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Supplemental Table S1 lists clinical characteristics for the study cohort. Figure S1 depicts results of batch correction. Figures S2 and S3 show comparisons between ERV levels and tumor content. Figure S4 shows ERV levels across different biopsy sites.

Supplemental Table S3 lists gene sets significantly enriched among genes up-regulated in VMP samples.

Next-generation sequencing of solid tumors has revealed variable signatures of immunogenicity across tumors, but underlying molecular characteristics driving such variation are not fully understood. Although expression of endogenous retrovirus (ERV)-containing transcripts can provide a source of tumor-specific neoantigen in some cancer models, associations between ERV levels and immunogenicity across different types of metastatic cancer are not well established. We performed bioinformatics analysis of genomic, transcriptomic, and clinical data across an integrated cohort of 199 patients with metastatic breast, colorectal, and pancreatic ductal adenocarcinoma tumors. Within each cancer type, we identified a subgroup of viral mimicry tumors in which increased ERV levels were coupled with transcriptional signatures of autonomous antiviral response and immunogenicity. In addition, viral mimicry colorectal and pancreatic tumors showed increased expression of DNA demethylation gene TET2. Taken together, these data demonstrate the existence of an ERV-associated viral mimicry phenotype across three distinct metastatic cancer types, while indicating links between ERV abundance, epigenetic dysregulation, and immunogenicity.

Supplemental Table S4 lists gene sets significantly enriched among genes down-regulated in VMP samples.

Supplemental Table S5 lists EGA accession numbers for each sample included in the study.

Supplemental Table S2 lists all genes differentially expressed in VMP samples.

Supplemental Data

Heatmap showing median gene expression levels (z-score) of genes involved in various pathways related to cellular metabolism. For each gene, within each of the four metabolic subgroups, expression values were assessed for significant deviation from zero using Wilcoxon signed rank test (mu = 0).

Supplementary Figures S1-7

Purpose:RNA-sequencing–based subtyping of pancreatic ductal adenocarcinoma (PDAC) has been reported by multiple research groups, each using different methodologies and patient cohorts. “Classical” and “basal-like” PDAC subtypes are associated with survival differences, with basal-like tumors associated with worse prognosis. We amalgamated various PDAC subtyping tools to evaluate the potential of such tools to be reliable in clinical practice.Experimental Design:Sequencing data for 574 PDAC tumors was obtained from prospective trials and retrospective public databases. Six published PDAC subtyping strategies (Moffitt regression tools, clustering-based Moffitt, Collisson, Bailey, and Karasinska subtypes) were used on each sample, and results were tested for subtype call consistency and association with survival.Results:Basal-like and classical subtype calls were concordant in 88% of patient samples, and survival outcomes were significantly different (P < 0.05) between prognostic subtypes. Twelve percent of tumors had subtype-discordant calls across the different methods, showing intermediate survival in univariate and multivariate survival analyses. Transcriptional profiles compatible with that of a hybrid subtype signature were observed for subtype-discordant tumors, in which classical and basal-like genes were concomitantly expressed. Subtype-discordant tumors showed intermediate molecular characteristics, including subtyping gene expression (P < 0.0001) and mutant KRAS allelic imbalance (P < 0.001).Conclusions:Nearly 1 in 6 patients with PDAC have tumors that fail to reliably fall into the classical or basal-like PDAC subtype categories, based on two regression tools aimed toward clinical practice. Rather, these patient tumors show intermediate prognostic and molecular traits. We propose close consideration of the non-binary nature of PDAC subtypes for future incorporation of subtyping into clinical practice.

Supplemental Table 2

Supplemental Figures and Tables

Supplemental Table 1

Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

Purpose:Identification of clinically actionable molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) is key to improving patient outcome. Intertumoral metabolic heterogeneity contributes to cancer survival and the balance between distinct metabolic pathways may influence PDAC outcome. We hypothesized that PDAC can be stratified into prognostic metabolic subgroups based on alterations in the expression of genes involved in glycolysis and cholesterol synthesis.Experimental Design:We performed bioinformatics analysis of genomic, transcriptomic, and clinical data in an integrated cohort of 325 resectable and nonresectable PDAC. The resectable datasets included retrospective The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) cohorts. The nonresectable PDAC cohort studies included prospective COMPASS, PanGen, and BC Cancer Personalized OncoGenomics program (POG).Results:On the basis of the median normalized expression of glycolytic and cholesterogenic genes, four subgroups were identified: quiescent, glycolytic, cholesterogenic, and mixed. Glycolytic tumors were associated with the shortest median survival in resectable (log-rank test P = 0.018) and metastatic settings (log-rank test P = 0.027). Patients with cholesterogenic tumors had the longest median survival. KRAS and MYC-amplified tumors had higher expression of glycolytic genes than tumors with normal or lost copies of the oncogenes (Wilcoxon rank sum test P = 0.015). Glycolytic tumors had the lowest expression of mitochondrial pyruvate carriers MPC1 and MPC2. Glycolytic and cholesterogenic gene expression correlated with the expression of prognostic PDAC subtype classifier genes.Conclusions:Metabolic classification specific to glycolytic and cholesterogenic pathways provides novel biological insight into previously established PDAC subtypes and may help develop personalized therapies targeting unique tumor metabolic profiles.See related commentary by Mehla and Singh, p. 6

Adrenocortical cancer (ACC) is a rare cancer of the adrenal gland. Several driver mutations have been identified in both primary and metastatic ACCs, but the therapeutic options are still limited. We performed whole-genome and transcriptome sequencing on seven patients with metastatic ACC. Integrative analysis of mutations, RNA expression changes, mutation signature, and homologous recombination deficiency (HRD) analysis was performed. Mutations affecting

Matched field processing (MFP) has been shown to be effective for remote sound source localization when the receiving array clearly records direct-path sound from a stationary source. Unfortunately, in imperfectly characterized confined environments, source motion, echoes, and reverberation commonly degrade localization performance. This poster presentation describes three acoustic technology development efforts focused on using matched-field processing, with and without the first reflections, (i) to track a moving source, (ii) to improve localization results by adjusting the receiving array geometry, and (iii) to determine the conditions under which a discrete scatterer may be localized. Experiments were conducted in a 1.0-meter-deep and 1.07-meter-diameter cylindrical water tank using a single sound projector, a receiving array of 16 hydrophones, and a linear actuator capable of moving the source at a speed of 0.5 m/s. Measured localization performance is reported for impulsive (100 micro-second) and lo...

Artificial time reversal (ATR) is a passive technique for blind deconvolution in an unknown multipath environment that relies on generic features of underwater sound fields. ATR has been found to be effective when the source is far from the receiving array and the receiving array properly resolves propagating modes or ray-path arrival angles throughout the bandwidth of the source signal. This presentation describes the results of an experimental investigation into ATR's performance for a near-field source in a highly reverberant environment. The experiments were conducted with nominally 0.1 ms pulses at frequencies from 20 kHz to 150 kHz in a 1.0-m-deep and 1.07-m-diameter cylindrical water tank having a reverberation time of ∼10 ms using a single sound projector and a linear receiving array of 16 hydrophones. The correlation coefficient between the original and the ATR-reconstructed signals is presented as a function of receiving-array and broadcast-signal characteristics and compared to equivalent signal reconstruction results from spherical-wave delay-and-sum beamforming. The intended application of this research lies in determining the acoustic signature of cavitation bubbles and other hydroacoustic sound sources in hydrodynamic test facilities. [Sponsored by ONR and by NAVSEA through the Naval Engineering Education Center.]

Matched field processing (MFP) has been shown to be effective for remote sound source localization when the receiving array clearly records direct-path sound. Unfortunately, in imperfectly characterized confined environments, echoes and reverberation commonly degrade localization performance. However, inclusion of first reflections in the requisite MFP field model should improve localization performance and such inclusion may be tractable as well. This presentation describes an acoustic technology development effort focused on source localization in a simple confined environment using both direct-path and once-reflected sounds. Experiments were conducted in a 1.0-m-deep and 1.07-m-diameter cylindrical water tank having a reverberation time of ~10 ms using a single sound projector and a linear receiving array of 16 hydrophones. Measured localization performance is reported for impulsive (100 μs) and longer duration sounds having frequencies from 20 to 150 kHz. Appropriate cropping of the signal coda and in...