Removal of Stomatin, a Membrane-Associated Cell Division Protein, Results in Specific Cellular Lipid Changes

Lipids are key constituents of all cells, which express thousands of different lipid species. In most cases, it is not known why cells synthesize such diverse lipidomes, nor what regulates their metabolism. Although it is known that dividing cells specifically regulate their lipid content and that the correct lipid complement is required for successful division, it is unclear how lipids connect with the cell division machinery. Here, we report that the membrane protein stomatin is involved in the cytokinesis step of cell division. Although it is not a lipid biosynthetic enzyme, depletion of stomatin causes cells to change their lipidomes. These changes include specific lipid species, like ether lipids, and lipid families like phosphatidylcholines. Addition of exogenous phosphatidylcholines rescues stomatin-induced defects. These data suggest that stomatin interfaces with lipid metabolism. Stomatin has multiple contacts with the plasma membrane and we identify which sites are required for its role in cell division, as well as associated lipid shifts. We also show that stomatin’s mobility on the plasma membrane changes during division, further supporting the requirement for a highly regulated physical interaction between membrane lipids and this newly identified cell division protein.

Correlation between cycle threshold and viral load through comparison of RT-PCR qualitative <em>versus</em> quantitative assay for SARS-CoV-2

Background and aims. Real-time reverse transcription polymerase chain reaction (RT-PCR) is the gold-standard assay to detect SARS-CoV-2, but it has limitations compared to viral load analysis. Quantitative detection improves surveillance, diagnosis, and prevention. We performed a comparative study of qualitative and quantitative tests for the diagnosis of COVID-19 on respiratory samples from patients screened for SARS-CoV-2 infection, and explored the correlation between viral load compared to the threshold cycle (Ct) value obtained in RT-PCR.Materials and methods. Sixty respiratory samples from patients affected by SARS-CoV-2 were subjected to both the qualitative (Allplex ™ 2019-nCoV Seegene) and the quantitative (Clonit® Quanty COVID-19) assays, and the relationship between viral load and Ct value was assessed by Spearman correlation analysis (ρ). In addition, the viral load of samples collected from a patient with symptomatic cancer was monitored. Results. The results show 100% agreement between the results obtained with quantitative assay and the reference standards, whereas 99.2% agreement was found for the qualitative test. A strong negative Spearman’s correlation between the Ct values of the N genes and RdRP gene was observed from qualitative assay values and viral loads.Conclusions. Quantitative assay has a higher sensitivity than qualitative assay, and viral load testing allows the clinicians to better orient themself in the choice of therapeutic treatment to be adopted. The constantly higher viral load of clinical cases considered, irrespective of the different therapies used, confirms that viral load monitoring could represent a great advantage in clinical practice.

HiPPO and PANDA: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data

High-dimensional mass cytometry (Cytometry by Time-Of-Flight; CyTOF) is a multiparametric single-cell approach that allows for more than 40 parameters to be evaluated simultaneously, opening the possibility to dissect cellular heterogeneity and elucidate functional interactions between different cell types. However, the complexity of these data makes analysis and interpretation daunting. We created High-throughput Population Profiler (HiPPO), a tool that reduces the complexity of the CyTOF data and allows homogeneous clusters of cells to be visualized in an intuitive manner. Each subpopulation is mapped to the Population Analysis Database (PANDA), an open-source, manually curated database containing protein expression profiles for selected markers of primary cells, allowing for cell type abundance in the analyzed samples to be monitored. Custom cell definitions can be submitted for targeted identifications. All cell clusters, regardless of their annotation status, are available for further analyses. HiPPO also conducts nonparametric tests to determine whether differences in protein expression levels between conditions are significant. HiPPO strikes a balance between diagnostic power and computational burden. Its minimal computational footprint allows for subpopulations in a heterogeneous sample to be identified and quantified quickly.

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

Muscle regeneration is a complex process governed by the interplay between several muscle-resident mononuclear cell populations. Following acute or chronic damage these cell populations are activated, communicate via cell-cell interactions and/or paracrine signals, influencing fate decisions via the activation or repression of internal signaling cascades. These are highly dynamic processes, occurring with distinct temporal and spatial kinetics. The main challenge toward a system level description of the muscle regeneration process is the integration of this plethora of inter- and intra-cellular interactions. We integrated the information on muscle regeneration in a web portal. The scientific content annotated in this portal is organized into two information layers representing relationships between different cell types and intracellular signaling-interactions, respectively. The annotation of the pathways governing the response of each cell type to a variety of stimuli/perturbations occurring during muscle regeneration takes advantage of the information stored in the SIGNOR database. Additional curation efforts have been carried out to increase the coverage of molecular interactions underlying muscle regeneration and to annotate cell-cell interactions. To facilitate the access to information on cell and molecular interactions in the context of muscle regeneration, we have developed Myo-REG, a web portal that captures and integrates published information on skeletal muscle regeneration. The muscle-centered resource we provide is one of a kind in the myology field. A friendly interface allows users to explore, approximately 100 cell interactions or to analyze intracellular pathways related to muscle regeneration. Finally, we discuss how data can be extracted from this portal to support in silico modeling experiments.

CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1

Ubiquitin binding domains (UBDs) are modular elements that bind non-covalently to ubiquitin and act as downstream effectors and amplifiers of the ubiquitination signal. With few exceptions, UBDs recognize the hydrophobic path centered on Ile44, including residues Leu8, Ile44, His68, and Val70. A variety of different orientations, which can be attributed to specific contacts between each UBD and surface residues surrounding the hydrophobic patch, specify how each class of UBD specifically contacts ubiquitin. Here, we describe the structural model of a novel ubiquitin-binding domain that we identified in NEDD4 binding protein 1 (N4BP1). By performing protein sequence analysis, mutagenesis, and nuclear magnetic resonance (NMR) spectroscopy of the ¹⁵N isotopically labeled protein, we demonstrate that a Phe-Pro motif in N4BP1 recognizes the canonical hydrophobic patch of ubiquitin. This recognition mode resembles the molecular mechanism evolved in the coupling of ubiquitin conjugation to endoplasmic-reticulum (ER) degradation (CUE) domain family, where an invariant proline, usually following a phenylalanine, is required for ubiquitin binding. Interestingly, this novel UBD, which is not evolutionary related to CUE domains, shares a 40% identity and 47% similarity with cullin binding domain associating with NEDD8 (CUBAN), a protein module that also recognizes the ubiquitin-like NEDD8. Based on these features, we dubbed the region spanning the C-terminal 50 residues of N4BP1 the CoCUN domain, for Cousin of CUBAN. By performing circular dichroism and ¹⁵N NMR chemical shift perturbation of N4BP1 in complex with ubiquitin, we demonstrate that the CoCUN domain lacks the NEDD8 binding properties observed in CUBAN. We also show that, in addition to mediating the interaction with ubiquitin and ubiquitinated substrates, both CUBAN and CoCUN are poly-ubiquitinated in cells. The structural and the functional characterization of this novel UBD can contribute to a deeper understanding of the molecular mechanisms governing N4BP1 function, providing at the same time a valuable tool for clarifying how the discrimination between ubiquitin and the highly related NEDD8 is achieved.

Effects of chronic antipsychotic treatment on neurophysiological correlates of the auditory oddball task in schizophrenia: A preliminary report from a multicentre study

Introduction

The effects of chronic antipsychotic administration on the human brain are debated. In particular, first-generation (FGAs) and second-generation antipsychotics (SGAs) seem to have different impacts on brain function and structure in subjects with schizophrenia. Few studies have investigated the effect of chronic administration of FGAs and SGAs on indices of brain function, such as event-related potentials (ERP) or neuropsychological performance.

Objectives

Within the Italian Network for Research on Psychoses study, subjects stabilized on FGAs or SGAs were compared on P300, an ERP component, thought to reflect attention, working memory and context integration and on neurocognitive indices.

Methods

ERPs were recorded in 110 chronic, stabilized patients with Schizophrenia (28 used FGAs) during a standard auditory oddball task. P300 latency and amplitude were assessed at Pz channel. MATRICS Consensus Cognitive Battery (MCCB) was used for cognitive assessment.

Results

Compared with the SGAs group, patients on FGAs showed significant increased P300 latency (P = 0.003; Cohen's d = 0.67) and significant decreased P300 amplitudes (P = 0.023; Cohen's d = 0.38). The two groups did not differ on psychopathology and MCCB scores. Multiple linear regressions revealed that “FGAs vs. SGAs” (β = 0.298, P = 0.002) and MCCB neurocognitive composite T-score (β = –0.273, P = 0.004) were independent predictors of P300 latency, whereas only age (β = –0.220, P = 0.027) was an independent predictor of P300 amplitude.

Conclusions

FGAs seem to affect the functional brain activity more than SGAs, particularly slowing cortical processing. Our results suggest that discrepant findings concerning P300 latency in schizophrenia might be related to the type of antipsychotic treatment used. Longitudinal studies are needed to further address this issue.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Relation between EEG source functional connectivity and the negative symptom severity in schizophrenia: a preliminary report from a multicentre study

Introduction

Neural dysconnectivity is hypothesized to be a key element in pathophysiology of schizophrenia. However, the relation of disordered connectivity with the different clinical characteristics of the syndrome is not fully elucidated.

Objectives

The current research investigated the relations between resting-state EEG Source Functional Connectivity (EEG-SFC) and the two main clusters of negative symptoms derived from the Brief Negative Symptom Scale, the Expressive Deficit (ED) and the Avolition (AV), in subjects with schizophrenia (SCZ) enrolled to the multicentre study of the Italian Network for Research on Psychoses.

Methods

Out of 97 chronic, stabilized SCZ included, we selected subjects according the lower and the upper quartile of the ED and AV value distribution: 25 were in upper and 24 in the lower quartile of ED (respectively, HIGH-ED and LOW-ED); 27 were in upper and 24 in the lower quartile of AV (respectively, HIGH-AV and LOW-AV). Fifty-five healthy controls (HC) were included, comparable to SCZ for gender, age and educational level. EEG-SFC analysis was based on the lagged phase synchronization (LPS) computed by eLORETA from 5 minutes resting-state EEG recordings in eyes closed condition. LPS indices were determined for each spectrum band and between all 28 regions of interest (ROI) pairs. Group differences were significant for corrected P-value < 0.05.

Results

SCZ had higher theta band LPS than HC. Respect to LOW-ED, HIGH-ED showed significant increased alpha LPS in fronto-cingulate, para-hippocampal and insular inter-hemispheric ROI pairs. No significant difference emerged between HIGH-AV and LOW-AV.

Conclusions

Subgrouping SCZ according to negative symptom severity reveals heterogeneous patterns of resting-state LPS connectivity.

Disclosure of interest

The authors have not supplied their declaration of competing interest.