Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ.

Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S using classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our findings suggest that Y432S induces structural alterations in domains responsible for nucleotide addition and ternary complex stabilization while retaining structural features consistent with possible catalysis in the active site. Calculations of the minimum energy path associated with the reaction mechanism of the wild type (WT) and Y432S Pol κ indicate that, while both enzymes are catalytically competent (in terms of energetics and the active site's geometries), the cancer mutation results in an endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on nonbonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP3- over dCTP4-.

Hallucination-Proneness is Associated With a Decrease in Robust Averaging of Perceptual Evidence.

BACKGROUND AND HYPOTHESIS: Hallucinations are characterized by disturbances in perceptual decision-making about environmental stimuli. When integrating across multiple stimuli to form a perceptual decision, typical observers engage in "robust averaging" by down-weighting extreme perceptual evidence, akin to a statistician excluding outlying data. Furthermore, observers adapt to contexts with more unreliable evidence by increasing this down-weighting strategy. Here, we test the hypothesis that hallucination-prone individuals (n = 38 high vs n = 91 low) would show a decrease in this robust averaging and diminished sensitivity to changes in evidence variance. STUDY DESIGN: We used a multielement perceptual averaging task to elicit dichotomous judgments about the "average color" (red/blue) of an array of stimuli in trials with varied strength (mean) and reliability (variance) of decision-relevant perceptual evidence. We fitted computational models to task behavior, with a focus on a log-posterior-ratio (LPR) model which integrates evidence as a function of the log odds of each perceptual option and produces a robust averaging effect. STUDY RESULTS: Hallucination-prone individuals demonstrated less robust averaging, seeming to weigh inlying and outlying extreme or untrustworthy evidence more equally. Furthermore, the model that integrated evidence as a function of the LPR of the two perceptual options and produced robust averaging showed poorer fit for the group prone to hallucinations. Finally, the weighting strategy in hallucination-prone individuals remained insensitive to evidence variance. CONCLUSIONS: Our findings provide empirical support for theoretical proposals regarding evidence integration aberrations in psychosis and alterations in the perceptual systems that track statistical regularities in environmental stimuli.

Computational drug discovery of an inhibitor of APOBEC3B as a treatment for epithelial cancers.

Cancer is one of the leading causes of death in the U.S., and tumorous cancers such as cervical, lung, breast, and ovarian cancers are the most common types. APOBEC3B is a nonessential cytidine deaminase found in humans and theorized to defend against viral infection. However, overexpression of APOBEC3B is linked to cancer in humans, which makes APOBEC3B a potential cancer treatment target through competitive inhibition for several tumorous cancers. Computational studies can help reveal a small molecule inhibitor using high-throughput virtual screening of millions of candidates with relatively little cost. This study aims to narrow the field of potential APOBEC3B inhibition candidates for future in vitro assays and provide an effective scaffold for drug design studies. Another goal of this project is to provide critical amino acid targets in the active site for future drug design studies. This study simulated 7.8 million drug candidates using high-throughput virtual screening and further processed the top scoring 241 molecules from AutoDock Vina, DOCK 6, and de novo design. Using virtual screening, de novo design, and molecular dynamics simulations, a competitive inhibitor candidate was discovered with an average binding free energy score of -46.03 kcal/mol, more than 10 kcal/mol better than the substrate control (dCMP). These results indicate that this molecule (or a structural derivative) may be an effective inhibitor of APOBEC3B and prevent host genome mutagenesis resulting from protein overexpression. Another important finding is the confirmation of essential amino acid targets, such as Tyr250 and Gln213 within the active site of APOBEC3B. Therefore, study used novel computational methods to provide a theoretical scaffold for future drug design studies that may prove useful as a treatment for epithelial cancers.Communicated by Ramaswamy H. Sarma.

The association between mental health stigma and face emotion recognition in individuals at risk for psychosis.

Self-stigma has been associated with reduced accuracy of face emotion recognition in individuals at clinical high risk for psychosis (CHR). Stigma may also relate to slowing of performance during cognitive tasks for which a negative stereotype is relevant. This study aimed to investigate the association of mental illness stigma with face emotion recognition among CHR individuals. Participants were 143 CHR individuals identified using the Structured Interview for Psychosis-Risk Syndromes (SIPS). Face emotion recognition was assessed using the Penn Emotion Recognition Task (ER-40). Stigma was assessed using discrimination, stereotype awareness, and stereotype agreement subscales of the Mental Health Attitudes Interview for CHR. We tested associations of ER-40 accuracy and response times with these stigma variables, including the role of clinical and demographic factors. Racial/ethnic minoritized participants had higher attenuated positive symptoms than non-minoritized participants. Longer ER-40 response times were correlated with greater stereotype agreement (r=.17, p=.045) and discrimination (r=.22, p=.012). A regression model predicting ER-40 response times revealed an interaction of stereotype agreement with minoritized status (p=.008), with slower response times for minoritized participants as stereotype agreement increased. Greater disorganized symptoms and male gender also predicted longer response times. ER-40 accuracy was not associated with stigma. Overall, minoritized CHR individuals with greater internalized stigma took longer to identify face emotions. Future research is needed to assess whether slower response times are specific to social cues, and if internalized stigma interferes with performance in real-world social situations. Reducing stigma may be an important target for interventions that aim to improve social skills.

Mismatch negativity and clinical trajectories in psychotic disorders: Five-year stability and predictive utility.

BACKGROUND: Mismatch negativity (MMN) amplitude is reduced in psychotic disorders and associated with symptoms and functioning. Due to these robust associations, it is often considered a biomarker for psychotic illness. The relationship between MMN and clinical outcomes has been examined well in early onset psychotic illness; however, its stability and predictive utility in chronic samples are not clear. METHOD: We examined the five-year stability of MMN amplitude over two timepoints in individuals with established psychotic disorders (cases; N = 132) and never-psychotic participants (NP; N = 170), as well as longitudinal associations with clinical symptoms and functioning. RESULTS: MMN amplitude exhibited good temporal stability (cases, r = 0.53; never-psychotic, r = 0.52). In cases, structural equation models revealed MMN amplitude to be a significant predictor of worsening auditory hallucinations (ß = 0.19), everyday functioning (ß = -0.13), and illness severity (ß = -0.12) at follow-up. Meanwhile, initial IQ (ß = -0.24), negative symptoms (ß = 0.23), and illness severity (ß = -0.16) were significant predictors of worsening MMN amplitude five years later. CONCLUSIONS: These results imply that MMN measures a neural deficit that is reasonably stable up to five years. Results support disordered cognition and negative symptoms as preceding reduced MMN, which then may operate as a mechanism driving reductions in everyday functioning and the worsening of auditory hallucinations in chronic psychotic disorders. This pattern may inform models of illness course, clarifying the relationships amongst biological mechanisms of predictive processing and clinical deficits in chronic psychosis and allowing us to better understand the mechanisms driving such impairments over time.

Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort.

Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumour types, including melanoma, glioma, leukaemia and cardiac angiosarcoma. We sequenced all coding exons of the POT1 gene in 2928 European-descent melanoma cases and 3298 controls, identifying 43 protein-changing genetic variants. We performed POT1-telomere binding assays for all missense and stop-gained variants, finding nine variants that impair or disrupt protein-telomere complex formation, and we further define the role of variants in the regulation of telomere length and complex formation through molecular dynamics simulations. We determine that POT1 coding variants are a minor contributor to melanoma burden in the general population, with only about 0.5% of melanoma cases carrying germline pathogenic variants in this gene, but should be screened in individuals with a strong family history of melanoma and/or multiple malignancies.

Pleasant and unpleasant odor identification ability is associated with distinct dimensions of negative symptoms transdiagnostically in psychotic disorders.

Negative symptoms are among the greatest sources of functional impairment for individuals with schizophrenia, yet their mechanisms remain poorly understood. Olfactory impairment is associated with negative symptoms. The processing of pleasant olfactory stimuli is subserved by reward-related neural circuitry while unpleasant olfactory processing is subserved by emotion-related neural circuitry, suggesting that these two odor dimensions may offer a window into differential mechanisms of negative symptoms. We examined whether pleasant and unpleasant odor identification bears differential relationships with avolition and inexpressivity dimensions of negative symptoms, whether these relationships are transdiagnostic, and whether pleasant and unpleasant odor processing also relate differently to other domains of functioning in a sample of individuals diagnosed with schizophrenia (N = 54), other psychotic disorders (N = 65), and never-psychotic adults (N = 160). Hierarchical regressions showed that pleasant odor identification was uniquely associated with avolition, while unpleasant odor identification was uniquely associated with inexpressivity. These relationships were largely transdiagnostic across groups. Additionally, pleasant and unpleasant odor identification displayed signs of specificity with other functional and cognitive measures. These results align with past work suggesting dissociable pathomechanisms of negative symptoms and provide a potential avenue for future work using valence-specific olfactory dysfunction as a semi-objective and low-cost marker for understanding and predicting the severity of specific negative symptom profiles.

The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation.

Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of mutated preleukemic cells. Individuals with CH are at an increased risk of developing hematopoietic malignancies. Here, we describe a novel animal model carrying a recurrent TET2 missense mutation frequently found in patients with CH and leukemia. In a fashion similar to CH, animals show signs of disease late in life when they develop a wide range of myeloid neoplasms, including acute myeloid leukemia (AML). Using single-cell transcriptomic profiling of the bone marrow, we show that disease progression in aged animals correlates with an enhanced inflammatory response and the emergence of an aberrant inflammatory monocytic cell population. The gene signature characteristic of this inflammatory population is associated with poor prognosis in patients with AML. Our study illustrates an example of collaboration between a genetic lesion found in CH and inflammation, leading to transformation and the establishment of blood neoplasms. SIGNIFICANCE: Progression from a preleukemic state to transformation, in the presence of TET2 mutations, is coupled with the emergence of inflammation and a novel population of inflammatory monocytes. Genes characteristic of this inflammatory population are associated with the worst prognosis in patients with AML. These studies connect inflammation to progression to leukemia. See related commentary by Pietras and DeGregori, p. 2234 . This article is highlighted in the In This Issue feature, p. 2221.

Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation.

The prediction of protein mutations that affect function may be exploited for multiple uses. In the context of disease variants, the prediction of compensatory mutations that reestablish functional phenotypes could aid in the development of genetic therapies. In this work, we present an integrated approach that combines coevolutionary analysis and molecular dynamics (MD) simulations to discover functional compensatory mutations. This approach is employed to investigate possible rescue mutations of a poly(ADP-ribose) polymerase 1 (PARP1) variant, PARP1 V762A, associated with lung cancer and follicular lymphoma. MD simulations show PARP1 V762A exhibits noticeable changes in structural and dynamical behavior compared with wild-type (WT) PARP1. Our integrated approach predicts A755E as a possible compensatory mutation based on coevolutionary information, and molecular simulations indicate that the PARP1 A755E/V762A double mutant exhibits similar structural and dynamical behavior to WT PARP1. Our methodology can be broadly applied to a large number of systems where single-nucleotide polymorphisms have been identified as connected to disease and can shed light on the biophysical effects of such changes as well as provide a way to discover potential mutants that could restore WT-like functionality. This can, in turn, be further utilized in the design of molecular therapeutics that aim to mimic such compensatory effect.

Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase.

Remdesivir was the first antiviral drug that received emergency use authorization from the United States Food and Drug Administration and is now formally approved to treat COVID-19. Remdesivir is a nucleotide analogue that targets the RNA-dependent RNA polymerase (RdRp) of coronaviruses, including SARS-CoV-2. The solution of multiple RdRp structures has been one of the main axes of research in the race against the SARS-CoV-2 virus. Several hypotheses of the mechanism of inhibition of RdRp by remdesivir have been proposed, although open questions remain. This work uses molecular dynamics simulations to explore the impact of remdesivir and two analogues as incoming nucleotides and of up to four incorporations of remdesivir along the primer strand on RdRp. The simulation results suggest that the overall structure and the dynamical behavior of RdRp are destabilized by remdesivir and the two analogues in the incoming position. The incorporation of remdesivir along the primer strand impacts specific non-bonded interactions between the nascent RNA and the polymerase subunit, as well as the overall dynamical networks on RdRp. The strongest impact on the structure and dynamics are observed after three incorporations, when remdesivir is located at position -A3, in agreement with previously reported experimental and computational results. Our results provide atomic-level details of the role played by remdesivir on the disruption of RNA synthesis by RdRp and the main drivers of these disruptions.

Dynamic interplay between life events and course of psychotic disorders: 10-year longitudinal study following first admission.

BACKGROUND: Life events (LEs) are a risk factor for first onset and relapse of psychotic disorders. However, the impact of LEs on specific symptoms - namely reality distortion, disorganization, negative symptoms, depression, and mania - remains unclear. Moreover, the differential effects of negative v. positive LEs are poorly understood. METHODS: The present study utilizes an epidemiologic cohort of patients (N = 428) ascertained at first-admission for psychosis and followed for a decade thereafter. Symptoms were assessed at 6-, 24-, 48-, and 120-month follow-ups. RESULTS: We examined symptom change within-person and found that negative events in the previous 6 months predicted an increase in reality distortion (ß = 0.07), disorganized (ß = 0.07), manic (ß = 0.08), and depressive symptoms (ß = 0.06), and a decrease in negative symptoms (ß = -0.08). Conversely, positive LEs predicted fewer reality distortion (ß = -0.04), disorganized (ß = -0.04), and negative (ß = -0.13) symptoms, and were unrelated to mood symptoms. A between-person approach to the same hypotheses confirmed that negative LEs predicted change in all symptoms, while positive LEs predicted change only in negative symptoms. In contrast, symptoms rarely predicted future LEs. CONCLUSIONS: These findings confirm that LEs have an effect on symptoms, and thus contribute to the burden of psychotic disorders. That LEs increase positive symptoms and decrease negative symptoms suggest at least two different mechanisms underlying the relationship between LEs and symptoms. Our findings underscore the need for increased symptom monitoring following negative LEs, as symptoms may worsen during that time.

Mismatch negativity amplitude in first-degree relatives of individuals with psychotic disorders: Links with cognition and schizotypy.

Mismatch negativity (MMN) amplitude is reliably reduced in psychotic disorders. While several studies have examined this effect in first-degree relatives of individuals with schizophrenia, few have sought to quantify deficits in relatives of individuals with other psychotic disorders. While some conclude that, compared to healthy subjects, first-degree relatives of schizophrenia show reduced MMN, others contradict this finding. Furthermore, though MMN is often shown to be associated with cognitive impairments and clinical symptoms in psychotic disorders, to our knowledge no studies have sought to fully examine these relationships in studies of first-degree relatives. The present study sought to clarify the extent of MMN amplitude reductions in a large sample of siblings of individuals with diverse psychotic disorders (n = 67), compared to probands with psychosis (n = 221) and never psychotic comparison subjects (n = 251). We further examined associations of MMN amplitude with cognition and schizotypal symptoms across these groups. We found that MMN amplitude was intact in siblings compared to probands. MMN amplitude was associated with cognition and schizotypal symptoms dimensionally across levels of familial risk. The present results imply that MMN reductions do not reflect genetic risk for psychotic disorders per se, and instead emerge as a result of, or in conjunction with, clinical features associated with psychosis. Such findings carry important implications for the utility of MMN amplitude as an indicator of inherited risk, and suggest that this component may be best conceptualized as an endophenotype for clinical symptoms and cognitive impairments, rather than risk for psychosis per se.

Conspiratorial Thinking During COVID-19: The Roles of Paranoia, Delusion-Proneness, and Intolerance of Uncertainty.

The COVID-19 global pandemic has left many feeling a sense of profound uncertainty about their world, safety, and livelihood. Sources espousing misinformation and conspiracy theories frequently offer information that can help make sense of this uncertainty. Individuals high in intolerance of uncertainty (IU) may be particularly impacted by the impoverished epistemic environment and may thus be more drawn to conspiratorial thinking (CT). In the present work, we show across 2 studies (N = 519) that COVID-19-specific CT is associated with higher levels of IU as well as delusion-proneness, and paranoia. Furthermore, delusion-proneness and paranoia explained the relationship between IU and CT and emerged as independent partial correlates of CT even when controlling for other facets of schizotypy. In contrast, anxiety did not explain the relationship between IU and CT. Overall, our findings highlight the importance of individual differences in IU, delusion-proneness and paranoia in the development of CT in the context of the acute uncertainty of a global crisis, in which conspiracy theories are more prevalent and salient. Informational intervention designs may benefit from leveraging the body of work demonstrating the efficacy of targeting IU to incite meaningful changes in thinking.

Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.

Selection of residues and other molecular fragments for inclusion in the quantum mechanics (QM) region for QM/molecular mechanics (MM) simulations is an important step for these calculations. Here, we present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analyses allows the determination of whether a residue needs to be included in the QM subsystem or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4-oxalocrotonate tautomerase (4OT) and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase λ (Polλ) with a third cation in the active site. Our results suggest that the combination of protein evolutionary and ELF analyses provides insights into residue/molecular fragment selection for QM/MM simulations.

Online Survey of the Impact of COVID-19 Risk and Cost Estimates on Worry and Health Behavior Compliance in Young Adults.

The novel coronavirus COVID-19 pandemic is associated with elevated rates of anxiety and relatively lower compliance with public health guidelines in younger adults. To develop strategies for reducing anxiety and increasing adherence with health guidelines, it is important to understand the factors that contribute to anxiety and health compliance in the context of COVID-19. Earlier research has shown that greater perceived risk of negative events and their costs are associated with increased anxiety and compliance with health behaviors, but it is unclear what role they play in a novel pandemic surrounded by uncertainty. In the present study we measured (1) perceived risk as the self-reported probability of being infected and experiencing serious symptoms due to COVID-19 and (2) perceived cost as financial, real-world, physical, social, and emotional consequences of being infected with COVID-19. Worry was assessed using the Penn State Worry Questionnaire (PWSQ) and health compliance was measured as endorsement of the World Health Organization (WHO) health directives for COVID-19. Our results showed that greater perceived risk and costs of contracting the COVID-19 virus were associated with greater worry and while only costs were associated with greater compliance with health behaviors. Neither self-reported worry nor its interaction with cost estimates was associated with increased engagement in health behaviors. Our results provide important insight into decision making mechanisms involved in both increased anxiety and health compliance in COVID-19 and have implications for developing psychoeducational and psychotherapeutic strategies to target both domains.

Moral Cognition About Harm in Anxiety Disorders: The Importance of Experienced Emotion.

Recent work has shown that emotional arousal influences decision-making in sacrificial moral dilemmas, with heightened levels of arousal associated with increased aversion to committing moral transgressions to maximize utilitarian outcomes. Patients with anxiety disorders experience pathologically heightened states of arousal and thus may be expected to exhibit reduced utilitarian responding on such dilemmas. Extant evidence has been mixed, however, regarding whether anxious patients differ in their moral decisions from controls, and no study has conducted a careful examination of emotions experienced during decision-making. We administered sacrificial moral dilemmas to a cohort of 95 patients from across the spectrum of anxiety disorders to test whether they differed from matched controls on a) utilitarian decision-making, and b) ratings of experienced emotion during the moral deliberative process. Results showed no group differences between patients and controls on endorsement of utilitarian sacrificial action or on reported experience of emotionality during the experiment. Additionally, exploratory analysis revealed that specific emotions were correlated with utilitarian judgments. These results are in line with the Dual Process Theory model's prediction that decreased utilitarian responding will be concomitant with an increased emotional arousal. Our findings support past work indicating that moral cognition is intact in anxiety disorders despite the emotional dysregulation characteristic of anxious psychopathology. Future work would benefit from the use of process-dissociation techniques to further clarify whether emotional or cognitive processes may differ in anxiety disorders during moral cognition.

Serendipitous re-sighting of a basking shark Cetorhinus maximus reveals inter-annual connectivity between American and European coastal hotspots.

Transatlantic stock mixing in basking sharks Cetorhinus maximus is supported by low genetic diversity in populations throughout the Atlantic Ocean. However, despite significant focus on the species' movements; >1500 individual sharks marked for recapture and >150 individuals equipped with remote tracking tags, only a single record of transatlantic movment has been previously recorded. Within this context, the seredipitous re-sighting of a female basking shark fitted with a satellite transmitter at Malin Head, Ireland 993 days later at Cape Cod, USA is noteworthy.

Comparison of DNA and RNA substrate effects on TET2 structure.

Ten-eleven translocation (TET) enzymes can perform the stepwise oxidation of 5-methylcytosine (5mC) to 5-carboxylcytosine on both single-stranded (ss) and double-stranded (ds) DNA and RNA. It has been established that TET2 has a preference for ds DNA substrates, but it can catalyze the oxidation reaction on both ssDNA and RNA. The reasons for this substrate preference have been investigated for only a substrate 5mC ribonucleotide in a DNA strand, but not other nucleic acid configurations (Biochemistry58 (2019) 411). We performed molecular dynamics simulations on TET2 with various ss and ds substrates in order to better understand the structural and dynamical reasons for TET2's preference to act on ds DNA. Our simulations show that substrates that have a ribonucleotide experience several disruptions in their overall backbone shape, hydrogen bonding character, and non-bonded interactions. These differences appear to lead to the instability of ribonucleotide in the active site, and provide further rational for TET2's experimental behavior.

Premorbid adjustment trajectories in schizophrenia and bipolar disorder: A transdiagnostic cluster analysis.

Despite the overlap between schizophrenia and bipolar disorder, neurodevelopmental abnormalities are thought to be associated primarily with schizophrenia. Transdiagnostic and empirical identification of subgroups based on premorbid adjustment (PMA) may enhance understanding of illness trajectories. 160 patients with bipolar I or II disorder (BD; n = 104) or schizophrenia or schizoaffective disorder (SZ; n = 56) were assessed on PMA course from childhood to late adolescence and current symptoms and functioning. A hierarchical cluster analysis was performed using social and academic PMA scores, resulting in three optimal clusters. Cluster 1 (n = 28 SZ, 65 BD) had normal social and academic PMA, the most education, and mildest current symptoms. Cluster 2 (n = 15 SZ, 24 BD) had normal social PMA but an impaired-declining academic course and had a greater proportion of males than Cluster 1. Cluster 3 (n = 13 SZ, 15 BD) had an impaired-stable social PMA and an impaired-declining academic course and the most severe current negative symptoms and childhood trauma. The proportions of SZ and BD diagnoses, current neurocognition, and functioning did not differ between clusters. These findings suggest shared neurodevelopmental abnormalities between SZ and BD, with subgroups exhibiting distinct PMA trajectories that cut across disorders.