Laura Poliseno

MicroRNAs (miRNAs) have the potential to regulate the expression of nearly every transcript in the cell, making the identification of miRNA–mRNA target interactions crucial for understanding their role in diverse biological processes. However, the identification of the miRNAs that regulate a given mRNA remains a challenge. Here, we describe miR-CATCHv2.0, an innovative method for the high-throughput identification of the miRNAs physically interacting with an mRNA of interest. We further highlight how miR-CATCHv2.0 overcomes key limitations of both current computational predictions and existing experimental strategies, enabling a more accurate and comprehensive characterization of physiologically relevant miRNA–mRNA interactions.

K-Rev Interaction Trapped protein-1 (KRIT1) is a scaffold protein that forms functional protein complexes involved in physiologically important signaling networks. While it is primarily recognized for its association with Cerebral Cavernous Malformations (CCMs), KRIT1 may also play critical roles in tumor formation and the acquisition of malignant phenotypes, regulating cell adhesion, cytoskeletal dynamics, and angiogenesis. In this study, we investigated the role of KRIT1 in cancer cell migration and metastasis, with a focus on identifying novel interacting proteins and characterizing the intracellular signaling pathways activated upon its loss. By using a yeast two-hybrid screening, we identified Kinesin Family Member 1C (KIF1C), a protein involved in regulating podosome and invadopodium elongation, as a novel binding partner of KRIT1, and the interaction was confirmed in melanoma and epithelial cancer cells. In silico docking and interaction interface analyses supported the KRIT1–KIF1C interaction, providing structural insight into the binding mode as shown experimentally. We also found that SRC and focal adhesion kinase (FAK) phosphorylation, as well as Ras homolog family member A (RhoA) expression, represent additional pathways affected by the loss of KRIT1. This study confirms our earlier hypothesis that KRIT1 functions as a tumor suppressor and uncovers a compelling link between its loss and enhanced cancer aggressiveness.

The field of non-coding RNA research is advancing at a breathtaking pace, continually uncovering new layers of regulatory complexity and functional diversity

The recalcitrance of Mycobacterium tuberculosis to antibiotic treatment has been broadly attributed to the impermeability of the organism's outer mycomembrane. However, the studies that support this inference have been indirect or reliant on bulk population measurements. We previously developed the Peptidoglycan Accessibility Click-Mediated AssessmeNt (PAC-MAN) method to covalently trap azide-modified small molecules in the peptidoglycan cell wall of live mycobacteria after they have traversed the mycomembrane. Using PAC-MAN, we now show that the mycomembrane differentially restricts access to fluorophores and antibiotic derivatives. Mycomembranes of both M. tuberculosis and the model organism Mycobacterium smegmatis discriminate between divergent classes of antibiotics as well as between antibiotics within a single family, the fluoroquinolones. By analyzing subpopulations of M. tuberculosis and M. smegmatis, we also found that some fluorophores and vancomycin are heterogeneously restricted by the mycomembrane. Our data indicate that the mycomembrane is a molecule- and cell-specific barrier to antibiotic permeation.

The BRAFV600E mutant kinase is widely studied as a cancer driver and therapeutic target. Here, we investigated how the annotation of the BRAF‐reference (ref) and BRAF‐X1 variants has evolved in public databases and addressed challenges posed by their discrimination and quantification from short‐read sequencing. We built IsoWorm, a bioinformatic pipeline tailored to discriminate and quantify BRAF variants, and employed it to analyze > 600 cancer cell lines and > 1000 cancer tissue samples. Using FLIBase, we reanalyzed TCGA data from > 9000 cancer tissue samples. We consistently found that BRAF‐X1 (now BRAF‐204) is very abundant in human cancer and its expression is 1.5–75 times greater than that of BRAF‐ref (now BRAF‐220). Crucially, we identified KIRP‐kidney renal papillary cell carcinoma as a cancer subtype in which a high BRAF‐204/BRAF‐220 ratio is an independent prognostic factor of poor outcome. Our in silico analyses establish BRAF as a mix of two protein‐coding transcript variants, with BRAF‐204 being more highly expressed than BRAF‐220. These findings prompt us to undertake the systematic benchmarking of BRAF‐204 against BRAF‐220 in terms of molecular mechanisms, biological activities, druggability, and clinical relevance.

The Non-coding Journal Editorial Board Members would like to congratulate Victor Ambros and Gary Ruvkun, who were jointly awarded the 2024 Nobel Prize in Physiology or Medicine for their groundbreaking discovery of microRNAs and the role of microRNAs in post-transcriptional gene regulation, uncovering a previously unknown layer of gene control in eukaryotes

Among bacteria used as anticancer vaccines, attenuated Listeria monocytogenes (Lm^at) stands out, because it spreads from one infected cancer cell to the next, induces a strong adaptive immune response, and is suitable for repeated injection cycles. Here, we use click chemistry to functionalize the Lm^at cell wall and turn the bacterium into an "intelligent carrier" of the chemotherapeutic drug doxorubicin. Doxorubicin-loaded Lm^at retains most of its biological properties and, compared to the control fluorophore-functionalized bacteria, shows enhanced cytotoxicity against melanoma cells both in vitro and in a xenograft model in zebrafish. Our results show that drugs can be covalently loaded on the Lm^at cell wall and pave the way to the development of new two-in-one therapeutic approaches combining immunotherapy with chemotherapy.