N⁶-Methyladenosine mRNA Forms Condensates to Promote AML Cell Survival

Messenger RNA can be posttranscriptionally regulated via modifications including N⁶-methyladenosine (m⁶A), and dysregulation of m⁶A modifications has been implicated in cancer. In myeloid leukemias, m⁶A has been shown to be required for tumorigenesis, but mechanisms by which m⁶A controls cell differentiation and survival are unknown. To investigate downstream effects of m⁶A, Cheng, Xie, and colleagues studied YTHDC1, a gene encoding a nuclear m⁶A reader. YTHDC1 scored as the top essential gene encoding a reader in a genome-wide CRISPR screen in acute myeloid leukemia (AML) cell lines. AML cell lines and primary patient samples expressed high levels of YTHDC1 mRNA and YTHDC1 protein, and knockdown of YTHDC1 inhibited cell proliferation, increased differentiation and apoptosis, and extended survival in a murine xenograft model. Given the intrinsically disordered regions within YTHDC1, recombinant EGFP–YTHDC1 was found to undergo droplet formation, which was enhanced in the presence of m⁶A-mRNA. Consistent with this observed liquid–liquid phase separation, endogenous EGFP-tagged YTHDC1 formed nuclear puncta and displayed liquid–liquid-like properties, providing evidence for YTHDC1-mediated condensate formation in AML cells. Nuclear YTHDC1–m⁶A condensates were essential for AML cell survival, as YTHDC1 mutants that were deficient in binding m⁶A were unable to form puncta and insufficient to rescue the decreased proliferation and increased differentiation observed upon YTHDC1 knockdown. RNA-sequencing analysis suggested that YTHDC1 promoted proliferation and inhibited myeloid differentiation, whereas protein–RNA interaction studies provided support for direct YTHDC1–m⁶A-mRNA binding and subsequent expression of mRNA targets, including MYC. The effects of YTHDC1 depletion on decreased proliferation and enhanced myeloid differentiation were partially rescued by MYC overexpression, highlighting MYC as an important functional target of YTHDC1. Nuclear YTHDC1–m⁶A condensates contributed to expression of m⁶A mRNA targets such as MYC by protecting mRNA from PAXT-driven nuclear exosome degradation. Together, this work describes a mechanism by which a nuclear reader promotes leukemogenesis via liquid–liquid phase separation and elucidates the functional role for m⁶A-modified mRNA in AML.

Cheng Y, Xie W, Pickering BF, Chu KL, Savino AM, Yang X, et al. N⁶-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer Cell 2021 May 27 [Epub ahead of print].

Note: Research Watch is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at http://cancerdiscovery.aacrjournals.org/CDNews.