Fig 2: PAX8 and MECOM sustain ovarian cancer growth.A Barplot showing sensitivity to PAX8 or MECOM KO as per CRISPR screens reported in DepMap portal. Bars are color coded by MECOM expression. B, C Tumor volume measurements of NIH:OVCAR3 cells bearing shRNAs against PAX8 (B) or MECOM (C). Trt start = day of starting daily doxycycline treatment. *P < 0.01 and ***P < 0.0001 signify significantly and highly significant differences to the respective vehicle (two-sided t test post hoc) on the last treatment day. Data are presented as mean ± SEM from n > 5 mice cohorts. D Western blot analysis of tumors from (B) 1 week after treatment start. E Boxplot of z-score expression of PAX8–MECOM Signature (Sig. Score) in TCGA ovarian cases (n = 608) binned according to MECOM (left) or PAX8 (right) expression quartiles. Boxplots represent median and first and third quartiles, and whiskers extend to 95th percentile. P values are based on two-sided Wilcoxon’s rank-sum test. F Kaplan–Meier curve of survival from TCGA ovarian and endometrial patients bearing high or low levels of Signature Score (top and bottom quartile, n = 746). P P value from log-rank test. Source data for Western blots and qPCRs are provided as a Source Data file.

Fig 3: CAP restores thyroid-specific gene expression and enhances radioiodine uptake of ATC cells. (A) 8505C cells were incubated with CAP (50‒200 µM) for 24 h and then the mRNA levels of TTF-1, TTF-2, PAX8, NIS, TSHR, and TPO were analyzed by qPCR. *P < 0.05, **P < 0.01, ***P < 0.001 vs. SC, one-way ANOVA. (B) 8505C cells were treated with different concentrations of CAP (50‒200 µM) for 24 h and then the protein levels of TTF-1, PAX8, NIS, TSHR, and TPO were analyzed by western blotting. Tubulin was used as an internal loading control. (C) 8505C cells were pretreated with CAP (200 µM) for 24 h followed by CHX (50 µg/ml) treatment for the indicated periods of time. Whole-cell lysate was extracted at each time point and immunoblotted with anti-TTF-1 or GAPDH antibody. GAPDH was used as a loading control. The protein bands were quantified by optical densitometry using ImageJ software, and the remaining protein levels of TTF-1 were plotted against time points. (D) After 8505C cells were treated with CAP for 24 h, the membranal and cytoplasmic proteins were extracted, respectively. The subcellular localization of NIS on membrane or cytoplasm was detected by western blotting. EGFR and tubulin served as membranal (Mem) and cytoplasmic (Cyto) loading controls, respectively. (E) 8505C cells were pretreated with CAP (50‒200 µM) for 24 h, followed by incubation with 37 kBq Na131I for additional 1 h in the presence or absence of 100 µM NaClO4. After three times of wash by ice-cold PBS, the radioactive iodine accumulated in 8505C cells was measured using a gamma-counter. **P < 0.01 vs. SC, one-way ANOVA. (F) 8505C cells were treated with the vehicle (DMSO), CAP (200 µM), rTSH (5 mU/ml), or CAP (200 µM) in combination with rTSH (5 mU/ml) for 24 h in the presence or absence of 100 µM NaClO4, and then the radioiodine uptake of cells was detected. **P < 0.01, ***P < 0.001, one-way ANOVA. The data shown represent mean ± SEM of three independent experiments (n = 3).

Fig 4: Core regulatory circuitry analysis identified PAX8 as a candidate oncogene in RCC. a Diagram of the experimental/computational pipeline to identify critical TFs in RCC. b CRC mapper output as TFs (x-axis) ranked by total degree (y-axis) in RCC. Total degree is a measure of a TFs’ contribution based on how often a given TF can participate in a regulatory interaction with the other TFs. c Sensitivity profile for CRC TFs (x-axis) in combined shRNA datasets (DRIVE, Achilles, Marcotte), where smaller values indicate that the cell line is more dependent on a given gene. Empty dots represent the sensitivity score for each TF in a RCC cell line. Colored dots represent the cell lines originally used in the CRC mapping. Shaded gray represents the distribution of sensitivity values for each TF in cell lines from other lineages. Horizontal dashed line at −1 represents the threshold for significant dependency. d Western blot validation of PAX8 knockdown efficacy in 786o cells infected with dox-inducible shRNAs. e Colony formation assay of 786o cells bearing various doxycycline-inducible shRNAs performed during 10 days. PLK1 is an essential gene in 786o cells and it is a positive control in this assay. f Cell cycle analysis by flow cytometry using PI-BrdU labeling in RCC cell lines bearing shPAX8_1581 upon 4 days of treatment with doxycycline

Fig 5: Bioinformatics analysis of TTFs and thyroid iodine-metabolizing genes in the combined GEO cohort of thyroid cancers. (A−F) Robust RMA expression values of TTF-1 (A), TTF-2 (B), PAX8 (C), TPO (D), TSHR (E), and SLC5A5 (F) were compared among normal thyroid tissues, PTCs, FTCs, PDTCs, and ATCs in the combined GEO cohort. *P < 0.05, **P < 0.01, ***P < 0.001, one-way ANOVA.