentation experiments for the first time. From the results of experiments on cells with different adherent shapes and different pairs of normal cells and cancer cells, we found additional force provided by membrane tension to be the main component of the force applied to the AFM probe, with decreased cell membrane tension being the essential reason for the greater softness of cancer cells than of normal cells. Hence, regulating membrane tension may become an important method for regulating the behavior of cancer cells.

Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks

Plasma membranes (PMs) act as primary cellular checkpoints for sensing signals and controlling solute transport. Membrane proteins communicate with intracellular processes through protein interaction networks. Deciphering these signaling networks provides crucial information for elucidating in vivo cellular regulation. Large-scale proteomics enables system-wide characterization of the membrane proteome, identification of ligand-receptor pairs, and elucidation of signals originating at membranes. In this review we assess recent progress in the development of mass spectrometry (MS)-based proteomic pipelines for determining membrane signaling pathways. We focus in particular on current techniques for the analysis of membrane protein phosphorylation and interaction, and how these proteins may be connected to downstream changes in gene expression, metabolism, and physiology.

Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics

We found that nuclear envelopes stabilize against surfactants in the presence of ethylene glycol (EG). We, therefore, developed a novel subcellular fractionation approach for proteomics using RIPA buffer containing EG and phase transfer surfactants. This method involves separating the cells into the cytoplasm, organelles, and nucleus, including intermediate filaments without ultracentrifugation. These fractions are directly applicable to sample preparation for shotgun proteomics as they have no mass spectrometry (MS)-incompatible chemicals, whereas those separated by traditional fractionation protocols require desalting. This protocol is successfully applied to subcellular fractionation with only 3.5 × 10⁵ cells. Here, it was combined with phosphoproteomics and proteomics to identify phosphorylation sites regulating protein subcellular localization. In total, 59 phosphorylation sites on 42 phosphopeptides and 32 proteins showing different enrichment patterns between phosphoproteomics and the corresponding proteomics were identified, which are potential candidate sites to regulate the protein subcellular localization, including serine 706 on CD44 and serine 22 on lamin A/C.

Imaging of human cells exposed to an antifungal antibiotic amphotericin B reveals the mechanisms associated with the drug toxicity and cell defence

Amphotericin B is an antibiotic used in pharmacotherapy of life-threatening mycotic infections. Unfortunately, the applicability of this antibiotic is associated with highly toxic side effects. In order to understand molecular mechanisms underlying toxicity of amphotericin B to patients, two cell lines, human normal colon epithelial cells (CCD 841 CoTr) and human colon adenocarcinoma cells (HT-29) were cultured in the presence of the drug and imaged with the application of fluorescence lifetime imaging microscopy and Raman scattering microscopy. The results of the cell viability assays confirm high toxicity of amphotericin B towards human cells. The images recorded demonstrate effective binding of amphotericin B to biomembranes. Analysis of the images reveals the operation of a defence mechanism based upon the elimination of molecules of the drug from living cells via formation of small amphotericin B-containing lipid vesicles. The fact that exosomes formed are devoid of cholesterol, as concluded on the basis of the results of Raman analysis, suggests that sequestration of sterols from the lipid phase of biomembranes is not a sole mechanism responsible for the toxic side effects of amphotericin B. Alternatively, the results imply that molecules of the drug present directly within the hydrophobic membrane core disturb the lipid membrane structure and affect their biological functions.

Cell-surface marker discovery for lung cancer

Lung cancer is the leading cause of cancer deaths in the United States. Novel lung cancer targeted therapeutic and molecular imaging agents are needed to improve outcomes and enable personalized care. Since these agents typically cannot cross the plasma membrane while carrying cytotoxic payload or imaging contrast, discovery of cell-surface targets is a necessary initial step. Herein, we report the discovery and characterization of lung cancer cell-surface markers for use in development of targeted agents. To identify putative cell-surface markers, existing microarray gene expression data from patient specimens were analyzed to select markers with differential expression in lung cancer compared to normal lung. Greater than 200 putative cell-surface markers were identified as being overexpressed in lung cancers. Ten cell-surface markers (CA9, CA12, CXorf61, DSG3, FAT2, GPR87, KISS1R, LYPD3, SLC7A11 and TMPRSS4) were selected based on differential mRNA expression in lung tumors vs. non-neoplastic lung samples and other normal tissues, and other considerations involving known biology and targeting moieties. Protein expression was confirmed by immunohistochemistry (IHC) staining and scoring of patient tumor and normal tissue samples. As further validation, marker expression was determined in lung cancer cell lines using microarray data and Kaplan–Meier survival analyses were performed for each of the markers using patient clinical data. High expression for six of the markers (CA9, CA12, CXorf61, GPR87, LYPD3, and SLC7A11) was significantly associated with worse survival. These markers should be useful for the development of novel targeted imaging probes or therapeutics for use in personalized care of lung cancer patients.

[Research Progress of Biomakers Proteomics-based in Lung Cancer]

蛋白组学技术可以应用于癌症研究来检测差异蛋白质表达以发现癌症生物标志物。肺癌的生物标志物在肺癌早期诊断、指导治疗和预后监测方面起着关键作用。因此，迫切需要确定新的早期诊断和预后指标以开辟新的治疗途径。本文简要介绍了基于蛋白质组学的肺癌生物标志物的最新研究报告。他包括作为诊断、预后和预测性的生物标志物，以及基于最近发表文献的基础上和我们所做的相关工作的总结。

ROS-mediated EB1 phosphorylation through Akt/GSK3β pathway: implication in cancer cell response to microtubule-targeting agents

Microtubule-targeting agents (MTAs) are largely administered in adults and children cancers. Better deciphering their mechanism of action is of prime importance to develop more convenient therapy strategies. Here, we addressed the question of how reactive oxygen species (ROS) generation by mitochondria can be necessary for MTA efficacy. We showed for the first time that EB1 associates with microtubules in a phosphorylation-dependent manner, under control of ROS. By using phospho-defective mutants, we further characterized the Serine 155 residue as critical for EB1 accumulation at microtubule plus-ends, and both cancer cell migration and proliferation. Phosphorylation of EB1 on the Threonine 166 residue triggered opposite effects, and was identified as a requisite molecular switch in MTA activities. We then showed that GSK3β activation was responsible for MTA-triggered EB1 phosphorylation, resulting from ROS-mediated inhibition of upstream Akt. We thus disclosed here a novel pathway by which generation of mitochondrial ROS modulates microtubule dynamics through phosphorylation of EB1, improving our fundamental knowledge about this oncogenic protein, and pointing out the need to re-examine the current dogma of microtubule targeting by MTAs. The present work also provides a strong mechanistic rational to the promising therapeutic strategies that currently combine MTAs with anti-Akt targeted therapies.

Stable isotope dilution mass spectrometry for membrane transporter quantitation

This review provides an introduction to stable isotope dilution mass spectrometry (MS) and its emerging applications in the analysis of membrane transporter proteins. Various approaches and application examples, for the generation and use of quantitation reference standards—either stable isotope-labeled peptides or proteins—are discussed as they apply to the MS quantitation of membrane proteins. Technological considerations for the sample preparation of membrane transporter proteins are also presented.

Inhibition of Raf-MEK-ERK and hypoxia pathways by Phyllanthus prevents metastasis in human lung (A549) cancer cell line

BACKGROUND

Lung cancer constitutes one of the malignancies with the greatest incidence and mortality rates with 1.6 million new cases and 1.4 million deaths each year. Prognosis remains poor due to deleterious development of multidrug resistance resulting in less than 15% lung cancer patients reaching five years survival. We have previously shown that Phyllanthus induced apoptosis in conjunction with its antimetastastic action. In the current study, we aimed to determine the signaling pathways utilized by Phyllanthus to exert its antimetastatic activities.

METHODS

Cancer 10-pathway reporter array was performed to screen the pathways affected by Phyllanthus in lung carcinoma cell line (A549) to exert its antimetastatic effects. Results from this array were then confirmed with western blotting, cell cycle analysis, zymography technique, and cell based ELISA assay for human total iNOS. Two-dimensional gel electrophoresis was subsequently carried out to study the differential protein expressions in A549 after treatment with Phyllanthus.

RESULTS

Phyllanthus was observed to cause antimetastatic activities by inhibiting ERK1/2 pathway via suppression of Raf protein. Inhibition of this pathway resulted in the suppression of MMP2, MMP7, and MMP9 expression to stop A549 metastasis. Phyllanthus also inhibits hypoxia pathway via inhibition of HIF-1α that led to reduced VEGF and iNOS expressions. Proteomic analysis revealed a number of proteins downregulated by Phyllanthus that were involved in metastatic processes, including invasion and mobility proteins (cytoskeletal proteins), transcriptional proteins (proliferating cell nuclear antigen; zinc finger protein), antiapoptotic protein (Bcl2) and various glycolytic enzymes. Among the four Phyllanthus species tested, P. urinaria showed the greatest antimetastatic activity.

CONCLUSIONS

Phyllanthus inhibits A549 metastasis by suppressing ERK1/2 and hypoxia pathways that led to suppression of various critical proteins for A549 invasion and migration.