Proteomic and phosphoproteomic profiling of urinary small extracellular vesicles in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most prevalent form of primary liver cancer and a major cause of cancer-related mortality worldwide. Small extracellular vesicles (sEVs) are heterogeneous populations of membrane-structured vesicles that can be found in many biological fluids and are currently considered as a potential source of disease-associated biomarkers for diagnosis. The purpose of this study was to define the proteomic and phosphoproteomic landscape of urinary sEVs in patients with HCC. Mass spectrometry-based methods were used to detect the global proteome and phosphoproteome profiles of sEVs isolated by differential ultracentrifugation. Label-free quantitation analysis showed that 348 differentially expressed proteins (DEPs) and 548 differentially expressed phosphoproteins (DEPPs) were identified in the HCC group. Among them, multiple phosphoproteins related to HCC, including HSP90AA1, IQGAP1, MTOR, and PRKCA, were shown to be upregulated in the HCC group. Pathway enrichment analysis indicated that the upregulated DEPPs participate in the regulation of autophagy, proteoglycans in cancer, and the MAPK/mTOR/Rap1 signaling pathway. Furthermore, kinase-substrate enrichment analysis revealed activation of MTOR, AKT1, MAP2Ks, and MAPKs family kinases in HCC-derived sEVs, indicating that dysregulation of the MAPK and mTOR signaling pathways may be the primary sEV-mediated molecular mechanisms involved in the development and progression of HCC. This study demonstrated that urinary sEVs are enriched in proteomic and phosphoproteomic signatures that could be further explored for their potential use in early HCC diagnostic and therapeutic applications.

A Mesoporous Gold Sensor Unveils Phospho PD-L1 in Extracellular Vesicles as a Proxy for PD-L1 Expression in Lung Cancer Tissue

Immune checkpoint inhibitors (ICIs) targeting programmed cell death ligand 1 (PD-L1), or its receptor, PD-1 have improved survival in patients with non-small-cell lung cancer (NSCLC). Assessment of PD-L1 expression requires tissue biopsy or fine needle aspiration that are currently used to identify patients most likely to respond to single agent anti-PD-1/PD-L1 therapy. However, obtaining sufficient tissue to generate a PD-L1 tissue proportion score (TPS) ≥ 50% using immunohistochemistry remains a challenge that potentially may be overcome by liquid biopsies. This study utilized a mesoporous gold sensor (MGS) assay to examine the phosphorylation status of PD-L1 in plasma extracellular vesicles (EV pPD-L1) and PD-L1 levels in plasma from NSCLC patient samples and their association with tumor PD-L1 TPS. The 3-dimensional mesoporous network of the electrodes provides a large surface area, high signal-to-noise ratio, and a superior electro-conductive framework, thereby significantly improving the detection sensitivity of PD-L1 nanosensing. Test (n = 20) (Pearson's r = 0.99) and validation (n = 45) (Pearson's r = 0.99) cohorts show that EV pPD-L1 status correlates linearly with the tumor PD-L1 TPS assessed by immunohistochemistry irrespective of the tumor stage, with 64% of patients overall showing detectable EV pPD-L1 levels in plasma. In contrast to the EV pPD-L1 results, plasma PD-L1 levels did not correlate with the tumor PD-L1 TPS score or EV pPD-L1 levels. These data demonstrate that EV pPD-L1 levels may be used to select patients for appropriate PD-1 and PD-L1 ICI therapy regimens in early, locally advanced, and advanced NSCLC and should be tested further in randomized controlled trials. Most importantly, the assay used has a less than 24h turnaround time, facilitating adoption of the test into the routine diagnostic evaluation of patients prior to therapy.

A Novel Label-Free Electrochemical Immunosensor for the Detection of Thyroid Transcription Factor 1 Using Ribbon-like Tungsten Disulfide-Reduced Graphene Oxide Nanohybrids and Gold Nanoparticles

Thyroid transcription factor 1 (TTF1) is an important cancer-related biomarker for clinical diagnosis, especially for carcinomas of lung and thyroid origin. Herein, a novel label-free electrochemical immunosensor was prepared for TTF1 detection based on nanohybrids of ribbon-like tungsten disulfide-reduced graphene oxide (WS2-rGO) and gold nanoparticles (AuNPs). The proposed immunosensor employed H2O2 as the electrochemical probe because of the excellent peroxidase-like activity of ribbon-like WS2-rGO. The introduction of AuNPs not only enhanced the electrocatalytic activity of the immunosensor, but also provided immobilization sites for binding TTF1 antibodies. The electrochemical signals can be greatly amplified due to their excellent electrochemical performance, which realized the sensitive determination of TTF1 with a wide linear range of 0.025-50 ng mL-1 and a lower detection limit of 0.016 ng mL-1 (S/N = 3). Moreover, the immunosensor exhibited high selectivity, good reproducibility, and robust stability, as well as the ability to detect TTF1 in human serum with satisfactory results. These observed properties of the immunosensor enhance its potential practicability in clinical applications. This method can also be used for the detection of other tumor biomarkers by using the corresponding antigen-antibody complex.

Potential Avenues for Exosomal Isolation and Detection Methods to Enhance Small-Cell Lung Cancer Analysis

Around the world, lung cancer has long been the main factor in cancer-related deaths, with small-cell lung cancer (SCLC) being the deadliest form of lung cancer. Cancer cell-derived exosomes and exosomal miRNAs are considered promising biomarkers for diagnosing and prognosis of various diseases, including SCLC. Due to the rapidity of SCLC metastasis, early detection and diagnosis can offer better diagnosis and prognosis and therefore increase the patient's chances of survival. Over the past several years, many methodologies have been developed for analyzing non-SCLC-derived exosomes. However, minimal advances have been made in SCLC-derived exosome analysis methodologies. This Review discusses the epidemiology and prominent biomarkers of SCLC. Followed by a discussion about the effective strategies for isolating and detecting SCLC-derived exosomes and exosomal miRNA, highlighting the critical challenges and limitations of current methodologies. Finally, an overview is provided detailing future perspectives for exosome-based SCLC research.

Liquid Biopsy Snapshots of Key Phosphoproteomic Pathways in Lung Cancer Patients for Diagnosis and Therapy Monitoring

Phosphorylation is a post-translational modification in proteins that changes protein conformation and activity for regulating signal transduction pathways. This mechanism is frequently impaired in lung cancer, resulting in permanently active constitutive phosphorylation to initiate tumor growth and/or reactivate pathways in response to therapy. We developed a multiplexed phosphoprotein analyzer chip (MPAC) that enables rapid (detection time: 5 min) and sensitive (LOD: 2 pg/μL) detection of protein phosphorylation and presents phosphoproteomic profiling of major phosphorylation pathways in lung cancer. We monitored phosphorylated receptors and downstream proteins involved in mitogen-activated protein kinase (MAPK) and PI3K/AKT/mTOR pathways in lung cancer cell line models and patient-derived extracellular vesicles (EV). Using kinase inhibitor drugs in cell line models, we found that the drug can inhibit the phosphorylation and/or activation of the kinase pathway. We then generated a phosphorylation heatmap by EV phosphoproteomic profiling of plasma samples isolated from 36 lung cancer patients and 8 noncancer individuals. The heatmap showed a clear difference between the noncancer and cancer samples and identify the specific proteins that are activated in the cancer samples. Our data also showed that MPAC could monitor immunotherapy responses by assessment of the phosphorylation states of the proteins, particularly for PD-L1. Finally, with a longitudinal study, we found that the phosphorylation levels of the proteins were indicative of a positive response to therapy. We believe that this study will lead to personalized treatment by providing a better understanding of the active and resistant pathways and will provide a tool for selecting combined and targeted therapies for precision medicine.

Point-of-care cancer diagnostic devices: From academic research to clinical translation

Early and timely diagnosis of cancer plays a decisive role in appropriate treatment and improves clinical outcomes, improving public health. Significant advances in biosensor technologies are leading to the development of point-of-care (POC) diagnostics, making the testing process faster, easier, cost-effective, and suitable for on-site measurements. Moreover, the incorporation of various nanomaterials into the sensing platforms has yielded POC testing (POCT) platforms with enhanced sensitivity, cost-effectiveness and simplified detection schemes. POC cancer diagnostic devices provide promising platforms for cancer biomarker detection as compared to conventional in vitro diagnostics, which are time-consuming and require sophisticated instrumentation, centralized laboratories, and experienced operators. Current innovative approaches in POC technologies, including biosensors, smartphone interfaces, and lab-on-a-chip (LOC) devices are expected to quickly transform the healthcare landscape. However, only a few cancer POC devices (e.g. lateral flow platforms) have been translated from research laboratories to clinical care, likely due to challenges include sampling procedures, low levels of sensitivity and specificity in clinical samples, system integration and signal readout requirements. In this review, we emphasize recent advances in POC diagnostic devices for cancer biomarker detection and discuss the critical challenges which must be surmounted to facilitate their translation into clinical settings.

Biomedical analysis of exosomes using biosensing methods: recent progress

Exosomes are membrane-bound extracellular vesicles (EVs) that are produced in the endosomal compartments of most eukaryotic cells; they play important roles in intercellular communication in diverse cellular processes and transmit different types of biomolecules. Endocytic pathways release exosomes, which have diameters ranging from 50 to 200 nm. The unique functions of exosomes have been introduced as cancer bio-markers due to the cargo (protein, DNA and RNA) of external exosomes (tetraspanin) and internal exosomes (syntenin). The early detection of cancer by exosomes can be an excellent method for the treatment of cancer. Although detection methods based on exosomes are important, they require extensive sample purification, have high false-positive rates, and encounter labeling difficulties due to the small size of exosomes. Here, we have reviewed three major types of biosensors, namely, electrochemical biosensors, optical biosensors and electrochemiluminescence biosensors for the detection of exosomes released from breast, ovarian, pancreatic, lung, and cervical cancer cells. In addition, the importance of nanomaterials and their applications in the biomedical analysis of exosomes are discussed. Although exosomes can be used to identify various types of external and internal biomarkers by conjugating with recognition elements, most designed biosensors are based on CD9 and CD63. Therefore, the development of novel biosensors for the selective and sensitive detection of exosomes is a current challenge. We hope that this review will serve as a beneficial study for improving exosome detection in clinical samples.

Exosomes and Nanoengineering: A Match Made for Precision Therapeutics

Targeted exosomal delivery systems for precision nanomedicine attract wide interest across areas of molecular cell biology, pharmaceutical sciences, and nanoengineering. Exosomes are naturally derived 50-150 nm nanovesicles that play important roles in cell-to-cell and/or cell-to-tissue communications and cross-species communication. Exosomes are also a promising class of novel drug delivery vehicles owing to their ability to shield their payload from chemical and enzymatic degradations as well as to evade recognition by and subsequent removal by the immune system. Combined with a new class of affinity ligands known as aptamers or chemical antibodies, molecularly targeted exosomes are poised to become the next generation of smartly engineered nanovesicles for precision medicine. Here, recent advances in targeted exosomal delivery systems engineered by aptamer for future strategies to promote human health using this class of human-derived nanovesicles are summarized.

Applications and strategies in nanodiagnosis and nanotherapy in lung cancer

Lung cancer is the second most common cancer and the leading cause of death in both men and women in the world. Lung cancer is heterogeneous in nature and diagnosis is often at an advanced stage as it develops silently in the lung and is frequently associated with high mortality rates. Despite the advances made in understanding the biology of lung cancer, progress in early diagnosis, cancer therapy modalities and considering the mechanisms of drug resistance, the prognosis and outcome still remains low for many patients. Nanotechnology is one of the fastest growing areas of research that can solve many biological problems such as cancer. A growing number of therapies based on using nanoparticles (NPs) have successfully entered the clinic to treat pain, cancer, and infectious diseases. Recent progress in nanotechnology has been encouraging and directed to developing novel nanoparticles that can be one step ahead of the cancer reducing the possibility of multi-drug resistance. Nanomedicine using NPs is continuingly impacting cancer diagnosis and treatment. Chemotherapy is often associated with limited targeting to the tumor, side effects and low solubility that leads to insufficient drug reaching the tumor. Overcoming these drawbacks of chemotherapy by equipping NPs with theranostic capability which is leading to the development of novel strategies. This review provides a synopsis of current progress in theranostic applications for lung cancer diagnosis and therapy using NPs including liposome, polymeric NPs, quantum dots, gold NPs, dendrimers, carbon nanotubes and magnetic NPs.

Exosome-specific tumor diagnosis via biomedical analysis of exosome-containing microRNA biomarkers

Exosome-containing microRNAs (exomiRs) can be employed as potential biomarkers for tumor diagnosis and have drawn much attention in the past few years. However, the separation of exosomes and the detection of exomiRs are still inconvenient or even difficult to implement. Thus, it is important to develop a simple, accurate, and reliable strategy for the separation of exosomes and the biomedical analysis of exomiRs. Herein, a novel exosome-specific tumor diagnosis strategy was constructed by integrating the rapid magnetic exosome-enrichment platform and the Ru(bpy)32+-polymer amplified electrochemiluminescence (ECL) strategy. This strategy realized the rapid and efficient capture of tumor-derived exosomes through a biological-affinity identification platform of the EpCAM antibody. The biomedical analysis of exomiRs achieved a preferable specificity and high sensitivity of 103 particles. Furthermore, we investigated the performance index for clinical blood samples from tumor patients; the results indicated that the exosome-specific tumor diagnosis strategy readily and consistently responded to exomiRs. These results indicated that the exosome-specific tumor diagnosis strategy provided new opportunities for the sensitive and efficient analysis of tumor-derived exomiRs. This strategy greatly simplified the biomedical analysis process and established the non-destructive detection mode of fluid biopsy for tumors.

Exosomes: Diagnostic Biomarkers and Therapeutic Delivery Vehicles for Cancer

Exosomes are described as nanoscale extracellular vesicles (EVs) secreted by multiple cell types and extensively distributed in various biological fluids. They contain multifarious bioactive molecules and transfer them to adjoining or distal cells through systemic circulation, participating in intracellular and intercellular communication, and modulating host-tumor cell interactions. Recent research has indicated that exosomes obtained from different biological fluids and their contents (proteins, nucleic acids, glycoconjugates, and lipids) can serve as biomarkers for cancer diagnosis, prognosis, and therapeutic response. Furthermore, the discovery of exosomes as therapeutic delivery vehicles has drawn much attention in antineoplastic drug delivery. They can be utilized for therapeutic delivery of proteins, genetic drugs, and chemotherapeutic drugs. Herein, this review summarizes the biogenesis, structure, and components of exosomes, focusing primarily on their two possible applications as diagnostic biomarkers and therapeutic delivery vehicles for cancers.

Phosphoproteome Profiling of Isogenic Cancer Cell-Derived Exosome Reveals HSP90 as a Potential Marker for Human Cholangiocarcinoma

The northeastern region of Thailand is well known to have a high incidence and mortality of cholangiocarcinoma (CCA). Protein phosphorylation status has been reported to reflect a key determinant of cellular physiology, but identification of phosphoproteins can be a problem due to the presence of phosphatase. Exosomes are stable toward circulating proteases and other enzymes in human blood and can be recognized before the onset of cancer progression. Here an in vitro metastatic model of isogenic CCA cells is used to provide insight into the phosphorylation levels of exosomal proteins derived from highly invasive cells. Gel-based and gel-free proteomics approaches are used to reveal the proteins differentially phosphorylated in relation to tumor cell phenotypes. Forty-three phosphoproteins are identified with a significant change in phosphorylation level. Phos-tag western blotting and immunohistochemistry staining are then employed to validate the candidate phosphoproteins. Heat shock protein 90 is successfully confirmed as being differentially phosphorylated in relation to tumor malignancy. Importantly, the aberrant phosphorylation of exosomal proteins might serve as a promising tool for the development of a biomarker for metastatic CCA.

An electrochemiluminescent aptasensor for amplified detection of exosomes from breast tumor cells (MCF-7 cells) based on G-quadruplex/hemin DNAzymes

Exosomes are non-invasive biomarkers for cancer diagnosis. Herein, we describe an electrochemiluminescent (ECL) aptasensor for the detection of exosomes from breast tumor cells. Mercaptopropionic acid (MPA)-modified Eu³⁺-doped CdS nanocrystals (MPA-CdS:Eu NCs) and H₂O₂ were used as ECL emitters and coreactant, respectively. The exosomes are recognized and captured by the CD63 aptamer, and then form a G-quadruplex/hemin DNAzyme, which efficiently catalyzes the decomposition of H₂O₂, resulting in the decreased ECL signal of MPA-CdS:Eu NCs. The exosomes from breast tumor cells (MCF-7 cells) can be detected in the range of 3.4 × 10⁵ to 1.7 × 10⁸ particles per mL. The limit of detection (LOD) was estimated to be 7.41 × 10⁴ particles per mL at a signal-to-noise ratio of 3. The aptasensor has been successfully used to detect exosomes in the serum.

Reading Conformational Changes in Proteins with a New Colloidal-Based Interfacial Biosensing System

Many biological events such as mutations or aberrant post-translational modifications can alter the conformation and/or folding stability of proteins and their subsequent biological function, which may trigger the onset of diseases like cancer. Evaluating protein folding is hence crucial for the diagnosis of these diseases. Yet, it is still challenging to detect changes in protein folding, especially if they are subtle, in a simple and highly sensitive manner with the current assays. Herein, we report a new colloidal-based interfacial biosensing approach for qualitative and quantitative profiling of various types of changes in protein folding; from denaturation to variant conformations in native proteins, such as protein activation via mutations or phosphorylation. The approach is based on the direct interfacial interaction of proteins freely available in solution with added tannic-acid-capped gold nanoparticles, to interrogate their folding status in their solubilized form. We found that under the optimized conditions, proteins can modulate colloids solvation according to their folding or conformational status, which can be visualized in a single step, by the naked eye, with minimal protein input requirements (limit of detection of 1 ng/μL). Protein folding detection was achieved regardless of protein topology and size without using conformation-specific antibodies and mutational analysis, which are the most common assays for sensing malfunctioning proteins. The approach showed excellent sensitivity, superior to circular dichroism, for the detection of the very subtle conformational changes induced by activating mutations and phosphorylation in epidermal growth factor receptor (EGFR) and extracellular signal-regulated kinase (ERK) proteins. This enabled their detection even in complex samples derived from lung cancer cells, which contained up to 95% excess of their wild-type forms. A broader clinical translation was shown via monitoring the action of conformation-restoring drugs, such as tyrosine kinase inhibitors, on EGFR conformation and its downstream protein network, using the ERK protein as a surrogate.

Exosome-mediated targeted delivery of miR-210 for angiogenic therapy after cerebral ischemia in mice

Background

Accumulating evidence shows that microRNA-210 (miR-210) holds great promise to improve angiogenesis for brain tissue repair after cerebral ischemia. However, safe and efficient delivery of miR-210 via intravenous administration is still a challenge. In the past decade, exosomes have emerged as a novel endogenous delivery system. Here, c(RGDyK) peptide is conjugated to exosomes, and they are loaded with cholesterol-modified miR-210 (RGD-exo:miR-210).

Results

In a transient middle cerebral artery occlusion (MCAO) mouse model, the RGD-exo:miR-210 targets the lesion region of the ischemic brain after intravenous administration, resulting in an increase in miR-210 at the site. Furthermore, RGD-exo:miR-210 are administered once every other day for 14 days, and the expressions of integrin β₃, vascular endothelial growth factor (VEGF) and CD34 are significantly upregulated. The animal survival rate is also enhanced.

Conclusions

These results suggest a strategy for the targeted delivery of miR-210 to ischemic brain and provide an angiogenic agent for the treatment of ischemic stroke.

Electronic supplementary material

The online version of this article (10.1186/s12951-019-0461-7) contains supplementary material, which is available to authorized users.