Faqing Huang

Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells

Nasopharyngeal carcinoma is a poorly differentiated upper respiratory tract cancer that highly expresses human folate receptors (hFR). Binding of folate to hFR triggers endocytosis. The folate was conjugated into adenosine 5′-monophosphate (AMP) by 1,6-hexanediamine linkages. After reverse HPLC to reach 93% purity, the folate–AMP, which can only be used for transcription initiation but not for chain extension, was incorporated into the 5′-end of bacteriophage phi29 motor pRNA. A 16:1 ratio of folate–AMP to ATP in transcription resulted in more than 60% of the pRNA containing folate. A pRNA with a 5′-overhang is needed to enhance the accessibility of the 5′ folate for specific receptor binding. Utilizing the engineered left/right interlocking loops, polyvalent dimeric pRNA nanoparticles were constructed using RNA nanotechnology to carry folate, a detection marker, and siRNA targeting at an antiapoptosis factor. The chimeric pRNAs were processed into ds-siRNA by Dicer. Incubation of nasopharyngeal epidermal carcinoma (KB) cells with the dimer resulted in its entry into cancer cells, and the subsequent silencing of the target gene. Such a protein-free RNA nanoparticle with undetectable antigenicity has a potential for repeated long-term administration for nasopharyngeal carcinoma as the effectiveness and specificity were confirmed by ex vivo delivery in the animal trial.

Facile Synthesis of Multivalent Folate-Block Copolymer Conjugates via Aqueous RAFT Polymerization: Targeted Delivery of siRNA and Subsequent Gene Suppression

Cell specific delivery of small interfering ribonucleic acid (siRNA) using well-defined multivalent folate-conjugated block copolymers is reported. Primary amine functional, biocompatible, hydrophilic-block-cationic copolymers were synthesized via aqueous reversible addition-fragmentation chain transfer (RAFT) polymerization. N-(2-hydroxypropyl)methacrylamide) (HPMA), a permanently hydrophilic monomer, was copolymerized with a primary amine containing monomer, N-(3-aminopropyl)methacrylamide (APMA). Poly(HPMA) confers biocompatibility, while APMA provides amine functionality, allowing conjugation of folate derivatives. HPMA-stat-APMA was chain extended with a cationic block, poly(N-[3-(dimethylamino)propyl]methacrylamide), to promote electrostatic complexation between the copolymer and the negatively charged phosphate backbone of siRNA. Notably, poly(HPMA) stabilizes the neutral complexes in aqueous solution, while APMA allows the conjugation of a targeting moiety, thus, dually circumventing problems associated with the delivery of genes via cationically charged complexes (universal transfection). Fluorescence microscopy and gene down-regulation studies indicate that these neutral complexes can be specifically delivered to cancer cells that overexpress folate receptors.

Effects of Oxidative Stress on Mouse Embryonic Stem Cell Proliferation, Apoptosis, Senescence, and Self-Renewal

Oxidative stress, associated with either normal metabolism or disease conditions, affects many cellular activities. Most of our knowledge in this field is derived from fully differentiated cells. Embryonic stem cells (ESCs) have attracted enormous attention for their potential applications in cell therapy, but little is known about how the unique properties of ESCs are affected by oxidative stress. We have investigated the effects of oxidative stress induced by H(2)O(2) on several cellular activities of mouse ESCs. Like differentiated cells, ESCs are sensitive to H(2)O(2)-induced apoptosis when continuously exposed to H(2)O(2) at the concentrations above 150 microM. However, unlike differentiated cells, ESCs are resistant to oxidative stress induced senescence. This is demonstrated by the results that when subjected to a short-term sublethal concentration and duration of H(2)O(2) treatment, fibroblasts enter the senescent state with enlarged flattened cell morphology concurrent with increased expression of senescence marker p21. On the contrary, ESCs neither show any sign of senescence nor express p21. Instead, ESCs enter a transient cell cycle arrest state, but they have remarkable recovery capacity to resume the normal cell proliferation rate without losing the ability of self-renewal and pluripotency. Our results further revealed that H(2)O(2) inhibits cell adhesion and the expression of cyclin D1, which are early events proceeding apoptosis and cell cycle arrest. In conclusion, our data suggest that ESCs are sensitive to H(2)O(2) toxicity, but may have unique mechanisms that prevent H(2)O(2)-induced senescence and protect self-renewal capacity.

NF‐κB, but not p38 MAP Kinase, is required for TNF‐α‐induced expression of cell adhesion molecules in endothelial cells

In response to inflammation stimuli, tumor necrosis factor‐α (TNF‐α) induces expression of cell adhesion molecules (CAMs) in endothelial cells (ECs). Studies have suggested that the nuclear factor‐κB (NF‐κB) and the p38 MAP kinase (p38) signaling pathways play central roles in this process, but conflicting results have been reported. The objective of this study is to determine the relative contributions of the two pathways to the effect of TNF‐α. Our initial data indicated that blockade of p38 activity by chemical inhibitor SB203580 (SB) at 10 µM moderately inhibited TNF‐α‐induced expression of three types of CAMs; ICAM‐1, VCAM‐1 and E‐selectin, indicating that p38 may be involved in the process. However, subsequent analysis revealed that neither 1 µM SB that could completely inhibit p38 nor specific knockdown of p38α and p38β with small interference RNA (siRNA) had an apparent effect, indicating that p38 activity is not essential for TNF‐α‐induced CAMs. The most definitive evidence to support this conclusion was from the experiments using cells differentiated from p38α knockout embryonic stem cells. We could show that deletion of p38α gene did not affect TNF‐α‐induced ICAM‐1 and VCAM‐1 expression when compared with wild‐type cells. We further demonstrated that inhibition of NF‐κB completely blocked TNF‐α‐induced expression of ICAM‐1, VCAM‐1 and E‐selectin. Taken together, our results clearly demonstrate that NF‐κB, but not p38, is critical for TNF‐α‐induced CAM expression. The inhibition of SB at 10 µM on TNF‐α‐induced ICAM‐1, VCAM‐1 and E‐selectin is likely due to the nonspecific effect of SB. J. Cell. Biochem. 105: 477–486, 2008.

Tailored Design of Au Nanoparticle-siRNA Carriers Utilizing Reversible Addition-Fragmentation Chain Transfer Polymers

The facile synthesis of polymer-stabilized Au nanoparticles (AuNPs) capable of forming neutral, sterically stable complexes with small interfering RNA (siRNA) is reported. The amine-containing cationic block of poly(N-2-hydroxypropyl methacrylamide(70)-block-N-[3-(dimethylamino)propyl] methacrylamide(24)) [P(HPMA(70)-b-DMAPMA(24))] was utilized to promote the in situ reduction of Au(3+) to AuNPs and subsequently bind small interfering RNA, while the nonimmunogenic, hydrophilic block provided steric stabilization. The ratio of [DMAPMA](0)/[Au(3+)](0) utilized in the reduction reaction was found to be critical to the production of polymer-stabilized AuNPs capable of complexing siRNA. Significant protection ( approximately 100 times) against nucleases was demonstrated by enzymatic tests, while gene down-regulation experiments indicated successful delivery of siRNA to cancerous cells.

RNA-Catalyzed Thioester Synthesis

A series of efficient ribozymes with thioester synthetase activities have been isolated from CoA-linked RNA libraries containing four different lengths (30N, 60N, 100N, and 140N) of random nucleotide regions. Competitive evolution of these size-heterogeneous CoA-RNA libraries resulted in an RNA size population in the order of 30N > 60N >> 100N > 140N. From isolated clones in the 30N and 60N size groups, two predominant RNA sequences, TES1 (30N) and TES33 (60N), have been shown to catalyze the synthesis of different thioesters using various acyl adenylates as the substrates. Together with our previous findings, the current results demonstrate a CoA thioester synthetic pathway catalyzed by individual metabolic ribozymes, and suggest a likely mechanism for thioester synthesis and utilization in an RNA world.

Synthesis of biotin–AMP conjugate for 5′ biotin labeling of RNA through one-step in vitro transcription

Biotin-labeled RNA has found broad applications in chemistry, biology and biomedicine. In this protocol, we describe a simple procedure for 5′ RNA biotin labeling by one-step in vitro transcription. A biotin–AMP (adenosine 5′-monophosphate) conjugate, biotin-HDAAMP (adenosine 5′-(6-aminohexyl) phosphoramide; where HDA is 1,6-hexanediamine), is chemically synthesized. Transcription initiation by biotin-HDAAMP under the T7 φ2.5 promoter produces 5′ biotin-labeled RNA with high labeling efficiency. The procedure is especially useful for biotin labeling of RNA that is larger than 60 nucleotides. In addition, the protocol provides an attractive alternative to chemical synthesis of biotin-labeled small RNA of less than 60 nucleotides, particularly when the desired quantity of RNA is low. The whole procedure, from chemical syntheses to isolated biotin-labeled RNA, can be completed within 2 weeks.

Novel cyanine-AMP conjugates for efficient 5′ RNA fluorescent labeling by one-step transcription and replacement of [γ-32P]ATP in RNA structural investigation

Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 φ2.5 promoter. Efficient fluorophore labeling of 5′ RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current work makes fluorescently labeled RNA readily available for broad applications in biochemistry, molecular biology, structural biology and biomedicine. In particular, site-specifically fluorophore-labeled large RNAs prepared by the current method may be used to investigate RNA structure, folding and mechanism by various fluorescence techniques. In addition, F550/570 and F650/670 may replace [γ-32P]ATP to prepare 5′ labeled RNA for RNA structural and functional investigation, thereby eliminating the need for the unstable and radio-hazardous [γ-32P]ATP.

Mouse embryonic stem cells lacking p38α and p38δ can differentiate to endothelial cells, smooth muscle cells, and epithelial cells

The p38 mitogen-activated protein (MAP) kinases (p38) are important signaling molecules that regulate various cellular processes. Four isoforms of p38 family, p38alpha, p38beta, p38gamma, and p38delta, have been identified in mammalian cells. Previous studies have shown that p38alpha knockout is embryonic lethal in mice. At the cellular level, p38alpha is abundantly expressed in mouse embryonic stem cells (ESCs), but p38alpha knockout (p38alpha-/-) ESCs can differentiate to endothelial cells (ECs), smooth muscle cells (SMCs), and neurons. We speculate that the lost function of p38alpha in p38alpha-/- ESCs may be compensated for by the redundant function of other isoforms. To test this hypothesis, we used siRNA approach to knock down the expression of p38delta, the second abundant isoform in ESCs. ESCs stably expressing p38delta siRNA were established from p38alpha-/- ESCs, resulting in 80% reduction of p38delta mRNA expression. However, these ESCs, deficient of both p38alpha and p38delta, could still differentiate into ECs and SMCs. We extended our investigation to test if these cells can differentiate into epithelial cells in which p38delta has been shown to regulate epidermis differentiation. Our results demonstrate again that ESC differentiation to epithelial cells is independent of p38alpha and p38delta. We conclude that p38alpha and p38delta are not essential for ESC differentiating into ECs, SMCs, or epithelial cells although numerous studies have shown that the two kinases regulate various cellular activities in aforementioned cells. Our results highlight the possibility that p38 MAP kinases may play less significant roles in ESC differentiation than in the regulation of cellular activities of fully differentiated somatic cells.

Optimal Random Libraries for the Isolation of Catalytic RNA

The relationship between ribozyme size and catalytic activity is of fundamental importance forRNA catalysis and molecular evolution in the RNA world. We have performed a series ofcompetitive in vitro selection experiments to probe the relationship using RNA librariescontaining size-heterogeneous random regions. Our experiments have established an inversecorrelation between RNA replication efficiency (the combined efficiency of PCR amplification,transcription, and reverse transcription) and RNA size. A number of ribozyme sequences havebeen isolated from different RNA size groups under competitive selection conditions.Comprehensive kinetic analysis on isolated ribozymes has revealed that large ribozymes do notconfer a significant catalytic superiority over smaller ones under most selection conditions, andactually impose two significant problems of replication inefficiency and RNA misfolding intoinactive conformations. The fraction of a misfolded ribozyme population is defined as alpha.Large ribozymes tend to possess high alpha values, which may significantly reduce ribozymeperformance. Our results suggest that a random region of around 60 nucleotides represents theoptimal balance between ribozyme catalytic activity, RNA misfolding (alpha), and replicationefficiency, and may therefore constitute the most advantageous RNA libraries for successfulisolation of functional RNA sequences.