The Multifunctionality of Exosomes; from the Garbage Bin of the Cell to a Next Generation Gene and Cellular Therapy

Exosomes are packaged with a variety of cellular cargo including RNA, DNA, lipids and proteins. For several decades now there has been ongoing debate as to what extent exosomes are the garbage bin of the cell or if these entities function as a distributer of cellular cargo which acts in a meaningful mechanistic way on target cells. Are the contents of exosomes unwanted excess cellular produce or are they selective nucleic acid packaged nanoparticles used to communicate in a paracrine fashion? Overexpressed RNAs and fragments of DNA have been shown to collect into exosomes which are jettisoned from cells in response to particular stimuli to maintain homeostasis suggesting exosomes are functional trash bins of the cell. Other studies however have deciphered selective packaging of particular nucleic acids into exosomes. Nucleic acids packaged into exosomes are increasingly reported to exert transcriptional control on recipient cells, supporting the notion that exosomes may provide a role in signaling and intracellular communication. We survey the literature and conclude that exosomes are multifunctional entities, with a plethora of roles that can each be taken advantage to functionally modulate cells. We also note that the potential utility of developing exosomes as a next generation genetic therapy may in future transform cellular therapies. We also depict three models of methodologies which can be adopted by researchers intending to package nucleic acid in exosomes for developing gene and cell therapy.

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Gene therapy promises accurate, targeted administration and overcoming drug resistance in diverse cancer cells

10.31219/osf.io/j34n6 ◽

2021 ◽

Author(s):

Moataz Dowaidar

Keyword(s):

Gene Therapy ◽

Drug Resistance ◽

Nucleic Acid ◽

Nucleic Acids ◽

Clinical Research ◽

Cancer Cells ◽

Cationic Lipids ◽

Target Cells ◽

Genetic Components ◽

Wide Range

Nucleic acid-based therapeutics such as siRNA and miRNA employ the silencing capabilities of the RNAi mechanism to affect the expression of one gene or several genes in target cells. Nucleic acid-based therapies enable accurate, targeted administration and overcoming drug resistance in diverse cancer cells. Several studies have shown that they can be utilized alongside pharmacological therapy to increase the efficacy of existing therapies. In addition, nucleic acid-based therapies have the potential to widen the spectrum of druggable targets for a range of diseases and emerge as a novel therapeutic technique for treating a number of diseases that are today untreatable. Nucleic acids are dependent on their effective distribution to target cells, which need correct complexation and encapsulation in a delivery mechanism. Although nucleic acids exist in a variety of forms and sizes, their physical and chemical commonality allow them to be loaded into a wide range of delivery vehicles. The primary biomaterials used to encapsulate genetic components were cationic lipids and polymers. Furthermore, the experiments focused particularly on effective transfection in target cells.Recent breakthroughs in NP-based RNA therapeutics have spurred a flood of clinical research, facing many challenges. In vivo, pharmacokinetics of different RNA-based medications must be researched to establish the viability and therapeutic potential of nucleic acid-based therapeutics. The U.S. Food and Drug Administration recently authorized many NP-based gene therapy. In 2019, Novartis authorized Zolgensma (onasemnogene abeparvovec-xioi) to treat spinal muscle atrophy. The first clinical research employing siRNA began in 2004 and is considered a milestone in nucleic acid-based drug development. Thirty clinical investigations have subsequently been completed. In 2018, the US FDA cleared Onpattro (Patisiran, Alnylam Pharmaceuticals) for the treatment of polyneuropathy caused by transthyretin amyloidosis.Several new generations of nucleic acid compositions employing polymer nanoparticles or liposomes are presently undergoing clinical testing. If allowed, the debut of nucleic acid-based treatments would represent a watershed event in immunotherapy. Advances in the design and development of biocompatible nanomaterials would allow us to overcome the above-mentioned problems and so show the potential to deliver nucleic acids in the treatment of a number of illnesses.

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Binding Of Immune Serine Proteases To Nucleic Acids Enhances Their Nuclear Localization and Promotes Their Cleavage Of Nucleic Acid-Binding Protein Substrates

Blood ◽

10.1182/blood.v122.21.3471.3471 ◽

2013 ◽

Vol 122 (21) ◽

pp. 3471-3471

Author(s):

Jennifer Whangbo ◽

Marshall Thomas ◽

Geoffrey McCrossan ◽

Aaron Deutsch ◽

Kimberly Martinod ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nuclear Localization ◽

Serine Proteases ◽

Rna Binding ◽

Nuclear Accumulation ◽

Target Cells ◽

Nucleic Acid Binding ◽

High Affinity ◽

Nucleic Acid Binding Proteins

Abstract When released from cytotoxic T lymphocytes and natural killer cells, Granzyme (Gzm) serine proteases induce programmed cell death of pathogen-infected cells and tumor cells. The Gzms rapidly accumulate in the target cell nucleus by an unknown mechanism. Many of the known substrates of GzmA and GzmB, the most abundant killer cell proteases, bind to DNA or RNA. Gzm substrates predicted by unbiased proteomics studies are also highly enriched for nucleic acid binding proteins. Here we show by fluorescence polarization assays that Gzms bind DNA and RNA with nanomolar affinity. We hypothesized that Gzm binding to nucleic acids enhances nuclear accumulation in target cells and facilitates their cleavage of nucleic acid-binding substrates. In fact, RNase treatment of cell lysates reduced cleavage of RNA binding protein (RBP) targets by GzmA and GzmB. Moreover, adding RNA to recombinant RBP substrates greatly enhanced in vitro cleavage by GzmB, but adding RNA to non-nucleic acid binding proteins did not. For example, exogenous RNA enhanced GzmB cleavage of recombinant hnRNP C1 (an RBP) but not LMNB1 (a non-RBP). In addition, GzmB cleaved the RNA-binding HuR protein efficiently only when it was bound to an HuR-binding RNA oligonucleotide, but not in the presence of an equal amount of non-binding RNA. Thus, nucleic acids facilitate Gzm cleavage of nucleic acid binding substrates. To evaluate whether nucleic acid binding influences Gzm trafficking in target cells, we incubated fixed target cells with RNase and then added Gzms. RNA degradation in target cells reduced Gzm cytosolic localization and increased nuclear accumulation. Similarly, pre-incubating Gzms with exogenous competitor DNA reduced Gzm nuclear localization. The Gzms form a monophyletic clade with other immune serine proteases including neutrophil elastase (NE) and cathepsin G (CATG). Upon neutrophil activation, NE translocates to the nucleus to drive the formation of neutrophil extracellular traps (NETs). NE and CATG, but not non-immune serine proteases such as trypsin and pancreatic elastase, also bind DNA with high affinity and localize to the nucleus of permeabilized cells. Consistent with this finding, competitor DNA also blocks the nuclear localization of NE. Moreover NE and CATG localization to NETs depends on DNA binding. Thus the antimicrobial activity of NETs may depend in part upon the affinity of these proteases for DNA. Our findings indicate that high affinity nucleic acid binding is a conserved and functionally important property of serine proteases involved in cell-mediated immunity. Disclosures: Lieberman: Alnylam Pharmaceuticals: Membership on an entity’s Board of Directors or advisory committees.

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Next-generation fluorescent nucleic acids probes for microscopic analysis of intracellular nucleic acids

Applied Microscopy ◽

10.1186/s42649-019-0017-1 ◽

2019 ◽

Vol 49 (1) ◽

Cited By ~ 1

Author(s):

Akimitsu Okamoto

Keyword(s):

Gene Expression ◽

Nucleic Acid ◽

Nucleic Acids ◽

Fluorescence Imaging ◽

Cell Function ◽

Microscopic Analysis ◽

Next Generation ◽

Nucleic Acid Probes ◽

Specific Fluorescence ◽

Methylated Dna

AbstractFluorescence imaging of nucleic acids is a very important technique necessary to understand gene expression and the resulting changes in cell function. This mini-review focuses on sequence-specific fluorescence imaging of intracellular RNA and methylated DNA using fluorescent nucleic acid probes. A couple of functional fluorescent nucleic acid probes developed by our laboratory are introduced and the examples of their application to fluorescence imaging of intracellular nucleic acids are described.

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Understanding In Vivo Fate of Nucleic Acid and Gene Medicines for the Rational Design of Drugs

Pharmaceutics ◽

10.3390/pharmaceutics13020159 ◽

2021 ◽

Vol 13 (2) ◽

pp. 159

Author(s):

Shintaro Fumoto ◽

Tsuyoshi Yamamoto ◽

Kazuya Okami ◽

Yuina Maemura ◽

Chisato Terada ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Rational Design ◽

Intracellular Localization ◽

Blood Stream ◽

The Body ◽

Endosomal Escape ◽

Target Cells ◽

Endocytosis Pathway

Nucleic acid and genetic medicines are increasingly being developed, owing to their potential to treat a variety of intractable diseases. A comprehensive understanding of the in vivo fate of these agents is vital for the rational design, discovery, and fast and straightforward development of the drugs. In case of intravascular administration of nucleic acids and genetic medicines, interaction with blood components, especially plasma proteins, is unavoidable. However, on the flip side, such interaction can be utilized wisely to manipulate the pharmacokinetics of the agents. In other words, plasma protein binding can help in suppressing the elimination of nucleic acids from the blood stream and deliver naked oligonucleotides and gene carriers into target cells. To control the distribution of these agents in the body, the ligand conjugation method is widely applied. It is also important to understand intracellular localization. In this context, endocytosis pathway, endosomal escape, and nuclear transport should be considered and discussed. Encapsulated nucleic acids and genes must be dissociated from the carriers to exert their activity. In this review, we summarize the in vivo fate of nucleic acid and gene medicines and provide guidelines for the rational design of drugs.

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Nucleic Acid Molecules Prepared by Monolayer Techniques

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100094140 ◽

1972 ◽

Vol 30 ◽

pp. 178-179

Author(s):

Dimitrij Lang

Keyword(s):

Electron Microscopy ◽

Standard Deviation ◽

Nucleic Acid ◽

Cytochrome C ◽

Nucleic Acids ◽

Contour Length ◽

Sample Standard Deviation ◽

Molecular Weights ◽

Length Measurements ◽

Protein Monolayer

The success of the protein monolayer technique for electron microscopy of individual DNA molecules is based on the prevention of aggregation and orientation of the molecules during drying on specimen grids. DNA adsorbs first to a surface-denatured, insoluble cytochrome c monolayer which is then transferred to grids, without major distortion, by touching. Fig. 1 shows three basic procedures which, modified or not, permit the study of various important properties of nucleic acids, either in concert with other methods or exclusively:1) Molecular weights relative to DNA standards as well as number distributions of molecular weights can be obtained from contour length measurements with a sample standard deviation between 1 and 4%.

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Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100124215 ◽

1992 ◽

Vol 50 (1) ◽

pp. 762-763

Author(s):

Stephen D. Jett

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nucleic Acid Binding ◽

Mobility Shift ◽

Carbon Coated ◽

Nucleoprotein Complexes ◽

Mobility Shift Assay ◽

Protein Nucleic Acid ◽

Gel Mobility Shift ◽

Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Physical Chemistry Chemical Physics ◽

10.1039/d0cp05759b ◽

2021 ◽

Vol 23 (1) ◽

pp. 219-228

Author(s):

Nabanita Saikia ◽

Mohamed Taha ◽

Ravindra Pandey

Keyword(s):

Nucleic Acid ◽

Boron Nitride ◽

Nucleic Acids ◽

Dynamic Stability ◽

Peptide Nucleic Acid ◽

Rational Design ◽

Peptide Nucleic Acids ◽

Boron Nitride Nanotubes ◽

Molecular Hybrids ◽

Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

The Analyst ◽

10.1039/d1an00765c ◽

2021 ◽

Author(s):

Qingteng Lai ◽

Wei Chen ◽

Yanke Zhang ◽

Zheng-Chun Liu

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Peptide Nucleic Acids ◽

Dna Probes ◽

Highly Sensitive ◽

Increased Sensitivity ◽

Acid Sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensor due to their higher stability and increased sensitivity than common DNA probes....

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Validating DNA Extraction Protocols for Bentonite Clay

mSphere ◽

10.1128/msphere.00334-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 3

Author(s):

Katja Engel ◽

Sara Coyotzi ◽

Melody A. Vachon ◽

Jennifer R. McKelvie ◽

Josh D. Neufeld

Keyword(s):

Microbial Community ◽

Nucleic Acid ◽

Nucleic Acids ◽

Dna Extraction ◽

Genomic Dna ◽

Bentonite Clay ◽

Dna Recovery ◽

Blocking Agents ◽

Clay Matrix ◽

Microbial Dna

ABSTRACT Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material “spiked” with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination. IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

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Peptide Nucleic Acids: Applications in Biomedical Sciences

Molecules ◽

10.3390/molecules25153317 ◽

2020 ◽

Vol 25 (15) ◽

pp. 3317

Author(s):

Eylon Yavin

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Peptide Nucleic Acid ◽

Peptide Nucleic Acids ◽

Biomedical Sciences

The DNA mimic, PNA (peptide nucleic acid), has been with us now for almost 3 decades [...]

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