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Ballesio, F.

Publications and source records attributed to Ballesio, F..

2 recordsLinked to original sources

A tumor metabolism-angiogenesis-immune axis governs immunotherapy responses

Despite the clinical success of immunotherapy, long-lasting benefit remains restricted to a subset of patients. Tumor metabolic adaptation is emerging as a key factor limiting immunotherapy efficacy. We previously found that glycolysis-low tumor variants, compared to the parental glycolytic tumors, better respond to neoadjuvant CTLA-4 immune checkpoint blockade (ICB) therapy. Here, we investigated new rational modalities to restore immune sensitivity of glycolytic tumors by studying how lowering the tumor-cell glycolytic capacity reshapes the tumor microenvironment (TME) to favor long-lasting systemic anti-tumor responses upon immunotherapy. We found that lowering glycolysis in cancer cells through LDHA-knock down (KD) results in TME displaying normalized vasculature, reduced angiogenic markers, increased high endothelial venules (HEVs), and enhanced recirculation of CD8+ T cells both in and out of the tumor. By leveraging public transcriptomic data sets from human solid cancers, we confirmed that glycolysis positively correlates with neo-angiogenesis and inversely correlates with features of vascular normalization and immune cytolytic activity. Moreover, a tumor signature that incorporates glycolysis- and angiogenesis-related genes as positive features, and normal vasculature, HEV, and immune cytolytic activity genes as negative features predicted poor outcomes better than the individual features across most human solid tumor types in the TCGA. To determine the therapeutic implication of these interrelated processes, we asked if targeting the vasculature would restore immunotherapy responses in glycolytic tumors. We found that combining low-dose anti-VEGFR2 with CTLA-4 blockade induces tumor regressions and protection from metastases in glycolytic tumors. These therapeutic effects were associated with vasculature normalization and increased abundance of HEVs and concentrations of lymphangiogenic factors in the TME of glycolytic tumors. Moreover, anti-VEGFR2 with anti-CTLA-4 restored recirculation of anti-tumor CD8+ T cells in and out of the TME in glycolytic tumors, with specific increases in intratumoral recruitment and activation of cytolytic CD62LCD44CD8 T cells expressing VEGFR2 and low levels of CTLA-4, suggesting potential novel direct synergistic effects of anti-VEGFR2 and anti-CTLA-4 on CD8+ T cells. Conversely, this combination opposed the beneficial immune and vascular TME features of LDHA-KD tumors, indicating tumor-metabolic-dependent effects. Accordingly, we found that standard combined regimens of anti-VEGF and ICB therapy improve survival with respect to ICB alone in patients with glycolysis-high but not glycolysis-low tumors. Together, these findings indicate that tumor cell glycolysis "primes" the TME for aberrant vascular architecture and T-cell exclusion, and that modulating the tumor vasculature can unravel these mechanisms restoring immune responsiveness. This suggests that tailoring anti-angiogenic and immunotherapy combinations to the tumor glycolytic state and associated vasculature profiles may restore immune surveillance and overcome therapy resistance.

immunology↗

Human lncRNAs harbor conserved modules embedded in different sequence contexts

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human lncRNA exons and identified 340 pairs of exons with high sequence and/or secondary structure similarity but embedded in a dissimilar sequence context. We grouped these pairs in 106 clusters based on their reciprocal similarities. These shared modules are highly conserved between humans and the four great ape species, display evidence of purifying selection and likely arose as a result of recent segmental duplications. Our analysis contributes to the understanding of the mechanisms driving the evolution of the non-coding genome and suggests additional strategies towards deciphering the functional complexity of this class of molecules. Author summaryThe Human genome includes more than 18,000 genes coding for RNAs that are not translated into proteins, called long non-coding RNAs (lncRNA). Mounting evolutionary and experimental evidence shows that a large amount of these RNAs have a specific function, mainly as regulators of a diverse set of biological processes. Here we set out to investigate whether these genes have a modular organization similar to that of protein-coding genes. Accordingly, we compared the sequence of all the exonic regions of human lncRNAs and identified 106 clusters of non-repetitive exonic modules shared between this class of genes. These modules display evidence of purifying selection, are highly conserved between humans and the four great ape species, and may represent distinct functional units that have been shuffled among multiple lncRNA genes, in a manner similar to the exon-shuffling process that is observed in the coding genome.

evolutionary biology↗