High-Throughput Nanoflow Proteomics Using a Dual-Column Electrospray Source.

With current trends in proteomics, especially regarding clinical and low input (to single cell) samples, it is increasingly important to both maximize the throughput of the analysis and maintain as much sensitivity as possible. The new generation of mass spectrometers (MS) are taking a huge leap in sensitivity, allowing analysis of samples with shorter liquid chromatography (LC) methods while digging as deep in the proteome. However, the throughput can be doubled by implementing a dual column nano-LC-MS configuration. For this purpose, we used a dual-column setup with a two-outlet electrospray source and compared it to a classic dual-column setup with a single-outlet source.

Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows.

Data-independent acquisition (DIA) has become a well-established method for MS-based proteomics. However, the list of options to analyze this type of data is quite extensive, and the use of spectral libraries has become an important factor in DIA data analysis. More specifically the use of in silico predicted libraries is gaining more interest. By working with a differential spike-in of human standard proteins (UPS2) in a constant yeast tryptic digest background, we evaluated the sensitivity, precision, and accuracy of the use of in silico predicted libraries in data DIA data analysis workflows compared to more established workflows. Three commonly used DIA software tools, DIA-NN, EncyclopeDIA, and Spectronaut, were each tested in spectral library mode and spectral library-free mode. In spectral library mode, we used independent spectral library prediction tools PROSIT and MS2PIP together with DeepLC, next to classical data-dependent acquisition (DDA)-based spectral libraries. In total, we benchmarked 12 computational workflows for DIA. Our comparison showed that DIA-NN reached the highest sensitivity while maintaining a good compromise on the reproducibility and accuracy levels in either library-free mode or using in silico predicted libraries pointing to a general benefit in using in silico predicted libraries.

The effect of dosage on the protective efficacy of whole-sporozoite formulations for immunization against malaria.

Immunization with Plasmodium sporozoites, either attenuated or administered under the cover of an antimalarial drug, can induce strong protection against malaria in pre-clinical murine models, as well as in human trials. Previous studies have suggested that whole-sporozoite (WSpz) formulations based on parasites with longer liver stage development induce higher protection, but a comparative analysis of four different WSpz formulations has not been reported. We employed a rodent model of malaria to analyze the effect of immunization dosage on the protective efficacy of WSpz formulations consisting of (i) early liver arresting genetically attenuated parasites (EA-GAP) or (ii) radiation-attenuated sporozoites (RAS), (iii) late arresting GAP (LA-GAP), and (iv) sporozoites administered under chemoprophylaxis, that are eliminated upon release into the bloodstream (CPS). Our results show that, unlike all other WSpz formulations, EA-GAP fails to confer complete protection against an infectious challenge at any immunization dosage employed, suggesting that a minimum threshold of liver development is required to elicit fully effective immune responses. Moreover, while immunization with RAS, LA-GAP and CPS WSpz yields comparable, dosage-dependent protection, protection by EA-GAP WSpz peaks at an intermediate dosage and markedly decreases thereafter. In-depth immunological analyses suggest that effector CD8+ T cells elicited by EA-GAP WSpz immunization have limited developmental plasticity, with a potential negative impact on the functional versatility of memory cells and, thus, on protective immunity. Our findings point towards dismissing EA-GAP from prioritization for WSpz malaria vaccination and enhance our understanding of the complexity of the protection elicited by these WSpz vaccine candidates, guiding their future optimization.

Images that speak: A Portuguese Photovoice study on the psychosocial experience of a migrant population from Cape Verde after a first episode of psychosis.

Several migrant populations have been identified worldwide as high-risk groups for psychosis because of their experience of social adversity. Recent evidence suggests that the local contexts in which these populations live should be addressed in their complexity to take into account individual and larger societal environmental aspects. This study aimed to assess the lived experiences of a group of migrant Cape Verdean patients, who had been recently hospitalized for a first episode of psychosis in a mental health service on the outskirts of Lisbon, Portugal. The study used Photovoice, a qualitative participatory research method in which people's experiences are documented through photography. Six individuals were recruited, and five weekly sessions were conducted to collect data that were analyzed thematically. Emergent themes addressed two main categories of well-being and illness. Participant concepts of well-being were rooted in a definition of freedom encompassing cultural expression, conveyed by familiar environments and supporting communities. Cultural differences may be experienced as important obstacles for well-being and can be associated with feelings of oppression and guilt. Participants' accounts focused on positive aspects of life despite illness and on personal concepts of recovery. The study findings contribute to knowledge of the dynamics of migrants' social experience and underscore the importance of socially and culturally informed mental healthcare institutions.

A genetically modified Plasmodium berghei parasite as a surrogate for whole-sporozoite vaccination against P. vivax malaria.

Two malaria parasite species, Plasmodium falciparum (Pf) and P. vivax (Pv) are responsible for most of the disease burden caused by malaria. Vaccine development against this disease has focused mainly on Pf. Whole-sporozoite (WSp) vaccination, targeting pre-erythrocytic (PE) parasite stages, is a promising strategy for immunization against malaria and several PfWSp-based vaccine candidates are currently undergoing clinical evaluation. In contrast, no WSp candidates have been developed for Pv, mainly due to constraints in the production of Pv sporozoites in the laboratory. Recently, we developed a novel approach for WSp vaccination against Pf based on the use of transgenic rodent P. berghei (Pb) sporozoites expressing immunogens of this human-infective parasite. We showed that this platform can be used to deliver PE Pf antigens, eliciting both targeted humoral responses and cross-species cellular immune responses against Pf. Here we explored this WSp platform for the delivery of Pv antigens. As the Pv circumsporozoite protein (CSP) is a leading vaccine candidate antigen, we generated a transgenic Pb parasite, PbviVac, that, in addition to its endogenous PbCSP, expresses PvCSP under the control of a strictly PE promoter. Immunofluorescence microscopy analyses confirmed that both the PbCSP and the PvCSP antigens are expressed in PbviVac sporozoites and liver stages and that PbviVac sporozoite infectivity of hepatic cells is similar to that of its wild-type Pb counterpart. Immunization of mice with PbviVac sporozoites elicits the production of anti-PvCSP antibodies that efficiently recognize and bind to Pv sporozoites. Our results warrant further development and evaluation of PbviVac as a surrogate for WSp vaccination against Pv malaria.

Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division.

Extracellular matrix (ECM) elasticity is perceived by cells via focal adhesion structures, which transduce mechanical cues into chemical signalling to conform cell behavior. Although the contribution of ECM compliance to the control of cell migration or division is extensively studied, little is reported regarding infectious processes. We study this phenomenon with the extraintestinal Escherichia coli pathogen UTI89. We show that UTI89 takes advantage, via its CNF1 toxin, of integrin mechanoactivation to trigger its invasion into cells. We identify the HACE1 E3 ligase-interacting protein Optineurin (OPTN) as a protein regulated by ECM stiffness. Functional analysis establishes a role of OPTN in bacterial invasion and integrin mechanical coupling and for stimulation of HACE1 E3 ligase activity towards the Rac1 GTPase. Consistent with a role of OPTN in cell mechanics, OPTN knockdown cells display defective integrin-mediated traction force buildup, associated with limited cellular invasion by UTI89. Nevertheless, OPTN knockdown cells display strong mechanochemical adhesion signalling, enhanced Rac1 activation and increased cyclin D1 translation, together with enhanced cell proliferation independent of ECM stiffness. Together, our data ascribe a new function to OPTN in mechanobiology.

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes.

Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screen for Listeria peptides presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detect 68 Listeria immunopeptides from 42 different bacterial proteins, including several known antigens. Peptides presented on different cell lines are often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations results in specific CD8+ T-cell responses and induces protection in vaccination challenge experiments in mice. Our results can serve as a starting point for the development of a clinical mRNA vaccine against Listeria and aid to improve attenuated Listeria vaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.

Prevalence of the Most Frequent Neuropsychiatric Diagnoses in Hospitalized SARS-CoV-2 Patients Evaluated by Liaison Psychiatry: Cross-Sectional Study.

INTRODUCTION: The SARS-CoV-2 infection has been associated with the acute onset of mental and behavioural symptoms and psychiatric disorders. The aim of this study was to assess the prevalence of the different neuropsychiatric diagnoses in hospitalized patients with SARS-CoV-2 infection assessed by Liaison Psychiatry. MATERIAL AND METHODS: We performed a cross-sectional study in a hospital near Lisbon, Portugal. We reviewed the electronic health records from all inpatients with a positive SARS-CoV-2 RT-PCR test that were assessed by the Liaison Psychiatry Unit (LPU) between February and December 2020. We reviewed relevant sociodemographic and clinical data, including 15 neuropsychiatric symptoms. The prevalence of psychiatric disorders was our main outcome. We also explored differences between two groups: patients with delirium (delirium group) and patients without delirium (no delirium group). RESULTS: We included 46 cases [Age: median = 67 years; interquartile range (IQR) = 24)], with 60.9% male individuals. Delirium was the most frequent diagnosis in our sample (43.5%), followed by major depressive disorder (21.7%). Patients with delirium were more likely to suffer from COVID-19 symptoms (delirium: 19/20, 95%; no delirium: 14/26, 53.8%; p = 0.02), and to have a longer time interval between a positive SARS-CoV-2 RT-PCR test and an evaluation by the LPU (delirium: median = 16.5 days, IQR = 16; no delirium: median = 8 days, IQR = 16.3; p = 0.045). Agitation (52.2%) and cognitive symptoms (47.8%) were the most reported neuropsychiatric symptoms. CONCLUSION: We found a high prevalence of delirium in our sample. This finding is in line with recent literature concerning hospitalized COVID-19 patients The higher frequency of COVID-19 symptoms found in the delirium group suggests a possible association between symptomatic SARS-CoV-2 infection and delirium onset.

Introdução: A infecção por SARS-CoV-2 tem sido associada ao desenvolvimento agudo de sintomas mentais e comportamentais e perturbações psiquiátricas. O objetivo deste estudo foi determinar a prevalência de diferentes diagnósticos neuropsiquiátricos em doentes hospitalizados com infeção SARS-CoV-2 avaliados pela Psiquiatria de Ligação. Material e Métodos: Realizámos um estudo transversal num hospital da região de Lisboa, em Portugal. Revimos os processos clínicos dos pacientes internados com um resultado RT-PCR positivo para SARS-CoV-2 avaliados pela Unidade de Psiquiatria de Ligação (UPL) entre fevereiro e dezembro de 2020. Incluímos dados sociodemográficos e clínicos, incluindo quinze sintomas neuropsiquiátricos. A incidência de diferentes diagnósticos psiquiátricos foi o nosso outcome primário. Explorámos também diferenças entre dois grupos: doentes com delirium e doentes sem delirium. Resultados: Incluímos 46 casos [Idade: mediana = 67 anos; amplitude interquartil (AIQ) = 24)], a maioria do sexo masculino (60,9%). Delirium foi o diagnóstico mais frequente na nossa amostra (43,5%), seguido de perturbação depressiva major (21,7%). Doentes com delirium tiveram uma prevalência maior de sintomas de COVID-19 (delirium: 19/20, 95%; sem delirium: 14/26, 53,8%; p = 0,02), bem como um intervalo de tempo mais longo entre um teste RT-PCR SARS-CoV-2 positivo e observação pela UPL (delirium: mediana = 16,5, AIQ = 16; sem delirium: mediana = 8, AIQ = 16,3; p = 0,045). Agitação (52,2%) e sintomas cognitivos (47,8%) foram os sintomas neuropsiquiátricos mais relatados. Conclusão: Foi encontrada na nossa amostra uma elevada prevalência de delirium. Este resultado está de acordo com literatura recente relativamente a doentes internados com COVID-19. A maior frequência de sintomas COVID-19 no grupo com delirium sugere uma possível associação entre infecção sintomática por SARS-CoV-2 e o desenvolvimento desta síndrome.

Proteome Profiling of RNF213 Depleted Cells Reveals Nitric Oxide Regulator DDAH1 Antilisterial Activity.

RNF213 is a large, poorly characterized interferon-induced protein. Mutations in RNF213 are associated with predisposition for Moyamoya disease (MMD), a rare cerebrovascular disorder. Recently, RNF213 was found to have broad antimicrobial activity in vitro and in vivo, yet the molecular mechanisms behind this function remain unclear. Using mass spectrometry-based proteomics and validation by real-time PCR we report here that knockdown of RNF213 leads to transcriptional upregulation of MVP and downregulation of CYR61, in line with reported pro- and anti-bacterial activities of these proteins. Knockdown of RNF213 also results in downregulation of DDAH1, which we discover to exert antimicrobial activity against Listeria monocytogenes infection. DDAH1 regulates production of nitric oxide (NO), a molecule with both vascular and antimicrobial effects. We show that NO production is reduced in macrophages from RNF213 KO mice, suggesting that RNF213 controls Listeria infection through regulation of DDAH1 transcription and production of NO. Our findings propose a potential mechanism for the antilisterial activity of RNF213 and highlight NO as a potential link between RNF213-mediated immune responses and the development of MMD.

Loss-of-Function Mutations in TRAF7 and KLF4 Cooperatively Activate RAS-Like GTPase Signaling and Promote Meningioma Development.

Meningiomas are the most common benign brain tumors. Mutations of the E3 ubiquitin ligase TRAF7 occur in 25% of meningiomas and commonly cooccur with mutations in KLF4, yet the functional link between TRAF7 and KLF4 mutations remains unclear. By generating an in vitro meningioma model derived from primary meningeal cells, we elucidated the cooperative interactions that promote meningioma development. By integrating TRAF7-driven ubiquitinome and proteome alterations in meningeal cells and the TRAF7 interactome, we identified TRAF7 as a proteostatic regulator of RAS-related small GTPases. Meningioma-associated TRAF7 mutations disrupted either its catalytic activity or its interaction with RAS GTPases. TRAF7 loss in meningeal cells altered actin dynamics and promoted anchorage-independent growth by inducing CDC42 and RAS signaling. TRAF deficiency-driven activation of the RAS/MAPK pathway promoted KLF4-dependent transcription that led to upregulation of the tumor-suppressive Semaphorin pathway, a negative regulator of small GTPases. KLF4 loss of function disrupted this negative feedback loop and enhanced mutant TRAF7-mediated cell transformation. Overall, this study provides new mechanistic insights into meningioma development, which could lead to novel treatment strategies. SIGNIFICANCE: The intricate molecular cross-talk between the ubiquitin ligase TRAF7 and the transcription factor KLF4 provides a first step toward the identification of new therapies for patients with meningioma.

Identification of the MuRF1 Skeletal Muscle Ubiquitylome Through Quantitative Proteomics.

MuRF1 (TRIM63) is a muscle-specific E3 ubiquitin ligase and component of the ubiquitin proteasome system. MuRF1 is transcriptionally upregulated under conditions that cause muscle loss, in both rodents and humans, and is a recognized marker of muscle atrophy. In this study, we used in vivo electroporation to determine whether MuRF1 overexpression alone can cause muscle atrophy and, in combination with ubiquitin proteomics, identify the endogenous MuRF1 substrates in skeletal muscle. Overexpression of MuRF1 in adult mice increases ubiquitination of myofibrillar and sarcoplasmic proteins, increases expression of genes associated with neuromuscular junction instability, and causes muscle atrophy. A total of 169 ubiquitination sites on 56 proteins were found to be regulated by MuRF1. MuRF1-mediated ubiquitination targeted both thick and thin filament contractile proteins, as well as, glycolytic enzymes, deubiquitinases, p62, and VCP. These data reveal a potential role for MuRF1 in not only the breakdown of the sarcomere but also the regulation of metabolism and other proteolytic pathways in skeletal muscle.

Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users.

Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.

Suicide and suicide attempts in adults: exploring suicide risk 24 months after a psychiatric emergency room visit

Objective: Suicide risk (including attempted and completed suicide) should be measured over short periods of time after contacting health services. The objective of this study was to identify the patterns of attempted and completed suicides within 24-months of a psychiatric emergency department visit, as well as to investigate predictive risk factors, including sociodemographic and clinical variables, previous suicidal behavior, and service utilization. Method: A convenience sample (n=147), recruited at a general hospital's psychiatric emergency room, included patients with suicidal ideation, suicidal plans or previous suicide attempts. These patients were followed for 24 months, focusing on two main outcomes: attempted and completed suicides. Results: After six months there were no completed suicides and 36 suicide attempts, while after 24 months there were seven completed suicides and 69 suicide attempts. A final logistic regression model for suicide attempts at 24 months identified somatic pathology and the number of previous psychiatric hospitalizations as predictive factors, with a good area under the receiver operating characteristic curve. Conclusions: The findings showed distinct patterns of attempted and completed suicides over time, indicating the importance of a systematic multidisciplinary suicide risk evaluation in psychiatric emergency rooms.

Suicide and suicide attempts in adults: exploring suicide risk 24 months after a psychiatric emergency room visit.

OBJECTIVE: Suicide risk (including attempted and completed suicide) should be measured over short periods of time after contacting health services. The objective of this study was to identify the patterns of attempted and completed suicides within 24-months of a psychiatric emergency department visit, as well as to investigate predictive risk factors, including sociodemographic and clinical variables, previous suicidal behavior, and service utilization. METHOD: A convenience sample (n=147), recruited at a general hospital's psychiatric emergency room, included patients with suicidal ideation, suicidal plans or previous suicide attempts. These patients were followed for 24 months, focusing on two main outcomes: attempted and completed suicides. RESULTS: After six months there were no completed suicides and 36 suicide attempts, while after 24 months there were seven completed suicides and 69 suicide attempts. A final logistic regression model for suicide attempts at 24 months identified somatic pathology and the number of previous psychiatric hospitalizations as predictive factors, with a good area under the receiver operating characteristic curve. CONCLUSIONS: The findings showed distinct patterns of attempted and completed suicides over time, indicating the importance of a systematic multidisciplinary suicide risk evaluation in psychiatric emergency rooms.

Wernicke-Korsakoff Syndrome: A Case Series in Liaison Psychiatry.

Wernicke-Korsakoff syndrome (WKS) is a life-threatening and underdiagnosed neuropsychiatric condition caused by thiamine deficiency that comprises Wernicke encephalopathy and Korsakoff syndrome. Although mainly associated with chronic alcoholism, WKS can arise from other circumstances. This report describes a series of cases of WKS that were clinically evaluated by liaison psychiatrists on a nonpsychiatric inpatient unit. The cases illustrate a deficit in the recognition and adequate treatment of WKS, demonstrating its clinical complexity and the need to improve physicians' knowledge.

Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control.

Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 µL of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 µg as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.

Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer.

Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including splicing switches correlating with disease progression. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, treatment with the AR antagonist bicalutamide (Casodex) induced mesenchymal splicing patterns of genes including FLNB and CTNND1. Our data reveals a new mechanism of splicing control in prostate cancer with important implications for disease progression.