Elucidation of the mutational landscape of human cancer has progressed rapidly and been accompanied by the development of therapeutics targeting mutant oncogenes. However, a comprehensive mapping of cancer dependencies has lagged behind and the discovery of therapeutic targets for counteracting tumor suppressor gene loss is needed. To identify vulnerabilities relevant to specific cancer subtypes, we conducted a large-scale RNAi screen in which viability effects of mRNA knockdown were assessed for 7,837 genes using an average of 20 shRNAs per gene in 398 cancer cell lines. We describe findings of this screen, outlining the classes of cancer dependency genes and their relationships to genetic, expression, and lineage features. In addition, we describe robust gene-interaction networks recapitulating both protein complexes and functional cooperation among complexes and pathways. This dataset along with a web portal is provided to the community to assist in the discovery and translation of new therapeutic approaches for cancer.

Data Fig. 3a-c, Supplementary Table 3). An interactive data browser for the atlases is publicly available (see 'Data availability'). Notably, our bulk RNA-seq and single-cell data were highly concordant, which indicates that our single-cell analytical approach did not introduce technical bias (Extended Data Fig. 3d).

Genetic studies have identified mutations in key regulators of the Wnt͞␤-catenin pathway in a variety of cancers, most frequently in colon cancers. However, whether the pathway is activated in clinical cancer samples is not easily determined, and therefore it is useful to find markers that could be surrogates to show activation of the Wnt͞␤-catenin pathway. Gene expression profiles were analyzed in SW620, a colon cancer cell line in which ␤-catenin levels are stabilized as a consequence of truncated adenomatous polyposis coli and were compared with profiles of the same cells transfected with antisense oligodeoxynucleotides. Treatment of cells with ␤-catenin antisense oligodeoxynucleotides resulted in a decrease in the levels of axin2 and human naked cuticle (hnkd) mRNAs. Interestingly, the proteins encoded by both of these mRNAs are known inhibitors of the ␤-catenin pathway. In 30 human cell lines derived from different origins, axin2 and hnkd were expressed only in human colon cancer cell lines that are known to have activating mutations in the Wnt͞␤-catenin pathway. Further, levels of both axin2 and hnkd mRNA were also found to be elevated in about 65% of laser microdissected cells from human colon tumors compared with laser microdissected cells of normal morphology from the same patient samples. The increased expression of axin2 and hnkd correlated with truncations in adenomatous polyposis coli in the same patient samples. These results reveal that it is possible to detect activation of a carcinogenic pathway in human cancer samples with specific markers.

Recent single-cell studies of cancer in both mice and humans have identified the emergence of a myofibroblast population specifically marked by the highly restricted leucine-rich-repeat-containing protein 15 (LRRC15)1–3. However, the molecular signals that underlie the development of LRRC15+ cancer-associated fibroblasts (CAFs) and their direct impact on anti-tumour immunity are uncharacterized. Here in mouse models of pancreatic cancer, we provide in vivo genetic evidence that TGFβ receptor type 2 signalling in healthy dermatopontin+ universal fibroblasts is essential for the development of cancer-associated LRRC15+ myofibroblasts. This axis also predominantly drives fibroblast lineage diversity in human cancers. Using newly developed Lrrc15–diphtheria toxin receptor knock-in mice to selectively deplete LRRC15+ CAFs, we show that depletion of this population markedly reduces the total tumour fibroblast content. Moreover, the CAF composition is recalibrated towards universal fibroblasts. This relieves direct suppression of tumour-infiltrating CD8+ T cells to enhance their effector function and augments tumour regression in response to anti-PDL1 immune checkpoint blockade. Collectively, these findings demonstrate that TGFβ-dependent LRRC15+ CAFs dictate the tumour-fibroblast setpoint to promote tumour growth. These cells also directly suppress CD8+ T cell function and limit responsiveness to checkpoint blockade. Development of treatments that restore the homeostatic fibroblast setpoint by reducing the population of pro-disease LRRC15+ myofibroblasts may improve patient survival and response to immunotherapy.

Combinatorial libraries of antibody heavy and light chains derived from the peripheral blood lymphocytes of an individual immunized with tetanus toxoid have been expressed in Escherichia coli by using phage A vectors. Screening of the libraries allowed identification of a large number of human monoclonal Fab fragments specific for tetanus toxoid.Initial studies suggested considerable sequence diversity in these antibodies. The method should allow the generation of many human monoclonal antibodies of interest and the dissection of human humoral immune responses.Mouse monoclonal antibodies are readily generated by the fusion procedure of Kohler and Milstein (1). However, for therapeutic applications, human monoclonal antibodies are preferred. Despite extensive efforts, including production of heterohybridomas (2), Epstein-Barr virus immortalization of human B cells (3) and "humanization" of mouse antibodies (4), no general method comparable to the Kohler-Milstein approach has emerged for the generation of human monoclonal antibodies (reviewed in ref. 2). Previously, a procedure was described for the production of mouse monoclonal antibodies based on antigen selection from a combinatorial library ofthe mouse antibody repertoire cloned in phage A (5). The procedure has recently been successfully applied to the isolation of mouse monoclonal antibodies specific for influenza virus hemagglutinin (6). The extension to human antibodies is not trivial. Mice can be hyperimmunized with antigen and the spleen, a rich source of antibody-producing cells, can be removed. Humans can be immunized or are immune to many antigens but only peripheral blood, a poor source of antibody-producing cells, is readily available.Here we show that the repertoire cloning approach can be applied for the generation of human monoclonal antibodies from peripheral blood lymphocytes (PBLs) and we speculate that, given appropriate donor selection, this may effectively constitute a general route to such antibodies. MATERIALS AND METHODSImmunization and Lymphocyte RNA Preparation. A healthy volunteer who had received the most recent tetanus toxoid immunization 18 months before this experiment was given a booster injection of 0.5 mg of diphtheria/tetanus toxoid intramuscularly. Seven days later, he was subjected to leukapheresis, processing 5 liters of blood resulting in 2.1 x 109 lymphocytes after additional density-gradient separation (Ficoll-Paque; Pharmacia); 0.5 x 109 cells each were taken for three parallel experiments: (i) untreated PBLs, RNA was isolated immediately by a guanidinium isothiocyanate method (7); (ii) in vitro antigen stimulation, in which the cells were cultured in the presence oftetanus toxoid (10 ,ug/ml) for 3 days in RPMI 1640 medium with 10%o human AB serum (GIBCO), after which the RNA was isolated as described above; (iii) panned antigen reactive cells, lymphocytes were incubated for 45 min with 60 nM biotin-tetanus toxoid, washed twice, and then poured onto Petri dishes coated with streptavidin and blocked with bovine ...