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Transfer of Functional Cargo in Exomeres.
Zhang Q, Higginbotham JN, Jeppesen DK, Yang YP, Li W, McKinley ET, Graves-Deal R, Ping J, Britain CM, Dorsett KA, Hartman CL, Ford DA, Allen RM, Vickers KC, Liu Q, Franklin JL, Bellis SL, Coffey RJ
(2019) Cell Rep 27: 940-954.e6
MeSH Terms: Amphiregulin, Animals, Cell Line, Tumor, Colonic Neoplasms, Dogs, ErbB Receptors, Exosomes, Humans, Lipids, Madin Darby Canine Kidney Cells, Mice, Mice, Knockout, Nanoparticles, Nucleic Acids, Particle Size, Principal Component Analysis, Proteome, Proteomics, Sialyltransferases
Show Abstract · Added April 24, 2019
Exomeres are a recently discovered type of extracellular nanoparticle with no known biological function. Herein, we describe a simple ultracentrifugation-based method for separation of exomeres from exosomes. Exomeres are enriched in Argonaute 1-3 and amyloid precursor protein. We identify distinct functions of exomeres mediated by two of their cargo, the β-galactoside α2,6-sialyltransferase 1 (ST6Gal-I) that α2,6- sialylates N-glycans, and the EGFR ligand, amphiregulin (AREG). Functional ST6Gal-I in exomeres can be transferred to cells, resulting in hypersialylation of recipient cell-surface proteins including β1-integrin. AREG-containing exomeres elicit prolonged EGFR and downstream signaling in recipient cells, modulate EGFR trafficking in normal intestinal organoids, and dramatically enhance the growth of colonic tumor organoids. This study provides a simplified method of exomere isolation and demonstrates that exomeres contain and can transfer functional cargo. These findings underscore the heterogeneity of nanoparticles and should accelerate advances in determining the composition and biological functions of exomeres.
Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.
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19 MeSH Terms
Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer Reveals Dynamic Insights into Treatment Efficacy and Disease Relapse.
Almodovar K, Iams WT, Meador CB, Zhao Z, York S, Horn L, Yan Y, Hernandez J, Chen H, Shyr Y, Lim LP, Raymond CK, Lovly CM
(2018) J Thorac Oncol 13: 112-123
MeSH Terms: Adult, Aged, Aged, 80 and over, Antineoplastic Combined Chemotherapy Protocols, Biomarkers, Tumor, Cell-Free Nucleic Acids, Female, Follow-Up Studies, Humans, Longitudinal Studies, Lung Neoplasms, Male, Middle Aged, Mutation, Neoplasm Recurrence, Local, Prospective Studies, Small Cell Lung Carcinoma, Survival Rate, Treatment Outcome
Show Abstract · Added April 3, 2018
INTRODUCTION - Patients with SCLC have a poor prognosis and limited treatment options. Because access to longitudinal tumor samples is very limited in patients with this disease, we chose to focus our studies on the characterization of plasma cell-free DNA (cfDNA) for rapid, noninvasive monitoring of disease burden.
METHODS - We developed a liquid biopsy assay that quantifies somatic variants in cfDNA. The assay detects single nucleotide variants, copy number alterations, and insertions or deletions in 14 genes that are frequently mutated in SCLC, including tumor protein p53 gene (TP53), retinoblastoma 1 gene (RB1), BRAF, KIT proto-oncogene receptor tyrosine kinase gene (KIT), notch 1 gene (NOTCH1), notch 2 gene (NOTCH2), notch 3 gene (NOTCH3), notch 4 gene (NOTCH4), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene (PIK3CA), phosphatase and tensin homolog gene (PTEN), fibroblast growth factor receptor 1 gene (FGFR1), v-myc avian myelocytomatosis viral oncogene homolog gene (MYC), v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog gene (MYCL1), and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog gene (MYCN).
RESULTS - Over the course of 26 months of peripheral blood collection, we examined 140 plasma samples from 27 patients. We detected disease-associated mutations in 85% of patient samples with mutant allele frequencies ranging from 0.1% to 87%. In our cohort, 59% of the patients had extensive-stage disease, and the most common mutations occurred in TP53 (70%) and RB1 (52%). In addition to mutations in TP53 and RB1, we detected alterations in 10 additional genes in our patient population (PTEN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, MYC, MYCL1, PIK3CA, KIT, and BRAF). The observed allele frequencies and copy number alterations tracked closely with treatment responses. Notably, in several cases analysis of cfDNA provided evidence of disease relapse before conventional imaging.
CONCLUSIONS - These results suggest that liquid biopsies are readily applicable in patients with SCLC and can potentially provide improved monitoring of disease burden, depth of response to treatment, and timely warning of disease relapse in patients with this disease.
Copyright © 2017 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.
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19 MeSH Terms
In vivo Raman spectral analysis of impaired cervical remodeling in a mouse model of delayed parturition.
O'Brien CM, Herington JL, Brown N, Pence IJ, Paria BC, Slaughter JC, Reese J, Mahadevan-Jansen A
(2017) Sci Rep 7: 6835
MeSH Terms: Animals, Cervix Uteri, Cyclooxygenase 1, Extracellular Matrix Proteins, Female, Lipid Metabolism, Membrane Proteins, Mice, Nucleic Acids, Spectrum Analysis, Raman, Term Birth, Uterine Contraction
Show Abstract · Added October 11, 2017
Monitoring cervical structure and composition during pregnancy has high potential for prediction of preterm birth (PTB), a problem affecting 15 million newborns annually. We use in vivo Raman spectroscopy, a label-free, light-based method that provides a molecular fingerprint to non-invasively investigate normal and impaired cervical remodeling. Prostaglandins stimulate uterine contractions and are clinically used for cervical ripening during pregnancy. Deletion of cyclooxygenase-1 (Cox-1), an enzyme involved in production of these prostaglandins, results in delayed parturition in mice. Contrary to expectation, Cox-1 null mice displayed normal uterine contractility; therefore, this study sought to determine whether cervical changes could explain the parturition differences in Cox-1 null mice and gestation-matched wild type (WT) controls. Raman spectral changes related to extracellular matrix proteins, lipids, and nucleic acids were tracked over pregnancy and found to be significantly delayed in Cox-1 null mice at term. A cervical basis for the parturition delay was confirmed by other ex vivo tests including decreased tissue distensibility, hydration, and elevated progesterone levels in the Cox-1 null mice at term. In conclusion, in vivo Raman spectroscopy non-invasively detected abnormal remodeling in the Cox-1 null mouse, and clearly demonstrated that the cervix plays a key role in their delayed parturition.
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12 MeSH Terms
Extracellular vesicles for liquid biopsy in prostate cancer: where are we and where are we headed?
Minciacchi VR, Zijlstra A, Rubin MA, Di Vizio D
(2017) Prostate Cancer Prostatic Dis 20: 251-258
MeSH Terms: Biomarkers, Tumor, Cell-Free Nucleic Acids, Extracellular Vesicles, Humans, Liquid Biopsy, Male, Neoplastic Cells, Circulating, Prostatic Neoplasms
Show Abstract · Added April 6, 2017
BACKGROUND - Extracellular vesicles (EVs) are a heterogeneous class of lipid bound particles shed by any cell in the body in physiological and pathological conditions. EVs play critical functions in intercellular communication. EVs can actively travel in intercellular matrices and eventually reach the circulation. They can also be released directly in biological fluids where they appear to be stable. Because the molecular content of EVs reflects the composition of the cell of origin, they have recently emerged as a promising source of biomarkers in a number of diseases. EV analysis is particularly attractive in cancer patients that frequently present with increased numbers of circulating EVs.
METHODS - We sought to review the current literature on the molecular profile of prostate cancer-derived EVs in model systems and patient biological fluids in an attempt to draw some practical and universal conclusions on the use of EVs as a tool for liquid biopsy in clinical specimens.
RESULTS - We discuss advantages and limitations of EV-based liquid biopsy approaches summarizing salient studies on protein, DNA and RNA. Several candidate biomarkers have been identified so far but these results are difficult to apply to the clinic. However, the field is rapidly moving toward the implementation of novel tools to isolate cancer-specific EVs that are free of benign EVs and extra-vesicular contaminants. This can be achieved by identifying markers that are exquisitely present in tumor cell-derived EVs. An important contribution might also derive from a better understanding of EV types that may play specific functions in tumor progression and that may be a source of cancer-specific markers.
CONCLUSIONS - EV analysis holds strong promises for the development of non-invasive biomarkers in patients with prostate cancer. Implementation of modern methods for EV isolation and characterization will enable to interrogate circulating EVs in vivo.
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8 MeSH Terms
Cerebrospinal fluid cell-free mitochondrial DNA is associated with HIV replication, iron transport, and mild HIV-associated neurocognitive impairment.
Mehta SR, Pérez-Santiago J, Hulgan T, Day TR, Barnholtz-Sloan J, Gittleman H, Letendre S, Ellis R, Heaton R, Patton S, Suben JD, Franklin D, Rosario D, Clifford DB, Collier AC, Marra CM, Gelman BB, McArthur J, McCutchan A, Morgello S, Simpson D, Connor J, Grant I, Kallianpur A
(2017) J Neuroinflammation 14: 72
MeSH Terms: AIDS Dementia Complex, Adult, Biomarkers, Cell-Free Nucleic Acids, Cohort Studies, Cross-Sectional Studies, DNA, Mitochondrial, Female, HIV, Humans, Iron, Male, Middle Aged, Viral Load, Virus Replication
Show Abstract · Added December 11, 2019
BACKGROUND - Mitochondria are abundant organelles critical for energy metabolism and brain function. Mitochondrial DNA (mtDNA), released during cellular injury and as part of the innate immune response to viral pathogens, contains CpG motifs that act as TLR-9 ligands. We investigated relationships between cerebrospinal fluid (CSF) cell-free mtDNA levels and HIV viral load (VL), biomarkers of inflammation and iron transport, and neurocognitive (NC) function in the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) cohort.
METHODS - We quantified cell-free mtDNA in CSF by droplet digital PCR in 332 CHARTER participants who underwent comprehensive neuropsychiatric evaluation. NC performance was assessed using the global deficit score (GDS) as either a continuous or a binary measure (GDS ≥ 0.5, impaired vs. GDS < 0.5, unimpaired). CSF, clinical, and biomarker data from the earliest available time point were analyzed. Cell-free mtDNA associations with CSF inflammation and iron-related biomarkers [CXCL10, IL-6, IL-8, TNF-a, transferrin (TF), ceruloplasmin (CP), and vascular endothelial growth factor (VEGF)], VL, and GDS were evaluated by multivariable regression.
RESULTS - CSF cell-free mtDNA levels were significantly lower in participants with undetectable (vs. detectable) VL in either plasma (p < 0.001) or CSF (p < 0.001) and in those on antiretroviral therapy (ART; p < 0.001). Participants on ART with undetectable VL in both CSF and plasma had lower mtDNA levels than those with detectable VL in both compartments (p = 0.001). Higher mtDNA levels were observed in participants in the highest vs. lowest tertile (T3 vs. T1) of CSF CXCL10 (T3 vs. T1, p < 0.001) and TNF-a (T3 vs. T1, p < 0.05) in unadjusted analyses. MtDNA levels also correlated with CSF leukocyte count. After adjusting for CSF leukocyte count and VL, mtDNA levels were also associated with other inflammation- and iron-related biomarkers in CSF, including TF (T3 vs. T1, p < 0.05) and CP (T3 vs. T1, p < 0.05). With additional correction for ART use, mtDNA was also negatively associated with CSF VEGF (p < 0.05) and IL-6 (p = 0.05). We observed no associations of CSF mtDNA levels with age or GDS-defined NC impairment.
CONCLUSIONS - CSF cell-free mtDNA levels were associated with HIV RNA and ART status, as well as with biomarkers of iron transport and VEGF, a growth factor with known effects on mitochondrial integrity and autophagy. CSF mtDNA may be a biomarker of iron dysregulation and/or neuroinflammation during HIV infection.
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Porous Silicon and Polymer Nanocomposites for Delivery of Peptide Nucleic Acids as Anti-MicroRNA Therapies.
Beavers KR, Werfel TA, Shen T, Kavanaugh TE, Kilchrist KV, Mares JW, Fain JS, Wiese CB, Vickers KC, Weiss SM, Duvall CL
(2016) Adv Mater 28: 7984-7992
MeSH Terms: Animals, Cell Line, Tumor, Colloids, Female, Humans, Mice, MicroRNAs, Nanocomposites, Peptide Nucleic Acids, Polymers, Porosity, RNAi Therapeutics, Silicon
Show Abstract · Added April 27, 2017
Self-assembled polymer/porous silicon nanocomposites overcome intracellular and systemic barriers for in vivo application of peptide nucleic acid (PNA) anti-microRNA therapeutics. Porous silicon (PSi) is leveraged as a biodegradable scaffold with high drug-cargo-loading capacity. Functionalization with a diblock polymer improves PSi nanoparticle colloidal stability, in vivo pharmacokinetics, and intracellular bioavailability through endosomal escape, enabling PNA to inhibit miR-122 in vivo.
© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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13 MeSH Terms
Shape-engineered multifunctional porous silicon nanoparticles by direct imprinting.
Mares JW, Fain JS, Beavers KR, Duvall CL, Weiss SM
(2015) Nanotechnology 26: 271001
MeSH Terms: Drug Carriers, Equipment Design, Models, Chemical, Molecular Imprinting, Nanoparticles, Nanotechnology, Peptide Nucleic Acids, Porosity, Silicon
Show Abstract · Added April 27, 2017
A versatile and scalable method for fabricating shape-engineered nano- and micrometer scale particles from mesoporous silicon (PSi) thin films is presented. This approach, based on the direct imprinting of porous substrates (DIPS) technique, facilitates the generation of particles with arbitrary shape, ranging in minimum dimension from approximately 100 nm to several micrometers, by carrying out high-pressure (>200 MPa) direct imprintation, followed by electrochemical etching of a sub-surface perforation layer and ultrasonication. PSi particles (PSPs) with a variety of geometries have been produced in quantities sufficient for biomedical applications (≫10 μg). Because the stamps can be reused over 150 times, this process is substantially more economical and efficient than the use of electron beam lithography and reactive ion etching for the fabrication of nanometer-scale PSPs directly. The versatility of this fabrication method is demonstrated by loading the DIPS-imprinted PSPs with a therapeutic peptide nucleic acid drug molecule, and by vapor deposition of an Au coating to facilitate the use of PSPs as a photothermal contrast agent.
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9 MeSH Terms
Effect of DNA-induced corrosion on passivated porous silicon biosensors.
Zhao Y, Lawrie JL, Beavers KR, Laibinis PE, Weiss SM
(2014) ACS Appl Mater Interfaces 6: 13510-9
MeSH Terms: Biosensing Techniques, Corrosion, DNA, DNA Probes, Magnesium, Optical Phenomena, Peptide Nucleic Acids, Porosity, Silanes, Silicon, Spectroscopy, Fourier Transform Infrared
Show Abstract · Added April 27, 2017
This work examines the influence of charge density and surface passivation on the DNA-induced corrosion of porous silicon (PSi) waveguides in order to improve PSi biosensor sensitivity, reliability, and reproducibility when exposed to negatively charged DNA molecules. Increasing the concentration of either DNA probes or targets enhances the corrosion process and masks binding events. While passivation of the PSi surface by oxidation and silanization is shown to diminish the corrosion rate and lead to a saturation in the changes by corrosion after about 2 h, complete mitigation can be achieved by replacing the DNA probe molecules with charge-neutral PNA probe molecules. A model to explain the DNA-induced corrosion behavior, consistent with experimental characterization of the PSi through Fourier transform infrared spectroscopy and prism coupling optical measurements, is also introduced.
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11 MeSH Terms
In situ synthesis of peptide nucleic acids in porous silicon for drug delivery and biosensing.
Beavers KR, Mares JW, Swartz CM, Zhao Y, Weiss SM, Duvall CL
(2014) Bioconjug Chem 25: 1192-7
MeSH Terms: Biosensing Techniques, Carcinoma, Hepatocellular, DNA, Drug Delivery Systems, Humans, Liver Neoplasms, Mass Spectrometry, MicroRNAs, Nanoparticles, Nucleic Acid Hybridization, Peptide Nucleic Acids, Porosity, Propylamines, Silanes, Silicon, Tumor Cells, Cultured
Show Abstract · Added April 27, 2017
Peptide nucleic acids (PNA) are a unique class of synthetic molecules that have a peptide backbone and can hybridize with nucleic acids. Here, a versatile method has been developed for the automated, in situ synthesis of PNA from a porous silicon (PSi) substrate for applications in gene therapy and biosensing. Nondestructive optical measurements were performed to monitor single base additions of PNA initiated from (3-aminopropyl)triethoxysilane attached to the surface of PSi films, and mass spectrometry was conducted to verify synthesis of the desired sequence. Comparison of in situ synthesis to postsynthesis surface conjugation of the full PNA molecules showed that surface mediated, in situ PNA synthesis increased loading 8-fold. For therapeutic proof-of-concept, controlled PNA release from PSi films was characterized in phosphate buffered saline, and PSi nanoparticles fabricated from PSi films containing in situ grown PNA complementary to micro-RNA (miR) 122 generated significant anti-miR activity in a Huh7 psiCHECK-miR122 cell line. The applicability of this platform for biosensing was also demonstrated using optical measurements that indicated selective hybridization of complementary DNA target molecules to PNA synthesized in situ on PSi films. These collective data confirm that we have established a novel PNA-PSi platform with broad utility in drug delivery and biosensing.
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16 MeSH Terms
A structure-specific nucleic acid-binding domain conserved among DNA repair proteins.
Mason AC, Rambo RP, Greer B, Pritchett M, Tainer JA, Cortez D, Eichman BF
(2014) Proc Natl Acad Sci U S A 111: 7618-23
MeSH Terms: Adenosine Triphosphate, Animals, Chromatography, Affinity, Chromatography, Agarose, Chromatography, Gel, Chromatography, Ion Exchange, Cloning, Molecular, Crystallization, DNA Helicases, DNA Repair, Hydrolysis, Likelihood Functions, Mice, Models, Molecular, Nucleic Acids, Protein Structure, Tertiary, Scattering, Small Angle, X-Ray Diffraction
Show Abstract · Added May 19, 2014
SMARCAL1, a DNA remodeling protein fundamental to genome integrity during replication, is the only gene associated with the developmental disorder Schimke immuno-osseous dysplasia (SIOD). SMARCAL1-deficient cells show collapsed replication forks, S-phase cell cycle arrest, increased chromosomal breaks, hypersensitivity to genotoxic agents, and chromosomal instability. The SMARCAL1 catalytic domain (SMARCAL1(CD)) is composed of an SNF2-type double-stranded DNA motor ATPase fused to a HARP domain of unknown function. The mechanisms by which SMARCAL1 and other DNA translocases repair replication forks are poorly understood, in part because of a lack of structural information on the domains outside of the common ATPase motor. In the present work, we determined the crystal structure of the SMARCAL1 HARP domain and examined its conformation and assembly in solution by small angle X-ray scattering. We report that this domain is conserved with the DNA mismatch and damage recognition domains of MutS/MSH and NER helicase XPB, respectively, as well as with the putative DNA specificity motif of the T4 phage fork regression protein UvsW. Loss of UvsW fork regression activity by deletion of this domain was rescued by its replacement with HARP, establishing the importance of this domain in UvsW and demonstrating a functional complementarity between these structurally homologous domains. Mutation of predicted DNA-binding residues in HARP dramatically reduced fork binding and regression activities of SMARCAL1(CD). Thus, this work has uncovered a conserved substrate recognition domain in DNA repair enzymes that couples ATP-hydrolysis to remodeling of a variety of DNA structures, and provides insight into this domain's role in replication fork stability and genome integrity.
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18 MeSH Terms