The increase in availability of whole genome sequences makes it possible to search for evidence of adaptation at an unprecedented scale. Despite recent progress, our understanding of the adaptive process is still very limited due to the difficulties in linking adaptive mutations to their phenotypic effects. In this study, we integrated different levels of biological information to pinpoint the ecologically relevant fitness effects and the underlying molecular and biochemical mechanisms of a putatively adaptive TE insertion in Drosophila melanogaster: the pogo transposon FBti0019627. We showed that other than being incorporated into Kmn1 transcript, FBti0019627 insertion also affects the polyadenylation signal choice of CG11699 gene. Consequently, only the short 3′UTR transcript of CG11699 gene is produced and the expression level of this gene is higher in flies with the insertion. Our results indicated that increased CG11699 expression leads to xenobiotic stress resistance through increased ALDH-III activity: flies with FBti0019627 insertion showed increased survival rate in response to benzaldehyde, a natural xenobiotic, and to carbofuran, a synthetic insecticide. Although differences in survival rate between flies with and without the insertion were not always significant, when they were, they were consistent with FBti0019627 mediating resistance to xenobiotics. Taken together, our results provide a plausible explanation for the increase in frequency of FBti0019627 in natural populations of D. melanogaster and add to the limited number of examples in which a natural genetic mutation has been linked to its ecologically relevant phenotype. Furthermore, the widespread distribution of TEs across the tree of life and conservation of stress response pathways across organisms make our results relevant not only for Drosophila, but for other organisms as well.

40% of colorectal cancer (CRC) patients undergoing curative resection of the primary tumor will develop metastases in the following years 1 . Therapies to prevent disease relapse remain an unmet medical need. Here we uncover the identity and features of the residual tumor cells responsible for CRC relapse. Analysis of single-cell transcriptomes of CRC patient samples revealed that the majority of poor prognosis genes are expressed by a unique tumor cell population that we named High Relapse Cells (HRCs). We established a human-like mouse model of microsatellite stable CRC that undergoes metastatic relapse following surgical resection of the primary tumor. Residual HRCs occult in mouse livers after primary CRC surgery gave rise to multiple cell types over time, including Lgr5+ stemlike tumor cells 2-4 , and caused overt metastatic disease. Using Emp1 (epithelial membrane Competitiveness (MINECO). HH is a Miguel Servet (CP14/00229) researcher funded by the

Summary The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with ∼400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among ∼1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action.

The standard of care for advanced colorectal cancer (CRC) includes treatment with chemotherapeutic drugs that target the cell proliferation machinery 1 . In CRC patients with overt metastases, chemotherapy initially halts tumor growth but, almost inevitably, disease progresses after some cycles of treatment. Adjuvant chemotherapy is also administered to eliminate minimal residual disease, yet it only diminishes the risk of relapse by 10-25% 2 . Previous studies have shown that patient-derived organoids predict responses to chemotherapy 3-6 . Therefore, we used them as models to investigate the mechanisms behind the limited benefit of these treatments. Whereas CRC organoids expand from highly proliferative Lgr5+ tumor cells, we discovered that lack of optimal stem cell growth conditions specifies a latent Lgr5+ cell population. These cells expressed the gene Mex3a, were largely insensitive to chemotherapy and regenerated the organoid culture after treatment. In mouse models of metastatic latency, Mex3a+ cells contributed marginally to metastatic outgrowth. However, after chemotherapy treatment, Mex3a+ cells produced large cell clones that regenerated metastatic disease. Using lineage-tracing analysis combined with single cell profiling, we showed that drug-tolerant persister Mex3a+ cells downregulate the WNT/Lgr5+ stem cell program immediately after chemotherapy and adopt a transient regenerative state