TYW5 Human

What is TYW5 and what is its basic function in humans?

TYW5 encodes tRNA-yW Synthesizing protein 5, a Jumonji C (JmjC)-domain-containing protein that functions as a tRNA modification enzyme. Unlike typical JMJD proteins that act as epigenetic regulators, TYW5 serves as an RNA hydroxylase that catalyzes the formation of the OHyW nucleoside through carbon hydroxylation, requiring 2-oxoglutarate (2-OG) and Fe²⁺ ion as cofactors . It plays a crucial role in the wybutosine biosynthesis pathway, where six enzymes (including TRMT5 and TYW1-5) work sequentially to transform the original nucleoside at position 37 of tRNAᴾʰᵉ into hydroxy wybutosine (OHyW) . Through homo-dimerization, TYW5 forms a large, positively-charged patch that facilitates tRNA binding . While its enzymatic function in tRNA modification has been characterized, recent research has revealed its important roles in neurodevelopment and psychiatric disorders, particularly schizophrenia .

How is TYW5 expression regulated in the human brain?

TYW5 expression in the human brain is regulated through several mechanisms, with genetic and environmental factors both playing important roles. Genetic studies have identified regulatory variants at the 2q33.1 locus, particularly rs796364 and rs281759, that significantly affect TYW5 expression . These variants disrupt the binding of transcription factors CTCF, RAD21, and FOXP2, leading to altered gene expression levels .

Additionally, the single nucleotide polymorphism (SNP) rs203772 has been associated with schizophrenia risk, with the risk allele corresponding to higher transcriptional levels of TYW5 in the prefrontal cortex . Expression analysis reveals that TYW5 is relatively stable and highly expressed across different regions of the human brain throughout the lifespan, suggesting its ongoing importance in brain function .

Environmental factors also influence TYW5 expression. Notably, TYW5 expression is significantly decreased under iron depletion conditions, which is particularly relevant since schizophrenia patients often show lower levels of iron in their blood compared to healthy controls . This suggests a potential interaction between genetic factors, environmental conditions, and TYW5 expression in the context of schizophrenia risk.

What is known about TYW5's cellular localization and expression pattern?

TYW5 exhibits a dual cellular localization pattern, being present in both the cytoplasm and nucleus across multiple cell types, including HEK293T, SH-SY5Y, SK-N-SH, mouse neural stem cells, and rat neurons . This localization pattern is consistent with its role in tRNA modification, as tRNA processing occurs in both cellular compartments.

Expression analysis across different neural cell types reveals that TYW5 is more highly expressed than FTCDNL1 (another gene in the vicinity of regulatory variants) . TYW5 shows particularly high expression in neural progenitor cells and 6-week-old forebrain neurons derived from human-induced pluripotent stem cells, suggesting important functions during neural development .

Spatio-temporal expression data indicate that TYW5 maintains stable and high expression across different regions of the human brain throughout development and adulthood . This consistent expression pattern underscores TYW5's potential importance in ongoing brain function beyond early developmental periods.

What evidence supports TYW5 as a risk gene for schizophrenia?

Multiple lines of evidence from integrative genomic analyses have established TYW5 as a schizophrenia risk gene:

This convergent evidence from multiple methodologies and populations strongly supports TYW5 as a genuine schizophrenia risk gene whose expression changes contribute to disease pathophysiology.

How do regulatory variants at 2q33.1 affect TYW5 expression and schizophrenia risk?

Two functional variants at the 2q33.1 locus, rs796364 and rs281759, have been identified as key regulators of TYW5 expression that contribute to schizophrenia risk . Through systematic investigation using reporter gene assays and electrophoretic mobility shift assays, these variants were found to disrupt the binding of transcription factors CTCF, RAD21, and FOXP2 .

These variants physically interact with the TYW5 gene through chromatin looping and show the most significant associations with TYW5 expression in the human brain . CRISPR-Cas9-mediated genome editing has confirmed their regulatory effect on TYW5 expression . Notably, these variants are not located within the TYW5 gene itself but rather act as distal regulators.

Although rs796364 is located in the promoter region of FTCDNL1, expression analyses across different neural cell types show that TYW5 expression is much higher than FTCDNL1 in the human brain . This suggests that these variants primarily affect schizophrenia risk by modulating TYW5 rather than FTCDNL1 expression.

The mechanism appears to involve long-range regulatory interactions, where these genetic variants alter the binding of transcription factors, leading to changes in chromatin architecture that affect TYW5 expression. This altered expression pattern, specifically the upregulation of TYW5, contributes to schizophrenia risk through effects on neurodevelopment and neuronal structure.

What neurobiological mechanisms link TYW5 to schizophrenia pathophysiology?

Several neurobiological mechanisms potentially link TYW5 to schizophrenia pathophysiology:

• Neurodevelopmental effects: TYW5 overexpression affects the proliferation and differentiation of neural stem cells, particularly impairing glial cell differentiation . After 3 days of neural stem cell differentiation, the ratio of GFAP-positive cells (a marker for glial cells) was significantly decreased in cells overexpressing TYW5 compared to controls . This aligns with the neurodevelopmental hypothesis of schizophrenia.

• Dendritic spine abnormalities: TYW5 overexpression alters dendritic spine density in neurons, an important neuronal structure frequently found to be dysregulated in schizophrenia . Since dendritic spines are the primary sites of excitatory synaptic transmission, these alterations may contribute to the cognitive symptoms of schizophrenia.

• Regulation of schizophrenia-associated genes: Transcriptome analysis revealed that TYW5 regulates the expression of several genes associated with schizophrenia, including Snap91, Ndrg4, Ier3, and Ip6k3 .

• Brain structural changes: Combined analysis of genotyping and MRI data showed that the TYW5-associated variant rs203772 is significantly associated with gray matter volume of the right middle frontal gyrus and left precuneus, brain regions implicated in schizophrenia .

• Involvement in schizophrenia-related pathways: TYW5 influences multiple pathways implicated in schizophrenia, including extracellular matrix-receptor interaction, focal adhesion, and the PI3K-Akt signaling pathway .

These mechanisms suggest that TYW5 dysregulation contributes to schizophrenia through effects on brain development, neuronal structure, and signaling pathways critical for proper brain function.

What approaches are used to study TYW5 expression in human brain tissues?

Researchers employ several complementary approaches to study TYW5 expression in human brain tissues:

• RNA sequencing (RNA-seq): Large-scale RNA-seq data from repositories such as PsychEncode has been used to compare TYW5 expression between 559 schizophrenia patients and 936 healthy controls across various brain regions . This approach provides comprehensive transcriptome-wide expression data with high sensitivity.

• Expression quantitative trait loci (eQTL) analysis: Brain eQTL studies identify genetic variants that influence gene expression levels in brain tissue. This approach has been instrumental in identifying variants like rs796364, rs281759, and rs203772 that regulate TYW5 expression . Integration of brain eQTL data with GWAS results helps establish causal relationships between gene expression and disease risk.

• Transcriptome-wide association studies (TWAS): This method integrates GWAS data with gene expression prediction models developed using reference panels like the CommonMind Consortium (CMC) and Lieber Institute for Brain Development (LIBD2) . FUSION software implementing various predictive models (LASSO, GBLUP, Elastic Net, and BSLM) has been used to identify association between predicted TYW5 expression and schizophrenia risk .

• Single-cell RNA sequencing: This technique allows examination of gene expression at the single-cell level, providing insights into cell-type-specific expression patterns of TYW5 across different neural cell populations.

• Immunohistochemistry and in situ hybridization: These techniques provide spatial information about TYW5 protein and mRNA expression within brain tissue sections, allowing visualization of expression patterns within their anatomical context.

These approaches provide a multi-dimensional understanding of TYW5 expression patterns in the human brain and how they relate to schizophrenia pathophysiology.

How can CRISPR-Cas9 genome editing be used to investigate TYW5 function?

CRISPR-Cas9 genome editing offers several powerful approaches for investigating TYW5 function:

• Validation of regulatory variants: CRISPR-Cas9 has been successfully used to confirm the regulatory effects of variants like rs796364 and rs281759 on TYW5 expression . By introducing specific mutations at these loci, researchers can directly observe how these genetic changes affect gene expression levels.

• Gene knockout studies: Complete deletion of TYW5 using CRISPR-Cas9 can help understand its function through loss-of-function phenotypes. This approach can be applied in cell culture models, including neural stem cells or iPSC-derived neurons, to assess effects on proliferation, differentiation, and morphology.

• Overexpression models: CRISPR-Cas9 systems with activator domains (CRISPRa) can be used to upregulate TYW5 expression, mimicking the increased expression observed in schizophrenia patients. This approach has been used to study the effects of TYW5 overexpression on neural stem cell proliferation and differentiation .

• Domain-specific mutations: CRISPR-Cas9 can introduce precise mutations in specific functional domains of TYW5, such as the JmjC domain or tRNA binding regions, to understand the importance of these domains for TYW5's neurobiological functions.

• Humanized models: CRISPR-Cas9 can be used to introduce human TYW5 variants into animal models, creating "humanized" systems to study the effects of human-specific genetic variation in a controlled experimental context.

These approaches can be applied across various model systems to comprehensively investigate TYW5's function and its role in schizophrenia pathophysiology, bridging the gap between genetic association and biological mechanism.

What cell culture models are appropriate for studying TYW5?

Several cell culture models have proven valuable for studying TYW5 function in the context of neurodevelopment and schizophrenia:

• Neural stem cells (NSCs): Mouse NSCs have been successfully used to study the effects of TYW5 overexpression on proliferation and differentiation . These cells can differentiate into both neurons and glial cells, making them ideal for studying neurodevelopmental effects. Studies have shown that TYW5 overexpression in mouse NSCs affects their differentiation into glial cells .

• Primary neurons: Rat cortical neurons (from embryonic day 18) have been used to investigate the effects of TYW5 on dendritic spine density and morphology . This model is particularly relevant for understanding TYW5's role in neuronal structure and synaptic function.

• Human induced pluripotent stem cells (iPSCs) and derived neurons: iPSCs from schizophrenia patients and healthy controls can be differentiated into neurons to study TYW5 expression and function in a disease-relevant human cellular context. These models preserve the genetic background of individuals with schizophrenia.

• Neuroblastoma cell lines: SH-SY5Y and SK-N-SH neuroblastoma cell lines have been used to study TYW5 localization and expression . While less physiologically relevant than primary neurons or iPSC-derived neurons, these cell lines offer advantages for high-throughput studies and genetic manipulations.

• HEK293T cells: Although not of neural origin, these cells have been used for molecular studies of TYW5, including protein localization and reporter gene assays for regulatory variants .

Each model system offers distinct advantages depending on the research question. Neural-derived cell types provide more disease-relevant contexts, while established cell lines may be more amenable to high-throughput molecular studies and genetic manipulations.

How does TYW5 affect dendritic spine formation and maturation?

TYW5 plays a critical role in dendritic spine formation and maturation, processes that are frequently dysregulated in schizophrenia . Experimental studies have shown that TYW5 overexpression in rat primary neurons significantly alters dendritic spine density . This finding is particularly relevant to schizophrenia pathophysiology, as abnormal dendritic spine density and morphology are well-documented features of the disorder.

The mechanisms through which TYW5 influences spine morphogenesis likely involve regulation of cytoskeletal proteins and signaling pathways that control spine formation, stability, and pruning. Transcriptome analysis of cells overexpressing TYW5 revealed effects on extracellular matrix-receptor interaction and focal adhesion pathways, both of which are involved in spine dynamics .

Dendritic spines are the primary sites of excitatory synaptic transmission, and their alterations can significantly affect neural circuit function. The impact of TYW5 on dendritic spines may therefore represent a key link between this gene and the cognitive symptoms of schizophrenia.

Further research using time-lapse imaging, super-resolution microscopy, and electrophysiological approaches could provide more detailed insights into how TYW5 dynamically regulates spine formation, maturation, and function. Understanding these mechanisms could potentially identify novel therapeutic targets for addressing the synaptic pathology associated with schizophrenia.

What are the downstream molecular pathways affected by TYW5 dysregulation?

Transcriptome analysis of neural stem cells overexpressing TYW5 has revealed several downstream molecular pathways affected by TYW5 dysregulation:

• Extracellular matrix-receptor interaction pathway: This pathway is crucial for cell adhesion, migration, and signaling during neurodevelopment . Disruption of this pathway may alter cell-cell and cell-matrix interactions critical for proper neural circuit formation.

• Focal adhesion pathway: This pathway mediates connections between the extracellular matrix and the cytoskeleton, influencing cell shape, mobility, and signal transduction . Alterations in focal adhesions may affect neuronal migration and synapse formation.

• PI3K-Akt signaling pathway: This pathway regulates various cellular processes including proliferation, survival, and metabolism, and has been implicated in schizophrenia . Dysregulation of this pathway may contribute to abnormal neuronal development and function.

Furthermore, TYW5 overexpression affects the expression of several schizophrenia-associated genes, including Snap91, Ndrg4, Ier3, and Ip6k3 . SNAP91 encodes a clathrin coat assembly protein involved in synaptic vesicle endocytosis, suggesting TYW5 may influence synaptic function .

These affected pathways provide mechanistic links between TYW5 dysregulation and the cellular and molecular alterations observed in schizophrenia. They also offer potential targets for therapeutic intervention aimed at normalizing neural development and function in individuals with TYW5-related risk variants.

How does TYW5's tRNA modification function relate to its role in schizophrenia?

The connection between TYW5's enzymatic function in tRNA modification and its role in schizophrenia presents a fascinating research question. TYW5 catalyzes a specific step in the wybutosine biosynthesis pathway, modifying position 37 of tRNAPhe by forming the OHyW nucleoside through carbon hydroxylation . This seemingly specialized molecular function raises intriguing questions about its relationship to neurodevelopment and psychiatric disorders.

One hypothesis is that altered tRNA modification due to TYW5 dysregulation could lead to changes in translation efficiency or accuracy, particularly for specific codons recognized by the modified tRNAPhe. This might result in altered protein synthesis during critical periods of neurodevelopment or in specific neuronal populations, contributing to schizophrenia-related phenotypes.

TYW5 expression is sensitive to iron levels, and schizophrenia patients often show lower blood iron levels . This connection suggests a potential link between environmental factors (iron availability), TYW5 function, and schizophrenia risk. Iron depletion could affect TYW5's enzymatic activity, potentially altering tRNA modification patterns and downstream translation processes.

Another possibility is that TYW5 has additional functions beyond tRNA modification that are more directly relevant to neurodevelopment. Many proteins have multiple cellular roles, and TYW5's presence in both the nucleus and cytoplasm might suggest additional activities .

Further research exploring the consequences of altered tRNA modification on the neuronal proteome, particularly during development and in schizophrenia-relevant cell types, could help elucidate the connection between TYW5's enzymatic function and its role in schizophrenia pathophysiology.

What is the relationship between TYW5 and other psychiatric disorders beyond schizophrenia?

While TYW5 has been most strongly linked to schizophrenia, preliminary evidence suggests potential associations with other psychiatric disorders. Exploration of associations between TYW5 and other psychiatric conditions has revealed suggestive associations with bipolar disorder, particularly with the variant rs73066802 (P = 2.61 × 10⁻⁵) .

This finding is not surprising given the substantial genetic overlap between schizophrenia and bipolar disorder. Both conditions involve similar neurodevelopmental pathways and share many genetic risk factors. The association with bipolar disorder suggests that TYW5 may influence neurobiological processes relevant to a broader spectrum of psychiatric conditions characterized by alterations in mood regulation and cognitive function.

The role of TYW5 in basic neurodevelopmental processes, including neural stem cell proliferation, differentiation, and dendritic spine formation , suggests it could potentially contribute to multiple disorders with neurodevelopmental components. These might include autism spectrum disorders, intellectual disability, or attention deficit hyperactivity disorder.

Cross-disorder genetic analyses and studies of TYW5 function in various neuropsychiatric disease models could provide insights into whether TYW5 influences shared neurobiological pathways or has disorder-specific effects. This broader perspective on TYW5's role in psychiatric illness could inform more integrative approaches to understanding and potentially treating these conditions.

What are potential therapeutic implications of targeting TYW5 in schizophrenia?

Given the evidence that TYW5 upregulation contributes to schizophrenia risk , developing therapeutic strategies that modulate TYW5 expression or function could represent a novel approach to treating the disorder. Several potential therapeutic implications and strategies can be considered:

• Small molecule inhibitors: Developing compounds that specifically inhibit TYW5's enzymatic activity could help normalize its function in schizophrenia patients. Since TYW5 is a JmjC-domain-containing protein that requires 2-oxoglutarate and Fe²⁺ as cofactors , structural insights from related enzymes could guide inhibitor design.

• RNA-based therapeutics: Antisense oligonucleotides or RNA interference approaches could specifically reduce TYW5 expression levels in patients with TYW5 upregulation, potentially reversing downstream effects on neurodevelopment and synaptic function.

• Targeting upstream regulators: Modulating the activity of transcription factors that regulate TYW5 expression, such as CTCF, RAD21, and FOXP2 , could provide an alternative approach to normalizing TYW5 levels.

• Iron supplementation strategies: Given that TYW5 expression is sensitive to iron levels and schizophrenia patients often show lower blood iron levels, investigating whether iron supplementation normalizes TYW5 function in relevant contexts could lead to relatively simple interventions for a subset of patients.

• Personalized medicine approaches: Genetic testing for TYW5-related variants could identify patients most likely to benefit from TYW5-targeted therapies, enabling a more personalized approach to schizophrenia treatment.

These therapeutic possibilities require extensive preclinical and clinical development, but they highlight how understanding specific genes like TYW5 in schizophrenia can open new avenues for therapeutic intervention beyond current symptom-based approaches.

How can multi-omics approaches advance our understanding of TYW5's role in brain development?

Multi-omics approaches can significantly advance our understanding of TYW5's role in brain development by providing a comprehensive and integrated view of its function across multiple biological levels:

• Genomics and epigenomics: Detailed mapping of regulatory elements affecting TYW5 expression, including enhancers, silencers, and chromatin modifications, can reveal how genetic variants influence TYW5 expression in different cell types and developmental stages.

• Transcriptomics at single-cell resolution: Single-cell RNA sequencing of developing brain tissue can identify cell populations where TYW5 is most highly expressed and reveal co-expression networks that suggest functional relationships.

• Proteomics and interactomics: Identifying TYW5's protein interaction partners in different neural cell types could reveal molecular mechanisms through which TYW5 influences neurodevelopment and synaptic function.

• Epitranscriptomics: Given TYW5's role in tRNA modification , comprehensive mapping of tRNA modifications in normal and TYW5-dysregulated conditions could elucidate how TYW5 affects the tRNA landscape and subsequent translational regulation.

• Metabolomics: Profiling metabolic changes associated with TYW5 dysregulation could identify affected biochemical pathways, particularly those involving iron metabolism given TYW5's sensitivity to iron levels .

• Spatial multi-omics: Technologies that preserve spatial information while measuring multiple molecular features could map how TYW5 influences molecular pathways across different brain regions during development.

• Longitudinal multi-omics: Collecting multi-omics data across developmental time points can capture the dynamic effects of TYW5 on brain development and maturation.

Integrating these diverse data types through advanced computational approaches could provide a systems-level understanding of how TYW5 contributes to neurodevelopment and schizophrenia risk, potentially identifying new biomarkers and therapeutic targets.

What methodological approaches are most promising for studying TYW5 in vivo?

Several methodological approaches hold promise for studying TYW5 function in vivo and its relevance to neurodevelopment and schizophrenia:

• Transgenic animal models: Developing animals with conditional overexpression or knockout of TYW5 would allow for detailed investigation of its role in neurodevelopment and behavior . These models could be designed with brain region-specific or cell-type-specific promoters to target TYW5 manipulation to relevant neural populations.

• In utero gene editing: CRISPR-Cas9 delivered to developing embryos could be used to manipulate TYW5 expression or introduce specific variants during early brain development, providing insights into its developmental functions.

• Human brain organoids: Derived from induced pluripotent stem cells, brain organoids provide a three-dimensional model of human brain development. Comparing organoids with different TYW5 expression levels or genetic variants could reveal effects on neural progenitor proliferation, differentiation, and organization.

• Longitudinal imaging: Techniques such as two-photon microscopy in animal models with fluorescently labeled TYW5 or neural structures could track dynamic changes in dendritic spine formation and neural circuit development associated with TYW5 manipulation.

• Functional assays: Electrophysiological recordings, calcium imaging, and behavioral testing in animals with altered TYW5 expression could connect molecular and cellular changes to functional outcomes relevant to schizophrenia.

• Patient-derived cellular models: iPSCs from individuals with TYW5 risk variants differentiated into neurons provide a human cellular context for studying TYW5's effects while preserving patient-specific genetic backgrounds.

• Environmental manipulation studies: Investigating how environmental factors such as iron availability interact with TYW5 genotype in animal models could reveal gene-environment interactions relevant to schizophrenia risk.

Combining these approaches would provide complementary insights into TYW5's in vivo function across multiple levels of analysis, from molecular mechanisms to behavioral outcomes.