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1.
Biology (Basel) ; 11(4)2022 Mar 25.
Article in English | MEDLINE | ID: mdl-35453708

ABSTRACT

Crohn's disease (CD) and rheumatoid arthritis (RA) are immune mediated inflammatory diseases. Several studies indicate a role for microRNAs (miRNAs) in the pathogenesis of a variety of autoimmune diseases, including CD and RA. Our study's goal was to investigate circulating miRNAs in CD and RA patients to identify potential new biomarkers for early detection and personalized therapeutic approaches for autoimmune diseases. For this study, subjects with CD (n = 7), RA (n = 8) and healthy controls (n = 7) were recruited, and plasma was collected for miRNA sequencing. Comparison of the expression patterns of miRNAs between CD and healthy patients identified 99 differentially expressed miRNAs. Out of these miRNAs, 4 were down regulated, while 95 were up regulated. Comparison of miRNAs between RA and healthy patients identified 57 differentially expressed miRNAs. Out of those, 12 were down regulated, while 45 were up regulated. For all the miRNAs down regulated in CD and RA patients, 420 GO terms for biological processes were similarly regulated between both groups. Therefore, the identification of new plasma miRNAs allows the emergence of new biomarkers that can assist in the diagnosis and treatment of CD and RA.

2.
J Gerontol A Biol Sci Med Sci ; 76(9): 1561-1570, 2021 08 13.
Article in English | MEDLINE | ID: mdl-34387333

ABSTRACT

The Ames dwarf (df/df) mouse is a well-established model for delayed aging. MicroRNAs (miRNAs), the most studied small noncoding RNAs (sncRNAs), may regulate ovarian aging to maintain a younger ovarian phenotype in df/df mice. In this study, we profile other types of ovarian sncRNAs, PIWI-interacting RNAs (piRNAs) and piRNA-like RNAs (piLRNAs), in young and aged df/df and normal mice. Half of the piRNAs derive from transfer RNA fragments (tRF-piRNAs). Aging and dwarfism alter the ovarian expression of these novel sncRNAs. Specific tRF-piRNAs that increased with age might target and decrease the expression of the breast cancer antiestrogen resistance protein 3 (BCAR3) gene in the ovaries of old df/df mice. A set of piLRNAs that decreased with age and map to D10Wsu102e mRNA may have trans-regulatory functions. Other piLRNAs that decreased with age potentially target and may de-repress transposable elements, leading to a beneficial impact on ovarian aging in df/df mice. These results identify unique responses in ovarian tissues with regard to aging and dwarfism. Overall, our findings highlight the complexity of the aging effects on gene expression and suggest that, in addition to miRNAs, piRNAs, piLRNAs, tRF-piRNAs, and their potential targets can be central players in the maintenance of a younger ovarian phenotype in df/df mice.


Subject(s)
Aging/genetics , Longevity/genetics , Ovary/metabolism , RNA, Small Interfering/metabolism , RNA, Small Untranslated/metabolism , Animals , Dwarfism, Pituitary/genetics , Female , Mice , Mice, Knockout , Oogenesis/genetics , Phenotype
3.
Biomark Cancer ; 10: 1179299X18759545, 2018.
Article in English | MEDLINE | ID: mdl-29497340

ABSTRACT

Extracellular RNAs are gaining clinical interest as biofluid-based noninvasive markers for diseases, especially cancer. In particular, derivatives of transfer RNA (tRNA) are emerging as a new class of small-noncoding RNAs with high biomarker potential. We and others previously reported alterations in serum levels of specific tRNA halves in disease states including cancer. Here, we explored seminal fluid for tRNA halves as potential markers of prostate cancer. We found that 5' tRNA halves are abundant in seminal fluid and are elevated in prostate cancer relative to noncancer patients. Importantly, most of these tRNA halves are also detectable in prostatic tissues, and a subset were increased in malignant relative to adjacent normal tissue. These findings emphasize the potential of 5' tRNA halves as noninvasive markers for prostate cancer screening and diagnosis and provide leads for future work to elucidate a putative role of the 5' tRNA halves in carcinogenesis.

4.
Biogerontology ; 19(2): 171-184, 2018 04.
Article in English | MEDLINE | ID: mdl-29335816

ABSTRACT

"Organ reserve" refers to the ability of an organ to successfully return to its original physiological state following repeated episodes of stress. Clinical evidence shows that organ reserve correlates with the ability of older adults to cope with an added workload or stress, suggesting a role in the process of aging. Although organ reserve is well documented clinically, it is not clearly defined at the molecular level. Interestingly, several metabolic pathways exhibit excess metabolic capacities (e.g., bioenergetics pathway, antioxidants system, plasticity). These pathways comprise molecular components that have an excess of quantity and/or activity than that required for basic physiological demand in vivo (e.g., mitochondrial complex IV or glycolytic enzymes). We propose that the excess in mtDNA copy number and tandem DNA repeats of telomeres are additional examples of intrinsically embedded structural components that could comprise excess capacity. These excess capacities may grant intermediary metabolism the ability to instantly cope with, or manage, added workload or stress. Therefore, excess metabolic capacities could be viewed as an innate mechanism of adaptability that substantiates organ reserve and contributes to the cellular defense systems. If metabolic excess capacities or organ reserves are impaired or exhausted, the ability of the cell to cope with stress is reduced. Under these circumstances cell senescence, transformation, or death occurs. In this review, we discuss excess metabolic and structural capacities as integrated metabolic pathways in relation to organ reserve and cellular aging.


Subject(s)
Aging/physiology , Adaptation, Physiological , Aging/genetics , Aging/metabolism , Animals , DNA, Mitochondrial/genetics , Electron Transport Complex IV/metabolism , Energy Metabolism , Glycolysis , Humans , Models, Biological , Neurons/metabolism , Pentose Phosphate Pathway , Telomere/genetics , Tissue Survival/physiology
5.
Aging Cell ; 16(5): 1200-1203, 2017 10.
Article in English | MEDLINE | ID: mdl-28677323

ABSTRACT

Caloric restriction (CR) is one of the most robust interventions shown to delay aging in diverse species, including rhesus monkeys (Macaca mulatta). Identification of factors involved in CR brings a promise of translatability to human health and aging. Here, we show that CR induced a profound change in abundance of circulating microRNAs (miRNAs) linked to growth and insulin signaling pathway, suggesting that miRNAs are involved in CR's mechanisms of action in primates. Deep sequencing of plasma RNA extracts enriched for short species revealed a total of 243 unique species of miRNAs including 47 novel species. Approximately 70% of the plasma miRNAs detected were conserved between rhesus monkeys and humans. CR induced or repressed 24 known and 10 novel miRNA species. Regression analysis revealed correlations between bodyweight, adiposity, and insulin sensitivity for 10 of the CR-regulated known miRNAs. Sequence alignment and target identification for these 10 miRNAs identify a role in signaling downstream of the insulin receptor. The highly abundant miR-125a-5p correlated positively with adiposity and negatively with insulin sensitivity and was negatively regulated by CR. Putative target pathways of CR-associated miRNAs were highly enriched for growth and insulin signaling that have previously been implicated in delayed aging. Clustering analysis further pointed to CR-induced miRNA regulation of ribosomal, mitochondrial, and spliceosomal pathways. These data are consistent with a model where CR recruits miRNA-based homeostatic mechanisms to coordinate a program of delayed aging.


Subject(s)
Aging/genetics , Caloric Restriction/methods , Gene Expression Regulation, Developmental , Insulin Resistance/genetics , MicroRNAs/genetics , Adiposity , Aging/metabolism , Animals , Conserved Sequence , Humans , Macaca mulatta , Male , MicroRNAs/blood , MicroRNAs/classification , Mitochondria/genetics , Mitochondria/metabolism , Principal Component Analysis , Receptor, Insulin/genetics , Receptor, Insulin/metabolism , Ribosomes/genetics , Ribosomes/metabolism , Signal Transduction , Spliceosomes/genetics , Spliceosomes/metabolism
6.
Genomics Insights ; 9: 29-39, 2016.
Article in English | MEDLINE | ID: mdl-27042094

ABSTRACT

In mammals, extracellular miRNAs circulate in biofluids as stable entities that are secreted by normal and diseased tissues, and can enter cells and regulate gene expression. Drosophila melanogaster is a proven system for the study of human diseases. They have an open circulatory system in which hemolymph (HL) circulates in direct contact with all internal organs, in a manner analogous to vertebrate blood plasma. Here, we show using deep sequencing that Drosophila HL contains RNase-resistant circulating miRNAs (HL-miRNAs). Limited subsets of body tissue miRNAs (BT-miRNAs) accumulated in HL, suggesting that they may be specifically released from cells or particularly stable in HL. Alternatively, they might arise from specific cells, such as hemocytes, that are in intimate contact with HL. Young and old flies accumulated unique populations of HL-miRNAs, suggesting that their accumulation is responsive to the physiological status of the fly. These HL-miRNAs in flies may function similar to the miRNAs circulating in mammalian biofluids. The discovery of these HL-miRNAs will provide a new venue for health and disease-related research in Drosophila.

7.
Redox Biol ; 6: 426-435, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26386875

ABSTRACT

Methylene blue (MB) delays cellular senescence, induces complex-IV, and activates Keap1/Nrf2; however, the molecular link of these effects to MB is unclear. Since MB is redox-active, we investigated its effect on the NAD/NADH ratio in IMR90 cells. The transient increase in NAD/NADH observed in MB-treated cells triggered an investigation of the energy regulator AMPK. MB induced AMPK phosphorylation in a transient pattern, which was followed by the induction of PGC1α and SURF1: both are inducers of mitochondrial and complex-IV biogenesis. Subsequently MB-treated cells exhibited >100% increase in complex-IV activity and a 28% decline in cellular oxidants. The telomeres erosion rate was also significantly lower in MB-treated cells. A previous research suggested that the pattern of AMPK activation (i.e., chronic or transient) determines the AMPK effect on cell senescence. We identified that the anti-senescence activity of MB (transient activator) was 8-times higher than that of AICAR (chronic activator). Since MB lacked an effect on cell cycle, an MB-dependent change to cell cycle is unlikely to contribute to the anti-senescence activity. The current findings in conjunction with the activation of Keap1/Nrf2 suggest a synchronized activation of the energy and cellular defense pathways as a possible key factor in MB's potent anti-senescence activity.


Subject(s)
Cellular Senescence/drug effects , Energy Metabolism/drug effects , Methylene Blue/pharmacology , Adenylate Kinase/metabolism , Aminoimidazole Carboxamide/analogs & derivatives , Aminoimidazole Carboxamide/pharmacology , Cell Cycle/drug effects , Cell Line , Drug Evaluation, Preclinical , Electron Transport Complex IV/metabolism , Humans , Mitochondria/drug effects , Mitochondria/metabolism , Mitochondrial Membranes/drug effects , Mitochondrial Membranes/metabolism , NAD/metabolism , Oxidation-Reduction , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha , Phosphorylation , Protein Processing, Post-Translational , Ribonucleotides/pharmacology , Telomere Homeostasis/drug effects , Transcription Factors/genetics , Transcription Factors/metabolism , Transcriptional Activation
8.
Mol Cell Biol ; 35(20): 3471-90, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26240283

ABSTRACT

The nuclear receptor hepatocyte nuclear factor 4α (HNF4α) is tumor suppressive in the liver but amplified in colon cancer, suggesting that it also might be oncogenic. To investigate whether this discrepancy is due to different HNF4α isoforms derived from its two promoters (P1 and P2), we generated Tet-On-inducible human colon cancer (HCT116) cell lines that express either the P1-driven (HNF4α2) or P2-driven (HNF4α8) isoform and analyzed them for tumor growth and global changes in gene expression (transcriptome sequencing [RNA-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]). The results show that while HNF4α2 acts as a tumor suppressor in the HCT116 tumor xenograft model, HNF4α8 does not. Each isoform regulates the expression of distinct sets of genes and recruits, colocalizes, and competes in a distinct fashion with the Wnt/ß-catenin mediator T-cell factor 4 (TCF4) at CTTTG motifs as well as at AP-1 motifs (TGAXTCA). Protein binding microarrays (PBMs) show that HNF4α and TCF4 share some but not all binding motifs and that single nucleotide polymorphisms (SNPs) in sites bound by both HNF4α and TCF4 can alter binding affinity in vitro, suggesting that they could play a role in cancer susceptibility in vivo. Thus, the HNF4α isoforms play distinct roles in colon cancer, which could be due to differential interactions with the Wnt/ß-catenin/TCF4 and AP-1 pathways.


Subject(s)
Colorectal Neoplasms/metabolism , Hepatocyte Nuclear Factor 1-alpha/metabolism , Hepatocyte Nuclear Factor 4/physiology , Transcription Factor AP-1/metabolism , Animals , Base Sequence , Binding, Competitive , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Consensus Sequence , Gene Expression Regulation, Neoplastic , Gene Ontology , HCT116 Cells , Humans , Male , Mice, Nude , Neoplasm Transplantation , Polymorphism, Single Nucleotide , Protein Binding , Protein Isoforms/physiology , Transcriptome , Tumor Burden
9.
Aging Cell ; 14(6): 1055-66, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26176567

ABSTRACT

Recent evidence demonstrates that serum levels of specific miRNAs significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 21 miRNAs during aging [genotype-by-age interaction (GbA)]. Genotype-by-age miRNAs showed four distinct expression patterns and significant overtargeting of transcripts involved in age-related processes. Functional enrichment analysis of putative and validated miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs modulated by age in the long-lived Ames mouse.


Subject(s)
Aging/genetics , Dwarfism, Pituitary/genetics , Longevity/genetics , MicroRNAs/blood , Animals , Base Sequence , Caloric Restriction , Female , Genotype , High-Throughput Nucleotide Sequencing , Insulin/metabolism , MAP Kinase Signaling System/genetics , Male , Mice , Mice, Knockout , MicroRNAs/genetics , Sequence Analysis, DNA , TOR Serine-Threonine Kinases/metabolism , Wnt Proteins/metabolism
10.
Oncotarget ; 6(22): 19246-63, 2015 Aug 07.
Article in English | MEDLINE | ID: mdl-26057471

ABSTRACT

The Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common human cancer, causing 350,000 individuals die worldwide each year. The overall prognosis in HNSCC patients has not significantly changed for the last decade. Complete understanding of the molecular mechanisms in HNSCC carcinogenesis could allow an earlier diagnosis and the use of more specific and effective therapies. In the present study we used deep sequencing to characterize small non-coding RNAs (sncRNAs) in serum from HNSCC patients and healthy donors. We identified, for the first time, a multi-marker signature of 3 major classes of circulating sncRNAs in HNSCC, revealing the presence of circulating novel and known miRNAs, and tRNA- and YRNA-derived small RNAs that were significantly deregulated in the sera of HNSCC patients compared to healthy controls. By implementing a triple-filtering approach we identified a subset of highly biologically relevant miRNA-mRNA interactions and we demonstrated that the same genes/pathways affected by somatic mutations in cancer are affected by changes in the abundance of miRNAs. Therefore, one important conclusion from our work is that during cancer development, there seems to be a convergence of oncogenic processes driven by somatic mutations and/or miRNA regulation affecting key cellular pathways.


Subject(s)
Biomarkers, Tumor/blood , Carcinoma, Squamous Cell/genetics , Head and Neck Neoplasms/genetics , MicroRNAs/blood , RNA, Untranslated/blood , Aged , Biomarkers, Tumor/genetics , Carcinoma, Squamous Cell/blood , Carcinoma, Squamous Cell/pathology , Female , Head and Neck Neoplasms/blood , Head and Neck Neoplasms/pathology , Humans , Male , MicroRNAs/genetics , Middle Aged , Mouth Neoplasms/blood , Mouth Neoplasms/genetics , Mouth Neoplasms/pathology , Neoplasm Staging , Prognosis , RNA, Untranslated/genetics , Squamous Cell Carcinoma of Head and Neck
11.
J Gerontol A Biol Sci Med Sci ; 70(12): 1479-89, 2015 Dec.
Article in English | MEDLINE | ID: mdl-25380600

ABSTRACT

Mesonordihydroguaiaretic acid (NDGA) extends murine lifespan. The studies reported here describe its dose dependence, effects on body weight, toxicity-related clinical chemistries, and mortality-related pathologies. In flies, we characterized its effects on lifespan, food consumption, body weight, and locomotion. B6C3F1 mice were fed AIN-93M diet supplemented with 1.5, 2.5, 3.5, or 4.5 g NDGA/kg diet (1.59, 2.65, 3.71 and 4.77 mg/kg body weight/day) beginning at 12 months of age. Only the 3.5 mg/kg diet produced a highly significant increase in lifespan, as judged by either the Mantel-Cox log-rank test (p = .008) or the Gehan-Breslow-Wilcoxon test (p = .009). NDGA did not alter food intake, but dose-responsively reduced weight, suggesting it decreased the absorption or increased the utilization of calories. NDGA significantly increased the incidence of liver, lung, and thymus tumors, and peritoneal hemorrhagic diathesis found at necropsy. However, clinical chemistries found little evidence for overt toxicity. While NDGA was not overtly toxic at its therapeutic dosage, its association with severe end of life pathologies does not support the idea that NDGA consumption will increase human lifespan or health-span. The less toxic derivatives of NDGA which are under development should be explored as anti-aging therapeutics.


Subject(s)
Antioxidants/pharmacology , Drosophila/physiology , Energy Metabolism/drug effects , Hemorrhagic Disorders/chemically induced , Homeostasis/drug effects , Longevity/drug effects , Masoprocol/pharmacology , Mice/physiology , Neoplasms/chemically induced , Neoplasms/mortality , Animals , Body Weight/drug effects , Dose-Response Relationship, Drug , Eating/drug effects , Male
12.
Metallomics ; 7(2): 309-21, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25525887

ABSTRACT

The majority of the heme-binding proteins possess a "heme-pocket" that stably binds to heme. Usually known as housekeeping heme-proteins, they participate in a variety of metabolic reactions (e.g., catalase). Heme also binds with lower affinity to the "Heme-Regulatory Motifs" (HRM) in specific regulatory proteins. This type of heme binding is known as exchangeable or regulatory heme (RH). Heme binding to HRM proteins regulates their function (e.g., Bach1). Although there are well-established methods for assaying total cellular heme (e.g., heme-proteins plus RH), currently there is no method available for measuring RH independent of the total heme (TH). The current study describes and validates a new method to measure intracellular RH. This method is based on the reconstitution of apo-horseradish peroxidase (apoHRP) with heme to form holoHRP. The resulting holoHRP activity is then measured with a colorimetric substrate. The results show that apoHRP specifically binds RH but not with heme from housekeeping heme-proteins. The RH assay detects intracellular RH. Furthermore, using conditions that create positive (hemin) or negative (N-methyl protoporphyrin IX) controls for heme in normal human fibroblasts (IMR90), the RH assay shows that RH is dynamic and independent of TH. We also demonstrated that short-term exposure to subcytotoxic concentrations of lead (Pb), mercury (Hg), or amyloid-ß (Aß) significantly alters intracellular RH with little effect on TH. In conclusion the RH assay is an effective assay to investigate intracellular RH concentration and demonstrates that RH represents ∼6% of total heme in IMR90 cells.


Subject(s)
Apoenzymes/metabolism , Enzyme Assays/methods , Heme/metabolism , Horseradish Peroxidase/metabolism , Intracellular Space/metabolism , Amyloid beta-Peptides/metabolism , Cell Line , Heme/biosynthesis , Humans , Lead/metabolism , Mercury/metabolism , Reference Standards , Substrate Specificity , Time Factors
13.
Biomark Cancer ; 6: 37-47, 2014.
Article in English | MEDLINE | ID: mdl-25520563

ABSTRACT

Small noncoding RNAs circulating in the blood may serve as signaling molecules because of their ability to carry out a variety of cellular functions. We have previously described tRNA- and YRNA-derived small RNAs circulating as components of larger complexes in the blood of humans and mice; the characteristics of these small RNAs imply specific processing, secretion, and physiological regulation. In this study, we have asked if changes in the serum abundance of these tRNA and YRNA fragments are associated with a diagnosis of cancer. We used deep sequencing and informatics analysis to catalog small RNAs in the sera of breast cancer cases and normal controls. 5' tRNA halves and YRNA fragments are abundant in both groups, but we found that a breast cancer diagnosis is associated with changes in levels of specific subtypes. This prompted us to look at existing sequence datasets of serum small RNAs from 42 breast cancer cases, taken at the time of diagnosis. We find significant changes in the levels of specific 5' tRNA halves and YRNA fragments associated with clinicopathologic characteristics of the cancer. Although these findings do not establish causality, they suggest that circulating 5' tRNA halves and YRNA fragments with known cellular functions may participate in breast cancer syndromes and have potential as circulating biomarkers. Larger studies with multiple types of cancer are needed to adequately evaluate their potential use for the development of noninvasive cancer screening.

14.
Ageing Res Rev ; 17: 86-98, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24607831

ABSTRACT

Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.


Subject(s)
Aging/blood , RNA, Small Untranslated/blood , Animals , Biomarkers/blood , Humans , RNA, Transfer/metabolism
15.
Mol Cell ; 53(1): 63-74, 2014 Jan 09.
Article in English | MEDLINE | ID: mdl-24289924

ABSTRACT

While p53 activation has long been studied, the mechanisms by which its targets genes are restored to their preactivation state are less clear. We report here that TAF1 phosphorylates p53 at Thr55, leading to dissociation of p53 from the p21 promoter and inactivation of transcription late in the DNA damage response. We further show that cellular ATP level might act as a molecular switch for Thr55 phosphorylation on the p21 promoter, indicating that TAF1 is a cellular ATP sensor. Upon DNA damage, cells undergo PARP-1-dependent ATP depletion, which is correlated with reduced TAF1 kinase activity and Thr55 phosphorylation, resulting in p21 activation. As cellular ATP levels recover, TAF1 is able to phosphorylate p53 on Thr55, which leads to dissociation of p53 from the p21 promoter. ChIP-sequencing analysis reveals p53 dissociates from promoters genome wide as cells recover from DNA damage, suggesting the general nature of this mechanism.


Subject(s)
DNA Damage , Histone Acetyltransferases/metabolism , Promoter Regions, Genetic , TATA-Binding Protein Associated Factors/metabolism , Transcription Factor TFIID/metabolism , Transcription, Genetic , Tumor Suppressor Protein p53/metabolism , Adenosine Triphosphate/genetics , Adenosine Triphosphate/metabolism , Cell Line , Cyclin-Dependent Kinase Inhibitor p21/genetics , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Genome-Wide Association Study , Histone Acetyltransferases/genetics , Humans , Phosphorylation/genetics , TATA-Binding Protein Associated Factors/genetics , Transcription Factor TFIID/genetics , Tumor Suppressor Protein p53/genetics
16.
Physiol Genomics ; 45(21): 990-8, 2013 Nov 01.
Article in English | MEDLINE | ID: mdl-24022222

ABSTRACT

Small noncoding RNAs carry out a variety of functions in eukaryotic cells, and in multiple species they can travel between cells, thus serving as signaling molecules. In mammals multiple small RNAs have been found to circulate in the blood, although in most cases the targets of these RNAs, and even their functions, are not well understood. YRNAs are small (84-112 nt) RNAs with poorly characterized functions, best known because they make up part of the Ro ribonucleoprotein autoantigens in connective tissue diseases. In surveying small RNAs present in the serum of healthy adult humans, we have found YRNA fragments of lengths 27 nt and 30-33 nt, derived from the 5'-ends of specific YRNAs and generated by cleavage within a predicted internal loop. Many of the YRNAs from which these fragments are derived were previously annotated only as pseudogenes, or predicted informatically. These 5'-YRNA fragments make up a large proportion of all small RNAs (including miRNAs) present in human serum. They are also present in plasma, are not present in exosomes or microvesicles, and circulate as part of a complex with a mass between 100 and 300 kDa. Mouse serum contains far fewer 5'-YRNA fragments, possibly reflecting the much greater copy number of YRNA genes and pseudogenes in humans. The function of the 5'-YRNA fragments is at present unknown, but the processing and secretion of specific YRNAs to produce 5'-end fragments that circulate in stable complexes are consistent with a signaling function.


Subject(s)
Pseudogenes/genetics , RNA Processing, Post-Transcriptional , RNA, Small Untranslated/genetics , RNA/genetics , Adult , Animals , Base Sequence , Blotting, Northern , DNA, Complementary/chemistry , DNA, Complementary/genetics , Humans , Male , Mice , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Small Untranslated/blood , RNA, Small Untranslated/chemistry , Ribonucleoproteins/genetics , Sequence Analysis, DNA
17.
BMC Genomics ; 14: 298, 2013 May 02.
Article in English | MEDLINE | ID: mdl-23638709

ABSTRACT

BACKGROUND: Small RNAs complex with proteins to mediate a variety of functions in animals and plants. Some small RNAs, particularly miRNAs, circulate in mammalian blood and may carry out a signaling function by entering target cells and modulating gene expression. The subject of this study is a set of circulating 30-33 nt RNAs that are processed derivatives of the 5' ends of a small subset of tRNA genes, and closely resemble cellular tRNA derivatives (tRFs, tiRNAs, half-tRNAs, 5' tRNA halves) previously shown to inhibit translation initiation in response to stress in cultured cells. RESULTS: In sequencing small RNAs extracted from mouse serum, we identified abundant 5' tRNA halves derived from a small subset of tRNAs, implying that they are produced by tRNA type-specific biogenesis and/or release. The 5' tRNA halves are not in exosomes or microvesicles, but circulate as particles of 100-300 kDa. The size of these particles suggest that the 5' tRNA halves are a component of a macromolecular complex; this is supported by the loss of 5' tRNA halves from serum or plasma treated with EDTA, a chelating agent, but their retention in plasma anticoagulated with heparin or citrate. A survey of somatic tissues reveals that 5' tRNA halves are concentrated within blood cells and hematopoietic tissues, but scant in other tissues, suggesting that they may be produced by blood cells. Serum levels of specific subtypes of 5' tRNA halves change markedly with age, either up or down, and these changes can be prevented by calorie restriction. CONCLUSIONS: We demonstrate that 5' tRNA halves circulate in the blood in a stable form, most likely as part of a nucleoprotein complex, and their serum levels are subject to regulation by age and calorie restriction. They may be produced by blood cells, but their cellular targets are not yet known. The characteristics of these circulating molecules, and their known function in suppression of translation initiation, suggest that they are a novel form of signaling molecule.


Subject(s)
Aging/genetics , Blood Cells/metabolism , Caloric Restriction , RNA, Transfer/blood , RNA, Transfer/genetics , Animals , Edetic Acid/pharmacology , Male , Mice , MicroRNAs/genetics , MicroRNAs/metabolism , Nucleoproteins/blood , Peptide Chain Initiation, Translational/drug effects , RNA, Transfer/drug effects , Tissue Distribution
18.
Aging (Albany NY) ; 5(2): 130-41, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23470454

ABSTRACT

MicroRNAs (miRNAs) function to modulate gene expression, and through this property they regulate a broad spectrum of cellular processes. They can circulate in blood and thereby mediate cell-to-cell communication. Aging involves changes in many cellular processes that are potentially regulated by miRNAs, and some evidence has implicated circulating miRNAs in the aging process. In order to initiate a comprehensive assessment of the role of circulating miRNAs in aging, we have used deep sequencing to characterize circulating miRNAs in the serum of young mice, old mice, and old mice maintained on calorie restriction (CR). Deep sequencing identifies a set of novel miRNAs, and also accurately measures all known miRNAs present in serum. This analysis demonstrates that the levels of many miRNAs circulating in the mouse are increased with age, and that the increases can be antagonized by CR. The genes targeted by this set of age-modulated miRNAs are predicted to regulate biological processes directly relevant to the manifestations of aging including metabolic changes, and the miRNAs themselves have been linked to diseases associated with old age. This finding implicates circulating miRNAs in the aging process, raising questions about their tissues of origin, their cellular targets, and their functional role in metabolic changes that occur with aging.


Subject(s)
Aging/genetics , Caloric Restriction/methods , High-Throughput Nucleotide Sequencing/methods , MicroRNAs/genetics , Aging/metabolism , Animals , Mice , MicroRNAs/blood , MicroRNAs/metabolism
19.
Age (Dordr) ; 35(6): 2099-109, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23314750

ABSTRACT

Chronic treatment with ß-adrenergic receptor (ßAR) agonists increases mortality and morbidity while ßAR antagonists (ß-blockers) decrease all-cause mortality for those at risk of cardiac disease. Levels of sympathetic nervous system ßAR agonists and ßAR activity increase with age, and this increase may hasten the development of age-related mortality. Here, we show that ß-blockers extend the life span of healthy metazoans. The ß-blockers metoprolol and nebivolol, administered in food daily beginning at 12 months of age, significantly increase the mean and median life span of isocalorically fed, male C3B6F1 mice, by 10 and 6.4%, respectively (P < 0.05). Neither drug affected the weight or food intake of the mice, indicating that induced CR is not responsible for these effects, and that energy absorption and utilization are not altered by the drugs. Both ß-blockers were investigated to control for their idiosyncratic, off-target effects. Metoprolol and nebivolol extended Drosophila life span, without affecting food intake or locomotion. Thus, ßAR antagonists are capable of directly extending the life span of two widely divergent metazoans, suggesting that these effects are phylogenetically highly conserved. Thus, long-term use of ß-blockers, which are generally well-tolerated, may enhance the longevity of healthy humans.


Subject(s)
Adrenergic beta-Antagonists/pharmacology , Aging/drug effects , Drosophila/growth & development , Energy Metabolism , Longevity/drug effects , Receptors, Adrenergic, beta/drug effects , Animals , Drosophila/drug effects , Male , Mice , Receptors, Adrenergic, beta/metabolism
20.
PLoS One ; 7(6): e39581, 2012.
Article in English | MEDLINE | ID: mdl-22737247

ABSTRACT

Statins such as simvastatin are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors and standard therapy for the prevention and treatment of cardiovascular diseases in mammals. Here we show that simvastatin significantly increased the mean and maximum lifespan of Drosophila melanogaster (Drosophila) and enhanced cardiac function in aging flies by significantly reducing heart arrhythmias and increasing the contraction proportion of the contraction/relaxation cycle. These results appeared independent of internal changes in ubiquinone or juvenile hormone levels. Rather, they appeared to involve decreased protein prenylation. Simvastatin decreased the membrane association (prenylation) of specific small Ras GTPases in mice. Both farnesyl (L744832) and type 1 geranylgeranyl transferase (GGTI-298) inhibitors increased Drosophila lifespan. These data are the most direct evidence to date that decreased protein prenylation can increase cardiac health and lifespan in any metazoan species, and may explain the pleiotropic (non-cholesterol related) health effects of statins.


Subject(s)
Hydroxymethylglutaryl-CoA Reductase Inhibitors/therapeutic use , Aging/drug effects , Animals , Behavior, Animal , Benzamides/pharmacology , Cardiovascular Diseases/drug therapy , Drosophila melanogaster , Feeding Behavior , Heart/drug effects , Longevity , Male , Methionine/analogs & derivatives , Methionine/pharmacology , Mice , Simvastatin/pharmacology , Ubiquinone/analogs & derivatives , Ubiquinone/pharmacology
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