Fig. 1: FOXQ1 interacts with the KMT2A/MLL1 complex in EMT.

a Network analysis (Cytoscape v 3.7.1) of the 100 most significant proteins bound to FOXQ1 identified through tandem affinity purification (TAP) and mass spectrometry proteomics. Fischer’s Exact T-test was conducted on candidate proteins’ normalized, mapped peptide counts. We highlighted several complexes, including four subunits that comprise the KMT2/MLL core complex (RbBP5, ASH2L, WDR5, and DPY30). FOXQ1 and LACZ TAP were performed in duplicate. b Co-immunoprecipitation of FOXQ1 from stable HMLE/FOXQ1 cells (with antibody against a C-terminal V5-epitope tag) validates protein interaction with the endogenous MLL core complex proteins (RbBP5, ASH2L, WDR5) within the context of EMT induction. c The binary interacting partner of FOXQ1 was assessed by GST pull-down. Purified GST-FOXQ1, or GST alone, was incubated at equimolar concentration with individual recombinant MLL core complex proteins (RbBP5, ASH2L, WDR5). Western blots were probed for with an antibody that recognizes the native protein as indicated. d–f Endogenous Co-IP of RbBP5, or IgG control, was performed in triple-negative breast cancer cell lines. IPs were probed with an antibody recognizing endogenous FOXQ1 to detect a protein interaction. d MDA-MB-231, e SUM1315, f MDA-MB-436. g Protein lysates from patient tumor samples of various types were used to test the endogenous interaction of FOXQ1 and RbBP5. Tumor lysates were subject to IP anti-RbBP5 antibody or IgG control. Samples were analyzed by western blot and probed with anti-FOXQ1 antibody. LG is a lung tumor tissue. CTG is an ovarian tumor tissue. B2926, TNBC1, and TNBC2 are all triple-negative breast cancer tumors. h–m HMLE/FOXQ1 cell lysate was utilized for immunoprecipitation toward identifying the KMT2/MLL enzymatic subunit(s) associated with FOXQ1. HMLE/FOXQ1 lysate was subject to IP with antibody against each of the six KMT2/MLL family members, alongside an IgG control, and assessed for the presence of FOXQ1 binding by western blots probed with anti-V5 antibody. An interaction was detected between FOXQ1 and KMT2A/MLL1 (h) and was absent in IP samples for other KMT2/MLL members (i–m). For panels b–m, representative images are presented (n = 3). Unprocessed western blot images are provided in Source data 2.