Rodriguez-Antona, C. | bioRxiv Science

bioRxiv2025

Identification of a novel papillary renal cell carcinoma molecular subtype characterized by HIF-pathway over-activation

PurposePapillary renal cell carcinoma (pRCC), the second most common subtype of renal cancer, exhibits heterogeneity in molecular features and response to targeted therapies, including antiangiogenic drugs. Discovering molecular biomarkers able to stratify pRCC patients into clinically relevant subgroups and understanding the underlying mechanisms are urgently needed to advance precision medicine. Here, we molecularly dissect a large pRCC series through the expression of the targets of hypoxia inducible factors (HIF), master regulators of angiogenesis, metabolic reprogramming and immune microenvironment. Experimental DesignWe merged and analyzed multi-omic and clinical data of 346 patients derived from two pRCC series (TCGA-KIRP and a Spanish metastatic series). Altered pathways and differences in tumor microenvironment were identified through tumor transcriptomic analyses. Tumor metabolome analysis was performed in selected cases. ResultsMolecular revision of driver mutations classified 302 patients as pRCC, while uncovering misclassified cases. Analysis of HIF targets gene expression identified a subset of pRCC tumors with increased HIF activity (31%; "HIF-active"). These tumors were characterized by high hypoxia scores, increased angiogenesis, low expression of Krebs cycle genes and mitochondrial activity, high immune infiltration and increased epithelial-mesenchymal transition (P<0.0001; each feature) and they were associated with increased metastasis risk and worse overall survival (P<0.005). Metabolome analyses revealed that HIF-active tumors accumulated L-2-hydroxyglutarate (L-2-HG), an oncometabolite that leads to pseudohypoxia by inhibiting HIF prolyl hydroxylases and preventing HIF degradation. L-2-HG-accumulation agreed with diminished L2HGDH expression, associated with losing one copy of the gene and low expression of PPARGC1A, which regulates its transcription. ConclusionsHIF-pathway overactivation defines a pseudohypoxic pRCC molecular subgroup characterized by high angiogenesis, immune infiltration and aggressive features. These findings advance our understanding of pRCC diversity, revealing potential clues for the variable response of patients to targeted therapies and paving the way to more personalized pRCC treatments.

cancer biology↗

bioRxiv2023

Tumour mitochondrial DNA mutations drive aerobic glycolysis to enhance checkpoint blockade

The mitochondrial genome encodes essential machinery for respiration and metabolic homeostasis but is paradoxically among the most common targets of somatic mutation in the cancer genome, with truncating mutations in respiratory complex I genes being most over-represented1. While mitochondrial DNA (mtDNA) mutations have been associated with both improved and worsened prognoses in several tumour lineages1-,3, whether these mutations are drivers or exert any functional effect on tumour biology remains controversial. Here we discovered that complex I-encoding mtDNA mutations are sufficient to remodel the tumour immune landscape and therapeutic resistance to immune checkpoint blockade. Using mtDNA base editing technology4 we engineered recurrent truncating mutations in the mtDNA-encoded complex I gene, Mt-Nd5, into murine models of melanoma. Mechanistically, these mutations promoted utilisation of pyruvate as a terminal electron acceptor and increased glycolytic flux without major effects on oxygen consumption, driven by an over-reduced NAD pool and NADH shuttling between GAPDH and MDH1, mediating a Warburg-like metabolic shift. In turn, without modifying tumour growth, this altered cancer cell-intrinsic metabolism reshaped the tumour microenvironment in both mice and humans, promoting an anti- tumour immune response characterised by loss of resident neutrophils. This subsequently sensitised tumours bearing high mtDNA mutant heteroplasmy to immune checkpoint blockade, with phenocopy of key metabolic changes being sufficient to mediate this effect. Strikingly, patient lesions bearing >50% mtDNA mutation heteroplasmy also demonstrated a >2.5-fold improved response rate to checkpoint inhibitor blockade. Taken together these data nominate mtDNA mutations as functional regulators of cancer metabolism and tumour biology, with potential for therapeutic exploitation and treatment stratification.

cancer biology↗