Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs.

Here we identify a low-cost diagnostic platform using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide (PMO) probe pairs, which upon binding target oligonucleotides undergo fluorescence resonance energy transfer (FRET). Using a target oligonucleotide derived from the Ebola virus (EBOV), we have derivatized PMO probes with either Alexa Fluor488 (donor) or tetramethylrhodamine (acceptor). Upon EBOV target oligonulceotide binding, observed changes in FRET between PMO probe pairs permit a 25 pM lower limit of detection; there is no off-target binding within a complex mixture of nucleic acids and other biomolecules present in human saliva. Equivalent levels of FRET occur using PMO probe pairs for single or double stranded oligonucleotide targets. High-affinity binding is retained under low-ionic strength conditions that disrupt oligonucleotide secondary structures (e.g., stem-loop structures), ensuring reliable target detection. Under these low-ionic strength conditions, rates of PMO probe binding to target oligonucleotides are increased 3-fold relative to conventional high-ionic strength conditions used for nucleic acid hybridization, with half-maximal binding occurring within 10 min. Our results indicate an ability to use PMO probe pairs to detect clinically relevant levels of EBOV and other oligonucleotide targets in complex biological samples without the need for nucleic acid amplification, and open the possibility of population screening that includes assays for the genomic integration of DNA based copies of viral RNA.

A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing.

The biological players involved in angiogenesis are only partially defined. Here, we report that endothelial cells (ECs) express a novel isoform of the cell-surface adhesion molecule L1CAM, termed L1-ΔTM. The splicing factor NOVA2, which binds directly to L1CAM pre-mRNA, is necessary and sufficient for the skipping of L1CAM transmembrane domain in ECs, leading to the release of soluble L1-ΔTM. The latter exerts high angiogenic function through both autocrine and paracrine activities. Mechanistically, L1-ΔTM-induced angiogenesis requires fibroblast growth factor receptor-1 signaling, implying a crosstalk between the two molecules. NOVA2 and L1-ΔTM are overexpressed in the vasculature of ovarian cancer, where L1-ΔTM levels correlate with tumor vascularization, supporting the involvement of NOVA2-mediated L1-ΔTM production in tumor angiogenesis. Finally, high NOVA2 expression is associated with poor outcome in ovarian cancer patients. Our results point to L1-ΔTM as a novel, EC-derived angiogenic factor which may represent a target for innovative antiangiogenic therapies.

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing's family of tumors.

Ewing's sarcoma treatment failures are associated with high mortality indicating a need for new therapeutic approaches. We used a k-mer counting approach to identify cancer-specific mRNA transcripts in 3 Ewing's Family Tumor (EFT) cell lines not found in the normal human transcriptome. Phosphorodiamidate morpholino oligomers targeting six EFT-specific transcripts were evaluated for cytotoxicity in TC-32 and CHLA-10 EFT lines and in HEK293 renal epithelial control cells. Average morpholino efficacy (EC50) was 0.66 ± 0.13 in TC-32, 0.25 ± 0.14 in CHLA-10 and 3.07 ± 5.02 µM in HEK293 control cells (ANOVA p < 0.01). Synergy was observed for a cocktail of 12 morpholinos at low dose (0.3 µM) in TC-32 cells, but not in CHLA-10 cells. Paired synergy was also observed in both EFT cell lines when the PHGDH pre-mRNA transcript was targeted in combination with XAGE1B or CYP4F22 transcripts. Antagonism was observed when CCND1 was targeted with XAGE1B or CYP4F22, or when IGFBP-2 was targeted with CCND1 or RBM11. This transcriptome profiling approach is highly effective for cancer drug discovery, as it identified new EWS-specific target genes (e.g. CYP4F22, RBM11 and IGBP-2), and predicted effective antisense agents (EC50 < 1 µM) that demonstrate both synergy and antagonism in combination therapy.

Tumor imaging using technetium-99m bound to pH-sensitive peptides.

Solid tumors often display metabolic abnormalities that consistently produce low pH in the extracellular space of poorly perfused tissue. These acidic regions may provide a mechanism for drug targeting. Peptides have been designed in such a manner that they exist in an anionic hydrophilic form at the pH of normal tissues, but then undergo a sharp transition to a non-ionic lipophilic form at reduced pH. Peptides were labeled with fluorescein or technetium-99m (99mTc) and evaluated in vitro and in two murine models of cancer. Our studies suggest that PAP-1, an 18 amino acid pH activated peptide with a pH of transition between hydrophilic and lipophilic forms (pT) of 6.4, will deliver fluorescein and 99mTc to tumors. Activation of PAP-1 by low pH and penetration into the plasma membrane of cells and tumors were confirmed using flow cytometry, fluorescence microscopy, and gamma scintigraphy. These results support our central hypothesis that PAP-1 may enable the selective delivery of macromolecules to tumors. This technology has potential for exploiting a common property of tumors to achieve highly specific medical intervention.

Invention and Early History of Morpholinos: From Pipe Dream to Practical Products.

Beginning with my concept in 1969 to treat disease at the nucleic acid level using antisense nucleic acids, antisense has evolved to the current Morpholino oligos. Morpholinos have been the dominant gene knockdown system in developmental biology. Lack of delivery technologies has limited their use in adult animals (including humans), though alteration in muscles in Duchenne muscular dystrophy (DMD) allows delivery into adult muscle. Morpholinos are currently in Phase 3 clinical trials for DMD and a Morpholino oligo for skipping dystrophin exon 51 has been approved by the US FDA. With improved delivery techniques, such as those in development at Gene Tools, therapeutic Morpholinos for many difficult-to-treat diseases will be possible. Initial applications are expected to be custom cocktails of delivery-enabled Morpholinos for treating cancers.

Endo-Porter: a novel reagent for safe, effective delivery of substances into cells.

Delivering large molecules into the cytosol of animal cells without damaging the cells has been one of the toughest challenges in biology. Endo-Porter is a weak-base amphiphilic peptide that was designed to deliver morpholino antisense oligomers and other non-ionic substances into the cytosol/nuclear compartment of cells by an endocytosis-mediated process that avoids damaging the plasma membrane of the cell. This prevents the loss of vital cell contents and the attendant high cell toxicity typical of most delivery systems. To deliver a substance into cells simply add that substance to the medium covering the cells, followed by addition of the pre-formulated Endo-Porter solution and swirl to mix. While most delivery reagents begin to show serious toxicity after just a few hours and are relatively ineffective in the presence of serum, delivery with Endo-Porter may be continued for 24 hours, or even 48 hours, without undue toxicity, and Endo-Porter is particularly effective in the presence of the 10% serum commonly used with cultured cells. The mechanism of delivery, entails rapid adsorption of Endo-Porter to cell surfaces, but this adsorption to the cell surface does not damage the plasma membrane. The membrane-bound Endo-Porter is rapidly endocytosed, along with any substances present in the medium (ie., the cargo one wishes to deliver). Upon subsequent acidification of the endosome (a natural process) the Endo-Porter contained within that endosome is converted to its poly-cationic form, which acts to permeabilize the endosomal membrane. This acid-induced permeabilization of the endosomal membrane allows any co-endocytosed cargo to pass from the endosome into the cytosol of the cell. This paper describes the basic design strategy used to develop Endo-Porter, test systems used to guide that development, and the effects of various structural parameters, including size and composition of the lipophilic face, size and composition of the weak-base face, and the relationship between peptide length and delivery efficiency in the presence of serum.

Custom cancer therapies: safe and effective treatments for most or all cancers.

Gene Tools, LLC has embarked on a program to develop safe and effective custom therapies for essentially all cancers. This entails: 1) identifying in each patient's cancer multiple molecular targets which are absent from that patient's normal cells, but are present in and essential to that patient's cancer; and 2) treating that patient with a custom cocktail of therapeutic agents effective for specifically inhibiting those selected targets in that patient's cancer.

Morpholino, siRNA, and S-DNA compared: impact of structure and mechanism of action on off-target effects and sequence specificity.

Generally a gene knockdown agent should achieve high sequence specificity and should lack off-target effects (non-antisense effects due to interactions with structures other than gene transcripts). Three major gene knockdown types are compared with respect to off-target effects and sequence specificities: 1) phosphorothioate-linked DNA (S-DNA); 2) short interfering RNA (siRNA); and, 3) Morpholino. S-DNAs cause multiple off-target effects, largely because their backbone sulfurs bind to many different proteins. S-DNAs also achieve poor sequence specificity because S-DNA/RNA duplexes as short as 7 base-pairs are cleaved by RNase H. siRNAs cause several off-target effects, but improved designs may soon avoid such effects. siRNAs also provide only limited sequence specificity because their short guide sequences largely determine which gene transcripts will be blocked or cleaved, and those guide sequences appear to recognize insufficient sequence information to uniquely target a selected gene transcript. This specificity limitation is inherent in their mechanism of action and so probably cannot be greatly improved. Morpholinos are virtually free of off-target effects--probably because they cannot interact electrostatically with proteins. Morpholinos also achieve exquisite sequence specificity--in large part because they must bind at least about 14 to 15 contiguous bases to block a gene transcript, and this constitutes sufficient sequence information to uniquely target a selected gene transcript. Because of their freedom from off-target effects, exquisite sequence specificity, complete stability in biological systems, and highly predictable targeting, Morpholinos dominate the most demanding of all gene knockdown applications, studies in developing embryos.

Mid-dilution on-line haemodiafiltration in a standard dialyser configuration.

BACKGROUND: Mid-dilution haemodiafiltration (HDF) results in an improved middle molecule removal compared with standard HDF. The OLpur MD 190 haemodiafilter represents a new dialyser design exclusively for mid-dilution on-line HDF. Compared with standard haemodialysers, structural changes in the headers allow the infusion of high replacement fluid volumes after a first post-dilution and before a second pre-dilution stage. METHODS: We compared in vitro the new device [blood flow (QB) 400 ml/min, substitution flow (QS) 100 and 200 ml/min, dialysate flow (QD) 800 ml/min] with a conventional high-flux dialyser of the same surface area in haemodialysis (HD) (QD 500 ml/min) and post-dilution HDF (at QS 60, QD = 500 ml/min and at QS 100, QD = 800 ml/min) modes. Subsequently, we performed an initial clinical application of the new device in six mid-dilution HDF treatments of five end-stage renal disease patients (QB 400 ml/min, QS 200 ml/min, QD 800 ml/min, treatment duration 205+/-23 min). RESULTS: In vitro urea and beta2-microglobulin clearances in mid-dilution HDF were, respectively, 309.2+/-5.5 and 144.4+/-15.2 ml/min (QS 100) and 321.6+/-4.1 and 204.9+/-4.1 ml/min (QS 200), compared with 278.6+/- 17.2 and 94.0+/-7.6 ml/min in HD, and 310.8+/-10.2 and 123.0+/-6.5 ml/min (QS 60) and 323.6+/-11.2 and 158.0+/-10.3 ml/min (QS 100) in post-dilution HDF. The in vivo trials showed the clinical utility of the device and confirmed the in vitro data: urea and beta2-microglobulin clearances were, respectively, 324.6+/- 10.9 and 207.9+/-29.3 ml/min, while reduction ratios were 75.0+/-5.5 and 83.6+/-4.7%. CONCLUSION: Our preliminary results need confirmation in a prospective cross-over study. However, the Nephros MD 190 haemodiafilter promises to be a true technological step ahead in terms of improved beta2-microglobulin removal.