ABSTRACT Chordomas are spinal neoplasms uniquely characterized by their overexpression of the transcription factor brachyury. Beyond its role as a biomarker, brachyury is critical for disease pathogenesis and therefore appears to be an attractive target for therapy. However, development of strategies targeting brachyury has had slow progress. Complete surgical resection, the current gold standard treatment, is not always feasible. Radiotherapy is the main adjuvant treatment, but unfortunately brachyury is known to mediate radio-resistance, as well as chemo- resistance. Thus, interest in novel T cell-based immunotherapies arose, but they too yielded poor results. We hypothesize that the latter is due to defective HLA class I antigen processing machinery (APM) component expression in chordoma cells. Indeed, T cell-based immunotherapies are dependent on the presentation of tumor antigen peptides to the host’s immune system, requiring that HLA class I APM is fully functional. Our analysis of a small number of surgically removed chordoma tumors has shown that HLA class I APM expression defects are frequent in chordoma cells. The underlying molecular mechanisms behind these defects have been poorly characterized. Our goal is therefore to investigate the mechanisms underlying HLA class I APM component expression defects in chordoma cells. We focus on brachyury and the protein tyrosine phosphatase SHP2 which we have previously shown to play a role in HLA class I APM component downregulation in other cancer types. We have found that higher SHP2 expression is associated with lower HLA class I APM component expression in chordoma cell lines, and that SHP2 expression is positively correlated with brachyury expression. Furthermore, YAP1, a direct target of brachyury in chordoma which is associated with HLA class I APM component downregulation in other tumor types, was found to interact with SHP2. This was demonstrated by the presence of a YAP1 binding site on conserved regions of the SHP2 promoter. In turn, SHP2 has been shown to suppress HLA class I APM component expression by inhibiting phosphorylation of STAT1, a transcription factor required for HLA class I APM component expression. Overall, these data support the model Brachyury YAP1 SHP2 pSTAT1 HLA class I APM, demonstrating a potential role of brachyury in HLA class I APM component downregulation in chordoma cells, via upregulation of SHP2. Therefore, we aim to: i) delineate the potential role of brachyury in HLA class I APM component downregulation in chordoma cells; ii) assess the in vivo ability of small molecule SHP2 inhibitor SHP099 to restore HLA class I APM component expression and functional activity in chordoma cells; and iii) assess the clinical significance of the hypothesized model by determining the association of HLA class I APM component expression with the expression of brachyury, YAP1 and SHP2 in surgically removed tumors. The results obtained will contribute to the rational design...