YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition

Abstract

The YTHDF protein family plays a critical role in cancer development by recognizing and regulating the stability of N6-methyladenosine (m⁶A)-modified RNA. Here, we reveal an autophagy-dependent mechanism controlling YTHDF protein levels. Using contact inhibition as a cellular model system, we show YTHDF proteins to be rapidly degraded, coinciding with increased autophagy and decreased mTOR activity. Upon pharmacological mTOR inhibition, YTHDF2 is also downregulated via lysosomal degradation. YTHDF2 selectively interacts with the autophagy modifier GABARAP L2 through LC3-interacting region (LIR) motifs in its unstructured N- and C-terminal regions. Autophagic YTHDF2 downregulation results in the co-degradation of its bound m⁶A-modified RNA clients. While YTHDF depletion induces cell death in contact-inhibition-deficient HCT116 cancer cells, contact-inhibited MRC5 and RPE1 cells remain unaffected. Our findings uncover a regulatory pathway that governs YTHDF protein stability with significant implications for cancer biology and cell fate determination and suggest the existence of an autophagy-mediated degradation pathway for m⁶A-modified RNA.

Keywords: CP: Cell biology; RNA binding; YTHDF; cancer; cellular homeostasis; contact inhibition; lysosomal degradation; m6A; selective autophagy.