(A) Efficacy studies of molecularly guided targeted therapy. BL0269 overexpressed HER2 and Src. Compared to the control group of median progression-free survival (PFS) of 13 days, a HER2 inhibitor lapatinib and a Src inhibitor ponatinib had little effect in suppressing tumor growth with a median PFS of 12 (p = 0.16) and 18 (p = 0.11) days, respectively. In contrast, lapatinib was very effective in BL0440 that expressed both HER2 and HER3 with PFS of 25.4 days versus 18.4 days in the control group (p = 0.0007). In BL0269 which also harbored a PIK3CA activation mutation H1047R, a PIK3CA inhibitor BEZ235 significantly suppressed tumor growth (p<0.0001). (B) Studies of efficacy and secondary resistance mechanisms of BGJ398 in BL0293. BL0293 overexpressed FGFR3. Compared to the control group of PFS at 9.5 days, an FGFR3 inhibitor BGJ398 significantly prolonged PFS to 18.5 days (p = 2. 61 X 10−6). Mice were sacrificed and PDXs were harvested (red arrows) before treatment, at Day 3 and at Day 17 (time of resistance) for western blot. Low levels of p-Akt and p-Erk at the baseline and at Day 3, suggesting low downstream signaling activity of FGFR3. Upon the development of resistance to BGJ398 at Day 17, both p-Akt and p-Erk levels increased, suggesting re-activation of the downstream signaling activity. BGJ398-resistant PDX BL0293 was re-implanted in NSG mice to form xenografts. Mice carrying BGJ398-resistant BL0293 were treated with PBS control, BGJ398, or a Raf inhibitor sorafenib plus a PIK3CA inhibitor BEZ235 combination. Compared to the BGJ398 group, treatment of BGJ398-resistant PDX with sorafenib and BEZ235 significantly prolonged PFS from 12 days to 22 days (p = 0.001). (C) Screening for effective chemotherapeutic agents. The first six PDXs were tested for sensitivity to cisplatin, gemcitabine or combination of both drugs. Only BL0440 was sensitive to cisplatin while only BL0269 and BL0479 were resistant to gemcitabine. Resistance to cisplatin could be overcome by gemcitabine, leaving four of these six PDXs sensitive to the combination therapy.