Exosomes, naturally derived nanovesicles secreted from various cell types, can serve as an effective platform for the delivery of various cargoes, because of their intrinsic ability such as long ...blood circulation and immune escapinge. However, unlike conventional synthetic nanoparticles, drug release from exosomes at defined targets is not controllable. Moreover, endowing exosomes with satisfactory cancer‐targeting ability is highly challenging. Here, for the first time, a biological and synthetic hybrid designer exosome is described with photoresponsive functionalities based on a donor cell‐assisted membrane modification strategy. Practically, the designer exosome effectively accumulates at target tumor sites via dual ligand‐mediated endocytosis. Then the localized hyperthermia induced by the conjunct gold nanorods under near‐infrared irradiation impacts the permeability of exosome membrane to enhance drug release from exosomes, thus inhibiting tumor relapse in a programmable manner. The designer exosome combines the merits of both synthetic materials and the natural nanovesicles. It not only preserves the intrinsic functionalities of native exosome, but also gains multiple abilities for efficient tumor targeting, controlled release, and thermal therapy like synthetic nanocarriers. The versatile designer exosome can provide functional platforms by engineering with more multifarious functionalities from synthetic materials to achieve individualized precise cancer therapy in the future.
A biological and synthetic hybrid designer exosome is presented with photoresponsive functionalities based on a donor cell‐assisted membrane modification strategy. The dual ligand engineered exosomes are shown to significantly increase accumulation at the target tumor site and can burst release drug under controllable near‐infrared irradiation in vitro and in vivo.
DNA molecules utilize adenine, thymine, cytosine, and guanine for coding genetic information. In addition to these four canonical nucleobases, DNA molecules also contain a variety of modified ...nucleobases that can control and regulate gene expression and chromosome structure. Elucidating the functions of DNA modifications relies on the sensitive detection, accurate quantification, and genome-wide mapping of these modifications in genomic DNA. The significant advances of techniques and methods in recent years have enabled the discovery and functional studies of a number of new modifications in DNA in both prokaryotes and eukaryotes. Mass spectrometry-based methods for analyzing DNA modifications have substantially advanced over the past decade, which has greatly stimulated the research of DNA epigenetic modifications. The emergence of next-generation sequencing technology provides complementary methodology to enable genome-wide mapping of modifications, which is very important to reveal the biological roles of DNA modifications. This perspective highlights the recent methodologies for the assessment of DNA modifications with focus on mass spectrometry and sequencing analytical strategies.
The discovery of reversible modifications in messenger RNA (mRNA) opens new research directions in RNA modification-mediated epigenetic regulation. Yeast is an extensively used model organism in ...molecular biology. Systematic investigation and profiling of modifications in yeast mRNA would promote our understanding of the physiological regulation mechanisms in yeast. However, due to the high abundance of ribosomal RNA (rRNA) and transfer RNA (tRNA) in total RNA, isolation of low abundance of mRNA frequently suffers from the contamination of rRNA and tRNA, which will lead to the false-positive determination and inaccurate quantification of modifications in mRNA. Therefore, obtaining high-purity mRNA is critical for precise determination and accurate quantification of modifications in mRNA, especially for studies that focus on discovering new ones. Herein, we proposed a successive orthogonal isolation method by combining polyT-based purification and agarose gel electrophoresis purification for extracting high-purity mRNA. With the extracted high-purity yeast mRNA, we systemically explored the modifications in yeast mRNA by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. The results showed that in addition to the previously reported eight kinds of modifications, two novel modifications of inosine (Ino) and 2'-
-methylinosine (Im) were identified to be prevalent in yeast mRNA. It is worth noting that Im was reported for the first time, to the best of our knowledge, to exist in living organisms in the three domains of life. Moreover, we observed that the levels of 10 kinds of modifications including Ino and Im in yeast mRNA exhibited dynamic change at different growth stages of yeast cells. Furthermore, Im in mRNA showed a significant decrease while in response to H
O
treatment. These results indicated that the two newly identified modifications in yeast mRNA were involved in yeast cell growth and response to environmental stress. Taken together, we reported two new modifications of Ino and Im in yeast mRNA, which expends the diversity of RNA modifications in yeast and also suggests new regulators for modulating yeast physiological functions.
We developed a novel strategy by oxidation-derivatization combined mass spectrometry analysis for the determination of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA. We reported ...the presence of 5-formylcytosine in RNA of mammals and found that ascorbic acid and hydroquinone can increase the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine in DNA and RNA.
Systemic analyses using large‐scale genomic profiles have successfully identified cancer‐driving somatic copy number variations (SCNVs) loci. However, functions of vast focal SCNVs in “protein‐coding ...gene desert” regions are largely unknown. The integrative analysis of long noncoding RNA (lncRNA) expression profiles with SCNVs in hepatocellular carcinoma (HCC) led us to identify the recurrent deletion of lncRNA‐PRAL (p53 regulation‐associated lncRNA) on chromosome 17p13.1, whose genomic alterations were significantly associated with reduced survival of HCC patients. We found that lncRNA‐PRAL could inhibit HCC growth and induce apoptosis in vivo and in vitro through p53. Subsequent investigations indicated that the three stem‐loop motifs at the 5′ end of lncRNA‐PRAL facilitated the combination of HSP90 and p53 and thus competitively inhibited MDM2‐dependent p53 ubiquitination, resulting in enhanced p53 stability. Additionally, in vivo lncRNA‐PRAL delivery efficiently reduced intrinsic tumors, indicating its potential therapeutic application. Conclusions: lncRNA‐PRAL, one of the key cancer‐driving SCNVs, is a crucial stimulus for HCC growth and may serve as a potential target for antitumor therapy. (Hepatology 2016;63:850‐863)
DNA methylation (5-methylcytosine, 5-mC) is the best characterized epigenetic mark that has regulatory roles in diverse biological processes. Recent investigation of RNA modifications also raises the ...possible functions of RNA adenine and cytosine methylations on gene regulation in the form of “RNA epigenetics.” Previous studies demonstrated global DNA hypomethylation in tumor tissues compared to healthy controls. However, DNA and RNA methylation in circulating tumor cells (CTCs) that are derived from tumors are still a mystery due to the lack of proper analytical methods. In this respect, here we established an effective CTCs capture system conjugated with a combined strategy of sample preparation for the captured CTCs lysis, nucleic acids digestion, and nucleosides extraction in one tube. The resulting nucleosides were then further analyzed by liquid chromatography–electrospray ionization–tandem mass spectrometry (LC-ESI-MS/MS). With the developed method, we are able to detect DNA and RNA methylation (5-methyl-2′-deoxycytidine, 5-methylcytidine, and N 6-methyladenosine) in a single cell. We then further successfully determined DNA and RNA methylation in CTCs from lung cancer patients. Our results demonstrated, for the first time, a significant decrease of DNA methylation (5-methyl-2′-deoxycytidine) and increase of RNA adenine and cytosine methylations (N 6-methyladenosine and 5-methylcytidine) in CTCs compared with whole blood cells. The discovery of DNA hypomethylation and RNA hypermethylation in CTCs in the current study together with previous reports of global DNA hypomethylation in tumor tissues suggest that nucleic acid modifications play important roles in the formation and development of cancer cells. This work constitutes the first step for the investigation of DNA and RNA methylation in CTCs, which may facilitate uncovering the metastasis mechanism of cancers in the future.
Hydrophilic materials in sample pretreatment Tang, Feng; Yu, Qiong-Wei; Yuan, Bi-Feng ...
TrAC, Trends in analytical chemistry (Regular ed.),
January 2017, 2017-01-00, Letnik:
86
Journal Article
Recenzirano
Sample pretreatment is a fundamental and essential step in almost all analytical procedures, especially for the analysis of biological and environmental samples with complex matrix. In the past ...decades, with the development of hydrophilic interaction liquid chromatography (HILIC) in the separation of polar compounds, hydrophilic materials have also been extensively applied in sample pretreatment in a variety of areas, including biological, pharmaceutical, clinical, toxicological, food and environmental analysis. We provide an overview of the hydrophilic materials, both commercially available and synthesized in-house, which improve the extraction of the most polar compounds in sample pretreatment. We describe the chemical properties and extraction performance of hydrophilic materials that relate to their retention capabilities toward polar compounds. In addition, the existed problems and possible trends of hydrophilic materials for sample pretreatment in the future are proposed.
•We survey applications of hydrophilic materials in sample pretreatment.•We review preparation and properties of hydrophilic materials in sample pretreatment.•We discuss the merits and problems of hydrophilic materials in sample pretreatment.•We prospect the future trends of hydrophilic materials in sample pretreatment.
RNA contains diverse modifications that exert an important influence in a variety of cellular processes. So far, more than 150 modifications have been identified in various RNA species, mainly in ...ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). In contrast to rRNA, tRNA, and mRNA, the known modifications in small RNA species have been primarily limited to 2′‐O‐ribose methylation in plants and inosine in mammals. The methylation of small RNAs in mammals is still unclear. Current methods widely used in the characterization of small RNAs are mainly based on the strategy of nucleic acid hybridization and sequencing, which cannot characterize modifications in small RNAs. Herein, we have systematically investigated modifications in small RNAs composed of 16–28 nucleotides (nt) by establishing an effective isolation and neutral enzymatic digestion of small RNAs in combination with liquid chromatography/electrospray ionization tandem mass spectrometry (LC‐ESI‐MS/MS). This method allowed us to simultaneously detect 57 different types of nucleoside modification. By using this approach, we revealed 24 modifications in small RNAs comprising 16–28 nt from human cells. In addition, we found that the obesity‐associated protein (FTO) may demethylate N6‐methyladenosine (m6A) and N6,2′‐O‐dimethyladenosine (m6Am) in small RNAs of 16–28 nt. Our study demonstrates the existence of diverse modifications in small RNAs composed of 16–28 nt, which may promote in‐depth understanding of the regulatory roles of noncoding RNAs.
Natural isolation: Modifications in small RNAs composed of 16–28 nucleotides (nt) by establishing an effective isolation and neutral enzymatic digestion of small RNAs in combination with liquid chromatography/electrospray ionization tandem mass spectrometry (LC‐ESI‐MS/MS; see figure) were systematically investigated . Our study demonstrates the existence of diverse modifications in small RNAs comprising 16–28 nt, which may promote in‐depth understanding of the regulatory roles of noncoding RNAs.
•We provide a comprehensive review of derivatization-based LC-MS studies.•We discuss the selection strategy for derivatization reagents.•We summarize the reaction mechanisms of representative ...derivatization reagents.•We describe the advancement of derivatization methods with advantages and prospects.•We summarize applications of derivatization in various research fields.
Liquid chromatography-mass spectrometry (LC-MS) is one of the most prominent analytical techniques, due to its inherent selectivity and sensitivity. In LC-MS, chemical derivatizations are frequently used to enhance the MS ionization efficiency and selectivity, to facilitate structure elucidation, and to improve the chromatographic separation. In this review, we present an overview of derivatization-based LC-MS analysis. We summarize the reaction mechanisms of representative derivatization reagents and the selection strategy to guide and to stimulate future studies. Furthermore, we emphasize applications of derivatization in peptide and protein analysis, metabolite analysis, environmental analysis, pharmaceutical analysis, food-safety evaluation and MS imaging.
PDF
