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.

Maximizing Analytical Performance in Biomolecular Discovery with LC-MS: Focus on Psychiatric Disorders.

In this review, we discuss the cutting-edge developments in mass spectrometry proteomics and metabolomics that have brought improvements for the identification of new disease-based biomarkers. A special focus is placed on psychiatric disorders, for example, schizophrenia, because they are considered to be not a single disease entity but rather a spectrum of disorders with many overlapping symptoms. This review includes descriptions of various types of commonly used mass spectrometry platforms for biomarker research, as well as complementary techniques to maximize data coverage, reduce sample heterogeneity, and work around potentially confounding factors. Finally, we summarize the different statistical methods that can be used for improving data quality to aid in reliability and interpretation of proteomics findings, as well as to enhance their translatability into clinical use and generalizability to new data sets. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 17 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms.

Long-term sequelae of coronavirus disease (COVID)-19 are frequent and of major concern. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the host gut microbiota, which is linked to disease severity in patients with COVID-19. Here, we report that the gut microbiota of post-COVID subjects had a remarkable predominance of Enterobacteriaceae strains with an antibiotic-resistant phenotype compared to healthy controls. Additionally, short-chain fatty acid (SCFA) levels were reduced in feces. Fecal transplantation from post-COVID subjects to germ-free mice led to lung inflammation and worse outcomes during pulmonary infection by multidrug-resistant Klebsiella pneumoniae. transplanted mice also exhibited poor cognitive performance. Overall, we show prolonged impacts of SARS-CoV-2 infection on the gut microbiota that persist after subjects have cleared the virus. Together, these data demonstrate that the gut microbiota can directly contribute to post-COVID sequelae, suggesting that it may be a potential therapeutic target.

Proteomic signatures of schizophrenia-sourced iPSC-derived neural cells and brain organoids are similar to patients' postmortem brains.

BACKGROUND: Schizophrenia is a complex and severe neuropsychiatric disorder, with a wide range of debilitating symptoms. Several aspects of its multifactorial complexity are still unknown, and some are accepted to be an early developmental deficiency with a more specifically neurodevelopmental origin. Understanding the timepoints of disturbances during neural cell differentiation processes could lead to an insight into the development of the disorder. In this context, human brain organoids and neural cells differentiated from patient-derived induced pluripotent stem cells are of great interest as a model to study the developmental origins of the disease. RESULTS: Here we evaluated the differential expression of proteins of schizophrenia patient-derived neural progenitors (NPCs), early neurons, and brain organoids in comparison to healthy individuals. Using bottom-up shotgun proteomics with a label-free approach for quantitative analysis, we found multiple dysregulated proteins since NPCs, modified, and disrupted the 21DIV neuronal differentiation, and cerebral organoids. Our experimental methods have shown impairments in pathways never before found in patient-derived induced pluripotent stem cells studies, such as spliceosomes and amino acid metabolism; but also, those such as axonal guidance and synaptogenesis, in line with postmortem tissue studies of schizophrenia patients. CONCLUSION: In conclusion, here we provide comprehensive, large-scale, protein-level data of different neural cell models that may uncover early events in brain development, underlying several of the mechanisms within the origins of schizophrenia.

UPLC-HDMSE to discover serum biomarkers in adults with type 1 diabetes.

Type 1 diabetes (T1D) is a complex disease with metabolic and functional changes that can alter an individual's proteome. An LC-MS/MS analytical method, in an HDMSE system, was used to identify differentially expressed proteins in the high abundance protein-depleted serum of T1D patients and healthy controls. Samples were processed in Progenesis QI for Proteomics software. A functional enrichment of the proteins was performed with Gene Ontology and ToppGene, and the interactions were visualized by STRING 11.5. As a result, 139 proteins were identified, 14 of which were downregulated in the serum of patients with T1D compared to controls. Most of the differentially expressed proteins were shown to be involved with the immune system, inflammation, and growth hormone stimulus response, and were associated with the progression of T1D. Differential protein expression data showed for the first-time changes in CPN2 expression levels in the serum of patients with T1D. Our findings indicate that these proteins are targets of interest for future investigations and for validation of protein biomarkers in T1D.

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 During Brain Development.

Several classes of post-translational modifications (PTMs) regulate various processes that occur during neurodevelopment. The first of these processes is the regulation of the cytoskeleton and cytoskeleton-associating proteins, responsible for the stability, reorganization, and binding of microtubules and actin filaments. Dysregulations in these PTMs lead to dysregulated brain volume and composition, structural defects, behavioral defects, and dendrite growth. The second class of processes involves gene regulation, from chromatin modulation to protein turnover and degradation. Proper gene expression during neurodevelopment is critical to ensure correctly matured cells; dysregulation of PTMs in these pathways leads to various altered morphological and behavioral phenotypes. The third class of processes that are affected by PTMs is cell signaling and signal transduction, vital to cell migration and axonal guidance. Neurodevelopment is a complex sequence of spatially and temporally regulated processes, and PTMs play important roles in this regulation. Most of the known modifications have yet to be studied in depth and much remains undiscovered about their roles in neurodevelopment and otherwise.

Histone Modifications in Neurological Disorders.

Post-translational modifications (PTMs) have a strong impact on many proteins across all kingdoms of life, affecting multiple functional and chemical properties of their protein recipients. With increasing knowledge about their functions, targets, and biological effects, dysregulations in PTMs have been implicated in various dysfunctions and diseases. One such target are histones, which compose the majority of the protein component of chromatin and the modulation of the 30+ PTMs that are known to affect them can have profound effects on chromatin state, gene expression, and DNA repair. In this review, the histone targets of PTMs are compiled in the context of neurological disorders, highlighting their specific biological roles and any previously implicated dysregulations in several classes of brain disease. Better understanding the pathogenic dysregulations of PTMs in such disorders can help to better understand their causes, as well as open doors to new possibilities for biomarkers and therapeutic targets.

PTMs: A Missing Piece for Schizophrenia Studies.

One of the closest regulatory mechanisms to a cellular phenotype is post-translational modifications (PTMs), a diverse class of changes that proteins can undergo to change various physical and functional properties. PTMs hold great potential to better understand multifactorial diseases and disorders like schizophrenia. The field of PTMomics is still expanding and developing, though several modifications have already been implicated in the etiology and treatment of schizophrenia. Nonetheless, much has yet to be uncovered due to the vast number of modifications that occur on proteins. Here, some of the most well-supported arguments for PTM dysregulation in schizophrenia are raised, leaving the door open for multiple other modifications and their potential.

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.

Postmortem Brains: What Can Proteomics Tell us About the Sources of Schizophrenia?

Modeling schizophrenia is challenging due to the uniquely human component of psychiatric disorders. Despite several advances in cellular and animal modeling, postmortem brain tissue derived from patients is still one of the extremely few sources of information that comprises brain complexity, human genetics, and patient experiences. Additionally, postmortem tissue from patients with schizophrenia can be used to drive hypotheses that can then be validated in other models, involving either other animals or an in vitro approach. While evaluating high-throughput and sensitive techniques, shotgun proteomics allows for the identification and quantitation of thousands of proteins present in biological systems. In the context of schizophrenia, proteomics can map differentially regulated proteins throughout brain regions of patients with schizophrenia, generating a large amount of information regarding the disorder's pathophysiology. In this chapter, our aim is to bring the literature up to date regarding proteomics tools applied to postmortem brains from patients with schizophrenia, additionally discussing new findings, roads, and perspectives for the comprehension of this severe disorder.

Modeling Schizophrenia In Vitro: Challenges and Insights on Studying Brain Cells.

One of the challenges in studying neuropsychiatric disorders is the difficulty in accessing brain tissue from living patients. Schizophrenia is a chronic mental illness that affects 1% of the population worldwide, and its development stems from genetic and environmental factors. In order to better understand the pathophysiology underlying schizophrenia, the development of efficient in vitro methods to model this disorder has been required. In addition to several in vitro models, induced pluripotent stem cells (iPSCs) arose as a powerful tool, enabling access to the genetic background of the donor. Moreover, genetic modification of these cells can improve studies of specific dysfunctions observed in the pathophysiology of several neuropsychiatric disorders, not only schizophrenia. Here, we summarize which in vitro models are currently available and their applications in schizophrenia research, describing their advantages and limitations. These technologies in the cell culture field hold great potential to contribute to a better understanding of the pathophysiology of schizophrenia in an integrated manner, in addition to testing potential therapeutic interventions based on the genetic background of the patient.

Known and Unexplored Post-Translational Modification Pathways in Schizophrenia.

Post-translational modifications (PTMs) of proteins occur in all domains of life, affecting various structural and functional properties. Multiple methods can be used to study PTMs depending on the biological question, which can vary widely. Schizophrenia is a widespread brain disorder that possesses many known contributing environmental factors and hundreds of genetic risk factors; however, a full picture of the mechanisms behind how and why this disorder occurs and how it can be treated remains unknown. Various PTMs have been found to be differentially expressed in several pathways that are dysregulated in schizophrenia, as seen in cell line and animal models, postmortem brain tissue from people with schizophrenia, and biological fluids like blood, plasma, and cerebrospinal fluid. Despite recent advances, several pathways have been completely left undisturbed by PTMomics and show great promise for better understanding of protein dynamics in schizophrenia, how the disease state occurs, and how it may be better treated in future therapies.

Proteomics and Schizophrenia: The Evolution of a Great Partnership.

The mass spectrometer is an instrument that observes particular masses of molecules of interest. Over the past century, it has grown to become a highly sensitive and robust tool in laboratorial and clinical research to identify and quantify thousands of proteins in a given sample in an unbiased manner leading to the quick rise in its use. This unbiased and high-throughput nature is extremely important in discovery-based studies, since no preset targets can be selected, as is the case with several other proteomic methods. In studying multifactorial diseases such as schizophrenia, mass-spectrometry-based proteomics has been frequently used and new improvements to the technique have been quickly taken advantage of. Over the past 15 years, mass spectrometry has evolved greatly, and with it, the proteomic analyses and data have evolved. In this chapter, a brief history of the evolution of mass spectrometry is covered along with how schizophrenia research has grown alongside this valuable methodology.

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.

Cannabinoids modulate proliferation, differentiation, and migration signaling pathways in oligodendrocytes.

Cannabinoid signaling, mainly via CB1 and CB2 receptors, plays an essential role in oligodendrocyte health and functions. However, the specific molecular signals associated with the activation or blockade of CB1 and CB2 receptors in this glial cell have yet to be elucidated. Mass spectrometry-based shotgun proteomics and in silico biology tools were used to determine which signaling pathways and molecular mechanisms are triggered in a human oligodendrocytic cell line (MO3.13) by several pharmacological stimuli: the phytocannabinoid cannabidiol (CBD); CB1 and CB2 agonists ACEA, HU308, and WIN55, 212-2; CB1 and CB2 antagonists AM251 and AM630; and endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG). The modulation of cannabinoid signaling in MO3.13 was found to affect pathways linked to cell proliferation, migration, and differentiation of oligodendrocyte progenitor cells. Additionally, we found that carbohydrate and lipid metabolism, as well as mitochondrial function, were modulated by these compounds. Comparing the proteome changes and upstream regulators among treatments, the highest overlap was between the CB1 and CB2 antagonists, followed by overlaps between AEA and 2-AG. Our study opens new windows of opportunities, suggesting that cannabinoid signaling in oligodendrocytes might be relevant in the context of demyelinating and neurodegenerative diseases. Proteomics data are available at ProteomeXchange (PXD031923).

Biological Applications for LC-MS-Based Proteomics.

Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.

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.

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.

Popliteal Cysts: A Systematic Review of Nonoperative and Operative Treatment.

BACKGROUND: Treatment methods for popliteal cysts have varied over the past several decades and have posed challenges to providers as recurrences were frequent. With greater understanding of relevant anatomy, both operative and nonoperative treatment methods have evolved to appropriately target relevant pathology and improve outcomes. The purposes of this review were to outline the evolution of treatment methods and to qualitatively summarize clinical outcomes. METHODS: We performed a systematic review on treatments for popliteal cysts to include publications from 1970 to 2019. Other inclusion criteria consisted of studies with ≥10 patients enrolled, studies with a patient age of ≥16 years, studies with an adequate description of the treatment technique, and studies with a Level of Evidence of IV or higher. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and literature quality was assessed using a modified Coleman methodology score. RESULTS: Thirty studies met inclusion criteria in this review. Nine studies discussed nonoperative treatment, and 21 studies discussed operative treatment. Eight of the 9 nonoperative treatment studies utilized corticosteroid injections. The most recent studies have advocated for ultrasound-guided intracystic injection with possible cyst fenestration. Most operative studies utilized an arthroscopic approach to enlarge the communication with the joint space. However, alternative treatment techniques are still utilized. CONCLUSIONS: The current literature on the treatment of popliteal cysts indicates that intracystic corticosteroid injection with cyst fenestration is an effective nonoperative treatment method. Arthroscopic surgical procedures with enlargement of the communication have been most widely studied, with positive results; however, further studies are needed to confirm superiority over other treatment methods. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.