A Top-Down Proteomic Assay to Evaluate KRAS4B-Compound Engagement

Development of new targeted inhibitors for oncogenic KRAS mutants may benefit from insight into how a given mutation influences the accessibility of protein residues and how compounds interact with mutant or wild-type KRAS proteins. Targeted proteomic analysis, a key validation step in the KRAS inhibitor development process, typically involves both intact mass- and peptide-based methods to confirm compound localization or quantify binding. However, these methods may not always provide a clear picture of the compound binding affinity for KRAS, how specific the compound is to the target KRAS residue, and how experimental conditions may impact these factors. To address this, we have developed a novel top-down proteomic assay to evaluate in vitro KRAS4B-compound engagement while assessing relative quantitation in parallel. We present two applications to demonstrate the capabilities of our assay: maleimide-biotin labeling of a KRAS4BG12D cysteine mutant panel and treatment of three KRAS4B proteins (WT, G12C, and G13C) with small molecule compounds. Our results show the time- or concentration-dependence of KRAS4B-compound engagement in context of the intact protein molecule while directly mapping the compound binding site.

Methodology of using acoustic emissions for enhancing rodent behavioral analysis

Rodent models of behavior used in the fields of neuroscience and psychology generate a wealth of multimodal data. For instance, as a rodent moves and behaves in its environment, muscle contractions apply subtle forces to any surface the animal contacts. These forces generate acoustic waves that propagate through the waveguide as Lamb and shear horizontal (SH) waves and contain information about the rodent's physiology, behavior, and underlying psychological state. If the information in these waves were to be tapped, it would provide a novel, non-invasive way to study rodent behavior. This article lays the foundations for using guided ultrasonic waves generated by a mouse's movement on an aluminum plate for detecting behavior and drawing inferences about acoustic startle responses. The experimental setup involves piezoelectric sensors capturing the waves generated by the rodent's movement, which are then stored as discrete acoustic emission (AE) hits using an amplitude threshold-based data acquisition system. This method of data acquisition ensures that data collection occurs only when the animal moves or behaves, and each movement/behavior is represented by values of features within the generated wavepackets (AE hits). Through open field tests with C57BL/6J mice, utilizing piezoelectric sensors and the DAQ system, it was observed that every movement/behavior of the animal generated Lamb wavepackets within the frequency range of 20 kHz to 100 kHz. Furthermore, rearing behavior in the animals also led to the generation of SH wavepackets in the frequency range of 75 kHz to 230 kHz. This criterion was subsequently employed to detect rearing behavior. In the acoustic startle response test, where the animals' responses to intense sound pulse were recorded, AE hits' features proved useful in quantifying the response. These experimental findings validate the proposed technology's practicality and demonstrate its capability to enhance studies of rodent behavior.

Refining the N-Termini of the SARS-CoV-2 Spike Protein and Its Discrete Receptor-Binding Domain

Previous work employing five SARS-CoV-2 spike protein receptor-binding domain (RBD) constructs, comprising versions originally developed by Mt. Sinai or the Ragon Institute and later optimized in-house, revealed potential heterogeneity which led to questions regarding variable seropositivity assay performance. Each construct was subjected to N-deglycosylation and subsequent intact mass analysis, revealing significant deviations from predicted theoretical mass for all five proteins. Complementary tandem MS/MS analysis revealed the presence of an additional pyroGlu residue on the N-termini of the two Mt. Sinai RBD constructs, as well as on the N-terminus of the full-length spike protein from which they were derived, thus explaining the observed mass shift and definitively establishing the spike protein N-terminal sequence. Moreover, the observed mass additions for the three Ragon Institute RBD constructs were identified as variable N-terminal cleavage points within the signal peptide sequence employed for recombinant expression. To resolve this issue and minimize heterogeneity for further seropositivity assay development, the best-performing RBD construct was further optimized to exhibit complete homogeneity, as determined by both intact mass and tandem MS/MS analysis. This new RBD construct has been validated for seropositivity assay performance, is available to the greater scientific community, and is recommended for use in future assay development.

Selection for contextual fear conditioning affects anxiety-like behaviors and gene expression

Conditioned fear and anxiety-like behaviors have many similarities at the neuroanatomical and pharmacological levels, but their genetic relationship is less well defined. We used short-term selection for contextual fear conditioning (FC) to produce outbred mouse lines with robust genetic differences in FC. The high and low selected lines showed differences in fear learning that were stable across various training parameters and were not secondary to differences in sensitivity to the unconditioned stimulus (foot shock). They also showed a divergence in fear potentiated startle, indicating that differences induced by selection generalized to another measure of fear learning. However, there were no differences in performance in a Pavlovian approach conditioning task or the Morris water maze, indicating no change in general learning ability. The high fear learning line showed greater anxiety-like behavior in the open field and zero maze, confirming a genetic relationship between FC and anxiety-like behavior. Gene expression analysis of the amygdala and hippocampus identified genes that were differentially expressed between the two lines. Quantitative trait locus (QTL) analysis identified several chromosomal regions that may underlie the behavioral response to selection; cis-acting expression QTL were identified in some of these regions, possibly identifying genes that underlie these behavioral QTL. These studies support the validity of a broad genetic construct that includes both learned fear and anxiety and provides a basis for further studies aimed at gene identification.

Conditioned and unconditioned behavioral-cognitive effects of a dopamine antagonist in rats

Many drugs need to be taken multiple times to achieve a therapeutic effect. Researchers have identified several mechanisms to account for the slow onset of drug action, including drug accumulation and structural changes induced by drugs. This article provides an example of a new mechanism to account for this change in drug action. Stimuli that accompany drug administration may come to evoke conditioned responses (CRs), and these CRs may be the basis for changes in drug efficacy. Specifically, this research shows that a dopamine antagonist, pimozide, changes response rates through the direct action of the drug but changes time perception through the CRs elicited by drug administration.

Combinations of clozapine and phencyclidine: effects on drug discrimination and behavioral inhibition in rats

Phencyclidine (PCP) produces psychotomimetic effects in humans that resemble schizophrenia symptoms. In an effort to screen compounds for antipsychotic activity, preclinical researchers have investigated whether these compounds block PCP-induced behaviors in animals. In the present study, the atypical antipsychotic clozapine was tested in combination with an active dose of PCP in two-lever drug discrimination and mixed signalled-unsignalled differential-reinforcement-of-low-rates (DRL) procedures. PCP produced distinctive effects in each task: it substituted for the training dose in PCP discrimination and it increased the number of responses with short (<3 s) interresponse times as well as increasing overall response rates in the DRL schedule. Acute dosing with clozapine failed to alter the behavioral effects of PCP in either procedure even when tested up to doses that produced pharmacological effects alone. These results suggest that acute dosing with clozapine would not affect behaviors most closely associated with PCP intoxication. Further, they bring into question the utility of using PCP combination procedures in animals to screen for antipsychotic potential. Since chronic dosing is required for therapeutic efficacy of antipsychotics, future studies should focus on investigation of chronic dosing effects of these drugs in combination with PCP.

Conditioned and unconditioned behavioral-cognitive effects of a dopamine antagonist in rats

Many drugs need to be taken multiple times to achieve a therapeutic effect. Researchers have identified several mechanisms to account for the slow onset of drug action, including drug accumulation and structural changes induced by drugs. This article provides an example of a new mechanism to account for this change in drug action. Stimuli that accompany drug administration may come to evoke conditioned responses (CRs), and these CRs may be the basis for changes in drug efficacy. Specifically, this research shows that a dopamine antagonist, pimozide, changes response rates through the direct action of the drug but changes time perception through the CRs elicited by drug administration.