ARID2 and PBRM1 mutant tumors alter KEAP1-NRF2 signatures.

GSEA of five NRF2 signatures was used. Normalized Enrichment Scores (NES) are shown in the heat map with Tumors (S2 Table) on the x-axis and Signatures (S3 Table) on the y-axis. A. NRF2 signature GSEA results for ARID2 mutant tumors. B. NRF2 signature GSEA results for PBRM1 mutant tumors.</p

Oncogenic signatures of mutant tumors.

Prior to the next generation sequencing and characterization of the tumor genome landscape, mutations in the SWI/SNF chromatin remodeling complex and the KEAP1-NRF2 signaling pathway were underappreciated. While these two classes of mutations appeared to independently contribute to tumor development, recent reports have demonstrated a mechanistic link between these two regulatory mechanisms in specific cancer types and cell models. In this work, we expand upon these data by exploring the relationship between mutations in BAF and PBAF subunits of the SWI/SNF complex and activation of NRF2 signal transduction across many cancer types. ARID1A/B mutations were strongly associated with NRF2 transcriptional activity in head and neck squamous carcinomas (HNSC). Many additional tumor types showed significant association between NRF2 signaling and mutation of specific components of the SWI/SNF complex. Different effects of BAF and PBAF mutations on the polarity of NRF2 signaling were observed. Overall, our results support a context-dependent functional link between SWI/SNF and NRF2 mutations across human cancers and implicate ARID1A inactivation in HPV-negative HNSC in promoting tumor progression and survival through activation of the KEAP1-NRF2 signaling pathway. The tumor-specific effects of these mutations open a new area of study for how mutations in the KEAP1-NRF2 pathway and the SWI/SNF complex contribute to cancer.</div

TCGA bioinformatic pipeline.

TCGA Firehose was used to download CNV, mutation, and gene expression data. CNV and mutation data were used to identify mutant tumors in genes for each group. Confounding mutations were then filtered from the treatment group. Gene expression data were used to calculate signal-to-noise ratios within each group. GSEA was performed using signal-to-noise ratios between control and treated groups for NRF2 gene signatures and Oncogene and Hallmark signatures.</p

Hallmark signatures of mutant tumors.

Prior to the next generation sequencing and characterization of the tumor genome landscape, mutations in the SWI/SNF chromatin remodeling complex and the KEAP1-NRF2 signaling pathway were underappreciated. While these two classes of mutations appeared to independently contribute to tumor development, recent reports have demonstrated a mechanistic link between these two regulatory mechanisms in specific cancer types and cell models. In this work, we expand upon these data by exploring the relationship between mutations in BAF and PBAF subunits of the SWI/SNF complex and activation of NRF2 signal transduction across many cancer types. ARID1A/B mutations were strongly associated with NRF2 transcriptional activity in head and neck squamous carcinomas (HNSC). Many additional tumor types showed significant association between NRF2 signaling and mutation of specific components of the SWI/SNF complex. Different effects of BAF and PBAF mutations on the polarity of NRF2 signaling were observed. Overall, our results support a context-dependent functional link between SWI/SNF and NRF2 mutations across human cancers and implicate ARID1A inactivation in HPV-negative HNSC in promoting tumor progression and survival through activation of the KEAP1-NRF2 signaling pathway. The tumor-specific effects of these mutations open a new area of study for how mutations in the KEAP1-NRF2 pathway and the SWI/SNF complex contribute to cancer.</div

ARID1A and ARID1B mutant tumors alter KEAP1-NRF2 signatures.

GSEA of five NRF2 signatures was used. Normalized Enrichment Scores (NES) are shown in the heat map with Tumors (S2 Table) on the x-axis and Signatures (S3 Table) on the y-axis. A. NRF2 signature GSEA results for KEAP1-NRF2 mutant tumors (positive control). B. NRF2 signature GSEA results for ARID1A mutant tumors C. NRF2 signature GSEA results for ARID1B mutant tumors. D. NRF2 signature GSEA results for HNSC tumors comparing the CPTAC and TCGA datasets.</p

Abbreviation of TCGA tumor types.

Prior to the next generation sequencing and characterization of the tumor genome landscape, mutations in the SWI/SNF chromatin remodeling complex and the KEAP1-NRF2 signaling pathway were underappreciated. While these two classes of mutations appeared to independently contribute to tumor development, recent reports have demonstrated a mechanistic link between these two regulatory mechanisms in specific cancer types and cell models. In this work, we expand upon these data by exploring the relationship between mutations in BAF and PBAF subunits of the SWI/SNF complex and activation of NRF2 signal transduction across many cancer types. ARID1A/B mutations were strongly associated with NRF2 transcriptional activity in head and neck squamous carcinomas (HNSC). Many additional tumor types showed significant association between NRF2 signaling and mutation of specific components of the SWI/SNF complex. Different effects of BAF and PBAF mutations on the polarity of NRF2 signaling were observed. Overall, our results support a context-dependent functional link between SWI/SNF and NRF2 mutations across human cancers and implicate ARID1A inactivation in HPV-negative HNSC in promoting tumor progression and survival through activation of the KEAP1-NRF2 signaling pathway. The tumor-specific effects of these mutations open a new area of study for how mutations in the KEAP1-NRF2 pathway and the SWI/SNF complex contribute to cancer.</div

Sample sizes of treatment and control groups for each tumor type.

Sample sizes of treatment and control groups for each tumor type.</p

NRF2 is one of the strongest pathway responses to SWI/SNF loss in hallmark and oncogene signatures.

A. Volcano plots of the canonical Hallmark Gene Set. Normalized Enrichment Scores (NES) are shown on the x-axis and p-adjusted values on the y-axis. HALLMARK_REACTIVE_OXYGEN_SPECIES (ROS) is the signature associated with NRF2 signaling. B. Volcano plots of the canonical Hallmark Gene Set. NES are shown on the x-axis and p-adjusted values on the y-axis. NFE2L2.V2 is the signature associated with NRF2 signaling.</p

Spotlite: Web Application and Augmented Algorithms for Predicting Co-Complexed Proteins from Affinity Purification – Mass Spectrometry Data

Protein–protein interactions defined by affinity purification and mass spectrometry (APMS) suffer from high false discovery rates. Consequently, lists of potential interactions must be pruned of contaminants before network construction and interpretation, historically an expensive, time-intensive, and error-prone task. In recent years, numerous computational methods were developed to identify genuine interactions from the hundreds of candidates. Here, comparative analysis of three popular algorithms, HGSCore, CompPASS, and SAINT, revealed complementarity in their classification accuracies, which is supported by their divergent scoring strategies. We improved each algorithm by an average area under a receiver operating characteristics curve increase of 16% by integrating a variety of indirect data known to correlate with established protein–protein interactions, including mRNA coexpression, gene ontologies, domain–domain binding affinities, and homologous protein interactions. Each APMS scoring approach was incorporated into a separate logistic regression model along with the indirect features; the resulting three classifiers demonstrate improved performance on five diverse APMS data sets. To facilitate APMS data scoring within the scientific community, we created Spotlite, a user-friendly and fast web application. Within Spotlite, data can be scored with the augmented classifiers, annotated, and visualized (http://cancer.unc.edu/majorlab/software.php). The utility of the Spotlite platform to reveal physical, functional, and disease-relevant characteristics within APMS data is established through a focused analysis of the KEAP1 E3 ubiquitin ligase

Sample sizes of co-occurring mutant tumors.

Prior to the next generation sequencing and characterization of the tumor genome landscape, mutations in the SWI/SNF chromatin remodeling complex and the KEAP1-NRF2 signaling pathway were underappreciated. While these two classes of mutations appeared to independently contribute to tumor development, recent reports have demonstrated a mechanistic link between these two regulatory mechanisms in specific cancer types and cell models. In this work, we expand upon these data by exploring the relationship between mutations in BAF and PBAF subunits of the SWI/SNF complex and activation of NRF2 signal transduction across many cancer types. ARID1A/B mutations were strongly associated with NRF2 transcriptional activity in head and neck squamous carcinomas (HNSC). Many additional tumor types showed significant association between NRF2 signaling and mutation of specific components of the SWI/SNF complex. Different effects of BAF and PBAF mutations on the polarity of NRF2 signaling were observed. Overall, our results support a context-dependent functional link between SWI/SNF and NRF2 mutations across human cancers and implicate ARID1A inactivation in HPV-negative HNSC in promoting tumor progression and survival through activation of the KEAP1-NRF2 signaling pathway. The tumor-specific effects of these mutations open a new area of study for how mutations in the KEAP1-NRF2 pathway and the SWI/SNF complex contribute to cancer.</div