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Results for “target validation”

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PubMed2005

Combinatorial microRNA target predictions.

MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript. Different combinations of microRNAs are expressed in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published microRNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results suggest widespread coordinate control executed by microRNAs. In particular, we experimentally validate common regulation of Mtpn by miR-375, miR-124 and let-7b and thus provide evidence for coordinate microRNA control in mammals.

Algorithms↗

PubMed2004

Technology insight: Identification of biomarkers with tissue microarray technology.

High-throughput technologies have been developed in the hope of increasing the pace of biomedical research, and accelerating the rate of translation from bench to bedside. Using such technology in target discovery has resulted in the need for systematic validation of the targets in an equally rapid manner. For example, gene expression microarrays have highlighted many potential targets in cancer, and tissue microarrays have emerged as a powerful tool to validate these targets by measuring tumor-specific protein expression and linking it to clinical outcome. Automated quantitative analysis of the tissue microarray 'spots' is beginning to take the technology a step further, removing observer bias, and providing standards for quality control and the potential for high-throughput analysis. The validation required for translation of tissue biomarkers from the research lab to the clinical lab will probably rely heavily on the combination of tissue microarray technology with automated quantitative analysis.

Biomarkers, Tumor↗

PubMed1999

Covert orienting and focusing of attention in children with attention deficit hyperactivity disorder.

Performance on the covert visuo-spatial attentional functions of orienting and focusing by a group of ADHD children (n = 20) was compared to that of age and sex-matched control children. In Experiment 1, responses were given to cued targets at valid and invalid locations. In Experiment 2, responses were given to targets presented in small, medium-sized or large visual field locations. For both experiments, the hypotheses that reaction times of ADHD children would be greater than those of control children and that performance would be asymmetrical, were supported. For Experiment 1, ADHD children showed bilaterally greater 'benefits' from having directed attention to the cued location and greater 'costs' in having to relocate the attentional focus than controls. In Experiment 2, the hypothesis that the function of focusing attention by ADHD children may show breakdown in the usual pattern of an increase in reaction time with focus area was partly supported by the finding of similar reaction times to targets presented in medium-sized and large regions of the left visual hemifield. These results have been interpreted as reflecting a stronger anchorage of attention by ADHD children upon a cued location and an inability to shift covert attention easily to an alternative location. The breakdown of the focusing function suggests adoption of similar time response sets across focus area size by the more compromised right hemisphere.

Attention↗

PubMed2004

A global approach combining proteome analysis and phenotypic screening with RNA interference yields novel apoptosis regulators.

Global approaches like proteome or transcriptome analyses have been performed extensively to identify candidate genes or proteins involved in biological and pathological processes. Here we describe the identification of proteins implicated in the regulation of apoptosis using proteome analysis and the functional validation of targets by RNA interference. A high-throughput platform for the validation of synthetic small interfering RNAs (siRNAs) by quantitative real-time PCR was established. Genes of the identified factors were silenced by automated siRNA transfection, and their role in apoptotic signaling was investigated. Using this strategy, nine new modulators of apoptosis were identified. A subsequent detailed study demonstrated that hepatoma-derived growth factor (HDGF) is required for TNFalpha-induced release of pro-apoptotic factors from mitochondria. The strategy described here may be used for hypothesis-free, global gene function analysis.

Apoptosis↗

PubMed2003

Chemical genomics strategy for the discovery of new anticancer agents.

Chemical genomics represents a cooperation of biology and chemistry to identify and intervene the biological targets. Small molecules with diverse structural characteristics should be used to validate the target through interfering with the biological processes. Because of the limitation of existing chemical libraries, the diversity can be exploited using both the molecular design techniques; structure-based design and ligand-based design. These methods can guide the selection of small molecules with optimal binding properties to desired biological targets. Studies of potential molecular targets for novel anticancer drug discovery including in silico screening, QSAR, and de novo design demonstrated the importance of chemical genomics strategy to find the chemical probes and drug lead compounds.

Animals↗

PubMed2006

Antiviral therapy targeting viral polymerase.

Viral DNA and RNA polymerases are enzymes, which are responsible for copying the genetic materials of viruses and are therefore central components in the life cycles of viruses. The polymerases are essentially required for the replication of viruses. The reverse transcriptase (RT) of the retroviruses and the hepadnaviruses is the sole viral enzyme required for the synthesis of DNA from viral RNA. Viral polymerases are therefore an extremely favorable target for the development of antiviral therapy. The success of anti-HIV-1 therapy using inhibitors specifically targeting HIV RT suggests that other viral polymerases can be the valid molecular targets for the design of antiviral drugs. Intensive structural and functional studies of viral polymerases have been conducted and have opened new avenues for the development of more effective antiviral therapy. This review summarizes the insights gained from recent structural and functional studies of antiviral agents, which target viral polymerases. The primary focus will be on hepatitis C virus (HCV), herpesviruses, HIV, hepatitis B virus (HBV) and influenza virus.

Antiviral Agents↗

PubMed2004

Genetic blockade of the insulin-like growth factor 1 receptor for human malignancy.

Growth factor receptor signals, including insulin-like growth factor (IGF)-1 receptor (IGF-1R), are required for carcinogenesis and tumour progression in many human malignancies. The concept of targeting specific tumorigenic receptors has been validated by successful clinical application of multiple new drugs, including trastuzumab and gefitinib. In this paper, we review strategies of the genetic blockade of IGF-1/IGF-1R that validate this receptor as a promising anticancer target. Adenoviruses efficiently transduce malignant epithelial cells in culture and are useful for such target validation and potentially also as clinical therapeutics. To block IGF-1R signalling, we constructed adenoviruses expressing antisense IGF-1R and two truncated IGF-1R (482 and 950 amino acids long, IGF-1R/482st and IGF-1R/950st, respectively) that function as dominant negative inhibitors (IGF-1R/dn). The truncated receptors were also cloned into tetracycline regulated expression vectors to study the effects of modulating this pathway without the use of viral vectors. Blocking for IGF-1R suppressed tumorigenicity both in vitro and invivo and effectively blocked both IGF-1 and IGF-2-induced activation of Akt-1. IGF-1R/dn expression increased radiation- and chemotherapy-induced apoptosis and these combination therapies with chemotherapy were very effective against tumours in mice. In an intraperitoneal dissemination mouse model, blockade of IGF-IR reduced dissemination and prolonged survival times. IGF-1R/482st was more effective than IGF-IR/950st due to its bystander effect. These studies confirm the validity of IGF-1R as a therapeutic target and genetic blockade as a potential strategy for several malignancies, including lung, colon and pancreatic carcinoma.

Animals↗

PubMed2005

Determining the basic psychometric properties of the Greek KDQOL-SF.

The aim of this study was to determine the basic psychometric properties, i.e. reliability and validity, of the Greek version of the Kidney Disease Quality of Life Short Form (KDQOL-SF). The instrument was self-administered to a homogenous group of 665 end stage renal disease patients in 20 dialysis units throughout Greece and the overall response rate was 72.6%. Reliability was demonstrated by Cronbach's alpha exceeding the recommended minimum value of 0.70 in all, except one, scales. Tests of item-internal consistency, after correction for overlap, resulted in correlations between items and their hypothesized scales, which exceeded the 0.40 standard in 94.5% of the cases. Item discriminant validity tests indicated 100% scaling success for six out of eight generic and disease-targeted scales. Validity was supported by the confirmation of expected correlations between scales and the overall health-rating item included in the instrument and with sociodemographic and self-reported health variables. Multiple stepwise linear regression analysis demonstrated that all disease-targeted scales were important predictors of SF-36 general health scales and the variance explained ranged from 37% to 57%. Overall, the psychometric properties of the KDQOL-SF, resulting from this first-time administration of the instrument to a Greek dialysis population, were good and the disease targeted scales were informative and of high internal consistency reliability. Cross-sectional construct validity is demonstrated, despite the lack of external validity criteria based on clinical ratings of severity. The results support administering the Greek KDQOL-SF in studies evaluating dialysis therapy and contribute to transnational comparison of findings.

Aged↗

PubMed2005

Identification and validation of the mitochondrial F1F0-ATPase as the molecular target of the immunomodulatory benzodiazepine Bz-423.

Bz-423 is a 1,4-benzodiazepine that suppresses disease in lupus-prone mice by selectively killing pathogenic lymphocytes, and it is less toxic compared to current lupus drugs. Cells exposed to Bz-423 rapidly generate O(2)(-) within mitochondria, and this reactive oxygen species is the signal initiating apoptosis. Phage display screening revealed that Bz-423 binds to the oligomycin sensitivity conferring protein (OSCP) component of the mitochondrial F(1)F(0)-ATPase. Bz-423 inhibited the F(1)F(0)-ATPase in vitro, and reconstitution experiments demonstrated that inhibition was mediated by the OSCP. This target was further validated by generating cells with reduced OSCP expression using RNA interference and studying the sensitivity of these cells to Bz-423. Our findings help explain the efficacy and selectivity of Bz-423 for autoimmune lymphocytes and highlight the OSCP as a target to guide the development of novel lupus therapeutics.

Adenosine Triphosphatases↗

PubMed1992

Differential accuracy in person perception across traits: examination of a functional hypothesis.

Although strangers can assess certain traits of unacquainted others with moderate validity, overall validity is low. Differential validity across traits may be due to (a) the extent to which targets display valid cues or (b) the extent to which perceivers validly use cues. A functionalist perspective suggests that valid cue utilization should vary with how important the consequences of accurate trait assessment are. It was predicted from this perspective that perceivers would judge strangers' sociosexuality more accurately than 3 other traits--social potency, social closeness, and stress reaction. Perceivers viewed 1-min videotaped segments of targets being interviewed and rated them on the 4 traits. Ratings were correlated with target-reported trait measures. As predicted, perceivers' ratings of male sociosexuality agreed relatively well with self-reports. This effect was moderated by sex of target and sex of perceiver.

Adult↗

PubMed1995

Event related potentials during covert orientation of visual attention: effects of cue validity and directionality.

Covert orientation of attention was studied in 30 adults who fixated warning cues and pressed a button at target onset. Directional cues (arrows) indicated the most probable (p = 0.8) side of target occurrence. Subjects responded fastest when validly cued, slowest to invalidly cued targets, and at an intermediate rate when the cue (a cross) was not directional. Directional cues took longer to evaluate (increased N1 and P2 latencies) and produced more focussed attention and greater response preparation (enhanced CNV and P3 amplitude) than non-directional cues. These findings indicate that the expectancy of a target can be manipulated by a spatial cue at three levels, sensory, attention, and response preparation, and lead to changes in the sensory perceptual processing of the target. Validly cued targets produced an increase in P1 amplitude reflecting attention enhanced sensory processing whereas invalidly cued targets increased N1 and P3 amplitudes reflecting the re-orientation of attention, and further processing and updating of information required of low probability stimuli respectively. P3 latency to invalidly cued targets was also delayed reflecting the additional processes required to shift attention to a new location. The P3 latency validity effect was smaller than that found for response time suggesting response execution may also be affected by spatial attention.

Aged↗

PubMed2026

Cross-Platform Proteomics and Machine Learning Algorithms Nominate Plasma Biomarkers of Stroke Diagnosis.

BACKGROUND: Blood-based biomarkers for stroke subtyping could improve triage in emergency settings. We used cross-platform proteomics to identify plasma biomarkers differentiating major stroke diagnostic groups. METHODS: We conducted a case-control study using 2 biorepositories. Plasma was collected in the emergency department from adults with suspected stroke before therapeutic intervention. Differentially enriched proteins were identified across acute ischemic stroke, intracerebral hemorrhage, transient ischemic attack, and stroke mimics using SomaScan discovery proteomics (Grady). Differentially enriched proteins were nominated using pairwise and multigroup comparisons and adjusted for clinical covariates. Protein panels were created using least absolute shrinkage and selection operator logistic regression. Internal validation used repeated nested cross-validation (rCV) and targeted mass spectrometry (MS), while external validation used data-independent acquisition  mass spectrometry in an independent cohort (Yale). RESULTS: We included 100 subjects (40 with acute ischemic stroke, 20 with intracerebral hemorrhage, 20 with transient ischemic attack, 20 with stroke mimics) in discovery and 80 subjects (20 per group) in external validation cohorts. SomaScan quantified 7307 proteins, of which 61 differentiated stroke subtypes. We identified 7 protein classifiers for acute ischemic stroke (rCV-area under the curve, 0.82 [95% CI, 0.78-0.86]), 6 for intracerebral hemorrhage (rCV-area under the curve, 0.70 [95% CI, 0.64-0.76]), 8 for transient ischemic attack (rCV-area under the curve, 0.78 [95% CI, 0.73-0.84]), and 7 for stroke mimics (rCV-area under the curve, 0.81 [95% CI, 0.77-0.86]). Targeted proteomics internally validated 11 proteins, and data-independent acquisition-mass spectrometry externally validated 32 proteins, including VTN (vitronectin), PLG (plasminogen), and S100A9 as top stroke mimics, transient ischemic attack, and intracerebral hemorrhage classifiers. CONCLUSIONS: This study highlights plasma proteomics as a valuable tool for discovering protein biomarkers of stroke diagnosis. These findings support further validation in larger, multicenter cohorts to facilitate biomarker-guided stroke diagnosis in acute care.

Humans↗

PubMed2026

Expression patterns of potential targets for antibody-directed therapy in metastatic castration-resistant prostate cancer patients.

INTRODUCTION: Survival in metastatic castration-resistant prostate cancer (mCRPC) patients remains limited and treatment is complicated by tumor heterogeneity. As antibody-based therapeutics emerge, identifying actionable antigen targets and patient subgroups most likely to benefit is essential. MATERIALS & METHODS: Gene expression of 62 antibody-targetable proteins was analyzed in 296 mCRPC biopsies. These genes encode proteins targeted by approved or investigational antibody-based cancer therapeutics. Associations between target expression with genomic classifications and transcriptomic subtypes were evaluated. Target expression was also assessed in tumors with low expression of established mCRPC targets. Subgroup-specific targets were validated in an independent cohort and single-cell transcriptomics. RESULTS: Established targets KLK2, FOLH1 (PSMA) and STEAP1 showed the highest median expression across the cohort. Target expression did not correlate with genomic classifications, including homologous recombination deficiency, microsatellite instability, CDK12, TP53, PTEN or AR alterations Target expression did associate with transcriptomic subtypes: CRPC-AR (driven by androgen receptor-signaling) and CRPC-SCL (stem cell-like features, AP-1/YAP/TAZ-driven), displayed the highest expression of multiple targets, including KLK2, FOLH1, and SLC44A4. CRPC-NE (neuroendocrine phenotype) showed heterogeneous expression, with high CD46 expression, whereas CRPC-WNT (Wnt-signaling driven) generally showed low target expression. Notably, CD46 was highly expressed in tumors with low KLK2, FOLH1, and STEAP1 expression, a subgroup associated with poor prognosis. CONCLUSIONS: Although several antibody targets showed broad expression in mCRPC-tumors, expression varied by transcriptomic subtype. Subgroups such as CRPC-WNT expressed fewer targets, suggesting the need for alternative therapeutic strategies. CD46 emerged as a promising target, with wide expression across multiple subtypes, including clinically challenging CRPC-NE and mCRPC tumors lacking expression of established targets.

Humans↗

PubMed2003

Modulation of small conductance calcium-activated potassium (SK) channels: a new challenge in medicinal chemistry.

Small conductance calcium-activated potassium (SK) channels are found in many types of neurons as well as in some other cell types. These channels are selective for K(+) and open when intracellular Ca(2+) rises to omega 500 nM. In neurons, this occurs during and after an action potential. Activation of SK channels hyperpolarizes the membrane, thus reducing cell excitability for several tens or hundreds of milliseconds. This phenomenon is called a afterhyperpolarization (AHP). Three subtypes of SK channels (SK1, SK2, SK3) have been cloned and exhibit a differential localization in the brain. SK channels may play a role in physiological and pathological conditions. They may be involved in the control of memory and cognition. Moreover, they are heavily expressed in the basal ganglia (in particular in the substantia nigra, pars compacta) and in the limbic system, suggesting that they may modulate motricity and emotional behaviour. Based on these facts, SK channel subtypes may be a suitable target for developing novel therapeutic agents, but more work is needed to validate these targets. Hence, there is a great need for selective ligands. Moreover, although the risk of peripheral side-effects for SK channel modulators appears to be low, some questions remain to be investigated. Currently, different molecules are known as SK channel modulators. Apamin is a very potent peptidic agent; it produces a strong blockade of these targets which is only very slowly reversible and it has limited selectivity. Dequalinium was found to be an effective blocker. Different chemical modulations on the dequalinium structure led to the discovery of highly potent bis-quinolinium derivatives such as UCL 1684. Other bis-(2-amino-benzimidazole) derivatives are in development. On the other hand, quaternary salts of bicuculline were reported to be effective in inhibiting AHPs. More recent developments on structurally-related molecules revealed that methyl-laudanosine is a new interesting tool for exploring SK channel pharmacology. Finally, a family of compounds has been shown to facilitate SK channel opening. Such compounds may be useful in treating disorders involving neuronal hyperexcitability.

Animals↗

PubMedDate not supplied

Deficits of the automatic orienting of attention in schizophrenic patients.

The automatic orienting of attention was studied in medicated non-psychotic schizophrenic patients and in matched controls using the Posner paradigm of covert orienting to peripheral cues. This paradigm allows determination of the "benefits" in performance when attention is moved in advance to target location ("valid" trials) and the "costs" in performance when attention has to be reoriented to target location after an incorrect directional cue ("invalid" trials). Compared to normals, schizophrenics showed reduced costs of invalid cueing and increased benefits of valid directional cueing. Schizophrenics did not show selective visual field asymmetries reported in similar studies. The decreased inhibition in the presence of incorrect directional cues may be related to a reduced tone of monoaminergic terminals possibly involved in the regulation of selective attention and arousal regulation.

Adult↗

PubMed2003

Genome-based drug discovery: prioritizing disease-susceptibility/disease-associated genes as novel drug targets for schizophrenia.

The search for new classes of antipsychotics based on novel targets identified from linkage/linkage association in diseased cohorts and microarray approaches using tissue from affected individuals is a high priority in central nervous system research. Genes linked to schizophrenia, a disease affecting 1% of the population, have been identified on nearly every chromosome of the human genome leading to a diverse choice of targets for validation. Interestingly, while the majority of currently used antipsychotic medications act by blocking dopamine receptors, there have been few genetic studies implicating the dopamine receptor family in disease etiology. Recently, four genes have been identified that encode dysbindin, neuroregulin, D-amino acid oxidase and G72, respectively, that support previous studies suggesting that schizophrenia may result from a hypofunction of glutamatergic neurotransmission. Linkage and microarray studies have similarly supported studies implicating the alpha 7 neuronal nicotinic receptor in the etiology of schizophrenia. Microarray studies using brain tissue from schizophrenic patients have shown changes in gene expression that number in the thousands, involving a number of proteins related to synaptic structure and function (PSYN gene group) and cellular metabolism. The majority of these proteins are not traditional drug discovery targets, nor are their functional roles in schizophrenia obvious, providing a challenge to validate them from the drug target identification/drug discovery perspective. The current state-of-the-art in genome-based approaches to schizophrenia, target discovery highlights a need for a multidisciplinary, integrative, null hypothesis-based approach to sort through these novel genes as drug targets.

Antipsychotic Agents↗

PubMed2026

CRISPGen: A deep generative framework for multi-objective CRISPR/Cas9 guide RNA design via Conditional Latent Diffusion and Dual-Critic Reinforcement Learning.

MOTIVATION: The CRISPR-Cas9 system offers transformative potential for precision genome editing, yet its clinical translation remains constrained by the risk of unintended off-target double-strand breaks. While current discriminative models excel at evaluating pre-specified candidate guides, resolving the fundamental antagonism between on-target cleavage efficiency and off-target specificity within a fixed sequence search space remains a major challenge. RESULTS: We present CRISPGen, a unified deep generative framework that reframes sgRNA design as a multi-objective constrained sequence synthesis problem. It integrates (i) DNABERT-2 genomic-language embeddings, (ii) a conditional latent diffusion generator conditioned on a user-specified on-target efficiency target, and (iii) a dual-critic reinforcement-learning (RL) stage that couples a frozen on-target efficiency critic with a cross-attention off-target discriminator (validation Pearson R=0.8157) trained on a unified corpus of experimental off-target events from six detection platforms. Across 1000 generated sgRNAs, CRISPGen reduces the mean off-target discriminator score by 99.7% relative to the pre-RL baseline and, under an exhaustive whole-genome screen of all 302,631,056 NGG PAM sites in GRCh38, yields zero perfect-match and only 55 one-mismatch genomic hits. We further show, transparently, that the internal on-target critic saturates under RL optimization - an instance of Goodhart's Law - and therefore assess on-target viability using an independent external CRISPRon screen (mean 47.10/100). Repeating the RL fine-tuning stage under three random seeds (with the diffusion generator, DNABERT-2 embeddings, and off-target discriminator held fixed) yields a stable operating point across seeds. Full diversity, per-mismatch, and reproducibility statistics are reported in the Results. AVAILABILITY: Source code is available at https://github.com/malekpouri/CRISPGen; the pre-trained checkpoints and the 3,000,000-sequence library are hosted on Hugging Face (https://huggingface.co/malekpouri/CRISPGen-Checkpoints) and archived on Zenodo under DOI 10.5281/zenodo.21428641.

CRISPR-Cas9↗

PubMed2005

Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms.

We present a new microRNA target prediction algorithm called TargetBoost, and show that the algorithm is stable and identifies more true targets than do existing algorithms. TargetBoost uses machine learning on a set of validated microRNA targets in lower organisms to create weighted sequence motifs that capture the binding characteristics between microRNAs and their targets. Existing algorithms require candidates to have (1) near-perfect complementarity between microRNAs' 5' end and their targets; (2) relatively high thermodynamic duplex stability; (3) multiple target sites in the target's 3' UTR; and (4) evolutionary conservation of the target between species. Most algorithms use one of the two first requirements in a seeding step, and use the three others as filters to improve the method's specificity. The initial seeding step determines an algorithm's sensitivity and also influences its specificity. As all algorithms may add filters to increase the specificity, we propose that methods should be compared before such filtering. We show that TargetBoost's weighted sequence motif approach is favorable to using both the duplex stability and the sequence complementarity steps. (TargetBoost is available as a Web tool from http://www.interagon.com/demo/.).

5' Untranslated Regions↗