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Results for “target validation”

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PubMed2005

Target motion measurement without implanted markers and its validation by comparison with manually obtained data.

For an effective radiotherapy the exact tumor location must be determined. The localization has to take into account patient's setup position as well as internal organ motion. Among the different localization methods, the use of a computer tomography (CT) scanner in the therapy room has been proposed recently. Achieving a CT with the patient on the therapy couch, a patient's treatment position is captured. We present a method to locate tumor considering internal organ motion and displacements due to respiration. We tested the method with prostate and lung patients. The method found the most probable tumor position as well as, for high-mobility tumors located in the lung, its trajectory during the respiratory cycle. The results of this novel method were validated by comparison with manually determined target position.

Female↗

PubMed2004

Application of proteomic technologies in the drug development process.

Proteins are the principal targets of drug discovery. Most large pharmaceutical companies now have a proteomics-oriented biotech or academic partner or have started their own proteomics division. Common applications of proteomics in the drug industry include target identification and validation, identification of efficacy and toxicity biomarkers from readily accessible biological fluids, and investigations into mechanisms of drug action or toxicity. Target identification and validation involves identifying proteins whose expression levels or activities change in disease states. These proteins may serve as potential therapeutic targets or may be used to classify patients for clinical trials. Proteomics technologies may also help identify protein-protein interactions that influence either the disease state or the proposed therapy. Efficacy biomarkers are used to assess whether target modulation has occurred. They are used for the characterization of disease models and to assess the effects and mechanism of action of lead candidates in animal models. Toxicity (safety) biomarkers are used to screen compounds in pre-clinical studies for target organ toxicities as well as later on in development during clinical trials. Complementary approaches such as metabolomics and genomics can be used in conjunction with proteomics throughout the drug development process to create more of a unified, systems biology approach.

Animals↗

PubMed2006

Characterization of five microRNA families in maize.

In recent years, microRNAs (miRNAs) have polarized the interest of the scientific community as a new category of gene expression regulators, present in both plants and animals. Plant miRNAs are involved in processes such as plant development, organ identity, and stress response. Nonetheless, knowledge of their functions is still incomplete, and it is conceivable that further new processes in which they are involved will be discovered. For these reasons, structural and functional characterization of MIR genes, that are also in crop species such as Zea mays L., becomes instrumental in addressing genetic and molecular mechanisms controlling phenotype determination and phenotypic adaptation to growing conditions. The present study contributes to the characterization of five miRNA families in maize, from the determination of their expression pattern in different maize tissues and genotypes, to the identification of putative targets by bioinformatic means and subsequent experimental validation of three targets by modified 5' RACE experiments. Furthermore, 30 different MIR genes belonging to these five miRNA families were analysed by their attribution to maize chromosomes using oat-maize addition lines and by investigating their phylogenetic relationship with genes from other cereals. In particular, sequence homology was determined by the reciprocal best BLAST hit approach, to define groups of homologous genes between maize, rice, and sorghum.

Chromosome Mapping↗

PubMed2002

Bioinformatics and the discovery of novel anti-microbial targets.

Genomic research is playing a critical role in the discovery of new anti-microbial drugs. The rapid increase in bacterial and eukaryotic genome sequences allows for new and innovative ways for obtaining antimicrobial protein targets. Here, we describe a two level strategy for target identification and validation using computers (in silico). First, large scale comparative analyses of genome sequences were used to identify highly conserved genes which might be essential for in vitro and/or in vivo survival of bacterial pathogens. Lab-based experiments provided confirmation or validation of the hypothesis of in silico essentiality for over 350 individual genes. Over 200 validated, broad spectrum; yet highly specific gene targets, were identified in community infection pathogens. The second part of the target discovery strategy is an in-depth evolutionary, structural and cellular analysis of key drug targets. As an example, phylogenetic and structural analyses suggest that sequence and binding-pocket conservation in FabH (beta-ketoacyl-ACP synthase III) would allow for the development of small molecule inhibitors not only effective against a broad species spectrum of community bacterial pathogens but also as potential new therapies for tuberculosis and malaria.

Animals↗

PubMed2001

Differential cognitive processing of Kanji and Kana words: do orthographic and semantic codes function in parallel in word matching task.

Relative engagements of the orthographic and semantic codes in Kanji and Hiragana word recognition were investigated. In Exp. 1, subjects judged whether the pairs of Kanji words (prime and target) presented sequentially were physically identical to each other in the word condition. In the sentence condition, subjects decided whether the target word was valid for the prime sentence presented in advance. The results showed that the response times to the target swords orthographically similar (to the prime) were significantly slower than to semantically related target words in the word condition and that this was also the case in the sentence condition. In Exp. 2, subjects judged whether the target word written in Hiragana was physically identical to the prime word in the word condition. In the sentence condition, subjects decided if the target word was valid for the previously presented prime sentence. Analysis indicated that response times to orthographically similar words were slower than to semantically related words in the word condition but not in the sentence condition wherein the response times to the semantically and orthographically similar words were largely the same. Based on these results, differential contributions of orthographic and semantic codes in cognitive processing of Japanese Kanji and Hiragana words was discussed.

Adult↗

PubMed2002

School height censuses are reliable and valid tools for small-area targeting of nutrition interventions in Honduras.

Nutrition program planners often need information on the relative burden of malnutrition in different communities, or administrative units, to decide where best to invest limited available resources. National nutrition surveys, however, rarely provide precise, representative findings at a finer level than that of large, subnational regions. The school height census is an alternative, low-cost approach that does provide disaggregated data on growth retardation at the local level. This study assessed the reliability and validity of the school height census for small-area targeting of nutrition interventions in Honduras. Reliability was assessed by examining the stability of small-area estimates of mean height-for-age Z-score over five consecutive years from 1993 to 1997. Validity was assessed by comparing municipality-level mean height-for-age Z-score in the 2001 school height census with the same parameter estimated in an anthropometric survey of children < 5 y old conducted in representative samples in 70 municipalities 3-7 mo earlier. The study found that stable estimates of mean height-for-age Z-score could be obtained at the level of municipalities or larger (intraclass correlation coefficients > or = 0.85). The school height census estimates of mean height-for-age Z-score at the municipality level were also valid, with the reference criterion the survey results for children > or = 1 y of age (Spearman's rank correlation = 0.74). School height censuses cannot provide reliable estimates of levels of growth retardation in individual schools. Wider use of school height censuses could make it much easier to identify communities that might benefit from targeted nutrition interventions.

Body Height↗

PubMed2004

Structural bioinformatic approaches to the discovery of new antimycobacterial drugs.

Integrated bioinformatic approaches to drug discovery exploit computational techniques to examine the flow of information from genome to structure to function. Informatics is being be used to accelerate and rationalize the process of antimycobacterial drug discovery and design, with the immediate goals to identify viable drug targets and produce a set of critically evaluated protein target models and corresponding set of probable lead compounds. Bioinformatic approaches are being successfully applied in the selection and prioritization of putative mycobacterial drug target genes; computational modelling and x-ray structure validation of protein targets with drug lead compounds; simulated docking and virtual screening of potential lead compounds; and lead validation and optimization using structure-activity and structure-function relationships. By identifying active sites, characterizing patterns of conserved residues and, where relevant, predicting catalytic residues, bioinformatics provides information to aid the design of selective and efficacious pharmacophores. In this review, we describe selected recent progress in antimycobacterial drug design, illustrating the strengths and limitations of current structural bioinformatic approaches as tools in the fight against tuberculosis.

Anti-Bacterial Agents↗

PubMed2005

Identification and validation of novel ERBB2 (HER2, NEU) targets including genes involved in angiogenesis.

V-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (ERBB2; synonyms HER2, NEU) encodes a transmembrane glycoprotein with tyrosine kinase-specific activity that acts as a major switch in different signal-transduction processes. ERBB2 amplification and overexpression have been found in a number of human cancers, including breast, ovary and kidney carcinoma. Our aim was to detect ERBB2-regulated target genes that contribute to its tumorigenic effect on a genomewide scale. The differential gene expression profile of ERBB2-transfected and wild-type mouse fibroblasts was monitored employing DNA microarrays. Regulated expression of selected genes was verified by RT-PCR and validated by Western blot analysis. Genome wide gene expression profiling identified (i) known targets of ERBB2 signaling, (ii) genes implicated in tumorigenesis but so far not associated with ERBB2 signaling as well as (iii) genes not yet associated with oncogenic transformation, including novel genes without functional annotation. We also found that at least a fraction of coexpressed genes are closely linked on the genome. ERBB2 overexpression suppresses the transcription of antiangiogenic factors (e.g., Sparc, Timp3, Serpinf1) but induces expression of angiogenic factors (e.g., Klf5, Tnfaip2, Sema3c). Profiling of ERBB2-dependent gene regulation revealed a compendium of potential diagnostic markers and putative therapeutic targets. Identification of coexpressed genes that colocalize in the genome may indicate gene regulatory mechanisms that require further study to evaluate functional coregulation. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html.)

Animals↗

PubMed2006

Use of a chemically modified antisense oligonucleotide library to identify and validate Eg5 (kinesin-like 1) as a target for antineoplastic drug development.

A library of 2'-methoxyethyl-modified antisense oligonucleotides (2'MOE ASO) targeting 1,510 different genes has been developed, validated, and used to identify cell cycle regulatory genes. The most effective molecular target identified was Eg5 (kinesin-like-1), which when inhibited gave the largest increase in 4N DNA in various tumor cells. The Eg5 ASO reduced Eg5 levels, inhibited proliferation, increased apoptosis, and altered the expression of other cell cycle proteins, including survivin and Aurora-A. To examine the therapeutic utility of the Eg5 ASO, the compound was also evaluated in xenograft models. Treatment with Eg5 ASO produced a statistically significant reduction of tumor growth, reduction in Eg5 expression in the tumors, and changes in histone phosphorylation, consistent with a loss of Eg5 protein expression. These data show, for the first time, the utility of a 2'MOE ASO library for high-throughput cell culture-based functional assays and suggest that an Eg5 ASO also has potential in a therapeutic strategy.

Animals↗

PubMed2000

Molecular targets and cancer therapeutics: discovery, development and clinical validation.

The AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics held in Washington, DC on 16-19 November 1999 provided a forum for cancer research clearly showing evolution of a target and mechanism-driven science. The notion of the tumor as a tissue composed of heterogeneous populations of normal and abnormal cells as viable targets is coming to the fore with the advent of agents directed toward non-malignant cell targets. Growth control rather than eradication as a treatment strategy for malignant disease is being tested preclinically and clinically. Among targets, kinases are in the lead with nuclear, cytoplasmic and membrane kinases being selectively inhibited by small molecules and macromolecules. First generation tumor vasculature-directed agents are progressing through early clinical studies. The interest in tumor vasculature as a target has renewed interest in imaging technology to discern biological effect and in tumor hypoxia. This has resulted in elucidation of molecular responses triggered by a low oxygen environment. Challenges remain in the areas of cellular and immune therapies. Dendritic cell-based vaccines are being tested preclinically in many systems. Interleukin-12 is proceeding through clinical trials. Apoptosis-protective molecules such as bcl-2, and apoptosis-stimulating molecules such as bax, are being pursued as targets for inhibition and activation, respectively. Finally, methods and technology to aid in the identification of new targets were highlighted. This perspective, while it is by no means an exhaustive review of the presentations, brings forward some of the main topics and interests that are current in cancer research. Targets were the topic but methods of target identification and the need for increased chemical diversity to selectively focus agents to targets with small differences were also major topics of discussion. Copyright 2000 Harcourt Publishers Ltd.

Journal Article↗

PubMed2026

SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.

The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.

CRISPR-Cas Systems↗

PubMed1997

Effects of altering brain cholinergic activity on covert orienting of attention: comparison of monkey and human performance.

Experiments were conducted to elucidate the role of the cholinergic neurotransmitter system in arousal and the orienting of attention to peripheral targets. Rhesus monkeys and humans fixated a visual stimulus and responded to the onset of visual targets presented randomly in two visual field locations. The target was preceded by a valid cue (cue and target at the same location), an invalid cue (cue and target to opposite locations), a double cue (cues to both spatial locations, target to one), or, the cue was omitted (no-cue, target to either location). Reaction times (RTs) to the onset of the target were recorded. For monkeys, systemic injections of nicotine (0.003-0.012 mg/kg) or atropine (0.001-0.01 mg/kg), but not saline control injections, reduced mean RTs for all trials, indicating general behavioral stimulation. In addition, nicotine significantly reduced RTs for invalid trials but had little additional effect on those for valid, double, or no-cue trials. Virtually identical effects were observed for human chronic tobacco smokers in performing the same task following cigarette smoking. Injections of atropine in monkeys had no effect on RTs for valid or invalid trials but significantly slowed RTs in double-cue trials that did not require the orienting of attention. These results suggest that in both species, the nicotinic cholinergic system may play a role in automatic sensory orienting. In addition, the muscarinic system may play a role in alerting to visual stimuli in monkeys.

Adolescent↗

PubMed1991

Contextual effects on choice reaction time and accuracy in acute and chronic schizophrenics. Impairment in selective attention or in the influence of prior learning?

Two hypotheses were tested concerning the nature of the cognitive dysfunction in schizophrenia: (a) that there is a broadening of selective attention; and (b) that there is an impairment in associational learning. RDC-diagnosed acute and chronic schizophrenics and normal controls carried out a choice reaction time (RT) task in which conflict between the correct response to a target (a letter in the centre of a computer screen) and that cued by simultaneously presented flankers (two letters either side of the target) increased RT. For 80 ('valid') trials, flankers and targets were consistent in the response cued (pressing a button with either left or right hand); on 8 ('invalid') trials they conflicted. On invalid trials there was a slowing of RT, and an increase of errors for left-hand responses. Chronic schizophrenics showed the same reactions to cue validity as normal controls, both groups differing significantly from acute schizophrenics. For the latter, the RT data supported hypothesis (b), but the error rates appeared to support hypothesis (a).

Acute Disease↗

PubMed1998

Hepatic lacI and cII mutation in transgenic (lambdaLIZ) rats treated with dimethylnitrosamine.

The recent introduction of a transgenic rat in vivo mutation assay is a much needed supplement to the transgenic mouse models and offers the tools necessary for collecting target tissue specific genotoxicity data in this species. The utility of the Big Blue(R) rat for the detection of in vivo mutations was investigated by studying spontaneous and dimethylnitrosamine (DMN)-induced hepatic mutations. High molecular weight DNA isolated from Big Blue(R) rat livers typically yielded good transgene rescue efficiency of up to 5x105 plaque forming units per packaging reaction. DMN, when administered by oral gavage at dose levels of 0.2, 0.6, 2.0, and 6.0 mg kg-1 day-1, induced up to a 4.5-fold increase in mutations at the highest dose level. There was no apparent difference between the lacI vs. cII target genes of the shuttle vector in either the background or DMN-induced mutant frequencies. These results suggest that the transgenic rat model is a useful tool for studying potential genotoxicity in target organs and, with further validation, the selectable cII target could be an attractive alternative to the conventional lacI color screening method for the detection of mutations in the lambdaLIZ shuttle vector.

Animals↗

PubMed2005

Mitotic kinesin inhibitors induce mitotic arrest and cell death in Taxol-resistant and -sensitive cancer cells.

Taxanes are powerful chemotherapy agents that target the microtubule cytoskeleton, leading to mitotic arrest and cell death; however, their clinical efficacy has been hampered due to the development of drug resistance. Therefore, other proteins involved in spindle assembly are being examined as potential targets for anticancer therapy. The mitotic kinesin, Eg5 is critical for proper spindle assembly; as such, inhibition of Eg5 leads to mitotic arrest making it a potential anticancer target. We wanted to validate Eg5 as a therapeutic target and determine if Eg5 inhibitors retain activity in Taxol-resistant cells. Using affinity chromatography we first show that the compound HR22C16 is an Eg5 inhibitor and does not interact with other microtubule motor proteins tested. Furthermore, HR22C16 along with its analogs, inhibit cell survival in both Taxol-sensitive and -resistant ovarian cancer cells with at least 15-fold greater efficacy than monastrol, the first generation Eg5 inhibitor. Further analysis with HR22C16-A1, the most potent HR22C16 analog, showed that it retains efficacy in PgP-overexpressing cells, suggesting that it is not a PgP substrate. We further show that HR22C16-A1 induces cell death following mitotic arrest via the intrinsic apoptotic pathway. Interestingly, the combination of HR22C16-A1 with Taxol results in an antagonistic antiproliferative and antimitotic effect, possibly due to the abrogation of Taxol-induced mitotic spindles by HR22C16-A1. Taken together, our results show that Eg5 inhibitors have promising anticancer activity and can be potentially used to overcome Taxol resistance in the clinical setting.

Antineoplastic Agents↗

PubMed2000

Selective attention to the chemosensory modality.

Previous studies have shown that behavioral responses to auditory, visual, and tactile stimuli are modulated by expectancies regarding the likely modality of an upcoming stimulus (see Spence & Driver, 1997). In the present study, we investigated whether people can also selectively attend to the chemosensory modality (involving responses to olfactory, chemical, and painful stimuli). Participants made speeded spatial discrimination responses (left vs. right) to an unpredictable sequence of odor and tactile targets. Odor stimuli were presented to either the left or the right nostril, embedded in a birhinally applied constant airstream. Tactile stimuli were presented to the left or the right hand. On each trial, a symbolic visual cue predicted the likely modality for the upcoming target (the cue was a valid predictor of the target modality on the majority of trials). Response latencies were faster when targets were presented in the expected modality than when they were presented in the unexpected modality, showing for the first time that behavioral responses to chemosensory stimuli can be modulated by selective attention.

Attention↗

PubMed2026

Sanguinarine as a multi-target therapeutic candidate for laryngeal cancer: insights from network pharmacology, molecular dynamics and in vitro validation.

OBJECTIVE: To identify the core targets and elucidate the potential molecular mechanisms of sanguinarine (SA) against laryngeal squamous cell carcinoma (LSCC), and to validate its antitumor effects in vitro. METHODS: Potential targets of SA were predicted using SwissTargetPrediction, TargetNet, and SuperPred and intersected with LSCC-related targets obtained from the GeneCards, OMIM, and DISEASES databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. A protein-protein interaction (PPI) network was constructed using the STRING database (combined score > 0.900), and topological parameters including degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), eigenvector centrality (EC), and local average connectivity (LAC) were calculated in Cytoscape to identify core genes based on median thresholds. Molecular docking and 100-ns molecular dynamics (MD) simulations were conducted for epidermal growth factor receptor (EGFR), Phosphatidylinositide-3-kinase catalytic subunit alpha (PIK3CA), phosphatidylinositol-4,5-biphosphate 3-kinase catalytic subunit β (PIK3CB), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD), and Non-Receptor Tyrosine Kinase (SRC). The effects of SA on LSCC were evaluated using CCK-8, colony formation, Transwell migration, and wound-healing assays in TU177 cells and TU212. RESULTS: A total of 213 common targets were identified, which were significantly enriched in PI3K-Akt signaling, EGFR tyrosine kinase inhibitor resistance, and adhesion- and migration-related pathways. The PPI network comprised 259 nodes and 259 edges, from which five core genes-PIK3CA, PIK3CB, PIK3CD, EGFR, and SRC-were identified. Molecular docking revealed strong binding affinities between SA and the PI3K family proteins (- 9.79 to - 10.96 kcal/mol), as well as EGFR (- 8.58 kcal/mol) and SRC (- 6.77 kcal/mol). MD simulations indicated greater stability of SA complexes with EGFR and PI3K family members compared with SRC. In vitro assays demonstrated that SA significantly inhibited TU177 cell and TU212 cell proliferation, colony formation, and migration. CONCLUSION: SA may exert anti-laryngeal cancer effects through synergistic multi-target inhibition centered on the EGFR/SRC/PI3K signaling axis, highlighting its potential as a promising therapeutic candidate for LSCC.

Humans↗

PubMed2004

The promise of genomics to identify novel therapeutic targets.

The cataloguing of the human genome has provided an unprecedented prospectus for target identification and drug discovery. A current analysis indicates that slightly more than 3000 unique protein encoding loci are potentially amenable to pharmacological intervention (the 'druggable genome', which can be queried at http://function.gnf.org/druggable). However, the assessment of genome sequence data has not resulted in the anticipated acceleration of novel therapeutic developments. The basis for this shortfall lies in the significant attrition rates endemic to preclinical/clinical development, as well as the often underestimated complexity of gene function in higher order biological systems. To address the latter issue, a number of strategies have emerged to facilitate genomics-driven target identification and validation, including cellular profiling of gene function, in silico modelling of gene networks, and systematic analyses of protein complexes. The expectation is that the integration of these and other systems-based technologies may enable the conversion of potential genomic targets into functionally validated molecules, and result in practicable gene-based drug discovery pipelines.

Animals↗