The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5΄-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites. Compared to PCR- or ELISA-based methods, this assay enables separate quantitation of non-phosphorylated full-length guide strands from 5΄-phosphorylated forms that may associate with RNA-induced silencing complexes (RISC). Biodistribution studies in mice indicated that ARC-520 guide strands predominantly accumulated in liver. 5΄-phosphorylation of guide strands was observed within 5 min after ARC-520 injection, and was detected for at least 4 weeks corresponding to the duration of HBV mRNA silencing. Guide strands detected in RISC by AGO2 immuno-isolation represented 16% of total 5΄-phosphorylated guide strands in liver, correlating with a 2.7 log10 reduction of HBsAg. The PNA method enables pharmacokinetic analysis of RNAi triggers, elucidates potential metabolic processing events and defines pharmacokinetic-pharmacodynamic relationships.

Chronic hepatitis B virus (HBV) infection is a major disease for which there remains an unmet medical need. Current therapies for chronic hepatitis B include reverse transcriptase inhibitors and interferon. These therapies either require life-long administration or have significant side effects and limited efficacy. We have taken a novel approach toward the treatment of chronic hepatitis B by developing an siRNA-based therapeutic. In contrast to current therapies, our approach has the promise of significantly decreasing viral protein load which is primarily responsible for disease progression. In our formulation, liver-tropic cholesterol-conjugated siRNAs against HBV (chol-siHBVs) are co-injected intravenously with a reversibly masked, hepatocyte-targeted melittin-like peptide (NAG-MLP). Co-injection of chol-siHBVs and NAG-MLP results in multi-log repression of viral RNA, proteins and viral DNA with long duration of effect in transient and transgenic mouse models of chronic HBV infection, without toxicity. Using a hybridization/HPLC-based method of detection, we are able to correlate the degree of repression of the virus with the amount of the active form of the siRNA guide strand in the liver. In addition, this form of the guide strand can be detected up to one month after a single administration, correlating with the duration of effect. High efficacy, a long duration of effect and establishment of a robust pharmacokinetic/ pharmacodynamic relationship in the liver suggest co-injection of NAG-MLP and cholsiHBVs holds great promise as a novel therapeutic for chronically HBV infected patients.

Chronic hepatitis B virus (HBV) infection is a major disease for which there remains an unmet medical need. Current therapies for chronic hepatitis B include reverse transcriptase inhibitors and interferon. These therapies either require life-long administration or have significant side effects and limited efficacy. We have taken a novel approach toward the treatment of chronic hepatitis B by developing an siRNA-based therapeutic. In contrast to current therapies, our approach has the promise of significantly decreasing viral protein load which is primarily responsible for disease progression. In our formulation, liver-tropic cholesterol-conjugated siRNAs against HBV (chol-siHBVs) are co-injected intravenously with a reversibly masked, hepatocyte-targeted melittin-like peptide (NAG-MLP). Co-injection of chol-siHBVs and NAG-MLP results in multi-log repression of viral RNA, proteins and viral DNA with long duration of effect in transient and transgenic mouse models of chronic HBV infection, without toxicity. Using a hybridization/HPLC-based method of detection, we are able to correlate the degree of repression of the virus with the amount of the active form of the siRNA guide strand in the liver. In addition, this form of the guide strand can be detected up to one month after a single administration, correlating with the duration of effect. High efficacy, a long duration of effect and establishment of a robust pharmacokinetic/ pharmacodynamic relationship in the liver suggest co-injection of NAG-MLP and cholsiHBVs holds great promise as a novel therapeutic for chronically HBV infected patients.

The efficacy of gene therapy mediated by plasmid DNA (pDNA) depends on the selection of suitable vectors and doses. Using hydrodynamic limb vein (HLV) injection to deliver naked pDNA to skeletal muscles of the limbs, we evaluated key parameters that affect expression in muscle from genes encoded in pDNA. Short-term and long-term promoter comparisons demonstrated that kinetics of expression differed between cytomegalovirus (CMV), muscle creatine kinase, and desmin promoters, but all gave stable expression from 2 to 49 weeks after delivery to mouse muscle. Expression from the CMV promoter was highest. For mice, rats, and rhesus monkeys, the linear range for pDNA dose response could be defined by the mass of pDNA relative to the mass of target muscle. Correlation between pDNA dose and expression was linear between a threshold dose of 75 μg/g and maximal expression at approximately 400 μg/g. One HLV injection into rats of a dose of CMV-LacZ yielding maximal expression resulted in an average transfection of 28% of all hind leg muscle and 40% of the gastrocnemius and soleus. Despite an immune reaction to the reporter gene in monkeys, a single injection transfected an average of 10% of all myofibers in the targeted muscle of the arms and legs and an average of 15% of myofibers in the gastrocnemius and soleus.

Evans blue dye (EBD) can be used in live mice to study muscle pathology or injury, including exercise-induced muscle damage. EBD is excluded from intact cell membranes but leaks into cells, including muscle fibers, when the cell membrane is ruptured. EBD can be visualized by its autofluorescence under a fluorescence microscope. EBD-stained myofibers can be quantified from microscope images of muscle cross-sections. These myofibers are often in clusters that lend themselves to morphometric analysis. When the damaged myofibers are interspersed among intact myofibers, however, a more suitable approach is to count individual myofibers in the field of view. A much faster approach to measure EBD in muscles from different strains of mice or between treatment groups is to extract the EBD from muscle samples and quantitate it using a spectrophotometric microplate reader. The advantages and disadvantages of using each of these approaches are discussed here. Curr. Protoc. Mouse Biol. 1:463-488 © 2011 by John Wiley & Sons, Inc.

Evans blue dye (EBD) is used to mark damaged and permeable muscle fibers in mouse models of muscular dystrophy and as an endpoint in therapeutic trials. We counted EBD‐positive muscle fibers and extracted EBD from muscles sampled throughout the hindlimbs in young adult and old mdx mice to determine if the natural variability in morphology would allow measurement of a functional improvement in one limb compared to the contralateral limb. Following one bout of rotarod or treadmill exercise that greatly increased serum creatine kinase levels, the number of EBD + muscle fibers in 12–19‐month‐old mdx mice increased 3‐fold, EBD in the muscles increased, and, importantly, contralateral pairs of muscles contained similar amounts of EBD. In contrast, the intra‐ and interlimb amounts of EBD in 2–7‐month‐old mdx mice were much too variable. A therapeutic effect can more readily be measured in old mdx mice. These results will be useful in the design of therapy protocols using the mdx mouse. Muscle Nerve, 2010

In these studies we delivered by hydrodynamic limb vein (HLV) injection plasmid DNA (pDNA) expressing the full-length mouse dystrophin gene to skeletal muscles throughout the hind limbs of the mdx mouse model for Duchenne muscular dystrophy (DMD). We evaluated the levels and stability of dystrophin expression and measured the resulting muscle protection, using Evans blue dye (EBD) to mark the damaged myofibers. Plasmid delivery was as efficient in the dystrophic mice as in wild-type mice and equally efficient in young adult and old mice, as long as the dose of pDNA was adjusted for the target muscle weight. The HLV gene delivery procedure was tolerated well by the dystrophic mice and repeat injections could be performed over an extended period of time. Multiple gene deliveries additively increased the amount of dystrophin protein and also increased the percentages of dystrophin-expressing myofibers. Plasmids expressing dystrophin from a cytomegalovirus (CMV) promoter construct containing the HMG1 intron provided stable dystrophin expression for the life of the mouse and provided significant benefit to the limbs. EBD staining showed that dystrophin gene delivery preserved myofibers in the CMV-HMGi-mDys-injected leg by 2.5- to 5-fold in large groups of muscles and by 2.5-fold throughout the injected legs, compared with the contralateral control legs injected with a nonexpressing plasmid. A similar degree of protection was measured in young adult mice evaluated soon after the last gene delivery and in aged mice injected over an extended period of time. This degree of protection resulted from 18 to 20% of the normal level of dystrophin protein, with 11-16% dystrophin-expressing myofibers. These studies show promise for the use of HLV injections to deliver therapeutic doses of full-length dystrophin-expressing plasmids for long-lasting protection of skeletal muscles in patients with DMD.

Various plasmids were delivered into rodent limb muscles by hydrodynamic limb vein (HLV) injection of naked plasmid DNA (pDNA). Some of the pDNA preparations caused significant muscle necrosis and associated muscle regeneration 3 to 4 days after the injection whereas others caused no muscle damage. Occurrence of muscle damage was independent of plasmid sequence, size, and encoded genes. It was batch dependent and correlated with the quantity of bacterial genomic DNA (gDNA) that copurified with the pDNA. To determine whether such an effect was due to bacterial DNA or simply to fragmented DNA, mice were treated by HLV injection with sheared bacterial or murine gDNA. As little as 20 μg of the large fragments of bacterial gDNA caused muscle damage that morphologically resembled damage caused by the toxic pDNA preparations, whereas murine gDNA caused no damage even at a 10-fold higher dose. Toxicity from the bacterial gDNA was not due to endotoxin and was eliminated by DNase digestion. We conclude that pDNA itself does not cause muscle damage and that purification methods for the preparation of therapeutic pDNA should be optimized for removal of bacterial gDNA.

Covalent modifications of histones play crucial roles in chromatin structure and genomic stability. Recently, we reported a novel modification of histones: biotinylation of lysine residues. Here we provide evidence that K12-biotinylated histone H4 (K12Bio H4) maps specifically to both heterochromatin (alpha satellite repeats in pericentromeric regions) and transcriptionally repressed chromatin (γ-G globin and interleukin-2) in human lymphoblastoma cells. The abundance of K12Bio H4 in these regions was similar to that of K9-dimethylated histone H3, a known marker for heterochromatin. Likewise, K8-biotinylated histone H4 (K8Bio H4) mapped to heterochromatin, but the relative enrichment was smaller compared with K12Bio H4. Stimulation of interleukin-2 transcriptional activity with phorbol-12-myristate-13-acetate and phytohemagglutinin caused a rapid depletion of K12Bio H4 in the gene promoter. These data are consistent with a novel role for biotin in chromatin structure and transcriptional activity of genes.

BACKGROUND:Placental transfer of nutrients and secretion of hormones is essential for normal fetal development.AIM OF THE STUDY:To determine whether biotin supply affects biotin homeostasis, proliferation rates, and progesterone secretion in placenta cells.METHODS:JAr choriocarcinoma cells were cultured in media containing deficient (25 pmol/L), physiological (250 pmol/L), or pharmacological concentrations (10,000 pmol/L) of biotin for three weeks; markers for biotin homeostasis, proliferation, and hormone secretion were quantified.RESULTS:Biotin concentrations in culture media correlated negatively with expression of the biotin transporter SMVT, as judged by cellular transport rates of biotin, abundance of SMVT protein, and transcriptional activity of SMVT reporter-gene constructs. Notwithstanding this homeostatic mechanism, biotin concentrations in media correlated positively with activities of biotin-dependent propionyl-CoA carboxylase, abundance of biotinylated carboxylases, and with biotinylation of histones. Biotin deficiency was associated with decreased rates of thymidine uptake into JAr cells [pmol thymidine/( 10(6) cells x 24 h)]: 1.6 +/- 0.1 (25 pmol/L biotin) versus 2.3 +/- 0.2 (250 pmol/L biotin) versus 3.7 +/- 0.4 (10,000 pmol/L biotin), suggesting that cell proliferation depends on biotin. Secretion of progesterone was reduced in biotin-deficient cells; this effect was caused by reduced generation of new cells in deficient media rather than by an immediate effect of biotin on progesterone secretion at the singlecell-level.CONCLUSIONS:This study provides evidence that choriocarcinoma cells cannot maintain normal activities of biotin-dependent metabolic pathways if biotin concentrations in culture media are low. It is uncertain whether activities of biotin-dependent pathways in placenta affect fetal development in vivo.

Biotin affects gene expression in mammals; however, the signaling pathways leading to biotindependent transcriptional activation and inactivation of genes are largely unknown. Members of the Sp/Krüppellike factor family of transcription factors (e.g., the ubiquitous Sp1 and Sp3) play important roles in the expression of numerous mammalian genes. We tested the hypothesis that the nuclear abundance of Sp1 and Sp3 depends on biotin in human T cells (Jurkat cells) mediating biotin-dependent gene expression. Jurkat cells were cultured in biotin-deficient (0.025 nmol/L) and biotin-supplemented (10 nmol/L) media for 5 wk prior to transcription factor analysis. The association of Sp1 and Sp3 with DNA-binding sites (GC box and CACCC box) was 76–149% greater in nuclear extracts from biotin-supplemented cells compared with biotin-deficient cells, as determined by electrophoretic mobility shift assays. The increased DNA-binding activity observed in biotin-supplemented cells was caused by increased transcription of genes encoding Sp1 and Sp3, as shown by mRNA levels and reporter-gene activities; increased transcription of Sp1 and Sp3 genes was associated with the increased abundance of Sp1 and Sp3 protein in nuclei. Notwithstanding the important role for phosphorylation of Sp1 and Sp3 in regulating DNA-binding activity, the present study suggests that the effects of biotin on phosphorylation of Sp1 and Sp3 are minor. The increased nuclear abundance of Sp1 and Sp3 in biotin-supplemented cells was associated with increased transcriptional activity of 5 -flanking regions in Sp1/Sp3-dependent genes in reporter-gene assays. This study provides evidence that some effects of biotin on gene expression might be mediated by the nuclear abundance of Sp1 and Sp3. J. Nutr. 133: 3409–3415, 2003.

Biotin affects gene expression in mammals; however, the signaling pathways leading to biotin-dependent transcriptional activation and inactivation of genes are largely unknown. Members of the Sp/Krüppel-like factor family of transcription factors (e.g., the ubiquitous Sp1 and Sp3) play important roles in the expression of numerous mammalian genes. We tested the hypothesis that the nuclear abundance of Sp1 and Sp3 depends on biotin in human T cells (Jurkat cells) mediating biotin-dependent gene expression. Jurkat cells were cultured in biotin-deficient (0.025 nmol/L) and biotin-supplemented (10 nmol/L) media for 5 wk prior to transcription factor analysis. The association of Sp1 and Sp3 with DNA-binding sites (GC box and CACCC box) was 76-149% greater in nuclear extracts from biotin-supplemented cells compared with biotin-deficient cells, as determined by electrophoretic mobility shift assays. The increased DNA-binding activity observed in biotin-supplemented cells was caused by increased transcription of genes encoding Sp1 and Sp3, as shown by mRNA levels and reporter-gene activities; increased transcription of Sp1 and Sp3 genes was associated with the increased abundance of Sp1 and Sp3 protein in nuclei. Notwithstanding the important role for phosphorylation of Sp1 and Sp3 in regulating DNA-binding activity, the present study suggests that the effects of biotin on phosphorylation of Sp1 and Sp3 are minor. The increased nuclear abundance of Sp1 and Sp3 in biotin-supplemented cells was associated with increased transcriptional activity of 5'-flanking regions in Sp1/Sp3-dependent genes in reporter-gene assays. This study provides evidence that some effects of biotin on gene expression might be mediated by the nuclear abundance of Sp1 and Sp3.

Background Posttranslational modifications of histones play important roles in processes such as regulation of gene expression and DNA repair. Recently, evidence has been provided that histones in human cells are modified by covalent attachment of biotin. Aim of the study To determine whether the reverse process (debiotinylation of histones) occurs in biological samples and whether debiotinylation is an enzyme-mediated process; and to characterize the enzyme that mediates debiotinylation of histones. Methods Plasma and lymphocytes from healthy adults and a biotinidase-deficient patient were used as sources of debiotinylating enzymes. Debiotinylation of histones by plasma and lymphocyte proteins was measured using a colorimetric 96-well plate assay. Results Histones were debiotinylated rapidly if incubated with human plasma or lysates of lymphocytes. The following observations are consistent with the hypothesis that debiotinylation is an enzyme-mediated process: (i) Hydrolysis was slower at 4 °C compared to 37 °C; (ii) debiotinylating activity was destroyed when biological samples were heated at 90 °C for 30 min preceding incubation with biotinylated histones; and (iii) rates of debiotinylation were pH dependent. Rates of histone debiotinylation were significantly decreased in biotinidase-deficient samples. Conclusion Debiotinylation of histones in human samples is an enzyme-mediated process that is at least partly catalyzed by biotinidase.

Here the hypothesis was tested that mono- carboxylate transporters (MCT) mediate biotin transport in human lymphoid cells. Uptake of (3H)biotin was measured in human lymphoid cells (peripheral blood mononuclear cells (PBMC) and Jurkat cells) under conditions known to affect MCT-mediated transport. When biotin uptake into PBMC was measured in the presence of excess concen- trations of competitors (MCT substrates) and MCT inhibi- tors, transport rates decreased significantly to <75 and <67%, respectively, of controls. Biotin uptake correlated with the concentration of protons in culture media, consis- tent with cotransport of protons and the carboxylate biotin by MCT. Efflux of biotin from PBMC was stimulated by extracellular lactate (a known substrate for MCT), consis- tent with countertransport of the two substrates by the same transporter. PBMC responded to proliferation with parallel increases of transport rates for both biotin and lactate, providing circumstantial evidence that the same transporter mediates uptake of the two substrates in PBMC. Transfection of Jurkat cells with an expression vec- tor encoding MCT1 caused a 50% increase in biotin uptake; in contrast, overexpression of MCT1 did not affect biotin uptake in various nonlymphoid cell lines. These findings are consistent with the hypothesis that MCT mediate biotin up- take in human lymphoid cells. J. Nutr. 133: 2703-2706, 2003.

Biotin supply may affect transcription of genes and biotinylation of proteins in cells. In this study, Jurkat cells were used to model effects of biotin supply on biotin homeostasis and interleukin-2 metabolism in immune cells. Cells were cultured in media containing deficient (25 pmol/L), physiologic (250 pmol/L), or pharma- cologic concentrations (10,000 pmol/L) of biotin for 4 wk. Activities of the biotin-dependent enzyme propionyl-CoA carboxylase paralleled the biotin concentrations in media (pmol bicarbonate fixed/(min 106 cells)): 1.9 0.7 (25 pmol/L biotin) vs. 19 1.2 (250 pmol/L biotin) vs. 40 2.0 (10,000 pmol/L biotin). Cells responded to biotin deficiency with increased expression of biotin transporter genes. Biotin-deficient cells maintained normal biotiny- lation of histones but contained reduced levels of biotinylated carboxylases, suggesting compartmentalization of intracellular biotin distribution. Rates of cell proliferation and activities of the apoptotic enzyme caspase-3 were similar among treatment groups, suggesting that net proliferation was not affected by biotin status. Net secretion of interleukin-2 by Jurkat cells was inversely associated with the biotin concentration in media (kU/(L 24 h 106 cells)): 21 1.8 (25 pmol/L biotin) vs. 15 5.4 (250 pmol/L biotin) vs. 6.1 1.8 (10,000 pmol/L biotin), suggesting increased secretion or decreased internalization of interleukin-2 by biotin-deficient cells. This study provides evidence that biotin supply affects biotinylation of proteins, gene expression and metabolism of interleukin-2 in Jurkat cells. The physiological significance of effects of biotin status on metabolism of interleukin-2 remains to be elaborated. J. Nutr. 132: 887- 892, 2002.