There is accumulating evidence that long noncoding RNAs (lncRNA), and the RNA-binding proteins (RBP) they interact with, are important regulators of tumor progression. To provide a comprehensive picture of the lncRNA landscape in cancer, Søndergaard and colleagues investigated a collection of roughly 2,300 previously identified RBPs to uncover altered RNAs in several different cancer cohorts. The authors observed increased RBP expression across tumor types and showed RBP expression had prognostic value for predicting patient survival. Knockdown of select RBPs in hepatocellular carcinoma cell lines led to the discovery of novel lncRNA-RBP pairs, such as between chaperonin complex subunit 3 (CCT3) and LINC00326, which had strong effects on the regulation of lipid metabolism and tumor progression.Expert Commentary: This study demonstrates the complexity of the lncRNA network in cancer and points towards potential diagnostic or therapeutic targets for liver cancer.Søndergaard JN, Sommerauer C, Atanasoai I, Hinte LC, Geng K, Guiducci G, et al. The CCT3-LINC00326 axis regulates hepatocarcinogenic lipid metabolism. Gut; Published online January 12, 2022; doi: 10.1136/gutjnl-2021-325109.Cancer evolution is a dynamic process, which influences tumor heterogeneity and therapeutic resistance among other features, but it has been difficult to quantify with existing techniques. Zhao and colleagues developed slide-DNA-seq to track chromosomal copy number alterations (CNA) in situ at high resolution. The method arrays spatially indexed barcoded beads upon which tissues can be laid for DNA analysis with spatial resolution. Slide-DNA-seq could also measure chromatin accessibility or DNA methylation status and could define cell types in the brain based on the density of mitochondrial DNA. Using a metastatic cell line injected intravenously to seed the liver, they differentiated cancer cells (with CNAs) from normal liver (lacking CNAs). Furthermore, after co-injecting two different metastatic lung tumor lines, clones could be distinguished based on their unique CNAs. Combining slide-DNA-seq with transcriptional analysis, they correlated differences in DNA copy number with transcriptional programs. Finally, they validated this approach in human colorectal cancer and showed that DNA variation as well as tumor cell density controlled the transcriptional signature of human tumor clones.Expert Commentary: Slide-DNA-seq measures DNA copy number alterations with spatial resolution to map clonal heterogeneity in cancer.Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, et al. Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Nature 2022;601:85–91.Immune checkpoint inhibitors have not yet demonstrated significant therapeutic impact in solid tumors in children. However, a subset of pediatric tumors, characterized by mutations directly affecting the DNA replication and repair machinery, has exceptionally high mutational burdens, is hypothesized to be highly immunogenic, and is nearly always fatal. In this study of hypermutant and ultrahypermutant tumors, Das and colleagues showed PD-1 inhibitor treatment resulted in greatly increased survival for many patients. In parallel, the authors demonstrated that biomarkers for response to immune checkpoint inhibitors (ICI) differed between hypermutant and ultrahypermutant cases. Finally, by examining lymphocyte abundance and rapid radiologic changes termed tumor “flare,” they found that this pseudoprogression often reflected expansion of T-cell clones and a productive immune response to the tumor.Expert Commentary: By examining an exceptional cohort of patients, this study revealed factors that do and do not contribute to ICI efficacy in pediatric patients, as well as identifying a new approach for a patient population that normally has extremely poor survival.Das A, Sudhaman S, Morgenstern D, Coblentz A, Chung J, Stone SC, et al. Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. Nature Medicine 2022;28:125–35.Although activating mutations in growth factor receptors and their downstream signaling pathways have been identified in hepatocellular carcinoma (HCC), no effective targeted treatments are currently available. A recent study by Guégan and colleagues, based on a shRNA screen of genes encoding kinases, identified the tyrosine kinase YES as a driver of HCC. Activation of YES in hepatocytes was sufficient to induce oncogenic transformation. Mechanistically, YES phosphorylates and activates the transcriptional coactivators YAP and TAZ to drive tumor progression. They showed that an experimentally derived gene signature of “high YES activity,” but not YES expression per se, predicts reduced survival in patients with HCC.Expert Commentary: This study warrants re-evaluating the use of SRC family kinase inhibitors in HCC, which is supported by the recent development of new potent inhibitors.Guégan JP, Lapouge M, Voisin L, Saba-El-Leil MK, Tanguay PL, Lévesque K, et al. Signaling by the tyrosine kinase Yes promotes liver cancer development. Sci Signal 2022; 15:eabj4743. doi: 10.1126/scisignal.abj4743.Monotherapy with drugs that target epigenetic regulators has largely failed in colorectal cancer, likely due to tumor heterogeneity and on-target toxicity. Berlin and colleagues examined the novel epigenetic regulator, lysine methyltransferase 9 (KMT9) in colorectal cancer progression, as it has been implicated in other tumor types. KMT9 methylates Histone H4 at lysine 12 (H4K12me1) to regulate transcription. They showed that KMT9 levels were upregulated in colorectal cancer and that KMT9 enriched with H4K12me1 at the promoters of genes, regulating proliferation of colorectal cancer cells. Knockout of KMT9 in colorectal cancer organoids reduced the viability and self-renewal capability of colorectal cancer tumor-initiating cells. This was true for organoids derived from inflammation- or APC mutant-driven colorectal cancer. Reduction in KMT9 levels resulted in a significant decline in expression of cell-cycle progression regulators and intestinal stem cell biomarkers. Additionally, using knockout mouse models, the authors demonstrated loss of KMT9 could reduce colorectal cancer progression without impacting the function of normal colon cells, supporting KMT9 as a cancer-specific epigenetic target for therapy.Expert Commentary: KMT9 is an important and druggable regulator of colorectal cancer progression that warrants further research to identify small molecule inhibitors.Berlin C, Cottard F, Willmann D, Urban S, Tirier SM, Marx L, et al. KMT9 controls stemness and growth of colorectal cancer. Cancer Res. 2022;82:210–20.Despite the excellent activity of the EGFR inhibitor osimertinib in the central nervous system (CNS), CNS progression is inevitable in EGFR mutant non-small cell lung cancer (NSCLC), and outcomes after CNS relapse are poor. Utilizing in vivo long-term treatment models, Biswas and colleagues generated relapsed brain metastases and identified tumoral S100A9 as a driver of brain metastases relapse in an EGFR-independent, ALDH1A1-, and retinoic acid–dependent manner. Genetic or pharmacologic inhibition of this pathway restored osimertinib sensitivity and significantly reduced the number of brain metastases. Furthermore, high S100A9 expression was associated with increased brain metastasis frequency and decreased duration of osimertinib response in patients.Expert Commentary: This study suggests that the combination of osimertinib with a retinoic acid receptor antagonist may prevent or delay CNS progression.Biswas AK, Han S, Tai Y, Ma W, Coker C, Quinn SA, et al. Targeting S100A9-ALDH1A1-retinoic acid signaling to suppress brain relapse in EGFR-mutant lung cancer. Cancer Discovery; Published OnlineFirst January 25, 2022; doi: 10.1158/2159-8290.CD-21-0910.Note: Breaking Insights are written by Cancer Research editors. Readers are encouraged to consult the articles referred to in each item for full details on the findings described.