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1.
Cell Host Microbe ; 31(7): 1185-1199.e10, 2023 07 12.
Article in English | MEDLINE | ID: mdl-37315561

ABSTRACT

Hemochorial placentas have evolved defense mechanisms to prevent the vertical transmission of viruses to the immunologically underdeveloped fetus. Unlike somatic cells that require pathogen-associated molecular patterns to stimulate interferon production, placental trophoblasts constitutively produce type III interferons (IFNL) through an unknown mechanism. We demonstrate that transcripts of short interspersed nuclear elements (SINEs) embedded in miRNA clusters within the placenta trigger a viral mimicry response that induces IFNL and confers antiviral protection. Alu SINEs within primate-specific chromosome 19 (C19MC) and B1 SINEs within rodent-specific microRNA cluster on chromosome 2 (C2MC) produce dsRNAs that activate RIG-I-like receptors (RLRs) and downstream IFNL production. Homozygous C2MC knockout mouse trophoblast stem (mTS) cells and placentas lose intrinsic IFN expression and antiviral protection, whereas B1 RNA overexpression restores C2MCΔ/Δ mTS cell viral resistance. Our results uncover a convergently evolved mechanism whereby SINE RNAs drive antiviral resistance in hemochorial placentas, placing SINEs as integral players in innate immunity.


Subject(s)
MicroRNAs , Animals , Mice , Female , Pregnancy , MicroRNAs/genetics , Placenta , Interferon Lambda , Antiviral Agents , Short Interspersed Nucleotide Elements
2.
Sci Signal ; 16(787): eadf6696, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37253090

ABSTRACT

Organ size is maintained by the controlled proliferation of distinct cell populations. In the mouse liver, hepatocytes in the midlobular zone that are positive for cyclin D1 (CCND1) repopulate the parenchyma at a constant rate to preserve liver mass. Here, we investigated how hepatocyte proliferation is supported by hepatic stellate cells (HSCs), pericytes that are in close proximity to hepatocytes. We used T cells to ablate nearly all HSCs in the murine liver, enabling the unbiased characterization of HSC functions. In the normal liver, complete loss of HSCs persisted for up to 10 weeks and caused a gradual reduction in liver mass and in the number of CCND1+ hepatocytes. We identified neurotrophin-3 (Ntf-3) as an HSC-produced factor that induced the proliferation of midlobular hepatocytes through the activation of tropomyosin receptor kinase B (TrkB). Treating HSC-depleted mice with Ntf-3 restored CCND1+ hepatocytes in the midlobular region and increased liver mass. These findings establish that HSCs form the mitogenic niche for midlobular hepatocytes and identify Ntf-3 as a hepatocyte growth factor.


Subject(s)
Hepatic Stellate Cells , Liver , Neurotrophin 3 , Animals , Mice , Cell Proliferation , Hepatic Stellate Cells/metabolism , Hepatocytes/metabolism , Liver/metabolism , Neurotrophin 3/metabolism
3.
Transplantation ; 106(4): 806-820, 2022 04 01.
Article in English | MEDLINE | ID: mdl-33979314

ABSTRACT

BACKGROUND: Acute rejection (AR) and recurrent hepatitis C virus (R-HCV) are significant complications in liver allograft recipients. Noninvasive diagnosis of intragraft pathologies may improve their management. METHODS: We performed small RNA sequencing and microRNA (miRNA) microarray profiling of RNA from sera matched to liver allograft biopsies from patients with nonimmune, nonviral (NINV) native liver disease. Absolute levels of informative miRNAs in 91 sera matched to 91 liver allograft biopsies were quantified using customized real-time quantitative PCR (RT-qPCR) assays: 30 biopsy-matched sera from 26 unique NINV patients and 61 biopsy-matched sera from 41 unique R-HCV patients. The association between biopsy diagnosis and miRNA abundance was analyzed by logistic regression and calculating the area under the receiver operating characteristic curve. RESULTS: Nine miRNAs-miR-22, miR-34a, miR-122, miR-148a, miR-192, miR-193b, miR-194, miR-210, and miR-885-5p-were identified by both sRNA-seq and TLDA to be associated with NINV-AR. Logistic regression analysis of absolute levels of miRNAs and goodness-of-fit of predictors identified a linear combination of miR-34a + miR-210 (P < 0.0001) as the best statistical model and miR-122 + miR-210 (P < 0.0001) as the best model that included miR-122. A different linear combination of miR-34a + miR-210 (P < 0.0001) was the best model for discriminating NINV-AR from R-HCV with intragraft inflammation, and miR-34a + miR-122 (P < 0.0001) was the best model for discriminating NINV-AR from R-HCV with intragraft fibrosis. CONCLUSIONS: Circulating levels of miRNAs, quantified using customized RT-qPCR assays, may offer a rapid and noninvasive means of diagnosing AR in human liver allografts and for discriminating AR from intragraft inflammation or fibrosis due to R-HCV.


Subject(s)
Graft Rejection , Hepatitis C, Chronic , Liver Transplantation , MicroRNAs , Allografts , Biomarkers , Hepatitis C, Chronic/surgery , Humans , Pilot Projects , Recurrence , Transcriptome
4.
Clin Chem ; 67(12): 1676-1688, 2021 11 26.
Article in English | MEDLINE | ID: mdl-34850840

ABSTRACT

BACKGROUND: Extracellular RNAs (exRNAs) in biofluids are amenable to quantitative analysis and proposed as noninvasive biomarkers for monitoring organ function. Cell-lineage-specific microRNAs (miRNAs) are present in plasma as soluble ribonucleoproteins or enclosed in exRNA carriers and transported through the vasculature. However, more extensive studies of healthy individuals are needed to gain insights into the variability of plasma miRNA abundance and composition. METHODS: The exRNA composition of platelet-depleted plasma collected twice from 236 healthy individuals was characterized by small RNA sequencing. Plasma of pregnant women featuring dramatically increased placental miRNAs and samples from subject P12 with noticeably increased epithelial- and neuroendocrine-origin miRNAs were included for comparison. The miRNA content of 10 000g and 100 000g pellet fractions of plasma generated by ultracentrifugation was also determined. Data analysis methods included Pearson correlation, differential gene expression, and unsupervised clustering. RESULTS: The abundance changes for more variable miRNAs in plasma of normal individuals correlated between coexpressed cell-lineage-specific miRNAs of the liver, neuroendocrine organs, epithelial cells, and muscle. ExRNA of pellet fractions contained <2% of total plasma miRNA with modest enrichment of lineage-specific and variable miRNAs compared to supernatant. The abundance fold changes of miRNAs observed in pregnancy and P12 compared to normal exceeded interquartile variability of healthy individuals. The neuroendocrine miRNA signature of P12 persisted for more than 4 years and was absent in other individuals. CONCLUSIONS: This study defines the framework and effect size for screening of extensive plasma collections for miRNA phenotypes and biomarker discovery.


Subject(s)
MicroRNAs , Sequence Analysis, RNA , Biomarkers , Female , Humans , MicroRNAs/blood , MicroRNAs/genetics , Phenotype , Placenta , Pregnancy , Pregnant Women , Sequence Analysis, RNA/methods
5.
Elife ; 102021 08 31.
Article in English | MEDLINE | ID: mdl-34463618

ABSTRACT

Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss-of-function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.


Subject(s)
Gene Regulatory Networks , MicroRNAs/genetics , RNA-Induced Silencing Complex/genetics , Animals , Female , Homeostasis , Mice , Mice, Transgenic , Peptides/metabolism , Pregnancy , Regeneration/genetics , Transgenes
6.
ESC Heart Fail ; 8(3): 1840-1849, 2021 06.
Article in English | MEDLINE | ID: mdl-33713567

ABSTRACT

AIMS: Allograft rejection following heart transplantation (HTx) is a serious complication even in the era of modern immunosuppressive regimens and causes up to a third of early deaths after HTx. Allograft rejection is mediated by a cascade of immune mechanisms leading to acute cellular rejection (ACR) and/or antibody-mediated rejection (AMR). The gold standard for monitoring allograft rejection is invasive endomyocardial biopsy that exposes patients to complications. Little is known about the potential of circulating miRNAs as biomarkers to detect cardiac allograft rejection. We here present a systematic analysis of circulating miRNAs as biomarkers and predictors for allograft rejection after HTx using next-generation small RNA sequencing. METHODS AND RESULTS: We used next-generation small RNA sequencing to investigate circulating miRNAs among HTx recipients (10 healthy controls, 10 heart failure patients, 13 ACR, and 10 AMR). MiRNA profiling was performed at different time points before, during, and after resolution of the rejection episode. We found three miRNAs with significantly increased serum levels in patients with biopsy-proven cardiac rejection when compared with patients without rejection: hsa-miR-139-5p, hsa-miR-151a-5p, and hsa-miR-186-5p. We identified miRNAs that may serve as potential predictors for the subsequent development of ACR: hsa-miR-29c-3p (ACR) and hsa-miR-486-5p (AMR). Overall, hsa-miR-486-5p was most strongly associated with acute rejection episodes. CONCLUSIONS: Monitoring cardiac allograft rejection using circulating miRNAs might represent an alternative strategy to invasive endomyocardial biopsy.


Subject(s)
Heart Transplantation , MicroRNAs , Allografts , Biomarkers , Graft Rejection/diagnosis , Humans , MicroRNAs/genetics
7.
Sci Rep ; 10(1): 3029, 2020 02 20.
Article in English | MEDLINE | ID: mdl-32080251

ABSTRACT

During implantation, cytotrophoblasts undergo epithelial-to-mesenchymal transition (EMT) as they differentiate into invasive extravillous trophoblasts (EVTs). The primate-specific microRNA cluster on chromosome 19 (C19MC) is exclusively expressed in the placenta, embryonic stem cells and certain cancers however, its role in EMT gene regulation is unknown. In situ hybridization for miR-517a/c, a C19MC cistron microRNA, in first trimester human placentas displayed strong expression in villous trophoblasts and a gradual decrease from proximal to distal cell columns as cytotrophoblasts differentiate into invasive EVTs. To investigate the role of C19MC in the regulation of EMT genes, we employed the CRISPR/dCas9 Synergistic Activation Mediator (SAM) system, which induced robust transcriptional activation of the entire C19MC cistron and resulted in suppression of EMT associated genes. Exposure of human iPSCs to hypoxia or differentiation of iPSCs into either cytotrophoblast-stem-like cells or EVT-like cells under hypoxia reduced C19MC expression and increased EMT genes. Furthermore, transcriptional activation of the C19MC cistron induced the expression of OCT4 and FGF4 and accelerated cellular reprogramming. This study establishes the CRISPR/dCas9 SAM as a powerful tool that enables activation of the entire C19MC cistron and uncovers its novel role in suppressing EMT genes critical for maintaining the epithelial cytotrophoblasts stem cell phenotype.


Subject(s)
Cellular Reprogramming/genetics , Chromosomes, Human, Pair 19/genetics , Epithelial-Mesenchymal Transition/genetics , MicroRNAs/genetics , Biomarkers/metabolism , Cell Differentiation/genetics , Cell Hypoxia/genetics , Female , Gene Expression Regulation , HEK293 Cells , Humans , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/metabolism , MicroRNAs/metabolism , Multigene Family , Placenta/metabolism , Pregnancy , Transcriptional Activation/genetics , Trophoblasts/metabolism
8.
JCI Insight ; 52019 04 11.
Article in English | MEDLINE | ID: mdl-30973829

ABSTRACT

Extracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. We performed conventional small-RNA-sequencing (sRNA-seq) and sRNA-seq with T4 polynucleotide kinase (PNK) end-treatment of total exRNA isolated from serum and platelet-poor EDTA, ACD, and heparin plasma to study the effect on ex-mRNA capture. Compared to conventional sRNA-seq PNK-treatment increased the detection of informative ex-mRNAs reads up to 50-fold. The exRNA pool was dominated by hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt reads originated from the coding sequences, in a pattern reminiscent of ribosome-profiling. Blood sample type had a considerable influence on the exRNA profile. On average approximately 350 to 1,100 distinct ex-mRNA transcripts were detected depending on plasma type. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to near 2,300. EDTA and ACD plasma showed a destabilizing effect on ex mRNA and non-coding RNA ribonucleoprotein complexes compared to other plasma types. In a proof-of-concept study, we investigated differences between the exRNA profiles of patients with acute coronary syndrome (ACS) and healthy controls. The improved tissue resolution of ex mRNAs after PNK-treatment enabled us to detect a neutrophil-signature in ACS that escaped detection by ex miRNA analysis.


Subject(s)
Acute Coronary Syndrome/genetics , Blood Cells/metabolism , Cell-Free Nucleic Acids/genetics , Liver/metabolism , Muscle, Skeletal/metabolism , RNA-Seq/methods , Acute Coronary Syndrome/blood , Adult , Aged , Biomarkers/blood , Case-Control Studies , Cell-Free Nucleic Acids/blood , Citric Acid , Edetic Acid , Erythrocytes/metabolism , Female , Glucose/analogs & derivatives , Heparin , High-Throughput Nucleotide Sequencing , Humans , Leukocytes, Mononuclear/metabolism , Male , Middle Aged , Monocytes/metabolism , Neutrophils/metabolism , Plasma , Polynucleotide 5'-Hydroxyl-Kinase , Proof of Concept Study , Sequence Analysis, RNA/methods , Serum , Specimen Handling
9.
J Am Soc Nephrol ; 30(4): 533-545, 2019 04.
Article in English | MEDLINE | ID: mdl-30846559

ABSTRACT

BACKGROUND: Recent single-cell RNA sequencing (scRNA-seq) analyses have offered much insight into cell-specific gene expression profiles in normal kidneys. However, in diseased kidneys, understanding of changes in specific cells, particularly glomerular cells, remains limited. METHODS: To elucidate the glomerular cell-specific gene expression changes in diabetic kidney disease, we performed scRNA-seq analysis of isolated glomerular cells from streptozotocin-induced diabetic endothelial nitric oxide synthase (eNOS)-deficient (eNOS-/-) mice and control eNOS-/- mice. RESULTS: We identified five distinct cell populations, including glomerular endothelial cells, mesangial cells, podocytes, immune cells, and tubular cells. Using scRNA-seq analysis, we confirmed the expression of glomerular cell-specific markers and also identified several new potential markers of glomerular cells. The number of immune cells was significantly higher in diabetic glomeruli compared with control glomeruli, and further cluster analysis showed that these immune cells were predominantly macrophages. Analysis of differential gene expression in endothelial and mesangial cells of diabetic and control mice showed dynamic changes in the pattern of expressed genes, many of which are known to be involved in diabetic kidney disease. Moreover, gene expression analysis showed variable responses of individual cells to diabetic injury. CONCLUSIONS: Our findings demonstrate the ability of scRNA-seq analysis in isolated glomerular cells from diabetic and control mice to reveal dynamic changes in gene expression in diabetic kidneys, with variable responses of individual cells. Such changes, which might not be apparent in bulk transcriptomic analysis of glomerular cells, may help identify important pathophysiologic factors contributing to the progression of diabetic kidney disease.


Subject(s)
Diabetic Nephropathies/genetics , Kidney Glomerulus/metabolism , Kidney Tubules/metabolism , Macrophages/metabolism , RNA, Small Cytoplasmic/analysis , Transcriptome , Animals , Diabetes Mellitus, Experimental/complications , Diabetic Nephropathies/etiology , Endothelial Cells/metabolism , Kidney Glomerulus/pathology , Kidney Tubules/pathology , Mesangial Cells/metabolism , Mice , Podocytes , Sequence Analysis, RNA , Single-Cell Analysis
10.
Nucleic Acids Res ; 47(2): 570-581, 2019 01 25.
Article in English | MEDLINE | ID: mdl-30517751

ABSTRACT

RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules represented functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.


Subject(s)
Gene Expression Regulation , RNA/metabolism , Ribonucleoproteins/metabolism , Base Sequence , Binding Sites , HEK293 Cells , Humans , RNA/chemistry , Ribonucleoproteins/classification
11.
Nat Commun ; 9(1): 4962, 2018 11 23.
Article in English | MEDLINE | ID: mdl-30470740

ABSTRACT

Activation of the Hippo pathway effector Yap underlies many liver cancers, however no germline or somatic mutations have been identified. Autophagy maintains essential metabolic functions of the liver, and autophagy-deficient murine models develop benign adenomas and hepatomegaly, which have been attributed to activation of the p62/Sqstm1-Nrf2 axis. Here, we show that Yap is an autophagy substrate and mediator of tissue remodeling and hepatocarcinogenesis independent of the p62/Sqstm1-Nrf2 axis. Hepatocyte-specific deletion of Atg7 promotes liver size, fibrosis, progenitor cell expansion, and hepatocarcinogenesis, which is rescued by concurrent deletion of Yap. Our results shed new light on mechanisms of Yap degradation and the sequence of events that follow disruption of autophagy, which is impaired in chronic liver disease.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Autophagy , Hepatocytes/cytology , Liver Neoplasms/metabolism , Liver Neoplasms/physiopathology , Liver/metabolism , Phosphoproteins/metabolism , Adaptor Proteins, Signal Transducing/genetics , Animals , Autophagy-Related Protein 7/genetics , Autophagy-Related Protein 7/metabolism , Carcinogenesis , Cell Cycle Proteins , Cell Differentiation , Female , Hepatocytes/metabolism , Humans , Liver/cytology , Liver/pathology , Liver Neoplasms/genetics , Male , Mice , Phosphoproteins/genetics , Proteolysis , Transcription Factors , YAP-Signaling Proteins
12.
Arterioscler Thromb Vasc Biol ; 38(6): 1321-1332, 2018 06.
Article in English | MEDLINE | ID: mdl-29724816

ABSTRACT

OBJECTIVE: Infantile hemangiomas (IHs) are the most common benign vascular neoplasms of infancy, characterized by a rapid growth phase followed by a spontaneous involution, or triggered by propranolol treatment by poorly understood mechanisms. LIN28/let-7 axis plays a central role in the regulation of stem cell self-renewal and tumorigenesis. However, the role of LIN28B/let-7 signaling in IH pathogenesis has not yet been elucidated. APPROACH AND RESULTS: LIN28B is highly expressed in proliferative IH and is less expressed in involuted and in propranolol-treated IH samples as measured by immunofluorescence staining and quantitative RT-PCR. Small RNA sequencing analysis of IH samples revealed a decrease in microRNAs that target LIN28B, including let-7, and an increase in microRNAs in the mir-498(46) cistron. Overexpression of LIN28B in HEK293 cells induced the expression of miR-516b in the mir-498(46) cistron. Propranolol treatment of induced pluripotent stem cells, which express mir-498(46) endogenously, reduced the expression of both LIN28B and mir-498(46) and increased the expression of let-7. Furthermore, propranolol treatment reduced the proliferation of induced pluripotent stem cells and induced epithelial-mesenchymal transition. CONCLUSIONS: This work uncovers the role of the LIN28B/let-7 switch in IH pathogenesis and provides a novel mechanism by which propranolol induces IH involution. Furthermore, it provides therapeutic implications for cancers in which the LIN28/let-7 pathway is imbalanced.


Subject(s)
Antineoplastic Agents/pharmacology , Hemangioma/drug therapy , Induced Pluripotent Stem Cells/drug effects , MicroRNAs/metabolism , Neoplastic Stem Cells/drug effects , Propranolol/pharmacology , RNA-Binding Proteins/metabolism , Signal Transduction/drug effects , Case-Control Studies , Cell Proliferation/drug effects , Cellular Senescence/drug effects , Epithelial-Mesenchymal Transition/drug effects , Gene Expression Regulation, Neoplastic , HEK293 Cells , Hemangioma/genetics , Hemangioma/metabolism , Hemangioma/pathology , Humans , Induced Pluripotent Stem Cells/metabolism , Induced Pluripotent Stem Cells/pathology , MicroRNAs/genetics , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , RNA-Binding Proteins/genetics
13.
Proc Natl Acad Sci U S A ; 115(23): E5334-E5343, 2018 06 05.
Article in English | MEDLINE | ID: mdl-29777089

ABSTRACT

Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample. We applied this method to characterize exRNAs from 312 plasma and serum samples collected from 13 healthy volunteers at 12 time points over a 2-month period. Small RNA cDNA library sequencing identified nearly twofold increased epithelial-, muscle-, and neuroendocrine-cell-specific miRNAs in females, while fasting and hormonal cycle showed little effect. External standardization helped to detect quantitative differences in erythrocyte and platelet-specific miRNA contributions and in miRNA concentrations between biofluids. It also helped to identify a study participant with a unique exRNA phenotype featuring a miRNA signature of up to 20-fold elevated endocrine-cell-specific miRNAs and twofold elevated total miRNA concentrations stable for over 1 year. Collectively, these results demonstrate an efficient and quantitative method to discern exRNA phenotypes and suggest that plasma and serum RNA profiles are stable over months and can be routinely monitored in long-term clinical studies.


Subject(s)
Cell-Free Nucleic Acids/blood , Adult , Biomarkers/blood , Cell-Free Nucleic Acids/genetics , Cell-Free Nucleic Acids/isolation & purification , Female , Gene Library , High-Throughput Nucleotide Sequencing , Humans , Male , MicroRNAs/blood , MicroRNAs/genetics
14.
JCI Insight ; 2(9)2017 May 04.
Article in English | MEDLINE | ID: mdl-28469080

ABSTRACT

Lupus nephritis is a leading cause of mortality among systemic lupus erythematosus (SLE) patients, and its heterogeneous nature poses a significant challenge to the development of effective diagnostics and treatments. Single cell RNA sequencing (scRNA-seq) offers a potential solution to dissect the heterogeneity of the disease and enables the study of similar cell types distant from the site of renal injury to identify novel biomarkers. We applied scRNA-seq to human renal and skin biopsy tissues and demonstrated that scRNA-seq can be performed on samples obtained during routine care. Chronicity index, IgG deposition, and quantity of proteinuria correlated with a transcriptomic-based score composed of IFN-inducible genes in renal tubular cells. Furthermore, analysis of cumulative expression profiles of single cell keratinocytes dissociated from nonlesional, non-sun-exposed skin of patients with lupus nephritis also revealed upregulation of IFN-inducible genes compared with keratinocytes isolated from healthy controls. This indicates the possible use of scRNA-seq analysis of skin biopsies as a biomarker of renal disease. These data support the potential utility of scRNA-seq to provide new insights into the pathogenesis of lupus nephritis and pave the way for exploiting a readily accessible tissue to reflect injury in the kidney.

15.
Exp Dermatol ; 24(12): 953-7, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26205579

ABSTRACT

Diphencyprone (DPCP) is a hapten that induces delayed-type hypersensitivity (DTH) reactions. MicroRNAs (miRNAs) are short non-coding RNAs that negatively regulate gene expression and have been implicated in various inflammatory skin diseases, but their role in DTH reactions is not well understood. We generated global miRNA expression profiles (using next-generation sequencing) of DPCP reactions in skin of seven healthy volunteers at 3, 14 and 120 days after challenge. Compared to placebo-treated sites, DPCP-challenged skin at 3 days (peak inflammation) had 127 miRNAs significantly deregulated. At 14 days (during resolution of inflammation), 43 miRNAs were deregulated and, at 120 days (when inflammation had completely resolved), six miRNAs were upregulated. While some miRNAs have been observed in psoriasis or atopic dermatitis, most of the deregulated miRNAs have not yet been studied in the context of skin biology or immunology. Across the three time points studied, many but not all miRNAs were uniquely expressed. As various miRNAs may influence T cell activation, this may indicate that the miRNAs exclusively expressed at different time points function to promote or resolve skin inflammation, and therefore, may inform on the paradoxical ability of DPCP to treat both autoimmune conditions (alopecia areata) and conditions of ineffective immunity (melanoma).


Subject(s)
Hypersensitivity, Delayed/genetics , Hypersensitivity, Delayed/immunology , MicroRNAs/genetics , MicroRNAs/metabolism , Skin/immunology , Skin/metabolism , Adult , Cyclopropanes/immunology , Female , Haptens/immunology , Humans , Hypersensitivity, Delayed/metabolism , Male , Middle Aged , Time Factors , Transcriptome , Young Adult
16.
J Clin Invest ; 124(9): 4102-14, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25133430

ABSTRACT

Drugs currently approved to coat stents used in percutaneous coronary interventions do not discriminate between proliferating vascular smooth muscle cells (VSMCs) and endothelial cells (ECs). This lack of discrimination delays reendothelialization and vascular healing, increasing the risk of late thrombosis following angioplasty. We developed a microRNA-based (miRNA-based) approach to inhibit proliferative VSMCs, thus preventing restenosis, while selectively promoting reendothelialization and preserving EC function. We used an adenoviral (Ad) vector that encodes cyclin-dependent kinase inhibitor p27(Kip1) (p27) with target sequences for EC-specific miR-126-3p at the 3' end (Ad-p27-126TS). Exogenous p27 overexpression was evaluated in vitro and in a rat arterial balloon injury model following transduction with Ad-p27-126TS, Ad-p27 (without miR-126 target sequences), or Ad-GFP (control). In vitro, Ad-p27-126TS protected the ability of ECs to proliferate, migrate, and form networks. At 2 and 4 weeks after injury, Ad-p27-126TS-treated animals exhibited reduced restenosis, complete reendothelialization, reduced hypercoagulability, and restoration of the vasodilatory response to acetylcholine to levels comparable to those in uninjured vessels. By incorporating miR-126-3p target sequences to leverage endogenous EC-specific miR-126, we overexpressed exogenous p27 in VSMCs, while selectively inhibiting p27 overexpression in ECs. Our proof-of-principle study demonstrates the potential of using a miRNA-based strategy as a therapeutic approach to specifically inhibit vascular restenosis while preserving EC function.


Subject(s)
Coronary Restenosis/prevention & control , Cyclin-Dependent Kinase Inhibitor p27/genetics , Endothelial Cells/physiology , MicroRNAs/genetics , Adenoviridae/genetics , Animals , Cells, Cultured , Humans , Male , Muscle, Smooth, Vascular/cytology , Muscle, Smooth, Vascular/physiology , Neointima , Percutaneous Coronary Intervention/adverse effects , Rats , Rats, Sprague-Dawley , Thrombophilia/therapy
17.
Proc Natl Acad Sci U S A ; 111(30): 11151-6, 2014 Jul 29.
Article in English | MEDLINE | ID: mdl-25012294

ABSTRACT

Heart failure (HF) is associated with high morbidity and mortality and its incidence is increasing worldwide. MicroRNAs (miRNAs) are potential markers and targets for diagnostic and therapeutic applications, respectively. We determined myocardial and circulating miRNA abundance and its changes in patients with stable and end-stage HF before and at different time points after mechanical unloading by a left ventricular assist device (LVAD) by small RNA sequencing. miRNA changes in failing heart tissues partially resembled that of fetal myocardium. Consistent with prototypical miRNA-target-mRNA interactions, target mRNA levels were negatively correlated with changes in abundance for highly expressed miRNAs in HF and fetal hearts. The circulating small RNA profile was dominated by miRNAs, and fragments of tRNAs and small cytoplasmic RNAs. Heart- and muscle-specific circulating miRNAs (myomirs) increased up to 140-fold in advanced HF, which coincided with a similar increase in cardiac troponin I (cTnI) protein, the established marker for heart injury. These extracellular changes nearly completely reversed 3 mo following initiation of LVAD support. In stable HF, circulating miRNAs showed less than fivefold differences compared with normal, and myomir and cTnI levels were only captured near the detection limit. These findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.


Subject(s)
Heart Failure/blood , MicroRNAs/blood , Myocardium/metabolism , RNA, Transfer/blood , Biomarkers/blood , Female , Heart Failure/pathology , Heart Failure/therapy , Heart-Assist Devices , Humans , Male , Myocardium/pathology , Troponin I/blood
18.
J Biol Chem ; 289(9): 5914-24, 2014 Feb 28.
Article in English | MEDLINE | ID: mdl-24407292

ABSTRACT

The mammalian heart, the body's largest energy consumer, has evolved robust mechanisms to tightly couple fuel supply with energy demand across a wide range of physiologic and pathophysiologic states, yet, when compared with other organs, relatively little is known about the molecular machinery that directly governs metabolic plasticity in the heart. Although previous studies have defined Kruppel-like factor 15 (KLF15) as a transcriptional repressor of pathologic cardiac hypertrophy, a direct role for the KLF family in cardiac metabolism has not been previously established. We show in human heart samples that KLF15 is induced after birth and reduced in heart failure, a myocardial expression pattern that parallels reliance on lipid oxidation. Isolated working heart studies and unbiased transcriptomic profiling in Klf15-deficient hearts demonstrate that KLF15 is an essential regulator of lipid flux and metabolic homeostasis in the adult myocardium. An important mechanism by which KLF15 regulates its direct transcriptional targets is via interaction with p300 and recruitment of this critical co-activator to promoters. This study establishes KLF15 as a key regulator of myocardial lipid utilization and is the first to implicate the KLF transcription factor family in cardiac metabolism.


Subject(s)
DNA-Binding Proteins/metabolism , Kruppel-Like Transcription Factors/metabolism , Lipid Metabolism , Muscle Proteins/metabolism , Myocardium/metabolism , Nuclear Proteins/metabolism , Transcription Factors/metabolism , Animals , Cardiomegaly/genetics , Cardiomegaly/metabolism , Cardiomegaly/pathology , Cell Line , DNA-Binding Proteins/genetics , E1A-Associated p300 Protein/genetics , E1A-Associated p300 Protein/metabolism , Heart Failure/genetics , Heart Failure/metabolism , Humans , Kruppel-Like Transcription Factors/genetics , Mice , Mice, Knockout , Muscle Proteins/genetics , Myocardium/pathology , Nuclear Proteins/genetics , Oxidation-Reduction , Transcription Factors/genetics
19.
Am J Cardiol ; 105(6): 862-4, 2010 Mar 15.
Article in English | MEDLINE | ID: mdl-20211333

ABSTRACT

Data suggest a link of aortic stenosis (AS) with calcium and bone metabolism. To further investigate this, the following parameters were analyzed in 38 patients with severe AS and in 38 age- and gender-matched controls, without obstructive coronary artery disease and with preserved renal function: calcium, phosphate, 1,25(OH(2))-vitamin D(3), intact parathyroid hormone (iPTH), and osteoprotegerin. Patients with AS had significantly higher serum levels of calcium (2.63 +/- 0.28 vs 2.48 +/- 0.23 mmol/L, p <0.01) and phosphate (1.56 +/- 0.33 vs 1.38 +/- 0.26 mmol/L, p <0.01) and increased calcium-phosphorus products (4.16 +/- 1.13 vs 3.44 +/- 0.89 mmol/L(2), p = 0.003). Notably, the iPTH concentration in the AS group was lower, and significantly more patients in the AS group had levels less than the study median of 60 ng/L. Osteoprotegerin was elevated in patients with AS, confirming reports in other populations (9.94 +/- 5.96 vs 6.73 +/- 4.28 pmol/L, p = 0.009). The relations of several parameters to iPTH were also altered (AS vs controls): calcium and iPTH, 0.071 +/- 0.034 versus 0.046 +/- 0.023, p <0.0001; phosphate and iPTH, 0.042 +/- 0.020 versus 0.025 +/- 0.013, p <0.0001; vitamin D and iPTH, 0.99 +/- 0.61 versus 0.63 +/- 0.46, p = 0.006; and osteoprotegerin and iPTH, 0.24 +/- 0.15 versus 0.12 +/- 0.09, p <0.0001. In conclusion, these data support a hypothesis connecting (severe) AS to altered calcium and bone homeostasis.


Subject(s)
Aortic Valve Stenosis/blood , Calcium/blood , Kidney Function Tests , Aged , Aortic Valve Stenosis/physiopathology , Cholecalciferol/blood , Creatinine/blood , Female , Humans , Male , Osteoprotegerin/blood , Parathyroid Hormone/blood , Phosphates/blood
20.
Cell Tissue Res ; 331(2): 401-12, 2008 Feb.
Article in English | MEDLINE | ID: mdl-17965884

ABSTRACT

Adhering junctions are generally grouped into desmosomes and adherens junctions based on their ultrastructural appearance and molecular composition. The armadillo-protein plakoglobin is common to both types of junctions, which are otherwise composed of mutually exclusive proteins. This view is based on observations in epithelial tissues but cannot easily be transferred to other cell types and tissues, as has become apparent during the last decade with the identification of new junctional proteins and the investigation of further non-epithelial junctions. Using a broad array of well-characterized specific antibodies against key junctional proteins in immunoblot reactions, high-resolution double-label laser scanning confocal microscopy, and immunoelectron microscopy, we describe a new type of adherens junction in human meningiomas and the human meningioma cell line HBL-52. This novel junction has a unique composition of proteins not found in any other tissue; it contains the desmosomal armadillo-protein plakophilin 2 together with the classic proteins of "epithelial" adherens junctions, i.e., E-cadherin (in some instances replaced by N-cadherin), alpha-catenin, beta-catenin, plakoglobin, and p120(ctn). Ultrastructurally, it is formed between two or three neighboring cells. For pragmatic reasons, we suggest the name "meningeal junction" for this new structure.


Subject(s)
Adherens Junctions/metabolism , Meningioma/pathology , Adherens Junctions/chemistry , Adult , Aged , Aged, 80 and over , Animals , Cadherins/metabolism , Cell Line, Tumor , Desmoplakins/metabolism , Female , Humans , Immunohistochemistry , Male , Meningioma/metabolism , Meningioma/ultrastructure , Middle Aged , Plakophilins/metabolism
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