Careful Target Selection Research Articles

RNAi-based drug design: considerations and future directions.

More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.

Big peptide drugs in a small molecule world.

A quarter of a century ago, designer peptide drugs finally broke through the glass ceiling. Despite the resistance by big pharma, biotechnology companies managed to develop injectable peptide-based drugs, first against orphan or other small volume diseases, and later for conditions affecting large patient populations such as type 2 diabetes. Even their lack of gastrointestinal absorption could be utilized to enable successful oral dosing against chronic constipation. The preference of peptide therapeutics over small molecule competitors against identical medical conditions can be achieved by careful target selection, intrachain and terminal amino acid modifications, appropriate conjugation to stability enhancers and chemical space expansion, innovative delivery and administration techniques and patient-focused marketing strategies. Unfortunately, however, pharmacoeconomical considerations, including the strength of big pharma to develop competing small molecule drugs, have somewhat limited the success of otherwise smart peptide-based therapeutics. Yet, with increasing improvement in peptide drug modification and formulation, these are continuing to gain significant, and growing, acceptance as desirable alternatives to small molecule compounds.

Discovery of new members of the nearby young stellar association in Cepheus

Context. Young field stars are hardly distinguishable from older ones because their space motion rapidly mixes them with the stellar population of the Galactic plane. Nevertheless, a careful target selection allows for young stars to be spotted throughout the sky. Aims. We aim to identify additional sources associated with the four young comoving stars that we discovered towards the CO Cepheus void and to provide a comprehensive view of the Cepheus association. Methods. Based on multivariate analysis methods, we have built an extended sample of 193 young star candidates, which are the optical and infrared counterparts of ROSAT All-Sky Survey and XMM-Newton X-ray sources. From optical spectroscopic observations, we measured their radial velocity with the cross-correlation technique. We derived their atmospheric parameters and projected rotational velocity with the code ROTFIT. We applied the subtraction of inactive templates to measure the lithium equivalent width, from which we infer their lithium abundance and age. Finally, we studied their kinematics using the second Gaia data release. Results. Our sample is mainly composed of young or active stars and multiple systems. We identify two distinct populations of young stars that are spatially and kinematically separated. Those with an age between 100 and 300 Myr are mostly projected towards the Galactic plane. In contrast, 23 of the 37 sources younger than 30 Myr are located in the CO Cepheus void, and 21 of them belong to the stellar kinematic group that we previously reported in this sky area. We report a total of 32 bona fide members and nine candidates for this nearby (distance = 157 ± 10 pc) young (age = 10–20 Myr) stellar association. According to the spatial distribution of its members, the original cluster is already dispersed and partially mixed with the local population of the Galactic plane.

Strategic Development of Tree Resistance Against Forest Pathogen and Insect Invasions in Defense-Free Space

• Invasive pathogens that cause stem cankers and wilts of trees, and insects that bore into bark and wood have proven extremely destructive to the world’s forests and particularly difficult to manage once established • Such pests are especially devastating when evolutionarily naive host trees lack adequate natural defenses • Modern tree improvement programs are increasingly capable of restoring such defenses and providing trees for planting that are capable of withstanding alien insects and pathogens • Careful target selection, early implementation and sustained support of these programs are important for their success • We provide a simplified framework to guide responses to invasive insects and pathogens and rapidly identify promising pests to target for development of host resistance

Plant-mediated RNAi silences midgut-expressed genes in congeneric lepidopteran insects in nature

BackgroundPlant-mediated RNAi (PMRi) silencing of insect genes has enormous potential for crop protection, but whether it works robustly under field conditions, particularly with lepidopteran pests, remains controversial. Wild tobacco Nicotiana attenuata and cultivated tobacco (N. tabacum) (Solanaceae) is attacked by two closely related specialist herbivores Manduca sexta and M. quinquemaculata (Lepidoptera, Sphingidae). When M. sexta larvae attack transgenic N. attenuata plants expressing double-stranded RNA(dsRNA) targeting M. sexta’s midgut-expressed genes, the nicotine-ingestion induced cytochrome P450 monooxygenase (invert repeat (ir)CYP6B46-plants) and the lyciumoside-IV-ingestion induced β-glucosidase1 (irBG1-plants), these larval genes which are important for the larvae’s response to ingested host toxins, are strongly silenced.ResultsHere we show that the PMRi procedure also silences the homologous genes in native M. quinquemaculata larvae feeding on irCYP6B46 and irBG1-transgenic N. attenuata plants in nature. The PMRi lines shared 98 and 96% sequence similarity with M. quinquemaculata homologous coding sequences, and CYP6B46 and BG1 transcripts were reduced by ca. 90 and 80%, without reducing the transcripts of the larvae’s most similar, potential off-target genes.ConclusionsWe conclude that the PMRi procedure can robustly and specifically silence genes in native congeneric insects that share sufficient sequence similarity and with the careful selection of targets, might protect crops from attack by congeneric-groups of insect pests.

Generation of inheritable and "transgene clean" targeted genome-modified rice in later generations using the CRISPR/Cas9 system.

The CRISPR/Cas9 system is becoming an important genome editing tool for crop breeding. Although it has been demonstrated that target mutations can be transmitted to the next generation, their inheritance pattern has not yet been fully elucidated. Here, we describe the CRISPR/Cas9-mediated genome editing of four different rice genes with the help of online target-design tools. High-frequency mutagenesis and a large percentage of putative biallelic mutations were observed in T0 generations. Nonetheless, our results also indicate that the progeny genotypes of biallelic T0 lines are frequently difficult to predict and that the transmission of mutations largely does not conform to classical genetic laws, which suggests that the mutations in T0 transgenic rice are mainly somatic mutations. Next, we followed the inheritance pattern of T1 plants. Regardless of the presence of the CRISPR/Cas9 transgene, the mutations in T1 lines were stably transmitted to later generations, indicating a standard germline transmission pattern. Off-target effects were also evaluated, and our results indicate that with careful target selection, off-target mutations are rare in CRISPR/Cas9-mediated rice gene editing. Taken together, our results indicate the promising production of inheritable and “transgene clean” targeted genome-modified rice in the T1 generation using the CRISPR/Cas9 system.

The gaia survey contribution to EChO target selection and characterization

The scientific output of the proposed EChO mission (in terms of spectroscopic characterization of the atmospheres of transiting extrasolar planets) will be maximized by a careful selection of targets and by a detailed characterization of the main physical parameters (such as masses and radii) of both the planets and their stellar hosts. To achieve this aim, the availability of high-quality data from other space-borne and ground-based programs will play a crucial role. Here we identify and discuss the elements of the Gaia catalogue that will be of utmost relevance for the selection and characterization of transiting planet systems to be observed by the proposed EChO mission.

Drug discovery for neglected diseases: molecular target-based and phenotypic approaches.

Drug discovery for neglected tropical diseases is carried out using both target-based and phenotypic approaches. In this paper, target-based approaches are discussed, with a particular focus on human African trypanosomiasis. Target-based drug discovery can be successful, but careful selection of targets is required. There are still very few fully validated drug targets in neglected diseases, and there is a high attrition rate in target-based drug discovery for these diseases. Phenotypic screening is a powerful method in both neglected and non-neglected diseases and has been very successfully used. Identification of molecular targets from phenotypic approaches can be a way to identify potential new drug targets.

Second-Generation Sequencing Supply an Effective Way to Screen RNAi Targets in Large Scale for Potential Application in Pest Insect Control

The key of RNAi approach success for potential insect pest control is mainly dependent on careful target selection and a convenient delivery system. We adopted second-generation sequencing technology to screen RNAi targets. Illumina's RNA-seq and digital gene expression tag profile (DGE-tag) technologies were used to screen optimal RNAi targets from Ostrinia furnalalis. Total 14690 stage specific genes were obtained which can be considered as potential targets, and 47 were confirmed by qRT-PCR. Ten larval stage specific expression genes were selected for RNAi test. When 50 ng/µl dsRNAs of the genes DS10 and DS28 were directly sprayed on the newly hatched larvae which placed on the filter paper, the larval mortalities were around 40∼50%, while the dsRNAs of ten genes were sprayed on the larvae along with artificial diet, the mortalities reached 73% to 100% at 5 d after treatment. The qRT-PCR analysis verified the correlation between larval mortality and the down-regulation of the target gene expression. Topically applied fluorescent dsRNA confirmed that dsRNA did penetrate the body wall and circulate in the body cavity. It seems likely that the combination of DGE-tag with RNA-seq is a rapid, high-throughput, cost less and an easy way to select the candidate target genes for RNAi. More importantly, it demonstrated that dsRNAs are able to penetrate the integument and cause larval developmental stunt and/or death in a lepidopteron insect. This finding largely broadens the target selection for RNAi from just gut-specific genes to the targets in whole insects and may lead to new strategies for designing RNAi-based technology against insect damage.

Stellar noise and planet detection. II. Radial-velocity noise induced by magnetic cycles

AbstractFor the 451 stars of the HARPS high precision program, we study correlations between the radial-velocity (RV) variation and other parameters of the Cross Correlated Function (CCF). After a careful target selection, we found a very good correlation between the slope of the RV-activity index (log(R'HK)) correlation and the Teff for dwarf stars. This correlation allow us to correct RV from magnetic cycles given the activity index and the Teff.

Construction and Validation of Tissue Microarrays of Ductal Carcinoma In Situ and Terminal Duct Lobular Units Associated With Invasive Breast Carcinoma

Construction of tissue microarrays (TMAs) to efficiently characterize large sets of noninvasive epithelial lesions in the breast by immunohistochemistry is an appealing investigative approach, but presents technical challenges. We report methodologic studies performed to optimize methods for building TMAs from noninvasive breast tissues collected in a large case-control study of breast cancer. Using a manual arraying technique with 2.0-mm diameter needles, we constructed TMAs from specimens obtained from 32 women with breast cancer containing the following targets: (1) 28 terminal duct lobular units (TDLUs); (2) 28 ductal carcinomas in situ, and (3) 23 invasive carcinomas. Using careful target selection, we achieved representation of approximately 80% of noninvasive targets with sustained preservation through section 30 of the TMAs. Immunohistochemical staining of TDLU targets demonstrated positive staining for estrogen receptor (ER) in 30.8% of tubules and for progesterone receptor (PR) in 50.0%. To establish an efficient method to evaluate staining results in TDLUs, we created a categorical scoring system to approximate the percentage of tubules containing positive stained cells (<10%, 10% to 50%, >or=50%), and compared the results with those obtained by tubule counting. Comparison between the two methods demonstrated exact agreement for 70.8% of ER and 79.2% of PR stains without two-category discrepancies. ER/PR expression levels in multiple (up to 4) noninvasive targets of the same tissue type (TDLU or DCIS) from a single block showed good correlation. These data suggest that it is feasible to produce TMAs of noninvasive breast structures, albeit with careful selection of targets, and that immunostains of such cores may permit efficient immunohistochemical characterization of peritumoral tissues. Additional exploration of this approach is needed.