TARDBP Human

What is the TARDBP gene and what does it encode?

TARDBP is a gene located on chromosome 1 that encodes the TAR DNA-binding protein 43 (TDP-43). TDP-43 is an RNA-binding and DNA-binding protein with multiple cellular functions, including regulation of gene expression and mediation of protein-protein interactions. It is widely expressed in various tissues and particularly important in the central nervous system. TDP-43 binds to heterogeneous ribonucleoproteins (hnRNPs) via its glycine-rich domain and is involved in multiple steps of RNA processing .

What is the prevalence of TARDBP mutations in neurodegenerative diseases?

TARDBP mutations are found in approximately 5% of familial ALS cases and 1-2% of sporadic ALS cases, though this prevalence varies widely across different populations (ranging from 0-12% in familial and 0-5% in sporadic cases). These mutations have also been identified in frontotemporal dementia (FTD) cases. More recently, TARDBP mutations have been observed in 1.4% of atypical parkinsonism cases, suggesting a broader role in neurodegenerative disorders .

Which domains of the TARDBP gene contain disease-causing mutations?

Most disease-causing mutations in TARDBP cluster in exon 6, which encodes the protein's C-terminal domain. This region contains the glycine-rich domain that regulates gene expression and mediates protein-protein interactions. Specific variants like p.Gly290Ala, p.Gly298Ser, p.N267S, p.A382T, and p.G348C have been identified in patients with neurodegenerative diseases .

How do TARDBP mutations lead to neurodegeneration?

TARDBP mutations appear to cause neurodegeneration through complex mechanisms involving both gain and loss of function. The mutations, particularly those affecting the glycine-rich domain, can alter TDP-43's ability to regulate gene expression and interact with other proteins. These alterations may disrupt RNA processing, affect protein homeostasis, and lead to pathological aggregation of TDP-43. Research has shown that mutations can create or disrupt serine residues, potentially affecting TDP-43 aggregation and function. Since TDP-43 is involved in multiple steps of RNA processing, dysregulation may impact numerous RNA and protein targets .

What is the relationship between TDP-43 and other neurodegenerative disease proteins?

Emerging evidence suggests interconnections between TDP-43 and other key proteins involved in neurodegeneration:

• Tau protein: TDP-43 may regulate tau exon 10 splicing, which generates the two isoforms 3R-tau and 4R-tau. TDP-43 also appears to bind the 3′-UTR of MAPT (microtubule-associated protein tau gene), promoting mRNA instability. Dysregulation of this interaction, possibly induced by mutated TDP-43, may lead to an altered ratio of 3R-tau/4R-tau, similar to effects induced by pathological MAPT mutations .

• Alpha-synuclein: In animal models, overexpression of wild-type TDP-43 potentiates mutant α-synuclein toxicity, leading to significant loss of dopaminergic neurons compared to single transgenic models. This suggests a synergistic relationship between these proteins in promoting neurodegeneration .

How does TDP-43 pathology manifest in different neurodegenerative conditions?

TDP-43 pathology is present in nearly all (97%) ALS cases and in approximately 50% of patients with frontotemporal lobar degeneration (FTLD-TDP). In patients with TARDBP mutations, TDP-43-positive inclusions can be found in many areas of the CNS, including remaining anterior horn cells in diseased spinal cord. The identification of mutations associated with both ALS and FTLD-TDP supports the concept that these conditions represent opposite ends of the same disease continuum .

What approaches are used to identify TARDBP mutations in patient cohorts?

Researchers typically employ direct sequencing of the TARDBP gene, particularly targeting exon 6 where most disease-causing mutations are located. For example, in the study by Kabashi et al., TARDBP was sequenced in 259 patients with ALS, FTLD, or both. After identifying variants, researchers use TaqMan-based SNP genotyping to screen for these variants in control groups matched for age and ethnic origin. Additional clinical, genetic, and pathological assessments are conducted in families with identified mutations to establish pathogenicity .
The process typically involves:

• PCR amplification of TARDBP exons

• Sanger sequencing or next-generation sequencing

• Comparison with control populations

• Cosegregation analysis in families

• In silico prediction of mutation effects

• Functional validation studies

What cellular and animal models are effective for studying TARDBP mutations?

Several model systems have been developed to study TARDBP mutations:

• iPSC-derived neurons: Researchers are using induced pluripotent stem cells (iPSCs) from patients with TARDBP mutations or CRISPR/Cas9 gene editing to generate neurons carrying specific mutations. This approach allows for studying the effects of mutations in human neurons in a more physiologically relevant context .

• CRISPR/Cas9 knock-in models: This technique enables the creation of specific mutations in cell lines or animal models. For example, researchers have generated homozygous knock-in iPSC lines carrying point mutations in TARDBP that express TDP-43 A382T or TDP-43 G348C at endogenous levels .

• Transgenic mice: Various transgenic mouse models expressing mutant TDP-43 have been developed to study disease mechanisms in vivo.

• Drosophila and zebrafish models: These organisms provide additional platforms for studying TARDBP mutations in vivo.

What are the key considerations in designing experiments to assess TDP-43 function?

When designing experiments to assess TDP-43 function, researchers should consider:

• Expression levels: TDP-43 is highly sensitive to expression levels, and both overexpression and knockdown can cause toxicity. Using endogenous expression systems or carefully controlled expression is critical.

• Cellular context: Different cell types may respond differently to TDP-43 mutations, with neurons being particularly vulnerable.

• Temporal dynamics: Acute versus chronic effects of TDP-43 dysfunction may differ.

• Subcellular localization: Tracking the distribution of TDP-43 between the nucleus and cytoplasm is important as mislocalization is a pathological hallmark.

• Downstream targets: Assessing effects on RNA processing, including splicing, stability, and transport of target RNAs.

• Protein interactions: Evaluating interactions with other proteins, particularly hnRNPs and other RNA-binding proteins.

• Post-translational modifications: Analyzing phosphorylation and other modifications that affect TDP-43 function and aggregation .

How is TARDBP conserved across species?

TARDBP is highly conserved across species, with a maximal divergence of only 3.4% among primates. This high level of conservation suggests critical functional importance. The gene exhibits characteristics typical of genes with multiple retropseudogenes: it produces short transcripts (coding for 61 to 414 amino acids), is widely and highly expressed, has low GC-content (47% average among 23 primate species), and is highly conserved .

What is known about TARDBP retropseudogenes in human evolution?

TARDBP has multiple retropseudogenes in primate genomes, which are non-functional copies of the gene formed through retrotransposition. The number of TARDBP retropseudogenes appears to be higher in apes compared to the average number of retrocopies per parental gene in their genomes. On average, ape genomes possess 2.9 retrocopies per parental gene, but five TARDBP retropseudogenes have been identified in each examined ape species. New World monkeys have an even higher number of TARDBP retropseudogenes, possibly related to a specific lineage expansion of L1PA1 and L1P3 subelements .
These retropseudogenes can be identified through BLASTN searches against whole genome sequences, looking for sequences containing all exons together and found on different chromosomes compared to the functional copy. The identified retropseudogenes have a similar length (mean 1128 bp, median 1193 bp) to the functional TARDBP gene (1245 bp), consistent with the slow rate of pseudogene length shortening over time .

How do specific TARDBP mutations correlate with clinical presentations?

Different TARDBP mutations may be associated with varying clinical presentations, as summarized in the table below:

What are the challenges in developing therapeutic approaches targeting TDP-43?

Developing therapeutics targeting TDP-43 presents several challenges:

• Mechanistic complexity: Both gain- and loss-of-function mechanisms have been proposed for TARDBP mutations, making it difficult to determine the optimal therapeutic approach.

• Essential protein: TDP-43 is essential for cellular function, so complete inhibition would likely be detrimental.

• Multiple downstream effects: TDP-43 regulates numerous RNA targets and interacts with many proteins, making it challenging to address all affected pathways.

• Diverse clinical presentations: TARDBP mutations are associated with a spectrum of clinical presentations, suggesting potentially diverse underlying mechanisms.

• Blood-brain barrier penetration: Developing compounds that effectively cross the blood-brain barrier remains a challenge for CNS-targeted therapeutics.

• Timing of intervention: Determining the optimal time point for therapeutic intervention in progressive neurodegenerative diseases is difficult.
  Potential therapeutic approaches being explored include antisense oligonucleotides to modulate TDP-43 expression, small molecules to prevent aggregation, and gene therapy approaches .

What are the key unanswered questions regarding TARDBP in human disease?

Several critical questions remain to be addressed:

• What are the primary mechanisms by which TARDBP mutations cause neurodegeneration?

• Why do TARDBP mutations predominantly affect specific neuronal populations?

• How do TARDBP mutations interact with other genetic and environmental risk factors?

• What is the full spectrum of clinical presentations associated with TARDBP mutations?

• Can TDP-43 pathology serve as a biomarker for disease progression or therapeutic response?

• What is the relationship between TDP-43 and other neurodegenerative disease proteins (tau, alpha-synuclein, etc.)?

• How do post-translational modifications affect TDP-43 function and aggregation?

What emerging technologies will advance TARDBP research?

Several emerging technologies hold promise for advancing TARDBP research:

• CRISPR/Cas9 gene editing: This technology allows for precise introduction of TARDBP mutations in cellular and animal models, as well as correction of mutations in patient-derived cells .

• Single-cell transcriptomics: This approach can reveal cell-type specific effects of TARDBP mutations and identify particularly vulnerable neuronal populations.

• Cryo-electron microscopy: This technique can provide structural insights into TDP-43 aggregates and how mutations affect protein conformation.

• Proteomics and interactomics: These approaches can identify the full complement of TDP-43 interacting partners and how mutations affect these interactions.

• In vivo imaging: Development of ligands that bind to TDP-43 aggregates could enable tracking of pathology in living patients.

• Organoids and advanced tissue culture models: These systems can better recapitulate the complex cellular environment of the human brain.