Development of novel antimiRzymes for targeted inhibition of miR-21 expression in solid cancer cells

MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the regulation of gene expression. Previous reports showed an over-expression of miRNA-21 (miR-21) in various cancer cells, and its up-regulation is closely related to cancer initiation, proliferation and metastasis. In this work, we envisioned the development of novel antimiRzymes (anti-miRNA-DNAzyme) that are capable of selectively targeting and cleaving miR-21 and inhibit its expression in cancer cells using the DNAzyme technique. For this purpose, we have designed different antimiRzyme candidates by systematically targeting different regions of miR-21. Our results demonstrated that RNV541, a potential arm-loop-arm type antimiRzyme, was very efficient (90%) to suppress miR-21 expression in U87MG malignant glioblastoma cell line at 200 nM concentration. In addition, RNV541 also inhibited miR-21 expression (50%) in MDA-MB-231 breast cancer cell line. For targeted delivery, we conjugated RNV541 with a transferrin receptor (TfR) targeting aptamer for TfR-mediated cancer cell delivery. As expected, the developed chimeric structure efficiently delivered the antimiRzyme RNV541 into TfR positive glioblastoma cells. TfR aptamer-RNV541 chimeric construct showed 52% inhibition of miR-21 expression in U87MG glioblastoma cells at 2000 nM concentration, without using any transfection reagents, making it a highly desirable strategy to tackle miR-21 over-expressed malignant cancers. Although these are in vitro based observations, based on our results, we firmly believe that our findings could be beneficial towards the development of targeted cancer therapeutics where conventional therapies face several challenges

Optimal query complexity for estimating the trace of a matrix

Given an implicit $n\times n$ matrix $A$ with oracle access $x^TA x$ for any $x\in \mathbb{R}^n$, we study the query complexity of randomized algorithms for estimating the trace of the matrix. This problem has many applications in quantum physics, machine learning, and pattern matching. Two metrics are commonly used for evaluating the estimators: i) variance; ii) a high probability multiplicative-approximation guarantee. Almost all the known estimators are of the form $\frac{1}{k}\sum_{i=1}^k x_i^T A x_i$ for $x_i\in \mathbb{R}^n$ being i.i.d. for some special distribution. Our main results are summarized as follows. We give an exact characterization of the minimum variance unbiased estimator in the broad class of linear nonadaptive estimators (which subsumes all the existing known estimators). We also consider the query complexity lower bounds for any (possibly nonlinear and adaptive) estimators: (1) We show that any estimator requires $\Omega(1/\epsilon)$ queries to have a guarantee of variance at most $\epsilon$. (2) We show that any estimator requires $\Omega(\frac{1}{\epsilon^2}\log \frac{1}{\delta})$ queries to achieve a $(1\pm\epsilon)$-multiplicative approximation guarantee with probability at least $1 - \delta$. Both above lower bounds are asymptotically tight. As a corollary, we also resolve a conjecture in the seminal work of Avron and Toledo (Journal of the ACM 2011) regarding the sample complexity of the Gaussian Estimator.Comment: full version of the paper in ICALP 201

Efficient epidermal growth factor receptor targeting oligonucleotide as a potential molecule for targeted cancer therapy

Epidermal growth factor receptor (EGFR) is associated with the progression of a wide range of cancers including breast, glioma, lung, and liver cancer. The observation that EGFR inhibition can limit the growth of EGFR positive cancers has led to the development of various EGFR inhibitors including monoclonal antibodies and small-molecule inhibitors. However, the reported toxicity and drug resistance greatly compromised the clinical outcome of such inhibitors. As a type of chemical antibodies, nucleic acid aptamer provides an opportunity to overcome the obstacles faced by current EGFR inhibitors. In this study, we have developed and investigated the therapeutic potential of a 27mer aptamer CL-4RNV616 containing 2′-O-Methyl RNA and DNA nucleotides. Our results showed that CL-4RNV616 not only displayed enhanced stability in human serum, but also effectively recognized and inhibited the proliferation of EGFR positive Huh-7 liver cancer, MDA-MB-231 breast cancer, and U87MG glioblastoma cells, with an IC50 value of 258.9 nM, 413.7 nM, and 567.9 nM, respectively. Furthermore, TUNEL apoptosis assay revealed that CL-4RNV616 efficiently induced apoptosis of cancer cells. In addition, clinical breast cancer biopsy-based immunostaining assay demonstrated that CL-4RNV616 had a comparable detection efficacy for EGFR positive breast cancer with commonly used commercial antibodies. Based on the results, we firmly believe that CL-4RNV616 could be useful in the development of targeted cancer therapeutics and diagnostics

Development of novel chemically-modified nucleic acid molecules for efficient inhibition of human MAPT gene expression

The hyperphosphorylation of the microtubule-associated protein tau (MAPT) has been implicated in various neurological diseases, including Alzheimer’s disease. It has been hypothesized that the reduction of MAPT would result in depolymerizing neurofibrillary tangles and could be a potential strategy for the treatment of Alzheimer’s disease and other tauopathies. In this study, we report the development of novel DNAzymes and splice-modulating antisense oligonucleotides (AOs) for the efficient inhibition of MAPT. We designed and synthesized a range of DNAzymes and 2ʹ-O-methyl (2’-OMe)-modified AOs on a phosphorothioate (PS) backbone targeting various exons across the MAPT gene transcript. Our results demonstrated that RNV563, an arm-loop-arm-type DNAzyme targeting exon 13, and an AO candidate AO4, targeting exon 4, efficiently downregulated MAPT RNA expression by 58% and 96%, respectively. In addition, AO4 also reduced the MAPT protein level by 74%. In line with our results, we believe that AO4 could be used as a potential therapeutic molecule for Alzheimer’s disease and other tauopathies

Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development

Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications

Final state effects on superfluid 4^{\bf 4}He in the deep inelastic regime

A study of Final State Effects (FSE) on the dynamic structure function of superfluid $^4$He in the Gersch--Rodriguez formalism is presented. The main ingredients needed in the calculation are the momentum distribution and the semidiagonal two--body density matrix. The influence of these ground state quantities on the FSE is analyzed. A variational form of $\rho_2$ is used, even though simpler forms turn out to give accurate results if properly chosen. Comparison to the experimental response at high momentum transfer is performed. The predicted response is quite sensitive to slight variations on the value of the condensate fraction, the best agreement with experiment being obtained with $n_0=0.082$. Sum rules of the FSE broadening function are also derived and commented. Finally, it is shown that Gersch--Rodriguez theory produces results as accurate as those coming from other more recent FSE theories.Comment: 20 pages, RevTex 3.0, 11 figures available upon request, to be appear in Phys. Rev.

Critical exponents in Ising spin glasses

We determine accurate values of ordering temperatures and critical exponents for Ising Spin Glass transitions in dimension 4, using a combination of finite size scaling and non-equilibrium scaling techniques. We find that the exponents $\eta$ and $z$ vary with the form of the interaction distribution, indicating non-universality at Ising spin glass transitions. These results confirm conclusions drawn from numerical data for dimension 3.Comment: 6 pages, RevTeX (or Latex, etc), 10 figures, Submitted to PR

Alpha-l-Locked nucleic acid-modified antisense oligonucleotides induce efficient splice modulation in vitro

Alpha-l-Locked nucleic acid (α-l-LNA) is a stereoisomeric analogue of locked nucleic acid (LNA), which possesses excellent biophysical properties and also exhibits high target binding affinity to complementary oligonucleotide sequences and resistance to nuclease degradations. Therefore, α-l-LNA nucleotides could be utilised to develop stable antisense oligonucleotides (AO), which can be truncated without compromising the integrity and efficacy of the AO. In this study, we explored the potential of α-l-LNA nucleotides-modified antisense oligonucleotides to modulate splicing by inducing Dmd exon-23 skipping in mdx mouse myoblasts in vitro. For this purpose, we have synthesised and systematically evaluated the efficacy of α-l-LNA-modified 2′-O-methyl phosphorothioate (2′-OMePS) AOs of three different sizes including 20mer, 18mer and 16mer AOs in parallel to fully-modified 2′-OMePS control AOs. Our results demonstrated that the 18mer and 16mer truncated AO variants showed slightly better exon-skipping efficacy when compared with the fully-23 modified 2′-OMePS control AOs, in addition to showing low cytotoxicity. As there was no previous report on using α-l-LNA-modified AOs in splice modulation, we firmly believe that this initial study could be beneficial to further explore and expand the scope of α-l-LNA-modified AO therapeutic molecules

A Multifractal Analysis of Asian Foreign Exchange Markets

We analyze the multifractal spectra of daily foreign exchange rates for Japan, Hong-Kong, Korea, and Thailand with respect to the United States Dollar from 1991 to 2005. We find that the return time series show multifractal spectrum features for all four cases. To observe the effect of the Asian currency crisis, we also estimate the multifractal spectra of limited series before and after the crisis. We find that the Korean and Thai foreign exchange markets experienced a significant increase in multifractality compared to Hong-Kong and Japan. We also show that the multifractality is stronge related to the presence of high values of returns in the series

Experimental evidence for the interplay between individual wealth and transaction network

We conduct a market experiment with human agents in order to explore the structure of transaction networks and to study the dynamics of wealth accumulation. The experiment is carried out on our platform for 97 days with 2,095 effective participants and 16,936 times of transactions. From these data, the hybrid distribution (log-normal bulk and power-law tail) in the wealth is observed and we demonstrate that the transaction networks in our market are always scale-free and disassortative even for those with the size of the order of few hundred. We further discover that the individual wealth is correlated with its degree by a power-law function which allows us to relate the exponent of the transaction network degree distribution to the Pareto index in wealth distribution.Comment: 6 pages, 7 figure