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The tumor immunosuppressive microenvironment (IME) significantly affects tumor occurrence, progression, and prognosis, but the underlying molecular mechanisms remain to make known. We investigated the prognostic significance of PDPN and its role in IME in glioma. Weighted gene co-expression network analysis (WGCNA) found PDPN closely related to IDH wildtype status and higher immune score. Correlation analysis suggested PDPN was highly positively relevant to immune checkpoints expression and immune checkpoints block responding status. Correlation analysis together with verification in vitro suggested PDPN highly positively relevant tumor-associated neutrophils (TANs) and tumor-associated macrophages (TAMs). Least absolute shrinkage and selection operator (LASSO) regression employed to develop the prediction model with TANs and TAMs markers showed that high risk scores predicted worse prognosis. We highlight that PDPN overexpression is an independent prognostic indicator, and promotes macrophage M2 polarization and neutrophil degranulation, ultimately devotes to the formation of an immunosuppressive tumor microenvironment. Our findings contribute to re-recognizing the role of PDPN in IDH wildtype gliomas and implicate promising target therapy combined with immunotherapy for this highly malignant tumor.

mRNA isoforms

Pharmacodynamic changes (pathways)

Response markers

Extended Materials and Methods with in depth details about experimental procedures and protocols

Pharmacodynamic markers

Supplementary tables 1 and 2; Clinical information about the patients that the PDX models were established from and pathways that are regulated in the sensitive tumors after buparlisib treatment, respectively.

Response markers (pathways)

Activation of PI3K signaling is frequently observed in triple-negative breast cancer (TNBC), yet PI3K inhibitors have shown limited clinical activity. To investigate intrinsic and adaptive mechanisms of resistance, we analyzed a panel of patient-derived xenograft models of TNBC with varying responsiveness to buparlisib, a pan-PI3K inhibitor. In a subset of patient-derived xenografts, resistance was associated with incomplete inhibition of PI3K signaling and upregulated MAPK/MEK signaling in response to buparlisib. Outlier phosphoproteome and kinome analyses identified novel candidates functionally important to buparlisib resistance, including NEK9 and MAP2K4. Knockdown of NEK9 or MAP2K4 reduced both baseline and feedback MAPK/MEK signaling and showed synthetic lethality with buparlisib in vitro. A complex in/del frameshift in PIK3CA decreased sensitivity to buparlisib via NEK9/MAP2K4–dependent mechanisms. In summary, our study supports a role for NEK9 and MAP2K4 in mediating buparlisib resistance and demonstrates the value of unbiased omic analyses in uncovering resistance mechanisms to targeted therapy.Significance: Integrative phosphoproteogenomic analysis is used to determine intrinsic resistance mechanisms of triple-negative breast tumors to PI3K inhibition. Cancer Res; 78(10); 2732–46. ©2018 AACR.

Supplementary Figures 1-10 supporting the study Mundt et al., "Proteomic profiling of PI3K inhibitor resistance"

PURPOSE Immune checkpoint blockade (ICB) in conjunction with chemotherapy is approved for the treatment of extensive-stage small-cell lung cancer (SCLC). Although specific genomic abnormalities such as KEAP1 and STK11 gene mutations are associated with resistance to ICB in non-SCLC, no genomic abnormality has been found in association with resistance to ICB in SCLC. MATERIALS AND METHODS We first analyzed a retrospective cohort of 42 patients with SCLC treated with single-agent ICB or ICB combination (data set A). We then validated our results in a large prospective clinical trial of 460 patients (CheckMate 032, data set B). DNA and RNA sequencing were performed. RESULTS In data set A, patients treated with ICB with RB1 wild-type (WT) had a median overall survival (OS) of 23.1 months (95% CI, 9 to 37.5), whereas the RB1 mutant OS was 5 months (95% CI, 2.5 to 26; P = .04). Differentially expressed gene analysis between RB1 mutant and RB1 WT samples indicated the enrichment of downregulated immune-related genes and an immune exclusion phenotype among RB1 mutant but not in the RB1 WT tumor samples. We then assessed results from 460 patients enrolled in CheckMate 032, a trial of nivolumab (NIVO) or NIVO + ipilimumab only in SCLC. In this large cohort, RB1 WT patients had significantly improved outcome with NIVO therapy compared with mutant patients (hazard ratio, 1.41; 95% CI, 1.02 to 2.01; P = .041). High RB1 loss-of-function (LOF) signature scores significantly associated with neuroendocrine subtypes (ASCL1 and NeuroD1). However, neuroendocrine subtypes did not associate with OS. Remarkably, patients with lower RB1 LOF scores had longer OS following treatment with NIVO. CONCLUSION SCLC patients with RB1 WT status or lower RB1 LOF signature scores by transcriptomics have better outcomes with ICB monotherapy.

Glioblastoma, IDH-wildtype (GBM, WHO grade 4) is the most common primary intracranial malignant tumor of adults and is characterized by an immunosuppressive tumor micro-environment (TME) and poor clinical outcomes. CLEC5A is a protein-coding gene involved in inflammatory and infectious diseases, where its activation enhances immune response. However, its role in GBM immune regulation is unclear. Seurat analysis of scRNA-seq data and CIBERSORTx analysis of GBM RNA-seq data showed that M2-like TAMs accounted for the largest proportion of immune cells in the GBM TME. Among CD163+ cells (M2-like TAM marker) in GBM, CLEC5A expression was most highly associated with overall patient survival. IHC on tumor microarrays (TMA) and analysis of Ivy GAP data indicated that CLEC5A and M2-like TAMs were preferentially expressed in tumor peri-necrotic zone. THP-1 cells exposed to GBM conditioned media showed increased CLEC5A and CD163 expression by RT-qPCR and Western blot compared to other immune-activating factors (IL-4, IL-13). CLEC5A overexpression in THP-1 cells enhanced their migration toward glioma cells in vitro, and also led to increased M2-like TAM biomarker expression. Cytokine antibody microarray results revealed that overexpressing CLEC5A in THP-1 cells also significantly increased the expression of IL-1β, IL-4, IL-6, IL-8, IL-10, IL-13, GM-CSF, and other cytokines, which all contribute to the immunosuppressive TME. In TCGA GBM data, tumors with higher CLEC5A expression were enriched in IL6-JAK-STAT3 signaling. In vivo, silencing CLEC5A delayed glioma growth and prolonged survival of tumor-bearing mice, and analysis of tumors showed reduced expression of CLEC5A, CD163 and Ki-67. Collectively, CLEC5A is expressed by M2-like TAMs and enhances M2-like TAM polarization, likely through IL6-JAK-STAT3 signaling.

Retrotransposons are genomic DNA sequences that copy them-selves to new genomic locations via RNA intermediates; LINE-1 is the only active and autonomous retrotransposon in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues but is derepressed in many cancers, where LINE-1 retrotransposition is correlated with p53 mutation and copy number alteration (CNA). In cell lines, inducing LINE-1 expression can cause double-strand breaks (DSBs) and replication stress. Reanalyzing multiomic data from breast, ovarian, endometrial, and colon cancers, we confirmed correlations between LINE-1 expression, p53 mutation status, and CNA. We observed a consistent correlation between LINE-1 expression and the abundance of DNA replication complex components, indicating that LINE-1 may also induce replication stress in human tumors. In endometrial cancer, high-quality phosphoproteomic data allowed us to identify the DSB-induced ATM-MRN-SMC S phase checkpoint pathway as the primary DNA damage response (DDR) pathway associated with LINE-1 expres-sion. Induction of LINE-1 expression in an in vitro model led to increased phosphorylation of MRN complex member RAD50, suggesting that LINE-1 directly activates this pathway.

BackgroundCheckMate 9KD (NCT03338790) is a non-randomized, multicohort, phase 2 trial of nivolumab plus other anticancer treatments for metastatic castration-resistant prostate cancer (mCRPC). We report results from cohorts A1 and A2 of CheckMate 9KD, specifically evaluating nivolumab plus rucaparib.MethodsCheckMate 9KD enrolled adult patients with histologically confirmed mCRPC, ongoing androgen deprivation therapy, and an Eastern Cooperative Oncology Group performance status of 0–1. Cohort A1 included patients with postchemotherapy mCRPC (1–2 prior taxane-based regimens) and ≤2 prior novel hormonal therapies (eg, abiraterone, enzalutamide, apalutamide); cohort A2 included patients with chemotherapy-naïve mCRPC and prior novel hormonal therapy. Patients received nivolumab 480 mg every 4 weeks plus rucaparib 600 mg two times per day (nivolumab dosing ≤2 years). Coprimary endpoints were objective response rate (ORR) per Prostate Cancer Clinical Trials Working Group 3 and prostate-specific antigen response rate (PSA50-RR; ≥50% PSA reduction) in all-treated patients and patients with homologous recombination deficiency (HRD)-positive tumors, determined before enrollment. Secondary endpoints included radiographic progression-free survival (rPFS), overall survival (OS), and safety.ResultsOutcomes (95% CI) among all-treated, HRD-positive, and BRCA1/2-positive populations for cohort A1 were confirmed ORR: 10.3% (3.9–21.2) (n=58), 17.2% (5.8–35.8) (n=29), and 33.3% (7.5–70.1) (n=9); confirmed PSA50-RR: 11.9% (5.9–20.8) (n=84), 18.2% (8.2–32.7) (n=44), and 41.7% (15.2–72.3) (n=12); median rPFS: 4.9 (3.7–5.7) (n=88), 5.8 (3.7–8.4) (n=45), and 5.6 (2.8–15.7) (n=12) months; and median OS: 13.9 (10.4–15.8) (n=88), 15.4 (11.4–18.2) (n=45), and 15.2 (3.0–not estimable) (n=12) months. For cohort A2 they were confirmed ORR: 15.4% (5.9–30.5) (n=39), 25.0% (8.7–49.1) (n=20), and 33.3% (7.5–70.1) (n=9); confirmed PSA50-RR: 27.3% (17.0–39.6) (n=66), 41.9 (24.5–60.9) (n=31), and 84.6% (54.6–98.1) (n=13); median rPFS: 8.1 (5.6–10.9) (n=71), 10.9 (6.7–12.0) (n=34), and 10.9 (5.6–12.0) (n=15) months; and median OS: 20.2 (14.1–22.8) (n=71), 22.7 (14.1–not estimable) (n=34), and 20.2 (11.1–not estimable) (n=15) months. In cohorts A1 and A2, respectively, the most common any-grade and grade 3–4 treatment-related adverse events (TRAEs) were nausea (40.9% and 40.8%) and anemia (20.5% and 14.1%). Discontinuation rates due to TRAEs were 27.3% and 23.9%, respectively.ConclusionsNivolumab plus rucaparib is active in patients with HRD-positive postchemotherapy or chemotherapy-naïve mCRPC, particularly those harboring BRCA1/2 mutations. Safety was as expected, with no new signals identified. Whether the addition of nivolumab incrementally improves outcomes versus rucaparib alone cannot be determined from this trial.Trial registration numberNCT03338790.

ACT001, which is derived from an ancient anti-inflammatory drug, has been shown to cross the blood-brain barrier in preclinical studies and has demonstrated anti-glioblastoma (GBM) activity in clinical trials. However, its pharmacological potential for anti-GBM immune response modulation remains unclear. The chemical structure of ACT001 indicates that it may bind to STAT3 and thus modulate antitumor immune response. Methods: Bioinformatics and immunohistochemistry (IHC) were used to assess STAT3 and PD-L1 expression in gliomas. Western blotting, RT-PCR and immunofluorescence were used to detect PD-L1 and p-STAT3 expression in glioma cells exposed to ACT001. Chromatin immunoprecipitation, an ACT001-Biotin probe, and a dual-luciferase reporter assay were used to detect direct modulation. The in vivo efficacy of ACT001 was evaluated in GL261 murine glioma model. Survival analyses were conducted using the log-rank (Mantel-Cox) test. Results: Bioinformatic analysis of 1,837 samples from 4 public glioma datasets showed that STAT3 mRNA expression was correlated with the degree of malignancy and therapeutic resistance and that STAT3 mRNA expression was related to immunosuppression, leukocyte infiltration, and PD-L1 expression. IHC staining of 53 tissue samples confirmed that relatively high phosphorylated STAT3 and PD-L1 protein expression was associated with a relatively advanced World Health Organization (WHO) glioma grade. Next, we confirmed that ACT001 treatment reduced PD-L1 expression and STAT3 phosphorylation. An ACT001-biotin probe was used to verify that ACT001 bound to STAT3. We also demonstrated that STAT3 bound to the PD-L1 promoter. The inhibition of PD-L1 expression and STAT3 phosphorylation by ACT001 could be rescued by STAT3 overexpression. Additionally, ACT001 inhibited GBM growth and decreased PD-L1 expression in vivo. The expression of the M2 markers CD206 and CD163 was decreased, while that of the antitumor immune markers iNOS and IFNγ was increased by ACT001 in vivo. Conclusion: Our results demonstrate that STAT3 plays a key role in immunosuppression of glioma and is inhibited by ACT001. ACT001 inhibits PD-L1 transcription and modulates anti-tumor immune response in glioma bearing mice. These findings will help us to understand the mechanism of ACT001 in GBM therapy.

Diffuse gliomas are a family of neoplastic diseases characterized by widespread infiltration of central nervous system structures by tumor cells displaying glial differentiation. Traditionally characterized by morphologic features of lineage and histologic differentiation, we now understand that diffuse gliomas contain multiple discrete molecular subsets, each with their own clinical and genetic characteristics. In the current molecular era, the World Health Organization 4th Edition update introduced classes of diffuse glioma according to the status of isocitrate dehydrogenase mutation, 1p/19q co-deletion, histone H3 mutation, and BRAF mutation. Additional studies have demonstrated the subset-specific prognostic significance and grading implications of epidermal growth factor receptor amplification, CDKN2A/B homozygous deletion, TERT promoter mutations, and whole chromosome 7 gain and whole chromosome 10 loss (+7/−10). These findings represent the beginning of the molecular era of diagnosis and grading. Additional studies will likely refine our current conceptions and further advance our ability to stratify risk and direct therapies. In this review, we discuss the current understanding of the molecular classification of diffuse gliomas.

Glioblastoma is the most common primary intracranial malignant tumor in adults and has high morbidity and high mortality. TMEM158 has been reported to promote the progression of solid tumors. However, its potential role in glioma is still unclear. Here, we found that TMEM158 expression in human glioma cells in the tumor core was significantly higher than that in noncancerous cells at the tumor edge using bioinformatics analysis. Cancer cells in patients with primary GBMs harbored significantly higher expression of TMEM158 than those in patients with WHO grade II or III gliomas. Interestingly, regardless of tumor grading, human glioma samples that were IDH1-wild-type (IDH1-WT) exhibited higher expression of TMEM158 than those with IDH1-mutant (IDH1-Mut). We also illustrated that TMEM158 mRNA expression was correlated with poor overall survival in glioma patients. Furthermore, we demonstrated that silencing TMEM158 inhibited the proliferation of glioma cells and that TMEM158 overexpression promoted the migration and invasion of glioma cells by stimulating the EMT process. We found that the underlying mechanism involves STAT3 activation mediating TMEM158-driven glioma progression. In vivo results further confirmed the inhibitory effect of the TMEM158 downregulation on glioma growth. Collectively, these findings further our understanding of the oncogenic function of TMEM158 in gliomas, which represents a potential therapeutic target, especially for GBMs.

BackgroundCell line perturbation data could be utilized as a reference for inferring underlying molecular processes in new gene expression profiles. It is important to develop accurate and computationally efficient algorithms to exploit biological knowledge in the growing compendium of existing perturbation data and harness these for new predictions.ResultsWe reframed the problem of inferring possible gene perturbation based on a reference perturbation database into a classification task and evaluated the application of deep neural network models to address this problem. Our results showed that a fully-connected multi-layer neural network was able to achieve up to 74.9% accuracy in a holdout test set, but the model generalizability was limited by consistency between training and testing data.ConclusionCapacity and flexibility enables neural network models to efficiently represent transcriptomic features associated with single gene knockdown perturbations. With consistent signals between training and testing sets, neural networks may be trained to classify new samples to experimentally confirmed molecular phenotypes.

Background. Glioma is the most common primary intracranial tumor and is associated with poor prognosis. Identifying effective biomarkers for glioma is particularly important. MXRA5, a secreted glycoprotein, is involved in cell adhesion and extracellular matrix remodeling and has been reported to be expressed in many cancers. However, the role and mechanism of action of MXRA5 in gliomas remain unclear. This study was aimed at investigating the role of MXRA5 at the transcriptome level and its clinical prognostic value. Methods. In this study, RNA microarray data of 301 glioma patients from the Chinese Glioma Genome Atlas (CGGA) were collected as a training cohort and RNA-seq data of 702 glioma samples from The Cancer Genome Atlas (TCGA) were used for validation. We analyzed the clinical and molecular characteristics as well as the prognostic value of MXRA5 in glioma. In addition, the expression level of MXRA was evaluated in 28 glioma tissue samples. Results. We found that MXRA5 expression was significantly upregulated in high-grade gliomas and IDH wild-type gliomas compared to controls. Receiver operating characteristic (ROC) analysis showed that MXRA5 is a potential marker of the mesenchymal subtype of glioblastoma multiforme (GBM). We found that MXRA5 expression is highly correlated with immune checkpoint molecule expression levels and tumor-associated macrophage infiltration. High MXRA5 expression could be used as an independent indicator of poor prognosis in glioma patients. Conclusion. Our study suggests that MXRA5 expression is associated with the clinicopathologic features and poor prognosis of gliomas. MXRA5 may play an important role in the immunosuppressive microenvironment of glioma. As a secreted glycoprotein, MXRA5 is a potential circulating biomarker for glioma, deserving further investigation.

Inhibitor of nuclear factor kappa‐B kinase subunit epsilon (IKBKE) plays critical roles in the proliferation, invasion, and epithelial‐mesenchymal transition (EMT) of glioblastoma (GBM). However, as an immune response factor, few studies have focused on the role of IKBKE in the glioblastoma‐mediated immunosuppressive microenvironment. Here, we found a higher IKBKE expression level in gliomas corresponding to higher malignancy of the tumor. The highest level of IKBKE expression was examined in the core region of GBM tissues as well as the mesenchymal subtype, which are featured with necrosis, immunocyte infiltration, and immunosuppression. Further in silico analysis demonstrated that the JAK/STAT as the signaling pathway most associated with IKBKE in mesenchymal GBM. The co‐expression patterns of IKBKE, pSTAT3, and PD‐L1 were detected within GBM tissues. Mechanistically, IKBKE could interact with STAT3 and thus enhancing the phosphorylation level of STAT3 and its nuclear translocation. In addition, pSTAT3 could transcriptionally regulate the expression of PD‐L1 through binding to its promoter. In vivo results further confirmed the inhibitory effect of the IKBKE downregulation on tumor growth. Collectively, our findings suggest IKBKE as the central node in the crosstalk between NF‐κB and STAT3 signaling within mesenchymal GBM. Targeting GBM through inhibiting IKBKE could restrain tumor growth and tumor‐mediated immunosuppressive environment., 1. Higher IKBKE expression was detected in higher grades of glioma. 2. IKBKE is enriched in mesenchymal GBM, which confers immunosuppressive signature. 3. IKBKE correlates with JAK/STAT signaling in MES GBM. 4. IKBKE activates the phosphorylation of STAT3, which transcriptionally regulates PD‐L1 expression.

Retrotransposons are genomic DNA sequences that are capable of copying themselves to new genomic locations via RNA intermediates; LINE-1 is the only retrotransposon that remains autonomous and active in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues, but LINE-1 is active in many cancers. Recent studies using LINE-1 constructs indicate that host cells activate a DNA damage response (DDR) to repair retrotransposition intermediates and resolve conflicts between LINE-1 and DNA replication. Using multi-omic data from the CPTAC project, we found correlations between LINE-1 expression and ATM-MRN-SMC DDR signalling in endometrial cancer and between LINE-1 and the ATR-CHEK1 pathway in p53 wild type breast cancer. This provides evidence that conflicts between LINE-1 and DNA replication occur in at least some human cancers. Furthermore, LINE-1 expression in these cancers is correlated with the total amount of copy number variation genome wide, indicating that, when active in cancer, pointing to a direct impact of LINE-1 associated DNA damage on genome structure. We also find that, in endometrial and ovarian cancer, LINE-1 expression is correlated with the expression of genes that drive cycle progression including E2F3, PLK1 and Aurora kinase B. This study provides evidence, supporting recent work in model cell lines, of a LINE-1/DDR connection in human tumors and raises the possibility of additional interactions between LINE-1 and the cell cycle.

Background: CheckMate 649, a randomized phase 3 study in advanced GC/GEJC/EAC, showed superior overall survival (OS) and an acceptable safety profile with 1L NIVO + chemo vs chemo, leading to approval in multiple countries. We present exploratory efficacy analyses by baseline tumor mutational burden (TMB) and gene expression signatures (GES) from CheckMate 649. Methods: Whole exome sequencing of baseline tumor tissue and matching blood was performed to derive TMB. TMB-high (H) was defined as ≥ 199 mutations/exome (Chang et al. Mol Diagn Ther 2019). RNA sequencing of baseline tumor tissue was performed to assess GES. GES included a 4-gene inflammatory (inflam) (Lei et al. Clin Cancer Res 2021), a proprietary 12-gene epithelial mesenchymal transition (EMT), 6-gene angiogenesis (angio) (McDermott et al. Nat Med 2018), and other stroma- and angiogenesis-related signatures. Results: Of 1581 patients (pts) randomized to receive NIVO + chemo or chemo, 685 (43%) were evaluable for TMB (NIVO + chemo 45%, chemo 41%), and 809 (51%) were evaluable for GES (NIVO + chemo 53%, chemo 49%). In pts with PD-ligand (L)1 combined positive score (CPS) ≥ 5, OS benefit with NIVO + chemo vs chemo was seen in TMB-H pts (HR 0.44), which accounted for 10% of this population, and non-TMB-H pts (HR 0.75) (Table). Similar results were observed when excluding MSI-H pts and will be presented. OS benefit was observed across multiple GES subgroups, although low EMT and angio signature tertiles were associated with greater OS benefit (Table). Similar results were observed with other stroma- and angiogenesis-related GES for all randomized pts and pts with PD-L1 CPS < 5 which will be presented. Conclusions: Although the magnitude of benefit was higher in TMB-H and EMT/angio-low pts, OS benefit with NIVO + chemo vs chemo was observed regardless of TMB, inflam, EMT, and angio GES status. Table PD-L1 CPS ≥ 5 TMB (N = 451) GES (N = 513) Inflam EMT Angio All evaluable HR (95% CI) 0.71 (0.58-0.87) 0.72 (0.59-0.87) High, n (%) 43 (10) 171 (33) 171 (33) 171 (33) HR (95% CI) 0.44 (0.21-0.93) 0.65 (0.45-0.93) 0.88 (0.64-1.22) 0.86 (0.61-1.20) Medium, n (%) - 171 (33) 171 (33) 171 (33) HR (95% CI) - 0.65 (0.47-0.91) 0.80 (0.57-1.12) 0.69 (0.50-0.97) Low, n (%) 408 (90) 171 (33) 171 (33) 171 (33) HR (95% CI) 0.75 (0.61-0.93) 0.77 (0.55-1.07) 0.57 (0.41-0.80) 0.62 (0.44-0.86) All randomized TMB (N = 685) GES (N = 809) Inflam EMT Angio All evaluable HR (95% CI) 0.79 (0.67-0.93) 0.78 (0.67-0.91) High, n (%) 57 (8) 270 (33) 270 (33) 270 (33) HR (95% CI) 0.48 (0.25-0.93) 0.70 (0.53-0.93) 0.88 (0.68-1.15) 0.91 (0.70-1.19) Medium, n (%) - 269 (33) 269 (33) 269 (33) HR (95% CI) - 0.83 (0.64-1.08) 0.84 (0.65-1.10) 0.79 (0.61-1.03) Low, n (%) 628 (92) 270 (33) 270 (33) 270 (33) HR (95% CI) 0.83 (0.70-0.99) 0.75 (0.58-0.97) 0.68 (0.52-0.88) 0.66 (0.51-0.86) HR data are NIVO + chemo vs chemo. Citation Format: Ming Lei, Yelena Y. Janjigian, Jaffer A. Ajani, Markus Moehler, Xuya Wang, Lin Shen, Marcelo Garrido, Carlos Gallardo, Kensei Yamaguchi, Lucjan Wyrwicz, Tomasz Skoczylas, Arinilda Bragagnoli, Tianshu Liu, Mustapha Tehfe, Elena Elimova, Mingshun Li, Valerie Poulart, Yu Wang, Parul Doshi, Kohei Shitara. Nivolumab (NIVO) plus chemotherapy (chemo) vs chemo as first-line (1L) treatment for advanced gastric cancer/gastroesophageal junction cancer/esophageal adenocarcinoma (GC/GEJC/EAC): CheckMate 649 biomarker analyses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT023.

Additional file 1: Figure S1. CLUSTAL Alignments of ORF2 protein sequences. ORF2p protein sequences were obtained from the L1Base database of reference L1Hs sequences. (A) Alignment of 146 full-length L1 sequences. (B) Alignment of 107 ORF2-intact L1 sequences. In the center tiles, black bars indicate amino acid positions where the L1 in that row differs from the CLUSTAL alignment consensus sequence. The ‘% agreement,’ or identity, at each amino acid position is quantified below the center tiles. On the right, the number of amino acid changes of a particular L1 compared to the immunogen, L1RP, is quantified.

Background Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. Results We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. Conclusions Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.

5038 Background: Accurate analysis of the genomic alteration landscape within tissue- and plasma-derived tumor DNA using next-generation sequencing (NGS) may provide insights into specific patient populations that benefit from different therapies. The interchangeable use of tissue- and plasma-based assessments may benefit patients when tissue availability is limited, a common occurrence in individuals with mCRPC. To understand the potential sources of technical and biological variability in this setting, we performed comprehensive comparative analyses across 3 NGS platforms, using samples from patients enrolled in CheckMate 9KD, a phase 2 study of nivolumab combined with docetaxel, rucaparib, or enzalutamide for patients with confirmed mCRPC (NCT03338790). Methods: We performed retrospective integrated analyses of sequence and structural alterations identified through comprehensive genomic profiling (CGP) of DNA obtained from formalin-fixed, paraffin-embedded tissue specimens and cell-free DNA obtained from plasma. Tissue-based analysis was performed using the FoundationOne assay (F1, 395 genes), while the FoundationACT (FACT, 70 genes) and GuardantOMNI (OMNI, 500 genes) assays were used for plasma-based analysis. Analysis was performed on samples from 103 patients for which datasets from all 3 assays were available. Inter-platform analysis considered variants with ≥ 0.50% variant allele fraction and common to the shared pairwise targeted regions, while excluding synonymous variants. Results: Through broad profiling of DNA obtained from tissue and plasma, we uncovered previously identified recurrent alteration of AR, TP53, PTEN, and TMPRSS2 fusion with ETS genes. Additionally, we found that 42% (F1), 45% (FACT), and 34% (OMNI) of patients harbored a combination of germline and somatic mutations in homologous recombination repair pathway genes. Across all samples, median tumor mutational burden was 3.5 mutations per megabase (mut/Mb) by F1 and 8.6 mut/Mb by OMNI. Inter-platform variant analyses demonstrated concordance of 52% for F1 vs FACT, 40% for F1 vs OMNI, and 75% for FACT vs OMNI. Conclusions: Overall, these data demonstrate the value of integrated tissue and liquid biopsy profiling in mCRPC. Both technical and biological sources of variation, including panel size, mutation detection algorithms, variant annotation and reporting, analytical performance, circulating tumor DNA levels, and tumor heterogeneity, may be captured differently by tissue- and plasma-based techniques, accounting for the discordance in reported results. Clinical trial information: NCT03338790.

5044 Background: CheckMate 9KD is a phase 2 trial of NIVO (anti-PD-1) combined with either rucaparib, docetaxel, or enzalutamide for mCRPC. PARP inhibitors, like rucaparib, increase cellular DNA damage, particularly in tumors with DNA repair defects, leading to genomic instability and cell death. This DNA damage promotes immune priming and adaptive PD-L1 upregulation. Consequently, dual PD-(L)1 and PARP inhibition is a plausible therapeutic strategy for mCRPC. We report final results for cohort A1 (NIVO + rucaparib for post-CT mCRPC) of CheckMate 9KD. Methods: Cohort A1 enrolled patients (pts) with post-CT mCRPC (1–2 prior taxane regimens), ongoing ADT, ≤ 2 prior novel hormonal therapies (abiraterone, enzalutamide, etc) for mCRPC, and no prior PARP inhibitor treatment. Pts received NIVO 480 mg Q4W + rucaparib 600 mg BID until disease progression/unacceptable toxicity (NIVO dosing limited to 2 yrs). Coprimary endpoints: objective response rate (ORR) per PCWG3 criteria and prostate-specific antigen response rate (PSA-RR; ≥ 50% PSA reduction) in all treated pts and pts with homologous recombination deficiency positive (HRD+) tumors, determined before enrollment. Secondary endpoints included radiographic progression-free survival (rPFS), overall survival (OS), and safety. Results: Of 88 treated pts, median age 66 yrs (range, 46–85), 34.1% had visceral metastases and 65.9% had measurable disease. Median follow-up was 11.9 mo. Pts had a median of 4.5 NIVO doses and 3.8 mo of rucaparib. The table summarizes primary and key secondary efficacy results, and shows better outcomes for HRD+ vs HRD–/not evaluable (NE) tumors. In pts with BRCA2 mutations, confirmed ORR was 37.5% (3/8 pts) and confirmed PSA-RR was 45.5% (5/11 pts). Any-grade treatment-related AEs (TRAEs) occurred in 93.2% of pts, most commonly nausea (40.9%) and fatigue (33.0%). Grade ≥ 3 TRAEs occurred in 54.5% of pts, most commonly anemia (20.5%) and neutropenia (10.2%). TRAEs led to discontinuation in 27.3% of pts. One pt had a stroke, considered related to rucaparib by the investigator, after 28 days on rucaparib and 2 NIVO doses and died 2 months later due to post-thrombolysis hematoma. Conclusions: NIVO + rucaparib is active in pts with HRD+ post-CT mCRPC, although the trial design and short follow-up limit assessment of benefits of the combination vs individual components. Pts with HRD– tumors did not appear to benefit from either drug. No new safety signals were observed with NIVO + rucaparib. Additional biomarker analyses are ongoing. Clinical trial information: NCT03338790. [Table: see text]

Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities., National Cancer Institute (U.S.) (Grant R01CA180006)

Changes in the DNA copy number of genes (copy number variation/CNV) are widespread in many cancers and affect the expression of tumor suppressors and oncogenes. Many of these CNVs arise from chromosomal aberrations that are the result of improperly repaired DNA damage. LINE-1 retrotransposons - genomic elements that cut DNA and then reverse transcribe themselves into the gap - are expressed in many cancers and likely contribute to DNA damage and CNV in cancer cells. Using multi-omic data from CPTAC, we developed cloud-based tools on the NCI funded Cancer Genomics Cloud to measure LINE-1 RNA, protein, phosphoprotein and insertion in five cancer types - breast, ovarian, endometrial, kidney and colon - and identified mutation, expression and phosphorylation correlates of LINE-1 expression. We found significant LINE-1 expression in all, but kidney cancer. LINE-1 expression was significantly correlated with global copy number variation in breast, endometrial and ovarian cancer, a trend that was reflected in the fact that we observed the highest LINE-1 expression in ovarian cancer, which is characterized by very high CNV, and the lowest LINE-1 expression in kidney cancer, which has less overall CNV. This correlation is mirrored in our finding that, in breast, ovarian and endometrial cancer, p53 mutants express more LINE-1, indicating that high LINE-1 expression occurs in a background that is tolerant of DNA damage and CNV. We also observed an association between LINE-1 expression and phosphorylation of 53BP1 in breast, colon and endometrial cancers. ATM phosphorylated 53BP1 localizes to double strand breaks and promotes repair by non-homologous end-joining (NHEJ). Taken together, this analysis supports the hypothesis that in many cancers LINE-1 contributes to DNA damage and copy number variation, perhaps involving mismatched repair by NHEJ. Funded by NCI Contract No. HHSN261200800001E Citation Format: Wilson H. McKerrow, Xuya Wang, Mark Grivainis, David Fenyö. Proteogenomic analysis points to relationship between LINE-1 retrotransposon expression and copy number variation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2129.

Background: Breast cancer has been extensively characterized molecularly with cohorts such as The Cancer Genome Atlas (TCGA). However, as the standard of care evolves, there is a need for contemporaneous datasets with more detailed treatment and outcomes data. The ORIEN Avatar database (M2Gen, Tampa, FL) consists of clinical and tumor sequencing data from treatment-naive or on-treatment biopsies. This study evaluates the quality of ORIEN Avatar's RNA-sequencing (RNASeq) data, interrogates the impact of prior treatment on PAM50 subtyping, and reports associations between breast cancer subtypes and estimated immune cell populations. Methods: In the ORIEN Avatar dataset, RNASeq data were prepared using a multistep normalization process. We assessed the quality of normalized RNASeq data using 3 modalities. Using a principal-component (PC) analysis, we interrogated the association of gene expression with potential technical and biological factors, including processing batch effects, preservation methods, and treatment status. We evaluated concordance between immunohistochemistry (IHC)-based subtyping and intrinsic subtyping using the PAM50 gene expression signature. Prevalence of in silico-derived tumor-infiltrating immune cell compositions in ORIEN Avatar compared with TCGA breast cancer samples was investigated. Results: The ORIEN Avatar breast cancer cohort comprised 560 patients with RNASeq data. The first 3 PCs (accounting for 11%, 9%, and 7% of total explained variance, respectively) were associated with biological factors, including PAM50 subtyping and HER2 receptor and hormone receptor (HR) status. PAM50 subtype was largely concordant with IHC subtype, per clinical record of biomarker testing, and prior treatment status did not impact PAM50 subtyping. We observed that 68% of basal samples were triple negative by IHC, 92% of luminal samples were HER2-negative and HR-positive by IHC, and 62% of HER2-enriched samples per RNASeq were HER2 receptor positive by IHC. Several in silico-derived tumor-infiltrating immune cell compositions, including activated CD4 memory T cells, M0 macrophages, and activated dendritic cells, were enriched in triple-negative breast cancer samples, consistent with TCGA. Correlative analysis of RNASeq data with other biomarker data and clinical outcome is planned. Conclusions: Our results using real-world (RW) ORIEN Avatar RNASeq data were consistent with molecular profiling of breast cancer assessed using IHC and TCGA. This proof-of-concept study found no association between prior treatment status and PAM50 intrinsic subtyping. Our analysis provides a framework to assess the quality of RW molecular profiling and highlights the feasibility of leveraging harmonized molecular data to replicate and discover novel biological evidence. Citation Format: Xuya Wang, Bin Li, Peter M. Szabo, Han Chang, Mustimbo Roberts, Alice M. Walsh. Immune contexture of breast cancer subtypes in real-world molecular data [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2117.

Background: Anti–programmed death-1/programmed death ligand 1 inhibitors have been approved for the treatment of advanced small cell lung cancer (SCLC) as a single disease entity. However, efforts to detect and characterize biologically distinct subtypes of SCLC based on gene expression profiling (GEP) have identified multiple subtypes of SCLC, with potential therapeutic implications. These SCLC subtypes can be characterized as neuroendocrine (NE) or non-NE by GEP. Mutation in the retinoblastoma (Rb) transcriptional corepressor 1 (RB1) gene occurs in 65–85% of patients with SCLC, and RB1 mutation may be associated with improved survival with chemotherapy. In this retrospective, exploratory analysis, we investigated the association of genomic and transcriptional biomarkers, including RB1 mutation, with response to immuno-oncology (I-O) in patients with SCLC. Methods: Biomarker evaluation was performed in baseline samples from patients with SCLC who received second-line or later nivolumab ± ipilimumab (NIVO±IPI) in CheckMate 032 (NCT01928394). RB1 wild type (RB1WT) or mutant (RB1MUT) status and tumor mutational burden (TMB) were determined by whole exome sequencing (WES). Gene expression signatures for SCLC transcriptional subtype (6 genes), Rb protein loss of function (LOF; 87 genes), and inflammation (4 genes) were determined using RNA sequencing. Results: Of 460 total samples from patients with SCLC, WES and GEP data were available for 279 and 286 samples, respectively. 166 patients (59%) carried frameshift, in-frame insertions or deletions, truncations, or stop-gained mutations in RB1. No differences in RB1 mutation frequency were observed between treatment arms. Overall survival (OS) with NIVO was lower in RB1MUT patients compared with RB1WT (HR = 1.46 [1.02–2.1]). RB1 mutation status was not associated with OS in patients receiving NIVO+IPI. Similar trends were observed for objective response rates. Moreover, stratifying patients based on an Rb protein LOF gene expression signature showed an association between Rb protein loss and lower OS with NIVO (HR = 1.3 [1.05–1.65]) and NIVO+IPI (HR = 1.2 [0.95–1.49]). RB1 mutation status also associated with NE transcriptional subtype (P < 0.0001). Stratification of patients into NE/non-NE subtypes was not associated with OS. TMB and inflammation signatures did not differ between NE and non-NE SCLC subtype or RB1 mutation status. Conclusion: This analysis of SCLC samples suggests that transcriptionally subtyping SCLC has limited clinical utility. Rb protein function, inflammatory gene signatures, and TMB may represent independent biomarkers of response to I-O in patients with SCLC, warranting further investigation to determine the predictive value of these biomarkers, alone and in combination. Citation Format: David Balli, Xuya Wang, Naiyer A. Rizvi, Timothy A. Chan, Afshin Dowlati, Parul Doshi, Han Chang. Association of retinoblastoma function with response to immuno-oncology treatment in patients with small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2047.

Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs' interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors.

Background The antitumor activity of programmed death-1 (PD-1)/PD-1 ligand 1 (PD-L1) inhibition alone is limited in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC). Combining immunotherapy with standard-of-care chemotherapy could improve outcomes in mCRPC. We report interim analysis results for the nivolumab + docetaxel (NIVO+DOCE) treatment arm from CheckMate 9KD. Methods CheckMate 9KD is a phase II study of NIVO in combination with DOCE, rucaparib, or enzalutamide. Eligible pts had confirmed metastatic adenocarcinoma of the prostate, ongoing androgen deprivation therapy, and evaluable tumor biopsy. Pts assigned to NIVO+DOCE (chemotherapy-naive and received ≤2 prior second-generation hormonal therapies) received NIVO 360mg every 3 weeks + DOCE 75mg/m2 every 3 weeks + prednisone 5mg twice daily for ≤10 cycles followed by NIVO 480mg every 4 weeks alone until disease progression or unacceptable toxicity (up to 2 years). Coprimary endpoints were objective response rate (ORR) and prostate-specific antigen response rate (PSA-RR; defined as≥50% PSA reduction from baseline). Secondary endpoints included radiographic progression-free survival (rPFS), and safety/tolerability in all treated pts. Association of biomarkers with efficacy was an exploratory endpoint. Results This interim analysis included 41 pts in the NIVO+DOCE arm with a minimum follow-up of 28 weeks, of whom 19 (46.3%) had measurable disease. At the time of the analysis, 24 (58.5%) had discontinued study treatment. ORR in pts with measurable disease was 36.8% (95% confidence interval [CI], 16.3–61.6) with 1 complete response and 6 partial responses. Confirmed PSA-RR was 46.3% (95% CI, 30.7–62.6). Median rPFS was 8.2 months (95% CI, 6.6–not estimable). The 6-month rPFS rate was 71.5%. Any-grade and grade 3/4 treatment-related adverse events occurred in 92.7% and 48.8% of pts, respectively. Associations of biomarkers are also evaluated. Conclusions The combination of NIVO+DOCE showed encouraging clinical activity in pts with mCRPC, with a safety profile consistent with those of the individual agents. A phase III trial is warranted to further evaluate NIVO+DOCE in mCRPC. Clinical trial identification NCT03338790. Editorial acknowledgement Professional medical writing assistance was provided by Nicolette Belletier, PhD, of Parexel, and funded by Bristol-Myers Squibb. Legal entity responsible for the study Bristol-Myers Squibb. Funding Bristol-Myers Squibb and Ono Pharmaceutical Company Limited. Disclosure K. Fizazi: Advisory / Consultancy: Janssen; Advisory / Consultancy: Astellas; Advisory / Consultancy: Bayer; Advisory / Consultancy: Orion. A. Rezazadeh Kalebasty: Advisory / Consultancy, Research grant / Funding (institution), Travel / Accommodation / Expenses: Genentech; Honoraria (self), Advisory / Consultancy, Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: Exelexis; Honoraria (self), Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: Janssen; Honoraria (self), Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: AZ; Advisory / Consultancy, Research grant / Funding (institution), Travel / Accommodation / Expenses: Bayer; Honoraria (self), Speaker Bureau / Expert testimony, Research grant / Funding (institution): BMS; Honoraria (self), Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: Eisai; Research grant / Funding (institution): Macrogenics; Honoraria (self), Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: Astellas; Research grant / Funding (institution): Beyond Spring; Research grant / Funding (institution): Bioclin/Rainier Therapeutics; Research grant / Funding (institution): Clovis; Research grant / Funding (institution): Bavarian; Research grant / Funding (institution): Nordic; Research grant / Funding (institution): Seattle Genetics; Honoraria (self), Advisory / Consultancy, Speaker Bureau / Expert testimony, Travel / Accommodation / Expenses: Novartis; Honoraria (self), Advisory / Consultancy, Speaker Bureau / Expert testimony, Travel / Accommodation / Expenses: Pfizer; Shareholder / Stockholder / Stock options: ECOM; Honoraria (self), Speaker Bureau / Expert testimony: Sanofi; Honoraria (self), Speaker Bureau / Expert testimony: Amgen; Travel / Accommodation / Expenses: Prometheus Labs. J.C. Vazquez Limon: Non-remunerated activity/ies, Personal Fees and non-financial support: AstraZeneca; Non-remunerated activity/ies, Non-financial support: Merck; Non-remunerated activity/ies, Personal fees: Roche; Non-remunerated activity/ies, Personal fees: Bristol-Myers Squibb. A.J. Armstrong: Research grant / Funding (institution): BMS; Advisory / Consultancy, Research grant / Funding (institution): Janssen; Advisory / Consultancy, Research grant / Funding (institution): Pfizer/Astellas; Advisory / Consultancy, Research grant / Funding (institution): Merck; Advisory / Consultancy, Speaker Bureau / Expert testimony, Research grant / Funding (institution): Dendreon; Advisory / Consultancy, Speaker Bureau / Expert testimony, Research grant / Funding (institution): Byer; Research grant / Funding (institution): Constellation; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Research grant / Funding (institution): Genentech/Roche; Advisory / Consultancy: Clovis. B. Sharkey: Full / Part-time employment: Bristol-Myers Squibb. A. Saci: Shareholder / Stockholder / Stock options, Full / Part-time employment: Bristol-Myers Squibb. J. Li: Shareholder / Stockholder / Stock options, Full / Part-time employment: Bristol-Myers Squibb. X. Wang: Full / Part-time employment: Bristol-Myers Squibb. M. Ciprotti: Full / Part-time employment: Bristol-Myers Squibb. P. Sathyanarayana: Shareholder / Stockholder / Stock options, Full / Part-time employment: Bristol-Myers Squibb. F. Saad: Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Astellas; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Janssen; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Bayer; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Sanofi; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): BMS; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Pfizer. D.P. Petrylak: Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy, Research grant / Funding (institution): Bayer; Advisory / Consultancy, Shareholder / Stockholder / Stock options: Bellicum; Research grant / Funding (institution): Clovis; Advisory / Consultancy, Research grant / Funding (institution): Dendreon; Research grant / Funding (institution): Eli Lilly; Research grant / Funding (institution): Endocyte ; Advisory / Consultancy: Exelixis; Advisory / Consultancy: Ferring; Research grant / Funding (institution): Genentech; Research grant / Funding (institution): Innocrin; Advisory / Consultancy, Research grant / Funding (institution): Johnson and Johnson; Research grant / Funding (institution): MedImmune; Research grant / Funding (institution): Merck; Advisory / Consultancy, Research grant / Funding (institution): Millineum; Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Progenics; Research grant / Funding (institution): Roche Labatories; Advisory / Consultancy, Research grant / Funding (institution): Sanofi Aventis; Research grant / Funding (institution): Sotio; Speaker Bureau / Expert testimony, Research grant / Funding (institution), Shareholder / Stockholder / Stock options: Tyme Pharmaceuticals. R.K. Pachynski: Advisory / Consultancy, Research grant / Funding (institution): BMS; Speaker Bureau / Expert testimony: Dendreon; Advisory / Consultancy: EMD Serono/Pfizer; Speaker Bureau / Expert testimony, Travel / Accommodation / Expenses: Genentech/Roche; Advisory / Consultancy, Speaker Bureau / Expert testimony: Genomic Health; Research grant / Funding (institution): Janssen; Advisory / Consultancy, Speaker Bureau / Expert testimony: AstraZeneca; Advisory / Consultancy, Speaker Bureau / Expert testimony: Sanofi; Speaker Bureau / Expert testimony: Merck; Advisory / Consultancy: Jounce Therapeutics. C. Drake: Advisory / Consultancy, Research grant / Funding (institution), Shareholder / Stockholder / Stock options: Compugen; Advisory / Consultancy: Roche/Genentech; Advisory / Consultancy, Research grant / Funding (institution): Janssen Oncology; Advisory / Consultancy: Pfizer; Advisory / Consultancy: Astellas Medivation; Advisory / Consultancy, Shareholder / Stockholder / Stock options: Tizona Therapeutics; Advisory / Consultancy: Merck; Advisory / Consultancy: Pierre Fabre; Advisory / Consultancy: F-Star; Advisory / Consultancy, Shareholder / Stockholder / Stock options: KLEO; Advisory / Consultancy, Shareholder / Stockholder / Stock options: Harpoon; Advisory / Consultancy, Shareholder / Stockholder / Stock options: Shattuck Labs; Advisory / Consultancy, Shareholder / Stockholder / Stock options: Werewolf; Advisory / Consultancy: Genocea; Advisory / Consultancy: Sanofi Aventis; Advisory / Consultancy, Licensing / Royalties: Amplimmune; Advisory / Consultancy, Licensing / Royalties: BMS; Advisory / Consultancy: EMD. All other authors have declared no conflicts of interest.

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (