TAF15 Human

What is TAF15 and what is its normal function in human cells?

TAF15 (TATA-box binding protein-associated factor 2N) is an RNA-binding protein belonging to the FET family, which also includes FUS (Fused in Sarcoma) and EWS (Ewing Sarcoma). In normal cellular physiology, TAF15 participates in transcriptional regulation and RNA processing. Studies have shown that TAF15 binds to approximately 4,900 RNA targets enriched for GGUA motifs in adult mouse brains .

Methodologically, researchers characterize TAF15's normal function through:

• RNA binding assays (CLIP-seq and RNA Bind-N-Seq technologies)

• Protein interaction studies using immunoprecipitation

• Transcriptomic analyses following TAF15 knockdown or knockout

Unlike its related protein FUS, TAF15 appears to have a minimal role in alternative splicing but contributes significantly to RNA turnover in human neural progenitors .

How does the structure of TAF15 compare with other FET family proteins?

TAF15 shares structural similarities with other FET proteins (FUS and EWS), particularly in its domain organization:

The filamentous structure of TAF15 in disease states involves residues 7-99 in the low-complexity domain, forming a characteristic 13-β-strand fold . This structure is distinct from filaments formed by other amyloidogenic proteins like tau or TDP-43, suggesting unique pathological mechanisms .

Researchers typically study these structural features through:

• Cryo-electron microscopy (cryo-EM) for filament structures

• X-ray crystallography for domain structure determination

• NMR spectroscopy for dynamic structural elements

What is the evidence for TAF15's role in frontotemporal dementia?

Recent breakthrough research has identified TAF15 as the key protein forming abnormal aggregates in a subset of frontotemporal dementia cases. Specifically:

• Cryo-EM studies revealed abundant TAF15 amyloid filaments in the brains of individuals with frontotemporal lobar degeneration (FTLD), particularly in cases previously designated as FTLD-FUS .

• The filament structures were consistent across multiple patients and brain regions, suggesting a specific pathological process .

• TAF15 filaments were found in the absence of FUS filaments, despite FUS often being present in the same inclusions .

• In approximately 10% of frontotemporal dementia cases where the causative protein was previously unknown, TAF15 has now been identified as the primary amyloidogenic protein .

Methodologically, researchers established this link through:

• Post-mortem brain tissue analysis using immunohistochemistry

• Protein extraction and characterization from affected brain regions

• Cryo-EM structural analysis of protein filaments

• Mass spectrometry verification of protein identity

How does TAF15 pathology differ between frontotemporal dementia and motor neuron diseases?

TAF15 pathology shows both similarities and differences in frontotemporal dementia and motor neuron diseases:

In studies of individuals with both upper and lower motor neuron pathology, TAF15 filaments with identical structure to those found in prefrontal and temporal cortices were observed in motor regions . This suggests that TAF15 proteinopathy may exist on a disease spectrum encompassing both frontotemporal dementia and motor neuron disease, analogous to the TDP-43 pathology spectrum .

Research approaches include:

• Comparative neuropathological analyses across disease phenotypes

• Regional protein extraction and filament characterization

• Clinicopathological correlation studies

• Animal modeling of region-specific TAF15 pathology

What are the optimal techniques for detecting and characterizing TAF15 aggregates in tissue samples?

Detecting and characterizing TAF15 aggregates requires a multi-modal approach:

• Immunohistochemistry/Immunofluorescence:

  • Primary antibodies: Anti-TAF15 (specifically recognizing epitopes outside the filament core)

  • Co-staining with FUS and transportin 1 antibodies to characterize inclusion composition

  • Controls should include known TAF15-positive cases and neurologically normal individuals

• Biochemical Extraction and Analysis:

  • Sequential extraction using increasing detergent strengths

  • Sarkosyl-insoluble fraction isolation for filamentous proteins

  • Western blotting with TAF15-specific antibodies

  • Mass spectrometry confirmation focusing on peptides mapping to the filament core region (residues 7-99)

• Structural Analysis:

  • Cryo-EM is the gold standard for filament structure determination

  • Sample preparation requires optimal tissue preservation and extraction protocols

  • Helical reconstruction techniques for filament structure solving

  • Resolution of 2.0-2.7 Å can be achieved with current methods

• Quantification Methods:

  • Stereological counting of TAF15-positive inclusions

  • Digital image analysis of immunostained sections

  • Regional distribution mapping correlating with clinical phenotypes

What cellular and animal models best recapitulate TAF15 pathology?

Developing accurate models for TAF15 pathology remains challenging. Current approaches include:

For cellular models, researchers should consider:

• Using human iPSC-derived motor neurons or cortical neurons

• Creating isogenic lines with TAF15 mutations or altered expression

• Evaluating both TAF15 loss-of-function and aggregation phenotypes

• Assessing RNA metabolism changes through transcriptomic approaches

For animal models, key methodological considerations include:

• Targeting expression to relevant neuronal populations

• Using brain region-specific inducible systems

• Validating models against human neuropathological findings

• Assessing both biochemical and behavioral phenotypes

How do TAF15's RNA binding properties differ from those of FUS and TDP-43?

TAF15, FUS, and TDP-43 show distinct RNA binding patterns and functional consequences:

Research approaches to characterize these differences include:

• CLIP-seq (Cross-linking immunoprecipitation followed by sequencing)

• RNA Bind-N-Seq for motif identification

• RNA stability assays following protein knockdown

• Alternative splicing analysis using RNA-seq

• Direct comparison studies in the same cellular systems

These differences suggest both overlapping and distinct pathological mechanisms when each protein forms aggregates in disease states .

What methodologies are most effective for studying TAF15-RNA interactions in disease states?

Studying TAF15-RNA interactions in disease contexts requires specialized approaches:

• Tissue-based RNA-protein interaction studies:

  • CLIP-seq adapted for post-mortem human brain tissue

  • Isolation of pathological inclusions followed by RNA extraction and sequencing

  • RNAscope in situ hybridization combined with TAF15 immunostaining

  • Single-cell approaches to capture cell-type specific interactions

• Biochemical approaches:

  • RNA immunoprecipitation from disease models

  • In vitro RNA binding assays with recombinant normal and mutant TAF15

  • Competition assays between TAF15, FUS, and other RNA-binding proteins

  • Structural studies of TAF15-RNA complexes

• Functional assessments:

  • RNA stability assays following TAF15 aggregation

  • Alternative splicing analysis in disease models

  • Translation efficiency measurements

  • RNA localization studies in the presence of TAF15 aggregates

• Advanced techniques:

  • APEX-seq for proximity labeling of RNAs near TAF15 aggregates

  • Single-molecule imaging of TAF15-RNA interactions

  • Massively parallel reporter assays for TAF15 binding sites

  • RNA modifications analysis in relation to TAF15 binding

How might the TAF15 filament structure inform therapeutic development for FTLD?

The high-resolution structure of TAF15 filaments (2.0-2.7 Å) provides crucial insights for therapeutic development:

• Structure-based drug design opportunities:

  • The 13-β-strand fold comprising residues 7-99 of TAF15 presents specific targets for small molecule binding

  • Stabilizing compounds that prevent further aggregation

  • Destabilizing agents that could promote disaggregation

  • Compounds targeting specific structural motifs unique to TAF15 filaments

• Immunotherapeutic approaches:

  • Generation of conformation-specific antibodies recognizing TAF15 filaments

  • Screening epitopes outside the filament core for accessible antibody targets

  • Developing intrabodies targeting pre-fibrillar species

• Diagnostic applications:

  • PET ligands based on TAF15 filament binding properties

  • CSF biomarkers detecting TAF15 fragments or conformations

  • Blood-based assays for TAF15 pathology

• Methodological considerations:

  • In silico screening against specific pockets in the TAF15 filament structure

  • Fragment-based drug discovery targeting the filament interface

  • Validation in cellular models expressing the same filament structure

  • Pharmacokinetic optimization for CNS penetration

This approach mirrors strategies already being developed for tau and Aβ in Alzheimer's disease , but requires TAF15-specific optimization.

What is the relationship between TAF15 aggregation and nuclear-cytoplasmic transport defects?

TAF15 aggregation and nuclear-cytoplasmic transport disruption appear interconnected:

• Evidence for transport disruption:

  • TAF15 contains a nuclear localization signal (NLS) outside the filament core

  • Transportin 1 is found in TAF15-containing inclusions

  • Cytoplasmic mislocalization precedes inclusion formation

• Potential mechanisms:

  • Sequestration of transportin 1 by TAF15 aggregates via NLS interactions

  • Competition between normal and aggregated TAF15 for transport machinery

  • Disruption of nuclear pore complex function by TAF15 aggregates

  • Secondary effects on nucleocytoplasmic transport of other essential cargoes

• Experimental approaches:

  • Live cell imaging of nuclear transport in TAF15 pathology models

  • Selective inhibition of transportin-mediated import

  • Rescue experiments restoring nuclear localization

  • Nucleocytoplasmic fractionation studies in disease models

• Therapeutic implications:

  • Targeting the TAF15-transportin 1 interaction

  • Enhancing nuclear import efficiency

  • Preventing cytoplasmic aggregation through chaperone enhancement

  • Combinatorial approaches addressing both aggregation and transport defects

This represents a critical area for future research, as nuclear-cytoplasmic transport defects may constitute both a consequence and driver of disease progression.

How does TAF15 proteinopathy compare to other amyloid proteinopathies in neurodegenerative diseases?

TAF15 joins a select group of proteins forming amyloid filaments in neurodegenerative diseases:

TAF15 proteinopathy shows distinct characteristics:

• Forms amyloid filaments specifically in FTLD-FET cases

• Involves an RNA-binding protein with specific RNA targets

• Co-occurs with other FET proteins in inclusions without them forming filaments

• Appears to have a disease spectrum spanning cognitive and motor phenotypes

Methodologically, researchers compare these proteinopathies through:

• Cryo-EM structural studies of isolated filaments

• Biochemical characterization of aggregation propensities

• Cellular models of seeding and spreading

• Comparative neuropathological analyses

What research gaps exist in understanding the interplay between TAF15, FUS, and EWS in pathological conditions?

Despite recent advances, significant questions remain about FET protein interactions in disease:

• Sequestration dynamics:

  • Why do TAF15 filaments form while FUS is present in inclusions but does not form filaments?

  • What molecular interactions determine which FET protein forms filaments?

  • Is there a protective mechanism preventing FUS fibrillization despite its aggregation propensity?

• Cross-seeding potential:

  • Can TAF15 filaments seed FUS or EWS aggregation?

  • Do subclinical aggregates of multiple FET proteins exist?

  • What determines the dominant protein in different disease contexts?

• Functional consequences:

  • How does loss of multiple FET proteins compare to single protein dysfunction?

  • Are there compensatory mechanisms between FET proteins?

  • Do FET proteins show cell-type specific vulnerabilities?

• Methodological approaches needed:

  • Development of FET protein-specific antibodies distinguishing native and pathological conformations

  • Cellular models expressing physiological levels of all FET proteins

  • Advanced imaging techniques to observe early aggregation events

  • Cross-species comparisons of FET protein interactions

The recent identification of TAF15 filaments challenges previous assumptions about FTLD-FUS and necessitates reevaluation of the role of each FET protein in disease .

What genetic factors might influence TAF15 aggregation propensity?

Several genetic factors may influence TAF15 aggregation:

• Direct genetic factors:

  • Variations in the TAF15 gene, particularly in the low-complexity domain (residues 7-99)

  • Mutations affecting TAF15 post-translational modifications

  • Alterations in nuclear localization signal or RNA-binding domains

  • Genetic modifiers of TAF15 expression levels

• Indirect genetic influences:

  • Genes involved in protein quality control (chaperones, degradation pathways)

  • RNA processing machinery components

  • Nuclear transport factors (transportin 1, nucleoporins)

  • Stress response mediators affecting phase separation properties

• Research approaches:

  • Genome-wide association studies in FTLD cohorts

  • Whole exome/genome sequencing of FTLD-FET cases

  • CRISPR screens for modifiers of TAF15 aggregation

  • Targeted sequencing of candidate genetic modifiers

• Translational potential:

  • Identification of at-risk individuals through genetic screening

  • Discovery of novel therapeutic targets

  • Development of personalized intervention strategies

  • Understanding of disease heterogeneity

A systematic evaluation of these factors would significantly advance our understanding of why TAF15 forms pathological aggregates in specific individuals.

How might TAF15-targeted therapies be developed and evaluated in preclinical models?

Development of TAF15-targeted therapies requires systematic approaches:

• Therapeutic strategies:

  • Antisense oligonucleotides (ASOs) reducing TAF15 expression

  • Small molecules preventing TAF15 aggregation or promoting clearance

  • Gene therapy approaches to modulate TAF15 levels or function

  • Immunotherapies targeting pathological TAF15 conformations

• Preclinical model development:

  • iPSC-derived neurons expressing TAF15 with enhanced aggregation propensity

  • Transgenic animals expressing human TAF15 in vulnerable neuronal populations

  • Viral vector-mediated TAF15 pathology induction

  • Ex vivo models using organotypic brain slices

• Evaluation methodologies:

  • Biochemical assessment of TAF15 aggregation and solubility

  • Imaging of TAF15 localization and inclusion formation

  • Transcriptomic analysis of TAF15-regulated RNA targets

  • Functional assessment of neuronal health and activity

  • Behavioral testing in animal models

• Translational considerations:

  • Development of target engagement biomarkers

  • Establishment of pharmacodynamic readouts

  • Determination of therapeutic window

  • Assessment of safety profile considering TAF15's normal functions

These approaches require close collaboration between structural biologists, medicinal chemists, neuroscientists, and clinicians to advance potential TAF15-directed therapies toward clinical application.

How can single-cell technologies advance our understanding of TAF15 pathology?

Single-cell technologies offer unique opportunities to understand TAF15 pathology:

• Single-cell transcriptomics:

  • Identification of cell-type specific responses to TAF15 aggregation

  • Characterization of transcriptional changes in individual affected neurons

  • Detection of compensatory mechanisms in resistant cells

  • Mapping disease progression at cellular resolution

• Single-cell proteomics:

  • Quantification of TAF15 protein levels in individual cells

  • Identification of protein interaction networks in affected vs. unaffected cells

  • Detection of post-translational modifications influencing aggregation

  • Assessment of protein quality control responses

• Spatial transcriptomics/proteomics:

  • Mapping TAF15 pathology in specific brain regions and circuits

  • Correlation with regional vulnerability patterns

  • Identification of microenvironmental factors influencing pathology

  • Assessment of non-cell autonomous effects

• Methodological considerations:

  • Sample preparation preserving cellular integrity and protein state

  • Analysis pipelines integrating multiple single-cell modalities

  • Validation in human post-mortem tissue and disease models

  • Computational approaches for trajectory analysis of disease progression

These technologies can reveal heterogeneity in TAF15 pathology that may be obscured in bulk tissue analyses, potentially identifying new therapeutic targets and biomarkers.

What are the most promising biomarker approaches for detecting TAF15 pathology in living patients?

Development of TAF15 pathology biomarkers represents a critical research need:

• Cerebrospinal fluid (CSF) biomarkers:

  • Total TAF15 protein levels in CSF

  • TAF15 fragments or modified forms specific to pathological states

  • Conformation-specific assays detecting misfolded TAF15

  • Ratios of TAF15 to other FET proteins

• Neuroimaging approaches:

  • PET ligands targeting TAF15 filaments

  • Functional MRI correlates of TAF15-associated network dysfunction

  • Structural imaging markers of regional atrophy patterns

  • Multimodal approaches combining structural and molecular imaging

• Blood-based biomarkers:

  • Plasma or serum TAF15 or fragments

  • Exosomal TAF15 from CNS origin

  • RNA profiles reflecting TAF15 dysfunction

  • Inflammatory markers associated with TAF15 pathology

• Methodological development needs:

  • Ultra-sensitive assays for TAF15 detection (e.g., SIMOA)

  • TAF15 filament-specific antibodies

  • TAF15 seed amplification assays (similar to α-synuclein PMCA/RT-QuIC)

  • Longitudinal studies correlating biomarker changes with clinical progression

The development of such biomarkers would enable earlier diagnosis, monitoring of disease progression, and evaluation of therapeutic efficacy in clinical trials targeting TAF15 pathology.