SUMMARY Through in-vivo selection of human cancer cell populations, we uncover a convergent and cooperative miRNA network that drives melanoma metastasis. We identify miR-1908, miR-199a-5p, and miR-199a-3p as endogenous promoters of metastatic invasion, angiogenesis, and colonization in melanoma. These miRNAs convergently target Apolipoprotein E (ApoE) and the heat-shock factor DNAJA4. Cancer-secreted ApoE suppresses invasion and metastatic endothelial recruitment (MER) by engaging melanoma-cell LRP1 and endothelial-cell LRP8 receptors, respectively–while DNAJA4 promotes ApoE expression. Expression levels of these miRNAs and ApoE correlate with human metastatic progression outcomes. Treatment of cells with locked nucleic acids (LNAs) targeting these miRNAs inhibits metastasis to multiple organs, while therapeutic delivery of these LNAs strongly suppresses melanoma metastasis. We thus identify miRNAs with dual cell-intrinsic/cell-extrinsic roles in cancer, reveal convergent cooperativity in a metastatic miRNA network, identify ApoE as an anti-angiogenic and metastasis-suppressive factor, and uncover multiple prognostic miRNAs with synergistic combinatorial therapeutic potential in melanoma.

Bacterial receptors typically contain modular architectures with distinct functional domains that combine to send signals in response to stimuli. Although the properties of individual components have been investigated in many contexts, there is little information about how diverse sets of modules work together in full-length receptors. Here we investigate the architecture of Aer2, a soluble gas-sensing receptor that has emerged as a model for PAS and poly-HAMP domain signaling. The crystal structure of the heme-binding PAS domain in the ferric, ligand-free form, in comparison to the previously determined cyanide-bound state, identifies conformational changes induced by ligand binding that are likely essential for the signaling mechanism. Heme-pocket alternations share some similarities with the heme-based PAS sensors FixL and EcDOS, but propagate to the Iβ-strand in a manner predicted to alter PAS-PAS associations and the downstream HAMP junction within full-length Aer2. SAXS of PAS and poly-HAMP domain fragments of increasing complexity allow unambiguous domain assignments and reveal a linear quaternary structure. The Aer2 PAS dimeric crystal structure fits well within ab initioSAXS molecular envelopes and pulsed-dipolar ESR measurements of inter-PAS distances confirm the crystallographic PAS arrangement within Aer2. Spectroscopic and pull-down assays fail to detect direct interactions between the PAS and HAMP domains. Overall, the Aer2 signaling mechanism differs from the E. coliAer paradigm, where side-on PAS-HAMP contacts are key. We propose an in-line model for Aer2 signaling, where ligand binding induces alterations in PAS domain structure and subunit association that is relayed through the poly-HAMP junction to downstream domains. ACCESSION NUMBERSThe coordinates and structure factors for the ferric Aer2 PAS domain have been deposited in the protein data bank with PDB ID 4HI4.

Through in vivo selection of multiple ER-negative human breast cancer populations for enhanced tumor-forming capacity, we have derived sub-populations that generate tumors more efficiently than their parental populations at low cell numbers. Tumorigenic-enriched (TE) sub-populations displayed increased expression of LAMA4, FOXQ1 and NAP1L3—genes that are also expressed at greater levels by independently derived metastatic sub-populations. These genes promote metastatic efficiency. FOXQ1 promotes LAMA4 expression, while LAMA4 enhances clonal expansion upon substratum-detachment in vitro, tumor re-initiation in multiple organs, and disseminated metastatic cell proliferation and colonization. LAMA4’s promotion of cancer cell proliferation and tumor re-initiation requires β1-integrin. Increased LAMA4 expression marks the transition of human pre-malignant breast lesions to malignant carcinomas, while tumoral LAMA4 over-expression predicts reduced relapse-free survival in ER-negative patients. Our findings reveal common features that govern primary and metastatic tumor re-initiation and identify a key molecular determinant of these processes.

Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA‐derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine‐tRNAGUA fragments in human cells—causing significant depletion of the precursor tRNA. Tyrosine‐tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation—revealing a dedicated tRNA‐regulated growth‐suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease‐dependent manner and inhibit hnRNPA1‐mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans‐acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon‐based regulatory response inherent to the genetic code.

Eukaryotic transfer RNAs can become selectively fragmented upon various stresses,generating tRNA-derived small RNA fragments (tRFs). Such tRNA fragmentation has been observed to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that in human cells, oxidative stress can rapidly generate tRFs derived from tyrosyl tRNA GUA -causing significant depletion of the precursor tRNA molecule. Tyrosyl tRNA GUA depletion impaired expression of a gene-set enriched in its cognate tyrosine codons, comprising growth and metabolic genes. Depletion of tyrosyl tRNA GUA or its downstream genes EPCAM, SCD, or USP3 repressed proliferation-revealing a tRNA-regulated growth suppressive pathway for oxidative stress response. Thus, tRNA fragmentation can both deplete a precursor tRNA molecule with codon-dependent regulatory consequences and also generate small-RNAs that interact with RNA binding proteins. Our findings reveal the existence of an underlying adaptive codon-based gene-regulatory logic inherent to the genetic code. RESEARCH HIGHLIGHTS• Stress-induced tyrosyl tRNA GUA fragmentation depletes precursor tRNA Tyr GUA and mature tRNA Tyr GUA • TRNA Tyr GUA depletion impairs expression of growth genes enriched in cognate tyrosine codons • This constitutes a growth suppressive adaptive stress response driven by codon-based logic