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1.
Nat Commun ; 15(1): 1581, 2024 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-38383524

RESUMEN

The high potential of siRNAs to silence oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, divalent lipid-conjugated siRNAs are optimized for in situ binding to albumin to improve pharmacokinetics and tumor delivery. Systematic variation of the siRNA conjugate structure reveals that the location of the linker branching site dictates tendency toward albumin association versus self-assembly, while the lipid hydrophobicity and reversibility of albumin binding also contribute to siRNA intracellular delivery. The lead structure increases tumor siRNA accumulation 12-fold in orthotopic triple negative breast cancer (TNBC) tumors over the parent siRNA. This structure achieves approximately 80% silencing of the anti-apoptotic oncogene MCL1 and yields better survival outcomes in three TNBC models than an MCL-1 small molecule inhibitor. These studies provide new structure-function insights on siRNA-lipid conjugate structures that are intravenously injected, associate in situ with serum albumin, and improve pharmacokinetics and tumor treatment efficacy.


Asunto(s)
Antineoplásicos , Neoplasias de la Mama Triple Negativas , Humanos , ARN Interferente Pequeño , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/genética , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Neoplasias de la Mama Triple Negativas/genética , Línea Celular Tumoral , Silenciador del Gen , Lípidos/química , Albúminas/genética
2.
bioRxiv ; 2023 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-36824780

RESUMEN

The high potential for therapeutic application of siRNAs to silence traditionally undruggable oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, siRNAs were optimized for in situ binding to albumin through C18 lipid modifications to improve pharmacokinetics and tumor delivery. Systematic variation of siRNA conjugates revealed a lead structure with divalent C18 lipids each linked through three repeats of hexaethylene glycol connected by phosphorothioate bonds. Importantly, we discovered that locating the branch site of the divalent lipid structure proximally (adjacent to the RNA) rather than at a more distal site (after the linker segment) promotes association with albumin, while minimizing self-assembly and lipoprotein association. Comparison to higher albumin affinity (diacid) lipid variants and siRNA directly conjugated to albumin underscored the importance of conjugate hydrophobicity and reversibility of albumin binding for siRNA delivery and bioactivity in tumors. The lead conjugate increased tumor siRNA accumulation 12-fold in orthotopic mouse models of triple negative breast cancer over the parent siRNA. When applied for silencing of the anti-apoptotic oncogene MCL-1, this structure achieved approximately 80% MCL1 silencing in orthotopic breast tumors. Furthermore, application of the lead conjugate structure to target MCL1 yielded better survival outcomes in three independent, orthotopic, triple negative breast cancer models than an MCL1 small molecule inhibitor. These studies provide new structure-function insights on optimally leveraging siRNA-lipid conjugate structures that associate in situ with plasma albumin for molecular-targeted cancer therapy.

3.
Nat Cell Biol ; 24(12): 1701-1713, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36474072

RESUMEN

Macrophages present a spectrum of phenotypes that mediate both the pathogenesis and resolution of atherosclerotic lesions. Inflammatory macrophage phenotypes are pro-atherogenic, but the stimulatory factors that promote these phenotypes remain incompletely defined. Here we demonstrate that microbial small RNAs (msRNA) are enriched on low-density lipoprotein (LDL) and drive pro-inflammatory macrophage polarization and cytokine secretion via activation of the RNA sensor toll-like receptor 8 (TLR8). Removal of msRNA cargo during LDL re-constitution yields particles that readily promote sterol loading but fail to stimulate inflammatory activation. Competitive antagonism of TLR8 with non-targeting locked nucleic acids was found to prevent native LDL-induced macrophage polarization in vitro, and re-organize lesion macrophage phenotypes in vivo, as determined by single-cell RNA sequencing. Critically, this was associated with reduced disease burden in distinct mouse models of atherosclerosis. These results identify LDL-msRNA as instigators of atherosclerosis-associated inflammation and support alternative functions of LDL beyond cholesterol transport.


Asunto(s)
Macrófagos , Receptor Toll-Like 8 , Animales , Ratones , Receptor Toll-Like 8/genética , ARN
4.
J Biol Chem ; 298(6): 101952, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35447119

RESUMEN

Extracellular small RNAs (sRNAs) are abundant in many biofluids, but little is known about their mechanisms of transport and stability in RNase-rich environments. We previously reported that high-density lipoproteins (HDLs) in mice were enriched with multiple classes of sRNAs derived from the endogenous transcriptome, but also from exogenous organisms. Here, we show that human HDL transports tRNA-derived sRNAs (tDRs) from host and nonhost species, the profiles of which were found to be altered in human atherosclerosis. We hypothesized that HDL binds to tDRs through apolipoprotein A-I (apoA-I) and that these interactions are conferred by RNA-specific features. We tested this using microscale thermophoresis and electrophoretic mobility shift assays and found that HDL binds to tDRs and other single-stranded sRNAs with strong affinity but did not bind to double-stranded RNA or DNA. Furthermore, we show that natural and synthetic RNA modifications influenced tDR binding to HDL. We demonstrate that reconstituted HDL bound to tDRs only in the presence of apoA-I, and purified apoA-I alone were able to bind sRNA. Conversely, phosphatidylcholine vesicles did not bind tDRs. In summary, we conclude that HDL binds to single-stranded sRNAs likely through nonionic interactions with apoA-I. These results highlight binding properties that likely enable extracellular RNA communication and provide a foundation for future studies to manipulate HDL-sRNA interactions for therapeutic approaches to prevent or treat disease.


Asunto(s)
Lipoproteínas HDL , ARN Pequeño no Traducido , Animales , Apolipoproteína A-I/metabolismo , Aterosclerosis , Humanos , Lipoproteínas HDL/química , Lipoproteínas HDL/metabolismo , Ratones , Fosfatidilcolinas , ARN Pequeño no Traducido/química
5.
Heliyon ; 7(12): e08519, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34934837

RESUMEN

Extracellular vesicles (EVs) are capable of transferring cargo from donor to recipient cells, but precisely how cargo content is regulated for export is mostly unknown. For miRNA cargo, we previously showed that when compared to isogenic colorectal cancer (CRC) cells expressing wild-type KRAS, a distinct subset of miRNAs are differentially enriched in EVs from KRAS mutant active CRC cells, with miR-100 being one of the most enriched. The mechanisms that could explain how miR-100 and other miRNAs are differentially exported into EVs have not been fully elucidated. Here, we tested the effect of N6-methyladenosine (m6A) modification on miRNA export into EVs by depletion of METTL3 and ALKBH5, a writer and eraser of m6A modification, respectively. While the effects of ALKBH5 knockdown were quite modest, decreased levels of METTL3 led to reduced cellular and extracellular levels of a subset of miRNAs that contain consensus sequences for m6A modification. Functional testing of EVs prepared from cells expressing shRNAs against METTL3 showed that they were less capable of conferring colony growth in 3D to wild-type KRAS cells and were also largely incapable of conferring the spread of cetuximab resistance. Our data support a role for METTL3 modification on cellular miRNA levels and export of specific miRNAs.

6.
High Educ (Dordr) ; : 1-17, 2021 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-34690358

RESUMEN

Despite the ubiquity of global university rankings coverage in media and academia, a concerted attempt to investigate the role of social media in ranking entrepreneurship remains absent. By drawing on an affect lens, we critically examine the social media activities of two commercial rankers: Times Higher Education (THE) and Quacquarelli Symonds Ltd (QS). Based on an analysis of THE's Twitter feed and QS' Facebook page between January and June 2020, we illuminate how rankers use social media for affective storytelling to frame and sell their expertise within global HE. First, we demonstrate how THE uses Twitter to engage an audience of institutions, governments, and administrators, reinforcing universities' increasingly aggressive behavior as market competitors. Next, we show how QS engages a student-oriented audience on Facebook, furthering the role of students as consumers. Before and during the COVID pandemic, we observed that both rankers amplified and mobilized precarity associated with performance and participation, selling hope to targeted audiences to market their expertise as solutions-a strategy that remained amidst the global pandemic. Based on our observation of the front stage of rankers' social media activities, we argue that rankers' deployment of social media as a form of affective infrastructure is conducive to further sustaining, diffusing, and normalizing rankings in HE globally.

7.
Diabetes ; 70(10): 2377-2390, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34233930

RESUMEN

Podocyte injury is important in development of diabetic nephropathy (DN). Although several studies have reported single-cell-based RNA sequencing (RNA-seq) of podocytes in type 1 DN (T1DN), the podocyte translating mRNA profile in type 2 DN (T2DN) has not previously been compared with that of T1DN. We analyzed the podocyte translatome in T2DN in podocin-Cre; Rosa26fsTRAP; eNOS-/-; db/db mice and compared it with that of streptozotocin-induced T1DN in podocin-Cre; Rosa26fsTRAP; eNOS-/- mice using translating ribosome affinity purification (TRAP) and RNA-seq. More than 125 genes were highly enriched in the podocyte ribosome. More podocyte TRAP genes were differentially expressed in T2DN than in T1DN. TGF-ß signaling pathway genes were upregulated, while MAPK pathway genes were downregulated only in T2DN, while ATP binding and cAMP-mediated signaling genes were downregulated only in T1DN. Genes regulating actin filament organization and apoptosis increased, while genes regulating VEGFR signaling and glomerular basement membrane components decreased in both type 1 and type 2 diabetic podocytes. A number of diabetes-induced genes not previously linked to podocyte injury were confirmed in both mouse and human DN. On the basis of differences and similarities in the podocyte translatome in T2DN and T1DN, investigators can identify factors underlying the pathophysiology of DN and novel therapeutic targets to treat diabetes-induced podocyte injury.


Asunto(s)
Nefropatías Diabéticas/genética , Nefropatías Diabéticas/metabolismo , Podocitos/metabolismo , Animales , Diabetes Mellitus Experimental/genética , Diabetes Mellitus Experimental/metabolismo , Diabetes Mellitus Experimental/patología , Diabetes Mellitus Tipo 1/complicaciones , Diabetes Mellitus Tipo 1/genética , Diabetes Mellitus Tipo 1/metabolismo , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/metabolismo , Nefropatías Diabéticas/patología , Perfilación de la Expresión Génica , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Especificidad de Órganos/genética , Podocitos/patología , Biosíntesis de Proteínas/genética , Proteoma/análisis , Proteoma/genética , Proteoma/metabolismo , ARN Mensajero/análisis , ARN Mensajero/genética , ARN Mensajero/metabolismo , RNA-Seq , Análisis de Secuencia de ARN , Estreptozocina , Transcriptoma
8.
Ann Rheum Dis ; 79(12): 1557-1564, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-32958509

RESUMEN

OBJECTIVES: To determine if plasma microbial small RNAs (sRNAs) are altered in patients with rheumatoid arthritis (RA) compared with control subjects, associated with RA disease-related features, and altered by disease-modifying antirheumatic drugs (DMARDs). METHODS: sRNA sequencing was performed on plasma from 165 patients with RA and 90 matched controls and a separate cohort of 70 patients with RA before and after starting a DMARD. Genome alignments for RA-associated bacteria, representative bacterial and fungal human microbiome genomes and environmental bacteria were performed. Microbial genome counts and individual sRNAs were compared across groups and correlated with disease features. False discovery rate was set at 0.05. RESULTS: Genome counts of Lactobacillus salivarius, Anaerobaculum hydrogeniformans, Staphylococcus epidermidis, Staphylococcus aureus, Paenisporosarcina spp, Facklamia hominis, Sphingobacterium spiritivorum, Lentibacillus amyloliquefaciens, Geobacillus spp, and Pseudomonas fluorescens were significantly decreased in the plasma of RA compared with control subjects. Three microbial transfer RNA-derived sRNAs were increased in RA versus controls and inversely associated with disease activity. Higher total microbial sRNA reads were associated with lower disease activity in RA. Baseline total microbial sRNAs were threefold higher among patients who improved with DMARD versus those who did not but did not change significantly after 6 months of treatment. CONCLUSION: Plasma microbial sRNA composition is altered in RA versus control subjects and associated with some measures of RA disease activity. DMARD treatment does not alter microbial sRNA abundance or composition, but increased abundance of microbial sRNAs at baseline was associated with disease activity improvement at 6 months.


Asunto(s)
Artritis Reumatoide/sangre , Artritis Reumatoide/microbiología , ARN Bacteriano/sangre , ARN de Hongos/sangre , ARN Pequeño no Traducido/sangre , Adulto , Anciano , Antirreumáticos/uso terapéutico , Artritis Reumatoide/patología , Estudios Transversales , Femenino , Humanos , Masculino , Persona de Mediana Edad , ARN Bacteriano/efectos de los fármacos , ARN de Hongos/efectos de los fármacos , ARN Pequeño no Traducido/efectos de los fármacos
9.
Diabetes ; 69(5): 813-822, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32312897

RESUMEN

Advances in small RNA sequencing have revealed the enormous diversity of small noncoding RNA (sRNA) classes in mammalian cells. At this point, most investigators in diabetes are aware of the success of microRNA (miRNA) research and appreciate the importance of posttranscriptional gene regulation in glycemic control. Nevertheless, miRNAs are just one of multiple classes of sRNAs and likely represent only a minor fraction of sRNA sequences in a given cell. Despite the widespread appreciation of sRNAs, very little research into non-miRNA sRNA function has been completed, likely due to some major barriers that present unique challenges for study. To emphasize the importance of sRNA research in cardiometabolic diseases, we highlight the success of miRNAs and competitive endogenous RNAs in cholesterol and glucose metabolism. Moreover, we argue that sequencing studies have demonstrated that miRNAs are just the tip of the iceberg for sRNAs. We are likely standing at the precipice of immense discovery for novel sRNA-mediated gene regulation in cardiometabolic diseases. To realize this potential, we must first address critical barriers with an open mind and refrain from viewing non-miRNA sRNA function through the lens of miRNAs, as they likely have their own set of distinct regulatory factors and functional mechanisms.


Asunto(s)
Enfermedades Cardiovasculares/metabolismo , Enfermedades Metabólicas/metabolismo , ARN Pequeño no Traducido/metabolismo , Diabetes Mellitus/metabolismo , Regulación de la Expresión Génica , Glucosa/metabolismo , Humanos , MicroARNs/genética , MicroARNs/metabolismo , ARN Pequeño no Traducido/genética
10.
ACR Open Rheumatol ; 2(2): 97-105, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31913579

RESUMEN

OBJECTIVE: Small RNA (sRNA) sequencing has revealed new sRNA classes beyond microRNAs (miRNAs). These sRNAs can regulate genes and act as biomarkers. The aim of this study was to determine if the endogenous plasma sRNA landscape is altered in patients with rheumatoid arthritis (RA) compared with control subjects and to determine its association with disease-related parameters in RA. METHODS: sRNA sequencing was performed on plasma from 165 RA and 90 control subjects who were frequency-matched for age, race, and sex. Endogenous sRNAs, such as miRNAs, isomiRs, sRNAs derived from small nuclear RNAs (snDRs), small nucleolar RNAs (snoDRs), Y RNAs (yDRs), transfer-derived RNAs (tDRs), long noncoding RNAs (lncDRs) as well as miscellaneous sRNAs (miscRNAs), were quantified using Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER). Individual and categories of sRNAs were compared between RA and controls, and significantly altered sRNAs and sRNA categories were correlated with disease activity and general laboratory measures in RA. RESULTS: Patients with RA had more miRNAs (1.42-fold, P = 0.01), more tDRs (1.14-fold, P = 0.04), and fewer yDRs (-1.41-fold, P = 0.009) compared with control subjects. Disease duration was inversely associated with yDRs. Disease-related parameters, such as Disease Activity Score-28 (DAS28), swollen joint count, and inflammatory markers were significantly positively associated with tDRs and miscRNAs, and miR-22-3p and related sequences and isomiRs were most significantly associated with DAS28. CONCLUSION: Endogenous plasma sRNAs are altered in RA compared with control subjects. Although individual miRNAs have been well studied and many are excellent biomarkers in RA, several non-miRNA sRNAs were significantly associated with disease-related parameters as classes and may represent novel biomarkers for RA.

11.
J Rheumatol ; 47(2): 188-196, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31092710

RESUMEN

OBJECTIVE: MicroRNA (miRNA) are short noncoding RNA that regulate genes and are both biomarkers and mediators of disease. We used small RNA (sRNA) sequencing and machine learning methodology to develop an miRNA panel to reliably differentiate between rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE) and control subjects. METHODS: Plasma samples from 167 RA and 91 control subjects who frequency-matched for age, race, and sex were used for sRNA sequencing. TIGER was used to analyze miRNA. DESeq2 and random forest analyses were used to identify a prioritized list of miRNA differentially expressed in patients with RA. Prioritized miRNA were validated by quantitative PCR, and lasso and logistic regression were used to select the final panel of 6 miRNA that best differentiated RA from controls. The panel was validated in a separate cohort of 12 SLE, 32 RA, and 32 control subjects. Panel efficacy was assessed by area under the receiver operative characteristic curve (AUC) analyses. RESULTS: The final panel included miR-22-3p, miR-24-3p, miR-96-5p, miR-134-5p, miR-140-3p, and miR-627-5p. The panel differentiated RA from control subjects in discovery (AUC = 0.81) and validation cohorts (AUC = 0.71), seronegative RA (AUC = 0.84), RA remission (AUC = 0.85), and patients with SLE (AUC = 0.80) versus controls. Pathway analysis showed upstream regulators and targets of panel miRNA are associated with pathways implicated in RA pathogenesis. CONCLUSION: An miRNA panel identified by a bioinformatic approach differentiated between RA or SLE patients and control subjects. The panel may represent an autoimmunity signature, perhaps related to inflammatory arthritis, which is not dependent on active disease or seropositivity.


Asunto(s)
Artritis Reumatoide/sangre , Biología Computacional/métodos , Lupus Eritematoso Sistémico/sangre , MicroARNs/sangre , MicroARNs/genética , Adulto , Área Bajo la Curva , Biomarcadores/sangre , Estudios de Cohortes , Femenino , Humanos , Modelos Logísticos , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ARN
12.
Sci Rep ; 9(1): 17387, 2019 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-31758005

RESUMEN

Extracellular vesicles (EVs) released by cells play a role in intercellular communication. Reporter and targeting proteins can be modified and exposed on the surface of EVs to investigate their half-life and biodistribution. A characterization of membrane-bound Gaussia luciferase (mbGluc) revealed that its signal was detected also in a form smaller than common EVs (<70 nm). We demonstrated that mbGluc initially exposed on the surface of EVs, likely undergoes proteolytic cleavage and processed fragments of the protein are released into the extracellular space in active form. Based on this observation, we developed a new assay to quantitatively track shedding of membrane proteins from the surface of EVs. We used this assay to show that ectodomain shedding in EVs is continuous and is mediated by specific proteases, e.g. metalloproteinases. Here, we present a novel tool to study membrane protein cleavage and release using both in vitro and in vivo models.


Asunto(s)
Copépodos/enzimología , Vesículas Extracelulares/metabolismo , Luciferasas/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas Recombinantes/metabolismo , Animales , Línea Celular Tumoral , Copépodos/genética , Copépodos/metabolismo , Femenino , Humanos , Luciferasas/genética , Proteínas de la Membrana/genética , Membranas/metabolismo , Ratones , Ratones Desnudos , Proteínas Recombinantes/genética , Vías Secretoras/genética , Distribución Tisular
13.
Cell Rep ; 27(3): 940-954.e6, 2019 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-30956133

RESUMEN

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 ß-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 ß1-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.


Asunto(s)
Exosomas/metabolismo , Nanopartículas/metabolismo , Anfirregulina/genética , Anfirregulina/metabolismo , Animales , Línea Celular Tumoral , Neoplasias del Colon/metabolismo , Neoplasias del Colon/patología , Perros , Receptores ErbB/química , Receptores ErbB/metabolismo , Exosomas/química , Humanos , Lípidos/análisis , Lípidos/química , Células de Riñón Canino Madin Darby , Ratones , Ratones Noqueados , Nanopartículas/química , Ácidos Nucleicos/análisis , Tamaño de la Partícula , Análisis de Componente Principal , Proteoma/análisis , Proteoma/metabolismo , Proteómica/métodos , Sialiltransferasas/análisis , Sialiltransferasas/metabolismo , beta-D-Galactósido alfa 2-6-Sialiltransferasa
14.
Annu Int Conf IEEE Eng Med Biol Soc ; 2018: 6112-6116, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-30441729

RESUMEN

Despite dramatic progress in the application of predictive modeling and data mining techniques to problems in modern medicine, a major challenge facing technical practitioners is that of delivering models to clinicians. We have developed an easily implementable framework for publishing predictive models written in R or Python in a way that allows them to be consumed by practically any downstream clinical application, as well as allowing them to be reused in a wide variety of environments without modification. The approach makes models available as web services embedded in containers and uses only open source technology. We provide a template, practical explanation and discussion of involved technologies for a model production framework. We currently use this framework to deliver a model for predicting readmission to hospital following discharge to skilled nursing facilities. The flexibility and simplicity of this methodology will allow it to be readily adopted at a wide variety of institutions. We also provide source code for an example model.


Asunto(s)
Minería de Datos , Programas Informáticos
15.
J Extracell Vesicles ; 7(1): 1506198, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30128086

RESUMEN

To comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), we developed a novel pipeline to overcome current limitations in analysis entitled, "Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER)". To demonstrate the power of this tool, sRNA-seq was performed on mouse lipoproteins, bile, urine and livers. A key advance for the TIGER pipeline is the ability to analyse both host and non-host sRNAs at genomic, parent RNA and individual fragment levels. TIGER was able to identify approximately 60% of sRNAs on lipoproteins and >85% of sRNAs in liver, bile and urine, a significant advance compared to existing software. Moreover, TIGER facilitated the comparison of lipoprotein sRNA signatures to disparate sample types at each level using hierarchical clustering, correlations, beta-dispersions, principal coordinate analysis and permutational multivariate analysis of variance. TIGER analysis was also used to quantify distinct features of exRNAs, including 5' miRNA variants, 3' miRNA non-templated additions and parent RNA positional coverage. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA.

16.
Am J Physiol Gastrointest Liver Physiol ; 315(5): G810-G823, 2018 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-30160993

RESUMEN

Colesevelam is a bile acid sequestrant approved to treat both hyperlipidemia and type 2 diabetes, but the mechanism for its glucose-lowering effects is not fully understood. The aim of this study was to investigate the role of hepatic microRNAs (miRNAs) as regulators of metabolic disease and to investigate the link between the cholesterol and glucose-lowering effects of colesevelam. To quantify the impact of colesevelam treatment in rodent models of diabetes, metabolic studies were performed in Zucker diabetic fatty (ZDF) rats and db/db mice. Colesevelam treatments significantly decreased plasma glucose levels and increased glycolysis in the absence of changes to insulin levels in ZDF rats and db/db mice. High-throughput sequencing and real-time PCR were used to quantify hepatic miRNA and mRNA changes, and the cholesterol-sensitive miR-96/182/183 cluster was found to be significantly increased in livers from ZDF rats treated with colesevelam compared with vehicle controls. Inhibition of miR-182 in vivo attenuated colesevelam-mediated improvements to glycemic control in db/db mice. Hepatic expression of mediator complex subunit 1 (MED1), a nuclear receptor coactivator, was significantly decreased with colesevelam treatments in db/db mice, and MED1 was experimentally validated to be a direct target of miR-96/182/183 in humans and mice. In summary, these results support that colesevelam likely improves glycemic control through hepatic miR-182-5p, a mechanism that directly links cholesterol and glucose metabolism. NEW & NOTEWORTHY Colesevelam lowers systemic glucose levels in Zucker diabetic fatty rats and db/db mice and increases hepatic levels of the sterol response element binding protein 2-responsive microRNA cluster miR-96/182/183. Inhibition of miR-182 in vivo reverses the glucose-lowering effects of colesevelam in db/db mice. Mediator complex subunit 1 (MED1) is a novel, direct target of the miR-96/182/183 cluster in mice and humans.


Asunto(s)
Ácidos y Sales Biliares/metabolismo , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Glucosa/metabolismo , Mucosa Intestinal/metabolismo , Hígado/metabolismo , MicroARNs/genética , Animales , Anticolesterolemiantes/farmacología , Anticolesterolemiantes/uso terapéutico , Clorhidrato de Colesevelam/farmacología , Clorhidrato de Colesevelam/uso terapéutico , Diabetes Mellitus Tipo 2/metabolismo , Glucólisis , Células HEK293 , Humanos , Hipoglucemiantes/farmacología , Hipoglucemiantes/uso terapéutico , Hígado/efectos de los fármacos , Masculino , Subunidad 1 del Complejo Mediador/genética , Subunidad 1 del Complejo Mediador/metabolismo , MicroARNs/metabolismo , Ratas , Ratas Zucker
17.
J Lipid Res ; 58(5): 941-954, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-28264879

RESUMEN

Idiopathic pulmonary alveolar proteinosis (PAP) is a rare lung disease characterized by accumulation of surfactant. Surfactant synthesis and secretion are restricted to epithelial type 2 (T2) pneumocytes (also called T2 cells). Clearance of surfactant is dependent upon T2 cells and macrophages. ABCG1 is highly expressed in both T2 cells and macrophages. ABCG1-deficient mice accumulate surfactant, lamellar body-loaded T2 cells, lipid-loaded macrophages, B-1 lymphocytes, and immunoglobulins, clearly demonstrating that ABCG1 has a critical role in pulmonary homeostasis. We identify a variant in the ABCG1 promoter in patients with PAP that results in impaired activation of ABCG1 by the liver X receptor α, suggesting that ABCG1 basal expression and/or induction in response to sterol/lipid loading is essential for normal lung function. We generated mice lacking ABCG1 specifically in either T2 cells or macrophages to determine the relative contribution of these cell types on surfactant lipid homeostasis. These results establish a critical role for T2 cell ABCG1 in controlling surfactant and overall lipid homeostasis in the lung and in the pathogenesis of human lung disease.


Asunto(s)
Transportador de Casetes de Unión a ATP, Subfamilia G, Miembro 1/metabolismo , Surfactantes Pulmonares/metabolismo , Células A549 , Transportador de Casetes de Unión a ATP, Subfamilia G, Miembro 1/deficiencia , Transportador de Casetes de Unión a ATP, Subfamilia G, Miembro 1/genética , Adulto , Células Epiteliales Alveolares/citología , Células Epiteliales Alveolares/metabolismo , Animales , Colesterol/biosíntesis , Colesterol/metabolismo , Femenino , Regulación de la Expresión Génica , Técnicas de Inactivación de Genes , Homeostasis , Humanos , Inmunoglobulinas/metabolismo , Macrófagos/citología , Macrófagos/metabolismo , Masculino , Ratones , Persona de Mediana Edad , Proteinosis Alveolar Pulmonar/metabolismo , Proteinosis Alveolar Pulmonar/patología
18.
J Vis Exp ; (117)2016 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-27929461

RESUMEN

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids. Nevertheless, to fully understand the impact of extracellular sRNAs as endocrine signals, it is important to determine which carriers are transporting and protecting them in biological fluids (e.g., plasma), which cells and tissues contribute to extracellular sRNA pools, and cells and tissues capable of accepting and utilizing extracellular sRNA. To accomplish these goals, it is critical to isolate highly pure populations of extracellular carriers for sRNA profiling and quantification. We have previously demonstrated that lipoproteins, particularly high-density lipoproteins (HDL), transport functional microRNAs (miRNA) between cells and HDL-miRNAs are significantly altered in disease. Here, we detail a new protocol that utilizes tandem HDL isolation with density-gradient ultracentrifugation (DGUC) and fast-protein-liquid chromatography (FPLC) to obtain highly pure HDL for downstream profiling and quantification of all sRNAs, including miRNAs, using both high-throughput sequencing and real-time PCR approaches. This protocol will be a valuable resource for the investigation of sRNAs on HDL.


Asunto(s)
Lipoproteínas HDL , ARN Pequeño no Traducido , Regulación de la Expresión Génica de las Plantas , Humanos , Lipoproteínas HDL/aislamiento & purificación , MicroARNs
19.
Metabolism ; 64(2): 263-73, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25467845

RESUMEN

OBJECTIVES: Our aim was to determine if chronic kidney disease (CKD) occurring in childhood impairs the normally vasoprotective functions of high-density lipoproteins (HDLs). MATERIALS AND METHODS: HDLs were isolated from children with end-stage renal disease on dialysis (ESRD), children with moderate CKD and controls with normal kidney function. Macrophage response to HDLs was studied as expression of inflammatory markers (MCP-1, TNF-α, IL-1ß) and chemotaxis. Human umbilical vein endothelial cells were used for expression of adhesion molecules (ICAM-1, VCAM-1, E-selectin) and adhesion. Cellular proliferation, apoptosis, and necrosis of endothelial cells were measured by MTS/PMS reagent-based assay, flow cytometry, and ELISA. Cholesterol efflux was assessed by gas chromatographic measurements of cholesterol in macrophages exposed to HDLs. RESULTS: Compared with HDL(Control), HDL(CKD) and HDL(ESRD) heightened the cytokine response and disrupted macrophage chemotaxis. HDL(Control) reduced endothelial expression of ICAM-1, VCAM-1, E-selectin, whereas HDL(CKD) and HDL(ESRD) were less effective and showed reduced capacity to protect endothelial cells against monocyte adhesion. Compared with a dramatically enhanced endothelial proliferation following injurious stimulus by HDL(Control), neither HDL(CKD) nor HDL(ESRD) caused proliferative effects. HDLs of all three groups were equally protective against apoptosis assessed by flow cytometry and cleaved caspase-3 activity. Compared to HDL(Control), HDL(CKD) and HDL(ESRD) trended toward reduced capacity as cholesterol acceptors. CONCLUSION: CKD in children impairs HDL function. Even in the absence of long-standing and concomitant risk factors, CKD alters specific HDL functions linked to control of inflammation and endothelial responses.


Asunto(s)
Enfermedades Cardiovasculares/prevención & control , Endotelio Vascular/metabolismo , Fallo Renal Crónico/fisiopatología , Lipoproteínas HDL/metabolismo , Macrófagos/metabolismo , Insuficiencia Renal Crónica/fisiopatología , Adolescente , Apoptosis , Transporte Biológico , Enfermedades Cardiovasculares/epidemiología , Enfermedades Cardiovasculares/etiología , Adhesión Celular , Línea Celular , Proliferación Celular , Células Cultivadas , Quimiotaxis , Niño , Preescolar , Colesterol/sangre , Colesterol/metabolismo , Técnicas de Cocultivo , Endotelio Vascular/citología , Endotelio Vascular/patología , Células Endoteliales de la Vena Umbilical Humana , Humanos , Lactante , Fallo Renal Crónico/sangre , Fallo Renal Crónico/metabolismo , Fallo Renal Crónico/patología , Lipoproteínas HDL/sangre , Macrófagos/citología , Macrófagos/patología , Insuficiencia Renal Crónica/sangre , Insuficiencia Renal Crónica/metabolismo , Insuficiencia Renal Crónica/patología , Factores de Riesgo , Índice de Severidad de la Enfermedad , Tennessee/epidemiología
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