Diving into the proteomic atlas of SARS-CoV-2 infected cells.

The COVID-19 pandemic was initiated by the rapid spread of a SARS-CoV-2 strain. Though mainly classified as a respiratory disease, SARS-CoV-2 infects multiple tissues throughout the human body, leading to a wide range of symptoms in patients. To better understand how SARS-CoV-2 affects the proteome from cells with different ontologies, this work generated an infectome atlas of 9 cell models, including cells from brain, blood, digestive system, and adipocyte tissue. Our data shows that SARS-CoV-2 infection mainly trigger dysregulations on proteins related to cellular structure and energy metabolism. Despite these pivotal processes, heterogeneity of infection was also observed, highlighting many proteins and pathways uniquely dysregulated in one cell type or ontological group. These data have been made searchable online via a tool that will permit future submissions of proteomic data ( https://reisdeoliveira.shinyapps.io/Infectome_App/ ) to enrich and expand this knowledgebase.

Myocardial proteome changes in aortic stenosis rats subjected to long-term aerobic exercise.

The effects of exercise training (ET) on the heart of aortic stenosis (AS) rats are controversial and the mechanisms involved in alterations induced by ET have been poorly clarified. In this study, we analyzed the myocardial proteome to identify proteins modulated by moderate-intensity aerobic ET in rats with chronic supravalvular AS. Wistar rats were divided into four groups: sedentary control (C-Sed), exercised control (C-Ex), sedentary aortic stenosis (AS-Sed), and exercised AS (AS-Ex). ET consisted of five treadmill running sessions per week for 16 weeks. Statistical analysis was performed by ANOVA or Kruskal-Wallis and Goodman tests. Results were discussed at a significance level of 5%. At the end of the experiment, AS-Ex rats had higher functional capacity, lower blood lactate concentration, and better cardiac structural and left ventricular (LV) functional parameters than the AS-Sed. Myocardial proteome analysis showed that AS-Sed had higher relative protein abundance related to the glycolytic pathway, oxidative stress, and inflammation, and lower relative protein abundance related to beta-oxidation than C-Sed. AS-Ex had higher abundance of one protein related to mitochondrial biogenesis and lower relative protein abundance associated with oxidative stress and inflammation than AS-Sed. Proteomic data were validated for proteins related to lipid and glycolytic metabolism. Chronic pressure overload changes the abundance of myocardial proteins that are mainly involved in lipid and glycolytic energy metabolism in rats. Moderate-intensity aerobic training attenuates changes in proteins related to oxidative stress and inflammation and increases the COX4I1 protein, related to mitochondrial biogenesis. Protein changes are combined with improved functional capacity, cardiac remodeling, and LV function in AS rats.

SARS-CoV-2 uses CD4 to infect T helper lymphocytes.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 infects mainly lungs and may cause several immune-related complications, such as lymphocytopenia and cytokine storm, which are associated with the severity of the disease and predict mortality. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is still not fully understood. Here, we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS- CoV-2 in T helper cells. This leads to impaired CD4 T cell function and may cause cell death. SARS-CoV-2-infected T helper cells express higher levels of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may contribute to a poor immune response in COVID-19 patients.

Analysis of Plasma Proteins Involved in Inflammation, Immune Response/Complement System, and Blood Coagulation upon Admission of COVID-19 Patients to Hospital May Help to Predict the Prognosis of the Disease.

The development of new approaches allowing for the early assessment of COVID-19 cases that are likely to become critical and the discovery of new therapeutic targets are urgently required. In this prospective cohort study, we performed proteomic and laboratory profiling of plasma from 163 COVID-19 patients admitted to Bauru State Hospital (Brazil) between 4 May 2020 and 4 July 2020. Plasma samples were collected upon admission for routine laboratory analyses and shotgun quantitative label-free proteomics. Based on the course of the disease, the patients were divided into three groups: (a) mild (n = 76) and (b) severe (n = 56) symptoms, whose patients were discharged without or with admission to an intensive care unit (ICU), respectively, and (c) critical (n = 31), a group consisting of patients who died after admission to an ICU. Based on our data, potential therapies for COVID-19 should target proteins involved in inflammation, the immune response and complement system, and blood coagulation. Other proteins that could potentially be employed in therapies against COVID-19 but that so far have not been associated with the disease are CD5L, VDBP, A1BG, C4BPA, PGLYRP2, SERPINC1, and APOH. Targeting these proteins' pathways might constitute potential new therapies or biomarkers of prognosis of the disease.

Plasma proteomic signature of major depressive episode in the elderly.

Depression is a complex and multifactorial disease, affecting about 6.5% of the elderly population in what is referred to as late-life depression (LLD). Despite its public health relevance, there is still limited information about the molecular mechanisms of LLD. We analyzed the blood plasma of 50 older adults, 19 with LLD and 31 controls, through untargeted mass spectrometry, and used systems biology tools to identify biochemical pathways and biological processes dysregulated in the disease. We found 96 differentially expressed proteins between LLD patients and control individuals. Using elastic-net regression, we generated a panel of 75 proteins that comprises a potential model for determining the molecular signature of LLD. We also showed that biological pathways related to vesicle-mediated transport and voltage-dependent calcium channels may be dysregulated in LLD. These data can help to build an understanding of the molecular basis of LLD, offering an integrated view of the biomolecular alterations that occur in this disorder. SIGNIFICANCE: Major depressive disorder in the elderly, called late-life depression (LLD), is a common and disabling disorder, with recent prevalence estimates of 6.5% in the general population. Despite the public health relevance, there is still limited information about the molecular mechanisms of LLD. The findings in this paper shed light on LLD heterogeneous biological mechanisms. We uncovered a potential novel biomolecular signature for LLD and biological pathways related to this condition which can be targets for the development of novel interventions for prevention, early diagnosis, and treatment of LLD.

Post-translational Modifications in Brain Diseases: A Future for Biomarkers.

Several omic fields have been used in the development of biomarker panels, most traditionally involving genetics and proteomics. The post-translational modification of proteins, however, is an important regulatory system of many biological processes, affecting a wide range of biochemical properties of proteins, including their binding, localization, activity, and stability. These modifications are not analyzed if not specifically searched for in proteomic workflows, making them an underrepresented source of important information in the field of biomarker research. Biomarkers can particularly benefit the diagnosis and prognosis of neurological and psychiatric diseases due to the difficulty of accessing tissue and distinguishing between multiple possible conditions. In this article, post-translational modifications in the context of brain disease are compiled, highlighting the potential that this data source holds for improving the field of medicine.

Morphological, cellular, and molecular basis of brain infection in COVID-19 patients.

Although increasing evidence confirms neuropsychiatric manifestations associated mainly with severe COVID-19 infection, long-term neuropsychiatric dysfunction (recently characterized as part of "long COVID-19" syndrome) has been frequently observed after mild infection. We show the spectrum of cerebral impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, ranging from long-term alterations in mildly infected individuals (orbitofrontal cortical atrophy, neurocognitive impairment, excessive fatigue and anxiety symptoms) to severe acute damage confirmed in brain tissue samples extracted from the orbitofrontal region (via endonasal transethmoidal access) from individuals who died of COVID-19. In an independent cohort of 26 individuals who died of COVID-19, we used histopathological signs of brain damage as a guide for possible SARS-CoV-2 brain infection and found that among the 5 individuals who exhibited those signs, all of them had genetic material of the virus in the brain. Brain tissue samples from these five patients also exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Supporting the hypothesis of astrocyte infection, neural stem cell-derived human astrocytes in vitro are susceptible to SARS-CoV-2 infection through a noncanonical mechanism that involves spike-NRP1 interaction. SARS-CoV-2-infected astrocytes manifested changes in energy metabolism and in key proteins and metabolites used to fuel neurons, as well as in the biogenesis of neurotransmitters. Moreover, human astrocyte infection elicits a secretory phenotype that reduces neuronal viability. Our data support the model in which SARS-CoV-2 reaches the brain, infects astrocytes, and consequently, leads to neuronal death or dysfunction. These deregulated processes could contribute to the structural and functional alterations seen in the brains of COVID-19 patients.

SARS-CoV-2 infection impacts carbon metabolism and depends on glutamine for replication in Syrian hamster astrocytes.

COVID-19 causes more than million deaths worldwide. Although much is understood about the immunopathogenesis of the lung disease, a lot remains to be known on the neurological impact of COVID-19. Here, we evaluated immunometabolic changes using astrocytes in vitro and dissected brain areas of SARS-CoV-2 infected Syrian hamsters. We show that SARS-CoV-2 alters proteins of carbon metabolism, glycolysis, and synaptic transmission, many of which are altered in neurological diseases. Real-time respirometry evidenced hyperactivation of glycolysis, further confirmed by metabolomics, with intense consumption of glucose, pyruvate, glutamine, and alpha ketoglutarate. Consistent with glutamine reduction, the blockade of glutaminolysis impaired viral replication and inflammatory response in vitro. SARS-CoV-2 was detected in vivo in hippocampus, cortex, and olfactory bulb of intranasally infected animals. Our data evidence an imbalance in important metabolic molecules and neurotransmitters in infected astrocytes. We suggest this may correlate with the neurological impairment observed during COVID-19, as memory loss, confusion, and cognitive impairment.

Corrigendum: Cannabidiol Displays Proteomic Similarities to Antipsychotics in Cuprizone-Exposed Human Oligodendrocytic Cell Line MO3.13.

[This corrects the article DOI: 10.3389/fnmol.2021.673144.].

Cannabidiol Displays Proteomic Similarities to Antipsychotics in Cuprizone-Exposed Human Oligodendrocytic Cell Line MO3.13.

Cannabidiol, a compound of Cannabis sativa, has been proposed as an alternative treatment of schizophrenia. Preclinical and clinical data have suggested that cannabidiol shares more similarity with atypical antipsychotics than typical, both of which are customarily used to manage schizophrenia symptoms. While oligodendrocytes are known to be relevant targets of antipsychotics, the biochemical knowledge in this regard is still limited. Here we evaluated the molecular pathways modulated by cannabidiol compared to the antipsychotics clozapine (atypical) and haloperidol (typical), additionally evaluating the effects of benztropine, a muscarinic receptor antagonist that displays a protective effect in oligodendrocytes and myelination. For this purpose, we employed nano-chromatography coupled with mass spectrometry to investigate the proteomic response to these drugs both in healthy oligodendrocytic cells and in a cuprizone-based toxicity model, using the human oligodendrocyte precursor cell line MO3.13. Cannabidiol shares similarities of biochemical pathways with clozapine and benztropine, in agreement with other studies that indicated an atypical antipsychotic profile. All drugs tested affected metabolic and gene expression pathways and cannabidiol, benztropine, and clozapine modulated cell proliferation and apoptosis when administered after cuprizone-induced toxicity. These general pathways are associated with cuprizone-induced cytotoxicity in MO3.13 cells, indicating a possible proteomic approach when acting against the toxic effects of cuprizone. In conclusion, although modeling oligodendrocytic cytotoxicity with cuprizone does not represent the entirety of the pathophysiology of oligodendrocyte impairments, these results provide insight into the mechanisms associated with the effects of cannabidiol and antipsychotics against cuprizone toxicity, offering new directions of study for myelin-related processes and deficits.

Human Blood Plasma Investigation Employing 2D UPLC-UDMSE Data-Independent Acquisition Proteomics.

Proteomic tools are especially useful when it comes to investigating complex samples such as human blood plasma, in which protein quantities can span across up to ten orders of magnitude. Ultra definition mass spectrometry, in combination with two-dimensional liquid chromatography, provides better coverage of complex proteomes and allows for better control of collision energy, keeping the fragmentation benefits of high collision energy associated with drift time measurements from ion mobility separation. Here, we present a protocol to assist in the identification of proteins in human blood plasma and other similar samples with a large dynamic range.

Molecular Mechanisms Associated with Antidepressant Treatment on Major Depression.

Major depressive disorder (MDD) is a complex and multifactorial psychiatric disorder that causes serious health, social, and economic concerns worldwide. The main treatment of the symptoms is through antidepressant (AD) drugs. However, not all patients respond properly to these drugs. Omic sciences are widely used to analyze not only biomarkers for the AD response but also their molecular mechanism. In this review, we aimed to focus on omics data to better understand the molecular mechanisms involving AD effects on MDD. We consistently found, from preclinical to clinical data, that glutamatergic transmission, immune/inflammatory processes, energy metabolism, oxidative stress, and lipid metabolism were associated with traditional and potential new ADs. Despite efforts of studies investigating biomarkers of response to ADs, which could contribute to personalized treatment, there is no biomarker panel available for clinical application. From clinical genomic studies, we found that the main findings contribute to the development of pharmacogenomic tests for AD efficacy for each patient. Several studies pointed at DRD2, PXDNL, CACNA1E, and CACNA2D1 genes as potential targets for MDD treatment and the efficacy and rapid-antidepressant effect of ketamine. Finally, more in-depth studies of the molecular targets pointed here are needed to determine the clinical relevance and provide further evidence for precision MDD treatment.

Human disease biomarker panels through systems biology.

As more uses for biomarkers are sought after for an increasing number of disease targets, single-target biomarkers are slowly giving way for biomarker panels. These panels incorporate various sources of biomolecular and clinical data to guarantee a higher robustness and power of separation for a clinical test. Multifactorial diseases such as psychiatric disorders show great potential for clinical use, assisting medical professionals during the analysis of risk and predisposition, disease diagnosis and prognosis, and treatment applicability and efficacy. More specific tests are also being developed to assist in ruling out, distinguishing between, and confirming suspicions of multifactorial diseases, as well as to predict which therapy option may be the best option for a given patient's biochemical profile. As more complex datasets are entering the field, involving multi-omic approaches, systems biology has stepped in to facilitate the discovery and validation steps during biomarker panel generation. Filtering biomolecules and clinical data, pre-validating and cross-validating potential biomarkers, generating final biomarker panels, and testing the robustness and applicability of those panels are all beginning to rely on machine learning and systems biology and research in this area will only benefit from advances in these approaches.

Fadiga cíclica e resistência torcional de instrumentos reciprocantes tratados termicamente tipo Gold / Cyclic fatigue and torsional resistance of Gold-type thermally treated reciprocating instruments

Objetivo: o objetivo do presente estudo foi avaliar a fadiga cíclica e torcional dos instrumentos WA1 e WaveOne Gold. Métodos: vinte instrumentos do sistema WA1 (25/0,07v) e vinte instrumentos do sistema WaveOne Gold (25/0,07v) foram utilizados. A resistência à fadiga cíclica foi testada, medindo o tempo até a fratura em um canal artificial curvo de aço inoxidável com ângulo de 80° e raio de curvatura de 3 mm (n = 10). O torque máximo e ângulo de rotação no momento da falha dos instrumentos (n = 10) foram medidos de acordo com a norma ISO 3630-1. A superfície de fratura de todos os fragmentos foi examinada com um microscópio eletrônico de varredura. Os resultados foram analisados estatisticamente usando o teste t de Student com um nível de significância de 5%. Resultados: não foram observadas diferenças na vida em fadiga cíclica dos instrumentos testados (p > 0,05). A força máxima de torção dos instrumentos WA1 foi menor do que os instrumentos WaveOne Gold (p < 0,05); entretanto, não foram observadas diferenças no ângulo máximo de rotação de ambos os sistemas (p > 0,05). A fotomicrografia eletrônica de varredura da superfície da fratura revelou características similares e típicas de fadiga cíclica e de falha por torção para os dois tipos de instrumentos. Conclusão: dentro dos resultados do presente estudo, pode-se concluir que os instrumentos WaveOne Gold e WA1 tiveram comportamento similar com relação à fadiga cíclica. No entanto, o instrumento WaveOne Gold apresentou maior deflexão angular à fratura por torção, em comparação aos instrumentos WA1 (AU).

Introduction: The aim of the present study was to evaluate the cyclic and torsional fatigue resistance of WA1 and WaveOne Gold instruments. Methods: Twenty instruments of the WA1 system (25/0.07v) and twenty instruments of the WaveOne Gold system (25/0.07v) were used. The cyclic fatigue resistance was tested by measuring the time to fracture in a stainless steel curved artificial canal with an angle of 80° and a radius of curvature of 3 mm (n = 10). The maximum torque and rotation angle at instrument failure (n = 10) were measured according to ISO 3630-1. The fracture surface of all the fragments was examined with a scanning electron microscope. The results were statistically analyzed using the student t-test with a significance level of 5%. Results: There were no differences in cyclic fatigue life of the tested instruments (P> 0.05). The maximum torsional force of the WA1 instruments was lower than the WaveOne Gold instruments (P <0.05); however, no differences were observed in the maximum rotation angle of both systems (P> 0.05). The scanning electron photomicrographs of the fracture surface revealed similar and typical characteristics of cyclic fatigue and torsional failure for the 2 types of instruments. Conclusion: Within the results of the present study, it can be concluded that WaveOne Gold and WA1 instruments had similar behavior regarding cyclic fatigue. However, WaveOne Gold instruments presented greater angular deflection to torsional fracture than WA1 instruments.

Proteomic Markers for Depression.

Major depressive disorder is a multifactorial disease, with molecular mechanisms not fully understood. A breakthrough could be reached with a panel of diagnostic biomarkers, which could be helpful to stratify patients and guide physicians to a better therapeutic choice, reducing the time between diagnostic and remission. This review brings the most recent works in proteomic biomarkers and highlights several potential proteins that could compose a panel of biomarkers to diagnostic and response to medication. These proteins are related to immune, inflammatory, and coagulatory systems and may also be linked to energy metabolism, oxidative stress, cell communication, and oligodendrogenesis.

Identifying Biomarker Candidates in the Blood Plasma or Serum Proteome.

Brain disorders are among the most complex and difficult to understand of human disorders in terms of pathophysiology and etiology. Differently from other human diseases such as cancer, which uses biomarkers in clinical practice, there are no prognostic and diagnostic biomarkers available for psychiatric disorders. Those associated with the likelihood of a successful medication are also not existent, impairing treatment strategies. Proteomics is a suitable tool for identifying such biomarkers to be validated and further implemented in the clinic. Here we present a protocol for the proteome analyses of blood plasma and serum collected in vivo, aiming for the discovery of potential biomarkers and the comprehension of the molecular bases of diseases and treatments.

Evaluation of the macroscopic growth degree of experimental endometriosis in rats.

PURPOSE: To evaluate macroscopically the growth degree of self-transplantation of endometriosis in rats. METHODS: Forty female rats, after a 7-day period for adpating and evaluating of the estrous cycle regularity, underwent tail abdominal midline laparotomy with 3-cm cuts. The average third of the left uterine horn was removed, 4mm x 4mm patches in liquid environment were made, and self-transplanted in the rat mesenterium with a single stitch, and the endometrial surface of the endometriotic implant facing the lumen of the peritoneal cavity. The rats were programmed to die after three weeks. The abdominal cavity displaying was held and self-transplants were identified and classified. RESULTS: The results achieved were: one case for degree 0 (2,5%), three cases for degree 1 (7,5%), eleven cases for degree II (27,5%) and twenty-five cases for degree III (62,5%). CONCLUSION: The experimental endometriosis development, through the self-transplantation technique, showed to be most common in degrees 3 and 2 of development.

Evaluation of the macroscopic growth degree of experimental endometriosis in rats

PURPOSE: To evaluate macroscopically the growth degree of self-transplantation of endometriosis in rats. METHODS: Forty female rats, after a 7-day period for adpating and evaluating of the estrous cycle regularity, underwent tail abdominal midline laparotomy with 3-cm cuts. The average third of the left uterine horn was removed, 4mm x 4mm patches in liquid environment were made, and self-transplanted in the rat mesenterium with a single stitch, and the endometrial surface of the endometriotic implant facing the lumen of the peritoneal cavity. The rats were programmed to die after three weeks. The abdominal cavity displaying was held and self-transplants were identified and classified. RESULTS: The results achieved were: one case for degree 0 (2,5 percent), three cases for degree 1 (7,5 percent), eleven cases for degree II (27,5 percent) and twenty-five cases for degree III (62,5 percent). CONCLUSION: The experimental endometriosis development, through the self-transplantation technique, showed to be most common in degrees 3 and 2 of development.

OBJETIVO: Avaliar macroscopicamente o grau de crescimento de autotransplantes de endometriose em ratos. MÉTODOS: Quarenta ratos fêmeas, após período de sete dias para adaptação e avaliação da regularidade do ciclo estral, foram submetidas à laparotomia mediana abdominal caudal com incisões de três cm. Foi retirado o terço médio do corno uterino esquerdo, feito retalhos de quatro mm x quatro mm em meio líquido, sendo em seguida autotransplantado no mesentério da rata com ponto simples, tomando o cuidado de manter a superfície mucosa voltada para luz abdominal. Após o período de três semanas as mortes das ratas foram programadas. Realizou-se a exposição da cavidade abdominal com identificação e classificação dos autotransplantes. RESULTADOS: os resultados encontrados foram: grau 0 obteve um caso (2,5 por cento), o grau I foi observado em três casos (7,5 por cento), o grau II com onze casos (27,5 por cento) e o grau III foi visto em vinte cinco casos (62,5 por cento). CONCLUSÃO:Desenvolve-se a endometriose experimental pela técnica do autotransplante com a maioria dos casos em grau 3 e 2 de desenvolvimento.