Hypoxic stimulation of DCLK1 transcription and alternative-promoter switching fuels tumor malignancy in clear cell renal cell carcinoma

Alterations in the diversity and abundance of oncogenic gene transcripts are key factors driving tumor initiation and progression. DCLK1, an emerging cancer stem cell marker, is activated during tumorigenesis, triggering cancer stemness and metastasis. It produces long or short isoforms through selective usage of alternative promoters (α- or β-promoter). However, the mechanism mediating DCLK1 activation and choice of AP model in cancer remains unclear. Herein, we reveal that DCLK1 is significantly activated, with a concomitant alternative-promoter model switch (β-to-α) towards the long variants (isoform 1 and 2) in clear cell renal cell carcinoma (ccRCC). During tumorigenesis, the α-promoter is initiated with an improved probability from 31.6% to 61.1%, whereas the initiation probability of the β-promoter declined from 68.4% to 38.9%. Mechanistically, this alteration is mediated by a hypoxia-HIF2α-PLOD2 axis, which further activates β-catenin to selectively bind and activate the α-promoter. Our findings also showed that the hyperactivated PLOD2-DCLK1-L axis in ccRCC is correlated with a higher EMT signature and predicts an unfavorable prognosis in ccRCC patients, while disrupting this signaling by pharmacological targeting of DCLK1-L significantly attenuated cancer malignancy both in vitro and in vivo. These findings couple hypoxia signaling to oncogenic alternative switching and highlight DCLK1-L as a promising therapeutic target for hypoxic PLOD2-rich ccRCCs.