SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.

Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination.

The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an α helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways.

Evolution of enhanced innate immune evasion by SARS-CoV-2.

The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.

DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.

Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.

PCprophet: a framework for protein complex prediction and differential analysis using proteomic data.

Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein profiles have shown promise. However, most approaches for interpreting cofractionation datasets to yield complex composition and rearrangements between samples depend considerably on protein-protein interaction inference. We introduce PCprophet, a toolkit built on size exclusion chromatography-sequential window acquisition of all theoretical mass spectrometry (SEC-SWATH-MS) data to predict protein complexes and characterize their changes across experimental conditions. We demonstrate improved performance of PCprophet over state-of-the-art approaches and introduce a Bayesian approach to analyze altered protein-protein interactions across conditions. We provide both command-line and graphical interfaces to support the application of PCprophet to any cofractionation MS dataset, independent of separation or quantitative liquid chromatography-MS workflow, for the detection and quantitative tracking of protein complexes and their physiological dynamics.

PCfun: a hybrid computational framework for systematic characterization of protein complex function.

In molecular biology, it is a general assumption that the ensemble of expressed molecules, their activities and interactions determine biological function, cellular states and phenotypes. Stable protein complexes-or macromolecular machines-are, in turn, the key functional entities mediating and modulating most biological processes. Although identifying protein complexes and their subunit composition can now be done inexpensively and at scale, determining their function remains challenging and labor intensive. This study describes Protein Complex Function predictor (PCfun), the first computational framework for the systematic annotation of protein complex functions using Gene Ontology (GO) terms. PCfun is built upon a word embedding using natural language processing techniques based on 1 million open access PubMed Central articles. Specifically, PCfun leverages two approaches for accurately identifying protein complex function, including: (i) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector and (ii) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing a hypergeometric statistical test to enrich the top NN GO terms within the child terms of the GO terms predicted by the RF models. The documentation and implementation of the PCfun package are available at https://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.

Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration.

While several computational methods have been developed to predict the functional relevance of phosphorylation sites, experimental analysis of the interdependency between protein phosphorylation and Protein-Protein Interactions (PPIs) remains challenging. Here, we describe an experimental strategy to establish interdependencies between protein phosphorylation and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein; (ii) assigning distinct proteoforms of the target protein to different protein complexes by native complex separation (AP-BNPAGE) and protein correlation profiling; and (iii) analyzing proteoforms and complexes in cells lacking regulators of the target protein. We applied this strategy to YAP1, a transcriptional co-activator for the control of organ size and tissue homeostasis that is highly phosphorylated and among the most connected proteins in human cells. We identified multiple YAP1 phosphosites associated with distinct complexes and inferred how both are controlled by Hippo pathway members. We detected a PTPN14/LATS1/YAP1 complex and suggest a model how PTPN14 inhibits YAP1 via augmenting WW domain-dependent complex formation and phosphorylation by LATS1/2.

Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.

Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.

Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion.

Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. With the development of data-independent technologies (DIA/SWATH-MS), it is now possible to analyze hundreds of samples with great reproducibility and quantitative accuracy. However, this technology benefits from empirically derived spectral libraries that define the detectable set of peptides and proteins. Here, we apply a simple and accessible tip-based workflow for the generation of spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized nonconventional proteases such as GluC and AspN together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 min of MS acquisition, including diagnostic Mycobacterium tuberculosis (Mtb) proteins that have previously been detectable primarily by antibody-based assays and intracellular proteins not previously described to be in plasma.

Body Dysmorphic Disorder in the Perspective of the Alternative DSM-5 Model for Personality Disorder: A Study on Italian Community-Dwelling Women.

To evaluate the relationships between body dysmorphic disorder (BDD) and Alternative DSM-5 Model for Personality Disorder (AMPD) criterion A and dysfunctional personality trait (i.e., criterion B) measures, 420 Italian community-dwelling women were administered three measures of BDD (i.e., the Body Dysmorphic Disorder Questionnaire, the Body Dysmorphic Disorder-Dimensional Scale, and the Appearance Anxiety Inventory), as well as the Level of Personality Functioning Scale-Brief Form (LPFS-BF) and the Personality Inventory for DSM-5-Short Form (PID-5-SF). The three BDD measures showed substantial convergent validity correlations and could be reliably cumulated to obtain the BDD Cumulative Index (BDDCI). Several significant, nonnegligible correlations were observed between the BDDCI as well as the LPFS-BF scale scores and PID-5-SF personality trait scale scores. Relative importance weight analysis results showed that LPFS-BF scale scores and PID-5-SF trait scale scores were substantial predictors of the BDDCI scores (R = 0.42, f = 0.72). In particular, AMPD criterion A impairment in self-functioning and AMPD criterion B depressivity, anhedonia, perseveration, separation insecurity, and cognitive and perceptual dysregulation were core components of the dysfunctional personality profile associated with BDD.

International Assessment of DSM-5 and ICD-11 Personality Disorder Traits: Toward a Common Nosology in DSM-5.1.

INTRODUCTION: The DSM-5 Alternative Model of Personality Disorders (AMPD) and the ICD-11 classification of personality disorders (PD) are largely commensurate and, when combined, they delineate 6 trait domains: negative affectivity, detachment, antagonism/dissociality, disinhibition, anankastia, and psychoticism. OBJECTIVE: The present study evaluated the international validity of a brief 36-item patient-report measure that portrays all 6 domains simultaneously including 18 primary subfacets. METHODS: We developed and employed a modified version of the Personality Inventory for DSM-5 - Brief Form Plus (PID5BF+). A total of 16,327 individuals were included, 2,347 of whom were patients. The expected 6-factor structure of facets was initially investigated in samples from Denmark (n = 584), Germany (n = 1,271), and the USA (n = 605) and subsequently replicated in both patient- and community samples from Italy, France, Switzerland, Belgium, Norway, Portugal, Spain, Poland, Czech Republic, the USA, and Brazil. Associations with interview-rated DSM-5 PD categories were also investigated. RESULTS: Findings generally supported the empirical soundness and international robustness of the 6 domains including meaningful associations with familiar interview-rated PD types. CONCLUSIONS: The modified PID5BF+ may be employed internationally by clinicians and researchers for brief and reliable assessment of the 6 combined DSM-5 and ICD-11 domains, including 18 primary subfacets. This 6-domain framework may inform a future nosology for DSM-5.1 that is more reasonably aligned with the authoritative ICD-11 codes than the current DSM-5 AMPD model. The 36-item modified PID5BF+ scoring key is provided in online supplementary Appendix A see www.karger.com/doi/10.1159/000507589 (for all online suppl. material).

Dysfunctional personality features, non-scientifically supported causal beliefs, and emotional problems during the first month of the COVID-19 pandemic in Italy.

The present study aimed at assessing the impact of demographic characteristics, maladaptive personality traits and causal beliefs about COVID-19 on perceived emotional problems in a sample of Italian community-dwelling adults (N = 1043) in the first month of the social distancing period due to the COVID-19 pandemic in Italy. Hierarchical logistic regression analysis results showed that dysfunctional personality domains and non-scientifically supported causal beliefs explained all the variance that was originally explained by demographic variables (i.e., age and gender). In particular, negative affectivity and detachment represented relevant risk factors for reduced emotional well-being in our sample. A significant positive association was observed also between emotional problems and supernatural causal beliefs on the COVID-19 infection. Our data supported the importance of considering the impact of quarantine measures on psychological well-being, while suggesting possible risk factors related to individual differences in personality and causal beliefs.

Emotional Responsiveness in Borderline Personality Disorder: The Role of Basal Hyperarousal and Self-Reported Emotional Regulation.

The present study aims to test the hypothesis of biological hyperarousal and hyperreactivity underpinning the dysfunctional emotional processes of borderline personality disorder (BPD). Self-reported (quality and intensity of emotions) and physiological (respiratory sinus arrhythmia [RSA] and heart rate) data were collected in 14 clinical subjects with BPD and in 14 control subjects (healthy controls [HCs]), during the administration of six video clips with different emotional contents. Our findings showed a constant hyperarousal state (lower RSA) in the clinical group, supporting the hypothesis of a biological vulnerability to emotional dysregulation. BPD patients showed lower self-reported happiness in positive stimuli compared with HCs and a significant association between emotional dysregulation and physiological hyperreactivity to neutral stimuli. Our data support the hypothesis of a constant condition of physiological preparedness to threat and danger in BPD subjects. Moreover, our results highlight the influence of self-reported ability in regulating emotions in explaining BPD responses to specific emotional situations.

Interview-based ratings of DSM-IV Axis II/DSM-5 Section II Personality Disorder symptoms in consecutively admitted insomnia patients: A comparison study with consecutively admitted psychotherapy patients matched on age and gender.

BACKGROUND: Selected personality features may represent important predisposing as well as perpetuating factors for insomnia, and previous studies stressed the importance to assess personality disorders in insomnia patients. METHODS: In order to evaluate the relationships between DSM-IV Axis II/DSM-5 Section II Personality Disorders (PDs) and insomnia, a sample of 171 consecutively admitted insomnia patients and a sample of 171 psychotherapy patients, matched on age and gender were administered the Italian translation of the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, Version 2.0 (SCID-II). Among insomnia patients, 52.0% (n = 89) received at least one DSM-IV Axis II/DSM-5 Section II PD diagnosis according to SCID-II assessment. RESULTS: Any PD base rate estimate in our insomnia patient sample was significantly and markedly higher than the median and mean base rate estimates for any PD in the general population. Within-group analyses showed that Narcissistic, Not otherwise specified PD, Histrionic PD, and Borderline PD represented the most frequently diagnosed-both dimensionally and categorically-DSM-IV Axis II/DSM-5 Section II PD features in our insomnia patient sample. When continuously-scored PDs were considered, insomnia patients showed a significantly lower number of Paranoid and Borderline PD features than psychotherapy patients; however, the corresponding effect size estimates suggested that these differences were modest. None of the categorically-scored PDs significantly differentiated insomnia patients from psychotherapy patients. CONCLUSIONS: As a whole, our findings seemed to suggest that personality dysfunction may play a role in insomnia, while stressing the need for a dimensional approach to the assessment of maladaptive personality traits even in insomnia patients.

Improving Family Functioning to (Hopefully) Improve Treatment Efficacy of Borderline Personality Disorder: An Opportunity Not to Dismiss.

People having intimate relationships with persons suffering from borderline personality disorder (BPD) - for instance, members of their family - are likely to be involved in stormy, roller coaster relationships. Thus, they may feel overwhelmed by extreme, unpredictable feelings and situations, even when they do not suffer from any mental disorder or have no problems with mentalization. As a consequence of living with a BPD relative, family members often experience an emotional and financial burden, and may blame themselves for their relative's illness or for not being able to do more to help. This can lead to emotional pain including anxiety, guilt, anger, frustration, despair, and hopelessness. Available evidence suggests a possible usefulness of family interventions for relatives of BPD persons. Starting from these background considerations, a qualitative review of the published literature on family interventions for relatives of BPD persons was carried out. The main findings concerning specific contents and available effectiveness data of psychoeducational family interventions, family skills training, and mentalization-based family programs are reported, in the perspective of 3 family intervention scenarios: (a) taking care of the family of origin of the BPD person; (b) taking care of the new family that the BPD person has started; (c) helping the BPD person to be an effective parent.

Dialectical Behavior Therapy Skills Training in Alcohol Dependence Treatment: Findings Based on an Open Trial.

BACKGROUND: Dialectical behavior therapy (DBT) has demonstrated efficacy in treating disorders such as alcohol dependence that are characterized by emotional dysregulation. Preliminary evidence has revealed the feasibility of DBT skills training (ST) as a stand-alone treatment for such disorders. Although emotional dysregulation plays a significant role in alcohol dependence, there are no previous reports of using DBT-ST to treat it. OBJECTIVES: The aim of this study was to evaluate the duration of abstinence and changes in emotional regulation in a 3-month DBT-ST program for alcohol-dependent patients and to look for relations between abstinence and emotional regulation. METHODS: We administered the Difficulties in Emotion Regulation Scale (DERS) and used urine toxicology screening to monitor alcohol/substance intake among the 244 subjects admitted to the program. RESULTS: Among the 157 patients who completed the treatment, 73.2% were abstinent at the end of the program, and their emotional regulation improved. Improvement was independent of the initial severity of both alcohol use and emotional dysregulation. For substance use outcomes, we found a partial mediation role of improved emotional regulation. CONCLUSIONS: This is the first open trial to show improved alcohol-related behavior and emotional regulation in alcohol-dependent patients treated with DBT-ST and to posit a partial but significant relation between improved emotional regulation and alcohol use outcomes. In the treatment of alcohol dependence, emotional regulation may be a relevant factor for therapists to consider.

Assessing Dimensions of Pathological Narcissism: Psychometric Properties of the Short Form of the Five-Factor Narcissism Inventory in a Sample of Italian University Students.

To evaluate the psychometric properties of the Italian translation of the Five-Factor Narcissism Inventory-Short Form (FFNI-SF), 1,063 Italian university students were administered the scale, along with the Pathological Narcissism Inventory (PNI) and the Measure of Disordered Personality Functioning (MDPF). In general, the FFNI-SF scales showed good internal consistency (median α = .76; median interitem r = .44) and structural analyses suggested a 3-component model of FFNI-SF scales that was similar to that reported by Sherman et al. (2015). FFNI-SF second-order scales yielded meaningful convergent and discriminant correlations with PNI second-order grandiose and vulnerable dimensions. Finally, FFNI-SF second-order scales correlated in expected ways with 2 dimensions of personality dysfunction.

Systems Training for Emotional Predictability and Problem Solving Program and Emotion Dysregulation: A Pilot Study.

The aim of this study was to assess the observed changes on emotion dysregulation obtained through the Systems Training for Emotional Predictability and Problem Solving (STEPPS) program. The sample is composed of 24 subjects with a personality disorder with borderline features. All participants filled out the Difficulties in Emotion Regulation Scale (DERS). There was a significant decrease in the DERS total score at the end of the treatment and at 6-month follow-up. Friedman test showed a significant decrease in suicide attempts and hospitalizations over time. The analysis of the DERS subscales showed that "goals" and "impulse" were the two dimensions on which the treatment acted and the changes were stable over time. STEPPS is associated with an improvement in emotion regulation and a reduction in the number of hospitalizations and suicide attempts. The treatment seems to act on the behavioral dimensions of emotion dysregulation like the ability to control impulsive behaviors and to achieve goals.

On the relationships between DSM-5 dysfunctional personality traits and social cognition deficits: A study in a sample of consecutively admitted Italian psychotherapy patients.

This study aims at testing the hypothesis that the Diagnostic and Statistical Manual of Mental Disorders fifth edition (DSM-5) alternative model of personality disorder (AMPD) traits may be significantly associated with deficits on 2 different social cognition tasks, namely, the Reading the Mind in the Eyes Test and the Movie for the Assessment of Social Cognition, in a sample of consecutively admitted inpatients and outpatients. The sample was composed of 181 consecutively admitted participants (57.5% women; mean age = 38.58 years). Correlation coefficients and partial correlation coefficients were computed in order to assess the associations among social cognition tasks, DSM-5 AMPD traits, and dimensionally assessed DSM-5 Section II personality disorders. Specific maladaptive traits listed in the DSM-5 AMPD were significantly associated with Reading the Mind in the Eyes Test scores and Movie for the Assessment of Social Cognition scores, even when the effect of selected DSM-5 Section II personality disorders was controlled for. Our results support the relevance of studying social cognitive functioning in subjects suffering from personality disorders.