Chromosomal Instability Drives Metastasis Through a Cytosolic DNA Response

Abstract

genetic diversity. This variation in LUAD has led to the development of genetic markers that have successfully guided drug therapies. Despite impressive initial clinical responses, there is variability in the extent of response even within homogeneous baskets and resistance to targeted and genotoxic therapies ultimately ensues. The extent of these failures is attributed to the topographic differences in genomes within tumors, or intratumoral heterogeneity, remains poorly studied which represents a major obstacle to tumor eradication. Tumors can have genetically distinct subclones that compete for space and resources and differentially resist therapy. Herein, we seek to elucidate subclone architecture in the most common type of lung cancer for the purpose of guiding radiotherapeutic strategies. Materials/Methods: We identified 405 candidate BRAF variants by analyzing targeted and genome-wide screen data from a collection of 48,397 tumors representing 35 cancers deposited in COSMIC. We selected 28 BRAF variants by random sampling and 7 variants considering local mutational density, evolutionary conservation and prior knowledge. We used site-directed mutagenesis to generate mutant clones and transferred alleles into lentiviral vectors. We generated 74 expression constructs adding wild-type and vector controls and representing biological replicates then stably-expressed each variant in bronchial epithelial cells (BEAS-2B). Total mRNA gene expression was assayed using RNAseq. Gene level copy number and mutational data were combined with estimates of the sample purity to infer the cancer cell fraction, or the proportion of cancer cells with the single nucleotide variant (CCFSNV) as follows: CCFSNV Z (VAF*(2+(ploidyCNV-2)*CCFCNV))/purity. Results: We identified BRAF driver mutations as predominately clonal in some cancers (melanoma) and subclonal in others (LUAD). Clonality was associated with the prevalence of V600 mutations and its selective amplification, a frequent occurrence in melanoma. We modelled the propagation and selection of tumors containing distinct categories of BRAF mutations to estimate their evolutionary trajectories. Hyperactivating BRAF mutant cells rapidly swept to clonality, resulting in a significant reduction of genetic diversity in the affected tumors. Mutations with differential activation of the Braf signaling pathway conferred a "softer" clonal sweep or remained subclonal maintaining tumor genetic diversity. Subclones containing BRAF variants had significant therapeutic implications for both targeted inhibitors of BRAF and/or MEK and genotoxic stress, conferring attenuated responses to both therapies. Conclusion: Our study uncovers patterns of distinct BRAF clonal evolutionary dynamics and nominates new radiotherapeutic strategies based on both the type of mutation and its subclone composition.

Lymph node metastasis in oral cancer is strongly associated with chromosomal instability and DNA repair defects

“…Additionally, we identified known NFKB targets and found that CCND1 , WT1 , CXCL5 , YY1 , CSF2 and SENP2 were significantly ( p < 0.05) upregulated in LN+ CI+ unstable tumors. Our result is consistent with a recent result on involvement of CI in metastasis mediated through NF‐kB.…”

“…Although CI is higher in LN+ tumors, significant increase in CNVs was observed only in HR DNA repair genes but not in NHEJ genes. It was shown in a recent study that CI tumor cells promote metastasis through noncanonical NFκB signaling. Our analysis of CNV and RNAseq data from TCGA‐HNSCC cohort recapitulates previously established findings from cell line studies.…”

Genes associated with increased brain metastasis risk in non–small cell lung cancer: Comprehensive genomic profiling of 61 resected brain metastases versus primary non–small cell lung cancer (Guangdong Association Study of Thoracic Oncology 1036)

“…14,15 Lastly, CNV events of multiple genes, including MET, VEGFA, KEAP1, ROS1, SMAD2, and SMAD4, were found exclusively in BMs (Fig. 14,15 Lastly, CNV events of multiple genes, including MET, VEGFA, KEAP1, ROS1, SMAD2, and SMAD4, were found exclusively in BMs (Fig.…”

STING pathway agonism as a cancer therapeutic

“…It will also be important to better understand the microenvironmental changes induced by type I IFNs elicited by STING pathway activation in both preclinical models and in patients that are responders or non‐responders to STING agonists. For example, chronic type I IFN signaling can reportedly have pro‐tumor effects including immune suppression and promote metastasis . Most STING agonist studies to date haven't encountered this issue because treatment is performed with 1 or a few doses that lead to a burst of IFN production that favors immune activation.…”