Upregulated levels of
TBXT, a transcription factor required during embryogenesis, have been detected in lung, prostate, breast, colon, adenoid cystic and oral squamous cell tumours where its expression is a significant predictor of poor prognosis. In addition,
TBXT is a biomarker of a rare cancer of the spinal column called chordoma. While the expression regulation of
TBXT is well studied in development, including its autoregulation, which is also detected in chordoma, it is unclear how its expression is initiated in cancers. Using circularised chromosome capture combined with sequencing (4C-seq) we have identified near-cis physical interactions with the
TBXT promoter in
TBXT expressing and non-expressing cancer cell lines for chordoma, lung, breast and prostate cancer. While many of the
TBXT genomic interactions are similar in the cancer types, some of the cell lines show exclusive interactions. A total of nine interactions to the
TBXT promoter were found to be distributed in open and active-histone marked genomic regions and three were selected for further testing as putative
TBXT regulatory elements using the Self-Transcribing Active Regulatory Region (STARR-seq) luciferase reporter in
TBXT expressing or non-expressing lung cancer cells. In addition, a human sequence, related to a mouse
TBXT cis-regulatory element (CRE) that drives expression in the mouse embryo and in
TBXT-expressing lung cancers cells, was tested for activity in this assay. Of the putative
TBXT regulatory elements, two showed significant enhancer activity in either non or
TBXT expressing cell lines using the reporter assay, however their activity was not linked to
TBXT expression levels, suggesting they do not regulate
TBXT expression in these cells. Overall, the study identifies a number of putative regulatory elements which need to be validated further, in
in vivo and
in vitro models, in addition to luciferase assays, to properly define whether they have a role in regulating expression of
TBXT in cancer.