Proteomics as a tool for understanding schizophrenia

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.

An overview of the human brain myelin proteome and differences associated with schizophrenia

OBJECTIVES

Disturbances in the myelin sheath drive disruptions in neural transmission and brain connectivity as seen in schizophrenia. Here, the myelin proteome was characterised in schizophrenia patients and healthy controls to visualise differences in proteomic profiles.

METHODS

A liquid chromatography tandem mass spectrometry-based shotgun proteomic analysis was performed of a myelin-enriched fraction of postmortem brain samples from schizophrenia patients (n = 12) and mentally healthy controls (n = 8). In silico pathway analyses were performed on the resulting data.

RESULTS

The present characterisation of the human myelinome led to the identification of 480 non-redundant proteins, of which 102 proteins are newly annotated to be associated with the myelinome. Levels of 172 of these proteins were altered between schizophrenia patients and controls. These proteins were mainly associated with glial cell differentiation, metabolism/energy, synaptic vesicle function and neurodegeneration. The hub proteins with the highest degree of connectivity in the network included multiple kinases and synaptic vesicle transport proteins.

CONCLUSIONS

Together these findings suggest disruptive effects on synaptic activity and therefore neural transmission and connectivity, consistent with the dysconnectivity hypothesis of schizophrenia. Further studies on these proteins may lead to the identification of potential drug targets related to the synaptic dysconnectivity in schizophrenia and other psychiatric and neurodegenerative disorders.

Enhanced mitochondrial autophagy (mitophagy) in oligodendrocytes might play a role in white matter pathology in schizophrenia

Disrupted white matter integrity is a typical feature of brain pathologic alterations in schizophrenia, which includes impaired myelination, decreased oligodendrocyte densities, distortion of their spatial distribution and deviations from normal oligodendrocyte cell morphology. While most genes expressed "in the remaining" oligodendrocytes are downregulated in schizophrenia, only a few are upregulated. To the latter group belong prohibitin 2 and DISC 1, which were recently identified as mitochondria-located mitophagy receptors. Their overexpression, together with greatly reduced numbers and densities of oligodendroglial mitochondria and the structurally "normal appearance of the remaining mitochondria" in these cells as reported by Uranova's group (Uranova et al., 2001, 2004, 2018), point to enhanced mitophagy in oligodendrocytes in schizophrenia, which is possibly even cell protective by preventing apoptosis. Since massive loss of white matter oligodendrocytes is a characteristic feature of schizophrenia, we assume that increased mitophagy is a late event in the development and/or further progression of white matter pathologic changes. Moreover, altered oligodendroglial mitophagy might in part result from antipsychotic treatment. Further studies are clearly needed to substantiate our hypothesis on enhanced mitochondrial autophagy in schizophrenia, whereby the "drug-naïve state" and the possible influence of antipsychotic treatment could be elegantly simulated using animal models of the disease.

Myelin: Methods for Purification and Proteome Analysis

Molecular characterization of myelin is a prerequisite for understanding the normal structure of the axon/myelin-unit in the healthy nervous system and abnormalities in myelin-related disorders. However, reliable molecular profiles necessitate very pure myelin membranes, in particular when considering the power of highly sensitive "omics"-data acquisition methods. Here, we recapitulate the history and recent applications of myelin purification. We then provide our laboratory protocols for the biochemical isolation of a highly pure myelin-enriched fraction from mouse brains and for its proteomic analysis. We also supply methodological modifications when investigating posttranslational modifications, RNA, or myelin from peripheral nerves. Notably, technical advancements in solubilizing myelin are beneficial for gel-based and gel-free myelin proteome analyses. We conclude this article by exemplifying the exceptional power of label-free proteomics in the mass-spectrometric quantification of myelin proteins.

A Clinician's Perspective on Biomarkers

Psychiatrists and mental health professionals regularly perform various clinical tasks (e.g., detection, differential diagnosis, prognostication, treatment selection and implementation). How well they perform each of these tasks has a direct impact on patient outcomes. Measurement-based care has brought greater precision to these tasks and has improved outcomes. This article provides an overview of the types of biomeasures and biomarkers, the clinical uses of biomarkers, and the challenges in their development and clinical use. Although still in their infancy, biomarkers hold the promise of bringing even greater precision and even better outcomes in mental health. Biomeasures that could become biomarkers include genetic, proteomic, metabolomic, and immunologic measures, as well as physiological, functional, and brain structural measures. Mechanistic markers reflect and are based on the specific pathobiological processes that are involved in the development of a clinically defined condition. Some clinically relevant biomarkers may rely on this mechanistic understanding while others may not. Clinical biomarkers serve three broadly defined goals. Diagnostic markers define what is wrong. Prognostic markers define what will happen in the natural course of the condition, although they may also predict the course of illness during treatment. Theranostic markers address issues pertinent to treatment by defining whether, when, whom, and how to treat. Other biomarkers may be used to monitor the overall effect of treatment regardless of the therapeutic effects or to monitor the specific therapeutic effects of the intervention on the disorder itself. Biomarkers can also be used to estimate susceptibility/risk of developing the condition or the biological consequences of having had the disorder.

Magnetic Resonance Spectroscopy in Schizophrenia: Evidence for Glutamatergic Dysfunction and Impaired Energy Metabolism

In the past couple of decades, major efforts were made to increase reliability of metabolic assessments by magnetic resonance methods. Magnetic resonance spectroscopy (MRS) has been valuable for providing in vivo evidence and investigating biomarkers in neuropsychiatric disorders, namely schizophrenia. Alterations of glutamate and glutamine levels in brains of schizophrenia patients relative to healthy subjects are generally interpreted as markers of glutamatergic dysfunction. However, only a small fraction of MRS-detectable glutamate is involved in neurotransmission. Here we review and discuss brain metabolic processes that involve glutamate and that are likely to be implicated in neuropsychiatric disorders.

Proteomics in the Diagnosis of Inborn Encephalopathies of Unknown Origin: A Myth or Reality

Synaptopathy underlies a great variety of neurological or neurodevelopmental disorders, including neurodegenerative diseases and the highly complex neuropsychiatric syndromes. Standard diagnostic assays in the majority of synaptopathies are insufficient to make an appropriate and fast diagnosis, which has spurred a search for more accurate diagnostic methods using recent technological advances. As synaptopathy phenotypes strictly depend on genetics and environmental factors, the best way to approach these diseases is the investigation of entire sets of protein characteristics. Thus, proteomics has emerged as a mainstay in the studies on synaptopathies, with mass spectrometry as a technology of choice. This review is an update on the proteomic methods and achievements in the understanding, diagnostics, and novel biomarkers of synaptopathies. The article also provides a critical point of view and future perspectives on the application of neuroproteomics in clinical practice.

Calcium as a Trojan horse in mental diseases-The role of PMCA and PMCA-interacting proteins in bipolar disorder and schizophrenia

Although first mentions about calcium disturbances in psychiatric diseases appeared more than 30 years ago, the most recent genomic and proteomic findings confirmed a significant role of Ca²⁺ and Ca²⁺-regulated pathways in development of neuropathological processes, including bipolar disorder and schizophrenia. Moreover, last decades have shown that due to multifactorial nature of both diseases, impairment in neuronal calcium homeostasis may depend not only on disturbed Ca²⁺ entry system, but also on altered extrusion system. A pivotal role in Ca²⁺ clearance mechanism is played by plasma membrane Ca²⁺-ATPase (PMCA), the enzyme responsible for returning the elevated levels of cytosolic Ca²⁺ back to the resting state. In this paper we summarize the current knowledge about the role of PMCA in bipolar disorder and schizophrenia pathologies, as well as the contribution of several proteins that by interaction with PMCA modify signal transduction mechanisms.

Consensus paper of the WFSBP Task Force on Biological Markers: Criteria for biomarkers and endophenotypes of schizophrenia, part III: Molecular mechanisms

OBJECTIVES

Despite progress in identifying molecular pathophysiological processes in schizophrenia, valid biomarkers are lacking for both the disease and treatment response.

METHODS

This comprehensive review summarises recent efforts to identify molecular mechanisms on the level of protein and gene expression and epigenetics, including DNA methylation, histone modifications and micro RNA expression. Furthermore, it summarises recent findings of alterations in lipid mediators and highlights inflammatory processes. The potential that this research will identify biomarkers of schizophrenia is discussed.

RESULTS

Recent studies have not identified clear biomarkers for schizophrenia. Although several molecular pathways have emerged as potential candidates for future research, a complete understanding of these metabolic pathways is required to reveal better treatment modalities for this disabling condition.

CONCLUSIONS

Large longitudinal cohort studies are essential that pair a thorough phenotypic and clinical evaluation for example with gene expression and proteome analysis in blood at multiple time points. This approach might identify biomarkers that allow patients to be stratified according to treatment response and ideally also allow treatment response to be predicted. Improved knowledge of molecular pathways and epigenetic mechanisms, including their potential association with environmental influences, will facilitate the discovery of biomarkers that could ultimately be effective tools in clinical practice.

Increased serum levels of apoptosis in deficit syndrome schizophrenia patients: a preliminary study

BACKGROUND

Schizophrenia is a chronic and debilitating disorder, the etiology of which remains unclear. Apoptosis is a programmed cell death mechanism that might be implicated in neuropsychiatric disorders, including schizophrenia. In this study, we aimed to compare the serum levels of apoptosis among deficit schizophrenia (DS) syndrome patients, nondeficit schizophrenia (NDS) patients, and healthy controls (HCs).

PATIENTS AND METHODS

After the inclusion and exclusion criteria were applied, 23 DS patients, 46 NDS patients, and 33 HCs were included in the study. The serum apoptosis levels were measured using a quantitative sandwich enzyme immunoassay with human monoclonal antibodies directed against DNA and histones.

RESULTS

There was a significant difference among the three groups in terms of the levels of apoptosis (F 2,96=16.58; P<0.001). The serum apoptosis levels in the DS and NDS groups were significantly higher than those in the HC group. Furthermore, the serum apoptosis levels in the DS group were significantly higher than the levels in the NDS group.

CONCLUSION

This study suggests that increased levels of apoptosis may be implicated in the pathophysiology of DS syndrome. However, further studies are needed to support the role of apoptosis in DS.

Proteome effects of antipsychotic drugs: Learning from preclinical models

Proteome-wide expression analyses are performed in the brain of schizophrenia patients to understand the biological basis of the disease and discover molecular paths for new clinical interventions. A major issue with postmortem analysis is the lack of tools to discern molecular modulation related to the disease from dysregulation due to medications. We review available proteome-wide analysis of antipsychotic treatment in rodents, highlighting shared dysregulated pathways that may contribute to an extended view of molecular processes underlying their pharmacological activity. Fourteen proteomic studies conducted with typical and atypical antipsychotic treatments were examined; hypothesis-based approaches are also briefly discussed. Treatment with antipsychotics mainly affects proteins belonging to metabolic pathways involved in energy generation, both in glycolytic and oxidative phosphorylation pathways, suggesting antipsychotics-induced impairments in metabolism. Nevertheless, schizophrenic patients show impaired glucose metabolism and mitochondrial dysfunctions independent of therapy. Other antipsychotics-induced changes shared by different studies implicate cytoskeletal and synaptic function proteins. The mechanism can be related to the reorganization of dendritic spines resulting from neural plasticity events induced by treatments affecting neurotransmitter circuitry. However, metabolic and plasticity pathways activated by antipsychotics can also play an authentic role in the etiopathological basis of schizophrenia.

Increased expression of NDEL1 and MBP genes in the peripheral blood of antipsychotic-naïve patients with first-episode psychosis

Schizophrenia is a multifactorial neurodevelopmental disorder with high heritability. First-episode psychosis (FEP) is a critical period for determining the disease prognosis and is especially helpful for identifying potential biomarkers associated with the onset and progression of the disorder. We investigated the mRNA expression of 12 schizophrenia-related genes in the blood of antipsychotic-naïve FEP patients (N=73) and healthy controls (N=73). To evaluate the influences of antipsychotic treatment and progression of the disorder, we compared the gene expression within patients before and after two months of treatment with risperidone (N=64). We observed a significantly increased myelin basic protein (MBP) and nuclear distribution protein nudE-like 1 (NDEL1) mRNA levels in FEP patients compared with controls. Comparing FEP before and after risperidone treatment, no significant differences were identified; however; a trend of relatively low NDEL1 expression was observed after risperidone treatment. Animals chronically treated with saline or risperidone exhibited no significant change in Ndel1 expression levels in the blood or the prefrontal cortex (PFC), suggesting that the trend of low NDEL1 expression observed in FEP patients after treatment is likely due to factors other than risperidone treatment (i.e., disease progression). In addition to the recognized association with schizophrenia, MBP and NDEL1 gene products also play an essential role in the functions that are deregulated in schizophrenia, such as neurodevelopment. Our data strengthen the importance of these biological processes in psychotic disorders, indicating that these changes can be detected peripherally and potentially represent putative novel blood biomarkers of susceptibility and disorder progression.

Gene expression analysis in blood of ultra-high risk subjects compared to first-episode of psychosis patients and controls

OBJECTIVES

This study aimed to investigate peripheral blood gene expression in ultra-high-risk subjects (UHR) compared to first-episode psychosis individuals (FEP) and healthy controls (HC).

METHODS

We enrolled 22 UHR, 66 FEP and 67 HC and investigated the expression of 12 genes using Taqman assays. We used the Univariate General Linear Model, as well as Bonferroni correction for multiple comparisons.

RESULTS

We found that UFD1L (ubiquitin fusion degradation 1 like (yeast)) gene was upregulated in UHR group compared to HC and FEP (P = 3.44 × 10^-6 ; P = 9.41 × 10^-6). MBP (myelin basic protein) was downregulated in UHR compared to FEP (P = 6.07 × 10^-6). DISC1 (disrupted in schizophrenia 1) was also upregulated in UHR compared to FEP but lost statistical significance when corrected for age.

CONCLUSIONS

These genes are directly related to neurodevelopmental processes and have been associated to schizophrenia. Recent findings described that DISC1 overexpression can disrupt MBP expression, thus, we think that these alterations in UHR individuals could be associated with a common process. UFD1L showed a different pattern of expression only for UHR group, suggesting that they can be under an acute endoplasmatic reticulum stress, demanding elevated levels of Ufd1. Further studies can improve knowledge on disease progression and putative targets to preventive strategies.

Glial cells as key players in schizophrenia pathology: recent insights and concepts of therapy

The past decade has witnessed an explosion of knowledge on the impact of glia for the neurobiological foundation of schizophrenia. A plethora of studies have shown structural and functional abnormalities in all three types of glial cells. There is convincing evidence of reduced numbers of oligodendrocytes, impaired cell maturation and altered gene expression of myelin/oligodendrocyte-related genes that may in part explain white matter abnormalities and disturbed inter- and intra-hemispheric connectivity, which are characteristic signs of schizophrenia. Earlier reports of astrogliosis could not be confirmed by later studies, although the expression of a variety of astrocyte-related genes is abnormal in psychosis. Since astrocytes play a key role in the synaptic metabolism of glutamate, GABA, monoamines and purines, astrocyte dysfunction may contribute to certain aspects of disturbed neurotransmission in schizophrenia. Finally, increased densities of microglial cells and aberrant expression of microglia-related surface markers in schizophrenia suggest that immunological/inflammatory factors are of considerable relevance for the pathophysiology of psychosis. This review describes current evidence for the multifaceted role of glial cells in schizophrenia and discusses efforts to develop glia-directed therapies for the treatment of the disease.

Mitochondrial dysfunction in schizophrenia: an evolutionary perspective

Schizophrenia (SCZ) is a severe psychiatric illness with a lifetime prevalence of 0.4 %. A disturbance of energy metabolism has been suggested as part of the etiopathogenesis of the disorder. Several lines of evidence have proposed a connection between etiopathogenesis of SCZ and human brain evolution, which was characterized by an increase in the energy requirement, demanding a co-evolution of the mitochondrial system. Mitochondria are key players in brain energy homeostasis and multiple lines of evidence suggest that the system is disrupted in SCZ. In this review, we will describe the current knowledge on pathways/system involved in the human brain evolution as well as the main theories regarding the evolutionary origin of SCZ. We will furthermore discuss the role of mitochondria in the context of brain energy metabolism and its role in the etiopathogenesis of SCZ. Understanding SCZ in the context of human brain evolution opens a new perspective to elucidate pathophysiological mechanisms involved in the origin and/or portions of the complex symptomatology of this severe mental disorder.