Resources for Researchers

Catalyzing TBXT Drug Discovery

TBXT, also called Brachyury, is a key driver and genetic dependency of chordoma, and is associated with disease progression in various other tumor types. With minimal expression in most normal tissues, targeting TBXT represents a promising therapeutic opportunity. Realizing that opportunity is a key pillar in our strategy to improve outcomes for chordoma patients.

  1. Resources for researchers
  2. Catalyzing TBXT Drug Discovery

Our approach

To bring TBXT targeting therapies to chordoma patients, the Chordoma Foundation is actively working to enable, de-risk and accelerate every stage of the TBXT drug discovery and development process through:

  • Funding basic research in TBXT function

  • Developing shared research-enabling resources, tools and datasets

  • Offering a range of discovery biology and translational research capabilities through Chordoma Foundation Labs

  • Collaborating with companies and researchers to enable efficient drug development

Working together

Leveraging our laboratory capabilities, we aim to collaborate with companies and researchers to advance TBXT-targeting molecules through all stages of development.

Our support is tailored to meet the specific needs of each program.

We invite you to get in touch with our team to explore how we can complement your unique expertise and interests to drug TBXT.

Hit identification and validation

We provide access to high-throughput screening assays to identify TBXT-targeting molecules and assess their potential. Our goal is to lower the entry barrier to targeting TBXT and enable rapid go/no-go decisions.

Hit-to-lead optimization

We can support iterative assay/design cycles to facilitate further optimization of TBXT-targeting compounds towards identification of lead candidates.

Lead optimization and beyond

We’re interested in entering into partnerships to advance candidates through lead optimization, preclinical development, and ultimately through IND filing and clinical development.

Available resources

Purified TBXT protein

  • Recombinant TBXT (full-length protein or the isolated DNA-binding domain) expressed in E.coli and purified using affinity and size-exclusion chromatography

  • Full-length TBXT (C-terminal AviTag)

  • DNA binding domain (coming soon)

Cell proliferation assays

Relevant data sets
Our partners at the Structural Genomics Consortium (SGC) have produced the following open access datasets relevant to TBXT drug discovery:

Preclinical chordoma models

  • We’ve assembled a collection of validated and well-characterized chordoma cell lines, CDX and PDX models which are available in our repositories. Learn more here.

Available capabilities

Engineered cell lines

  • We engineered chordoma and other TBXT-positive tumor cell lines to express a doxycycline-inducible TBXT shRNA. Inducible TBXT knockdown has been validated by Western blots, immunofluorescence, and/or RT-PCR. These lines also constitutively express GFP. The following engineered cell lines are available via collaboration with CF Labs:
    • U-CH1 (chordoma) TBXT shRNA
    • H460 (NSCLC) TBXT shRNA
    • SW480 (colorectal) TBXT shRNA

Binding and structural assays

  • Surface plasmon resonance (SPR): We use a Biacore 8K SPR System to discover TBXT ligands. Purified, biotinylated TBXT is immobilized on a streptavidin-coated sensor chip and binding of compounds to TBXT is assessed using steady-state affinity. You can learn more about our protocol here.

  • Biomolecular NMR (coming soon)

  • Crystallography (coming soon)

  • Structural bioinformatics (coming soon)

TBXT reporter assay

  • To determine whether compounds functionally inhibit TBXT, we engineered H460 cells to express GFP downstream of a TBXT response element. We can assess TBXT inhibition in high throughput by monitoring GFP levels using a fluorescence plate reader.

Functional assays

  • Gene reporter assay to assess inhibition of TBXT’s transcriptional activity

  • qRT-PCR to measure expression of TBXT target genes including TBXT, YAP1, and KRT8

Xenograft efficacy studies

Mechanism of action studies

  • DNA-binding inhibition (electrophoretic mobility shift assay/DNA gel-shift assay protocol)

  • TBXT degradation and rescue assay

Why TBXT?

TBXT expression is a near-universal hallmark of chordoma. This transcription factor is an essential regulator of embryonic notochord development, and a growing body of evidence suggests it is a master regulator of chordoma and required for tumor growth. Notably, functional genomics studies have identified TBXT as a key genetic essentiality in chordoma cells. It also appears to be minimally expressed in healthy adult tissues – making it an attractive therapeutic target.

Beyond chordoma, TBXT has also been associated with tumor progression, therapy resistance, and poor patient outcomes in several other cancers, including lung, colon, breast, and prostate.

This underscores TBXT's potential value as a drug target with relevance well beyond chordoma.

(Photo: Chordoma patient Dimitrios visits Chordoma Foundation Labs with his father, Theodore)

More about TBXT’s role in chordoma and other solid tumors

Engage with us

If you are a company or investigator interested in exploring TBXT as a therapeutic target, we welcome you to reach out to learn more about how we can support your efforts.

Or, if you’re a funder or donor whose goal is to make a meaningful impact in the fight against chordoma and other TBXT-associated cancers like lung, colon, breast, and prostate, we invite you to consider a contribution to this work.

Some notable outcomes of our TBXT drug discovery efforts: