LRPPRC promotes glycolysis by stabilising LDHA mRNA and its knockdown plus glutamine inhibitor induces synthetic lethality via m⁶A modification in triple-negative breast cancer

Abstract

Background: Targeted therapy for triple-negative breast cancer (TNBC) remains a challenge. N6-methyladenosine (m⁶A) is the most abundant internal mRNA modification in eukaryotes, and it regulates the homeostasis and function of modified RNA transcripts in cancer. However, the role of leucine-rich pentatricopeptide repeat containing protein (LRPPRC) as an m⁶A reader in TNBC remains poorly understood.

Methods: Western blotting, reverse transcription-polymerase chain reaction (RT-qPCR) and immunohistochemistry were used to investigate LRPPRC expression levels. Dot blotting and colorimetric enzyme linked immunosorbent assay (ELISA) were employed to detect m⁶A levels. In vitro functional assays and in vivo xenograft mouse model were utilised to examine the role of LRPPRC in TNBC progression. Liquid chromatography-mass spectrometry/mass spectrometry and Seahorse assays were conducted to verify the effect of LRPPRC on glycolysis. MeRIP-sequencing, RNA-sequencing, MeRIP assays, RNA immunoprecipitation assays, RNA pull-down assays and RNA stability assays were used to identify the target genes of LRPPRC. Patient-derived xenografts and organoids were employed to substantiate the synthetic lethality induced by LRPPRC knockdown plus glutaminase inhibition.

Results: The expressions of LRPPRC and m⁶A RNA were elevated in TNBC, and the m⁶A modification site could be recognised by LRPPRC. LRPPRC promoted the proliferation, metastasis and glycolysis of TNBC cells both in vivo and in vitro. We identified lactate dehydrogenase A (LDHA) as a novel direct target of LRPPRC, which recognised the m⁶A site of LDHA mRNA and enhanced the stability of LDHA mRNA to promote glycolysis. Furthermore, while LRPPRC knockdown reduced glycolysis, glutaminolysis was enhanced. Moreover, the effect of LRPPRC on WD40 repeat domain-containing protein 76 (WDR76) mRNA stability was impaired in an m⁶A-dependent manner. Then, LRPPRC knockdown plus a glutaminase inhibition led to synthetic lethality.

Conclusions: Our study demonstrated that LRPPRC promoted TNBC progression by regulating metabolic reprogramming via m⁶A modification. These characteristics shed light on the novel combination targeted therapy strategies to combat TNBC.

Keywords

LDHA / LRPPRC / metabolic reprogramming / N ⁶-methyladenosine / synthetic lethal / triple-negative breast cancer

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2024 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.