Stromal Signature Research Articles

Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis.

Benign prostatic hyperplasia (BPH) is the most common cause of lower urinary tract symptoms in men. Current treatments target prostate physiology rather than BPH pathophysiology and are only partially effective. Here, we applied next-generation sequencing to gain new insight into BPH. By RNAseq, we uncovered transcriptional heterogeneity among BPH cases, where a 65-gene BPH stromal signature correlated with symptom severity. Stromal signaling molecules BMP5 and CXCL13 were enriched in BPH while estrogen regulated pathways were depleted. Notably, BMP5 addition to cultured prostatic myofibroblasts altered their expression profile towards a BPH profile that included the BPH stromal signature. RNAseq also suggested an altered cellular milieu in BPH, which we verified by immunohistochemistry and single-cell RNAseq. In particular, BPH tissues exhibited enrichment of myofibroblast subsets, whilst depletion of neuroendocrine cells and an estrogen receptor (ESR1)-positive fibroblast cell type residing near epithelium. By whole-exome sequencing, we uncovered somatic single-nucleotide variants (SNVs) in BPH, of uncertain pathogenic significance but indicative of clonal cell expansions. Thus, genomic characterization of BPH has identified a clinically-relevant stromal signature and new candidate disease pathways (including a likely role for BMP5 signaling), and reveals BPH to be not merely a hyperplasia, but rather a fundamental re-landscaping of cell types.

Schlafen-11 expression is associated with immune signatures and basal-like phenotype in breast cancer.

Breast cancer (BC) is a heterogeneous disorder, with variable response to systemic chemotherapy. Likewise, BC shows highly complex immune activation patterns, only in part reflecting classical histopathological subtyping. Schlafen-11 (SLFN11) is a nuclear protein we independently described as causal factor of sensitivity to DNA damaging agents (DDA) in cancer cell line models. SLFN11 has been reported as a predictive biomarker for DDA and PARP inhibitors in human neoplasms. SLFN11 has been implicated in several immune processes such as thymocyte maturation and antiviral response through the activation of interferon signaling pathway, suggesting its potential relevance as a link between immunity and cancer. In the present work, we investigated the transcriptional landscape of SLFN11, its potential prognostic value, and the clinico-pathological associations with its variability in BC. We assessed SLFN11 determinants in a gene expression meta-set of 5061 breast cancer patients annotated with clinical data and multigene signatures. We found that 537 transcripts are highly correlated with SLFN11, identifying "immune response", "lymphocyte activation", and "T cell activation" as top Gene Ontology processes. We established a strong association of SLFN11 with stromal signatures of basal-like phenotype and response to chemotherapy in estrogen receptor negative (ER-) BC. We identified a distinct subgroup of patients, characterized by high SLFN11 levels, ER- status, basal-like phenotype, immune activation, and younger age. Finally, we observed an independent positive predictive role for SLFN11 in BC. Our findings are suggestive of a relevant role for SLFN11 in BC and its immune and molecular variability.

Bioinformatics Analysis of Stromal Molecular Signatures Associated with Breast and Prostate Cancer.

This study aimed to identify stromal molecular signatures associated with breast and prostate cancer. The microarray data GSE26910 was downloaded from Gene Expression Omnibus database, including six invasive breast tumor stroma, six matched normal controls, six invasive prostate tumor stroma, and six matched controls. The differentially expressed genes (DEGs) in invasive breast and prostate tumors stroma were, respectively, identified. Then common stromal genes (B_P.DEGs) were further screened. Protein-protein interaction (PPI) network was constructed and Gene Ontology analysis was performed. Besides, gene-chemical interactions were mapped in Comparative Toxicogenomics Database to screen the chemicals related to feature genes. The results showed that, in total, 16 B_P.DEGs were identified. Thereinto, only seven B_P.DEGs were mapped into PPI, and only four functional modules (adenylate cyclase activating polypeptide 1 (pituitary) receptor type I (ADCYAP1R1) module, aspartoacylase (ASPA) module, glutathione S-transferase mu 5 (GSTM5) module, and periplakin (PPL) module) were involved in important biological processes associated with cancer progression. In addition, the chemicals, such as dihydrotestosterone, apocarotenal, testosterone, and progesterone, were screened for the roles of feature genes in the progression of breast and prostate cancer. In conclusion, ADCYAP1R1, GSTM5, and PPL were stromal molecular signatures and might play a key role in the progression of breast and prostate cancer.

PF510 A 14‐GENE SIGNATURE ASSOCIATED TO CHOLESTEROL METABOLISM IDENTIFIES M1‐LIKE TUMOR‐INFILTRATING MACROPHAGES AND PREDICTS PATIENT SURVIVAL IN DIFFUSE LARGE B CELL LYMPHOMA

Background:Diffuse large B cell lymphoma (DLBCL) is a heterogeneous disease with high variability in clinical outcome, genetic features and cells of origin (COO). Gene expression profiling (GEP) studies have identified stromal signatures reflecting extracellular matrix deposition and macrophage infiltration as predictive of favorable outcome to standard immune‐chemotherapy. However, while a reliable gene panel has been recently developed to detect stromal compartment, no reproducible macrophage biomarkers applicable to clinical practice are currently available. Tumor‐associated macrophages (TAM) can display a M1‐like phenotype with an antitumor activity, or act as M2‐like subpopulation promoting angiogenesis and tumor progression. As described for many immune cells, environmental and metabolic signals including oxygen, cytokine and nutrient gradients induce profound reprogramming also in macrophages and their precursors. In particular, the cholesterol metabolism, mainly regulated by the nuclear liver X receptors (LXRα and LXRβ), is known to control functional polarization, inflammatory response and apoptosis processes.Aims:We investigated whether LXRs may play a role in DLBCL biology and modulate the function of macrophages in tumor microenvironment, ultimately affecting prognosis.Methods:We first examined the expression level of LXRα and LXRβ, encoded by NR1H3 and NR1H2 genes respectively, throughout several B‐cell lymphomas GEP from different tissues and used CIBERSORT deconvolution algorithm to analyze DLBCL microenvironment composition according to NR1H3 expression. Furthermore, Gene set enrichment analyses (GSEA), in vitro studies and in situ RNA hybridization were used to correlate NR1H3 with a particular TAM subpopulation. Then, we identified a panel of 50 genes closely related to LXRα by using a machine learning approach (Random Forest), and explored their prognostic potential in a validation cohort of 210 fresh frozen DLBCLs. Finally, we analyzed the expression level of 14 genes functionally selected from the whole LXRα panel by NanoString technology in an independent cohort of 148 formalin fixed paraffin embedded (FFPE) specimens.Results:LXRα but not LXRβ was found upregulated in non‐malignant cells showing a strong association with M1‐like macrophages by combining GSEA, in situ and in vitro results. Hierarchical clustering analysis of the 50‐gene signature associated to LXRα identified three patient groups with heterogeneous clinical behavior in the cohort of 210 fresh/frozen DLBCLs. Notably, this difference was strikingly evident when the panel of 14 functionally‐selected genes was used to stratify an independent cohort of 148 DLBCLs by NanoString, identifying two main prognostic subgroups. In particular, cases with low expression of the selected genes showed a significant adverse outcome in term of overall survival and progression free survival compared to those with intermediate and high expression (Figure 1). Moreover, this difference was independent from COO, and identified a group of GCB‐DLBCLs with unexpected less favorable outcome.Summary/Conclusion:We characterized macrophages functionally and demonstrated that the metabolic regulator LXRα may represent a reliable functional biomarker of M1‐like macrophages in DLBCL. Furthermore, we identified a robust prognostic panel of 14 genes closely related to cholesterol metabolism and routinely applicable to FFPE samples. The panel recognizes distinct prognostic subgroups of DLBCLs independently from their COO, providing the rationale to design clinical trials exploring new immunomodulatory drugs.image

Comprehensive molecular characterization of clinical response in ramucirumab-treated gastric cancer patients: Phase II trial with integrated genomic profiling.

4064 Background: The absence of tumor cells enables an enriched stromal environment to generate RNA signatures and through assembling genes involved in tumor stroma, four distinct stromal signatures that reflected biological processes such as signature vascular mature (VM), vascular mature/inflammatory (VMI), vascular immature/noninflammatory (VINI) and inflammatory alone (I) depending on mature of vasculature. We hypothesized that these stromal specific signatures may provide additional information to the pre-existing TCGA/ACRG subtypes when predicting response to anti-angiogenesis agent such as ramucirumab. Methods: We conducted a single-center phase II trial in which we treated 61 unselected patients with metastatic GC with ramucirumab plus paclitaxel as second line therapy and performed pre-planned integrated genomic profiling. Results: Sixty-two patients were enrolled in this study between May 2014 and June 2017. The cut-off date for treatment outcome analysis was January 2, 2019, at which time response evaluations were available for 57 patients with a median follow-up of 30.2months. In an intent-to-treat analysis cohort, there was no CR and 22 patients achieved confirmed PRs resulting in an ORR of 35.5% (95% CI: 23.6 – 47.4). The response rate to ramucirumab was considerably enriched in VM/VMI group (29.2%) (P = 0.0003) when compared to I ( < 10%) or VINI group ( < 10%). The strongest response defined by maximal response to ramucirumab was shown in GC patients with VM/VMI signatures. Of note, VM/VMI patients had prolonged duration of response to ramucirumab/paclitaxel demonstrating that these patients not only respond to ramucirumab but also had durable response. Conclusions: This is the first study to demonstrate a clinically robust correlation between stromal-based signature and response to anti-angiogenesis inhibitor in GC. Clinical trial information: 02628951.

164 – Establishment of a Nomogram Comprising of Immune and Stromal Gene Signature for Predicting Survival and Identification of Poor Molecular Subtypes in Pancreatic Ductal Adenocarcinoma

164 – Establishment of a Nomogram Comprising of Immune and Stromal Gene Signature for Predicting Survival and Identification of Poor Molecular Subtypes in Pancreatic Ductal Adenocarcinoma

A modular transcriptome map of mature B cell lymphomas

BackgroundGerminal center-derived B cell lymphomas are tumors of the lymphoid tissues representing one of the most heterogeneous malignancies. Here we characterize the variety of transcriptomic phenotypes of this disease based on 873 biopsy specimens collected in the German Cancer Aid MMML (Molecular Mechanisms in Malignant Lymphoma) consortium. They include diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), Burkitt’s lymphoma, mixed FL/DLBCL lymphomas, primary mediastinal large B cell lymphoma, multiple myeloma, IRF4-rearranged large cell lymphoma, MYC-negative Burkitt-like lymphoma with chr. 11q aberration and mantle cell lymphoma.MethodsWe apply self-organizing map (SOM) machine learning to microarray-derived expression data to generate a holistic view on the transcriptome landscape of lymphomas, to describe the multidimensional nature of gene regulation and to pursue a modular view on co-expression. Expression data were complemented by pathological, genetic and clinical characteristics.ResultsWe present a transcriptome map of B cell lymphomas that allows visual comparison between the SOM portraits of different lymphoma strata and individual cases. It decomposes into one dozen modules of co-expressed genes related to different functional categories, to genetic defects and to the pathogenesis of lymphomas. On a molecular level, this disease rather forms a continuum of expression states than clearly separated phenotypes. We introduced the concept of combinatorial pattern types (PATs) that stratifies the lymphomas into nine PAT groups and, on a coarser level, into five prominent cancer hallmark types with proliferation, inflammation and stroma signatures. Inflammation signatures in combination with healthy B cell and tonsil characteristics associate with better overall survival rates, while proliferation in combination with inflammation and plasma cell characteristics worsens it. A phenotypic similarity tree is presented that reveals possible progression paths along the transcriptional dimensions. Our analysis provided a novel look on the transition range between FL and DLBCL, on DLBCL with poor prognosis showing expression patterns resembling that of Burkitt’s lymphoma and particularly on ‘double-hit’ MYC and BCL2 transformed lymphomas.ConclusionsThe transcriptome map provides a tool that aggregates, refines and visualizes the data collected in the MMML study and interprets them in the light of previous knowledge to provide orientation and support in current and future studies on lymphomas and on other cancer entities.

Compartmentalized gut lymph node drainage dictates adaptive immune responses.

The intestinal immune system has the challenging task of tolerating foreign nutrients and the commensal microbiome, while excluding or eliminating ingested pathogens. Failure in such balance leads to severe diseases such as inflammatory bowel diseases (IBD), food allergies or invasive gastrointestinal infections1. Multiple immune mechanisms are therefore in place to maintain tissue integrity, including balanced generation of effector T (TH) cells and FOXP3+ regulatory T (pTreg) cells, which mediate resistance to pathogens and regulate excessive immune activation, respectively1–4. The gut–draining lymph nodes (gLNs) are critical sites for orchestrating adaptive immunity to luminal perturbations5–7. However, how they manage to simultaneously support tolerogenic and inflammatory reactions is incompletely understood. Here we report that gLNs are immunologically unique according to the functional gut segment they drain. Stromal and dendritic cell gene signatures as well as T cell polarization against the same luminal antigen differed between gLNs, the proximal small intestine–draining gLNs preferentially giving rise to tolerogenic and the distal gLNs to pro-inflammatory T cell responses. This segregation permitted targeting distal gLNs for vaccination and maintenance of duodenal pTreg cell induction during colonic infection. Conversely, the compartmentalized dichotomy was perturbed by surgical removal of select distal gLNs and duodenal infection, impacting both lymphoid organ and tissue immune responses. Our findings reveal that the conflict between tolerogenic and inflammatory intestinal responses is in part resolved by discrete gLN drainage, and encourage gut segment-specific antigen targeting for therapeutic immune modulation.

Metabolic reprogramming of the stromal epigenome in ovarian cancer metastasis

High grade serous ovarian cancer (HGSOC) is characterized by early metastasis throughout the peritoneal cavity and a poor clinical outcome. During the metastatic process, ovarian cancer cells interact with diverse cell populations, including mesothelial cells, adipocytes, and cancer‐associated fibroblasts (CAFs). Ovarian cancer CAFs have well‐described roles in promoting the growth and progression of ovarian cancer by secreting pro‐proliferative cytokines and oncogenic extracellular matrix components (ECM). To better understand the proteomic changes that occur during metastasis in both tumor and stromal compartments, laser‐capture microdissection was coupled to label‐free, quantitative proteomics to independently characterize the proteomes of both tumor and stromal compartments in a cohort of HGSOC patients. We identified a conserved stromal proteomic signature associated with metastasis which included high expression of nicotinamide N‐methyltransferase (NNMT) in the metastatic stroma. NNMT is a metabolic enzyme that catalyzes the methylation of nicotinamide and consumes S‐adenosyl methionine (SAM), thus depleting cellular methylation potential and reducing methylation of DNA and proteins. NNMT regulated the expression of thousands of genes and was necessary and sufficient for the reprogramming of normal fibroblasts to CAFs. Stromal NNMT expression altered multiple metabolic pathways and led to a significant reduction in cellular SAM pools. Attenuated DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) were associated with global changes in gene expression. Using genetic and small‐molecule inhibitor strategies, we found that stromal NNMT activity promoted the progression and metastasis of ovarian cancer. This study provides support to the idea that stromal methyltransferase activities can be targeted to normalize the metastatic stroma and should be further explored as treatment targets for cancer.Support or Funding InformationThis work was supported by a Marsha Rivkin Foundation award (MAE), National Cancer Institute (NCI) grants CA111882 and CA211916 (EL), the Harris Family Foundation (MAE and SDY), the Ludwig Institute for Cancer Research (EL), NIH grant CA175399 and DP2GM128199 (REM), V Foundation for Cancer Research (V2016‐020 to REM), the Körber Foundation/Körber European Science Prize (MM), the Max‐Planck Society for the Advancement of Science (MM), the Novo Nordisk Foundation (Grant agreement NNF14CC0001 and NNF15CC0001; FC and MM), and University of Chicago Cancer Center Support Grant P30CA014599.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Abstract P4-06-03: Unravelling triple-negative breast cancer tumor microenvironment heterogeneity using an integrative multiomic analysis

Abstract Introduction: Triple negative breast cancer (TNBC) constitute 10-20% of all breast cancers and is associated with a worse prognosis and limited treatment options. Recent trials evaluating immune checkpoint blockade in TNBC demonstrated encouraging results for a subset of patients. TNBC is highly heterogeneous and its tumour microenvironment (TME) has been recognized as a critical determinant of its behavior and clinical outcome. Genome-wide gene expression profiling analyses have already improved our understanding of the complexity of this disease and have defined 6 different molecular subtypes namely Basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal stem-like (MSL) and luminal androgen receptor (LAR), exhibiting distinct biological and clinical characteristic. In this study, we aim to dissect the molecular diversity of the TME and more specifically to assess the immune landscape according to TNBC molecular subtypes. Methods: A cohort of 485 TNBC patient with publicly available data (RNA-Seq and Illumina HT-12 v3) from the METABRIC and the TCGA consortia were used in the gene expression analysis. Gene signatures reflecting different features or cellular components (immune, stromal, angiogenesis, lymphangiogenesis, hypoxia, metabolism) of the TME were used to evaluate multiple biological processes known to contribute to tumorogenesis. A compendium of 17 immune specific gene signatures and T cell localisation classification were used to evaluate the immune composition and spatial pattern of immune infiltrates. All parameters were compared using a logistic regression model to evaluate their relative contribution according to each molecular subtype. Results: Our analyses demonstrated that each molecular subtype exhibits different TME profiles, as well as specific immune composition and localisation. IM tumors were associated with the highest expression of immune-related gene signatures, enriched with adaptive immune cells and with a fully inflamed spatial pattern. MSL tumors were mostly associated with the expression of Lymphangiogenesis and Stromal TME signatures. They also exhibited some immune activity through the expression of immune gene signatures capturing innate immune and adaptive immunosuppressive cells. This subtype was mainly associated with margin restricted and to some extent with fully inflamed spatial pattern. BL1 tumors were associated with the expression of Metabolism TME signatures, along with fully inflamed and stroma restricted spatial pattern. To a lesser extent, this subtype was also associated with activated DC and CD4 Tem cells. LAR and M tumors exhibited an immune cold phenotype. They were associated with Stromal and Metabolism TME signatures, enriched in margin restricted spatial pattern and negatively associated with every immune cells. Conclusions: Our results demonstrate for the first time the huge heterogeneity that characterizes the TME of TNBCs. Identification of specific TME profiles could help to design more rationale and appropriate synergistic therapeutic combinations targeting TME elements in this high-risk disease. Citation Format: Bareche Y, Buisseret L, Gruosso T, Girard E, Venet D, Dupont F, Desmedt C, Park M, Rothé F, Stagg J, Sotiriou C. Unravelling triple-negative breast cancer tumor microenvironment heterogeneity using an integrative multiomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-06-03.

Abstract P5-11-04: Anti-proliferative effect of oral metronomic vinorelbine (mVNB) in PAM50 Luminal/HER2-negative early breast cancer (SOLTI-1501 VENTANA): A randomized, three-arm, window-of-opportunity study

Abstract BACKGROUND: The anti-proliferative effect of mVNB alone or in combination with endocrine therapy in patients with hormone receptor-positive/HER2- breast cancer (BC) has been scarcely addressed. METHODS: Postmenopausal women with untreated stage I-III BC were randomized (1:1:1) to receive 3 weeks of letrozole (LTZ) 2.5mg/day, oral mVNB 50mg 3 days/week or the combination. The 1ary objective was to evaluate, within PAM50 Luminal A/B disease, if the anti-proliferative effect of mVNB+LTZ was superior to monotherapy. An anti-proliferative effect was defined as the mean relative decrease of the PAM50 11-gene Proliferation Score in each arm. 2ary objectives included safety and the comparison of the anti-proliferative effect between arms. An unplanned analysis of stromal tumor infiltrating lymphocytes (sTILs) was performed. PAM50 analyses were performed using the nCounter®-based Breast Cancer 360TM panel. Changes in the expression of 790 genes/signatures tracking multiple biological processes from tumor cells and the microenvironment were evaluated within each arm using paired (surgery vs. baseline) univariate analyses. P-values were corrected for multiple comparisons using false discovery rate (FDR). RESULTS: A total of 61 patients were randomized and 54 paired samples (89%) were analyzed. Main patient characteristics were mean age 67, mean tumor size 1.7 cm, stage I (55.7%) and grade 1-2 (90%). Grade 3 toxicities occurred in 3.3% of cases. Baseline samples were Luminal A (72.3%) or B (27.7%). The anti-proliferative effect of mVNB+LTZ (-73.2%) was superior to both monotherapy arms combined (-49.9%; p=0.001) and mVNB (-19.1%; p<0.001). The anti-proliferative effect of mVNB+LTZ (-73.2%) was higher compared to LTZ (-65.7%) but did not reach statistical significance (p=0.328). Across the mVNB+LTZ, LTZ and VNB arms, 413 (52.3%), 403 (51.0%) and 21 (2.6%) genes/signatures were found differentially expressed (FDR<5%) between baseline and surgery samples. Compared to mVNB+LTZ baseline samples, surgical samples showed higher expression of AP-1 transcription factor subunits FOS and JUN, inflammatory chemokines (e.g. CCL4 and IL6), stromal-related genes (e.g. CAV1 and stroma signature) and immune infiltration (e.g. CD8 T-cell signature) and lower expression of proliferation-related genes (e.g. MKI67 and UBE2C), estrogen receptor-signaling and Risk of Recurrence. Of the 413 genes found differentially expressed in surgical samples compared to baseline samples in the mVNB+LTZ arm, 108 (26.2%) were not found in the LTZ arm. Among them, high expression of LAG3, CD24, CD84 and CCR5. Under the microscope, sTILs (≥10% at week 3) were observed in 6.6% (mVNB), 15% (LTZ) and 26% (mVNB+LTZ) of the cases. In tumors with ≤10% TILs at baseline, an increase in TILs was observed following LTZ (p=0.049) and mVNB+LTZ (p=0.012). CONCLUSIONS: mVNB is well-tolerated and presents antiproliferative activity alone and in combination with LTZ. The increase of activated CD8 T-cells or TILs observed with LTZ+mVNB opens the possibility of studying combinations with immunotherapy. Further investigation comparing these biological results with other metronomic schedules or combinations is warranted. Citation Format: Prat A, Adamo B, Pascual T, Perez Fidalgo JA, Blanch S, Martínez N, Gomez Pardo P, Lopez Gonzalez A, Murillo Jaso L, Amillano K, Vidal M, Paré L, Canes J, Galvan P, Gonzalez Farre B, Ortega Cebrián V, Gonzalez X, Bellet Ezquerra M, Villagrasa P, Ciruelos E. Anti-proliferative effect of oral metronomic vinorelbine (mVNB) in PAM50 Luminal/HER2-negative early breast cancer (SOLTI-1501 VENTANA): A randomized, three-arm, window-of-opportunity study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-04.

Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-Sparing Trimodality Therapy for Muscle-Invasive Bladder Cancer

BackgroundBladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC), and biomarkers to inform therapy selection are needed. ObjectiveTo evaluate the prognostic value of immune and stromal signatures in MIBC treated with TMT. Design, setting, and participantsWe used a clinical-grade platform to perform transcriptome-wide gene expression profiling of primary tumors from 136 MIBC patients treated with TMT at a single institution. We observed 60 overall survival events at 5yr, and median follow-up time for patients without an event was 5.0yr (interquartile range 3.1, 5.0). Expression data from another cohort of 223 MIBC patients treated with neoadjuvant chemotherapy (NAC) and RC were also analyzed. Outcome measurements and statistical analysisMolecular subtype, immune, and stromal signatures were evaluated for associations with disease-specific survival (DSS) and overall survival (OS) in TMT patients, and in patients treated with NAC and RC. Results and limitationsGene expression profiling of TMT cases identified luminal (N=40), luminal-infiltrated (N=26), basal (N=54), and claudin-low (N=16) subtypes. Signatures of T-cell activation and interferon gamma signaling were associated with improved DSS in the TMT cohort (hazard ratio 0.30 [0.14–0.65], p=0.002 for T cells), but not in the NAC and RC cohort. Conversely, a stromal signature was associated with worse DSS in the NAC and RC cohort (p=0.006), but not in the TMT cohort. This study is limited by its retrospective nature. ConclusionsHigher immune infiltration in MIBC is associated with improved DSS after TMT, whereas higher stromal infiltration is associated with shorter DSS after NAC and RC. Additional studies should be conducted to determine whether gene expression profiling can predict treatment response. Patient summaryWe used gene expression profiling to study the association between tumor microenvironment and outcomes following bladder preservation therapy for invasive bladder cancer. We found that outcomes varied with immune and stromal signatures within the tumor. We conclude that gene expression profiling has potential to guide treatment decisions in bladder cancer.

Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue

BackgroundGene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methodsHere, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression digitally quantified by NanoString technology on a validation set of 175 formalin-fixed, paraffin-embedded DLBCLs from two randomized trials. Data from an unsupervised clustering analysis were used to build a model of clustering assignment, whose prognostic value was also assessed on an independent cohort of 40 cases. All tissue samples consisted of pretreatment biopsies of advanced-stage DLBCLs treated by comparable R-CHOP/R-CHOP-like regimens. ResultsIn silico analysis demonstrated that higher proportion of myofibroblasts (MFs), dendritic cells, and CD4+ T cells correlated with better outcomes and the expression of genes in our panel is associated with a risk of overall and progression-free survival. In a multivariate Cox model, the microenvironment genes retained high prognostic performance independently of the cell-of-origin (COO), and integration of the two prognosticators (COO + TME) improved survival prediction in both validation set and independent cohort. Moreover, the major contribution of MF-related genes to the panel and Gene Set Enrichment Analysis suggested a strong influence of extracellular matrix determinants in DLBCL biology. ConclusionsOur study identified new prognostic categories of DLBCL, providing an easy-to-apply gene panel that powerfully predicts patients’ survival. Moreover, owing to its relationship with specific stromal and immune components, the panel may acquire a predictive relevance in clinical trials exploring new drugs with known impact on TME.

A New Stromal Signature Applicable to Formalin-Fixed Paraffin-Embedded Tissues Identifies Patients at Risk in Prospective Clinical Trials of the German High-Grade Non-Hodgkin Lymphoma Study Group

Diffuse large B-cell-lymphoma (DLBCL) is a heterogeneous disease in its sites of origin, genetic alterations, and clinical behavior. Gene expression profiling (GEP) has led to the identification of two molecular subtypes, GCB-like and ABC-like DLBCL, that follow different molecular circuits and hence, likely represent different diseases. Next to the ABC-like GEP, the rearrangement and/or expression of MYC and TP53 mutations in tumors characterize patient subsets with inferior prognosis. However, the clinical impact of cell of origin (COO) subtyping and the identification of prognostic biomarkers differ between studies. In many clinical trials, patients identified “at risk” experience cure and long-time survival. Important factors modulating the impact of tumor cell-specific factors may be conferred by the host microenvironment, and stromal signatures have been shown to be correlated to survival in DLBCL. The robust analysis of stromal signatures is hampered by the lack of assays applicable to routinely used formalin-fixed paraffin-embedded (FFPE) materials. We have constructed a molecular signature applicable to FFPE, interrogating the quantitative and qualitative composition of the microenvironment in DLBCL. The signature was trained using an algorithm that extracts prognostic information out of the ratios of pairs of genes. The genes that drive prognosis are expressed in T-cells and macrophages and have function in the communication between both cell types. The model was validated using the NanoString assay in a cohort of 466 DLBCL patients enrolled in 7 prospective clinical trials (MInT, MegaCHOEP phase III and observation, RICOVER-60, RICOVER-noRTh, DENSER, SMARTER) of the German High grade non-Hodgkin's lymphoma study group (DSHNHL). Grouping of the patients into quartiles according to the expression of the continuous stromal signature score (ranging from -1.880to 4.441) resulted in three quartiles (Q1-3) with comparable clinical behavior (stromal signature low). Patients from quartile 4 (Q4), however, characterized by high expression of the signature (stromal signature high), showed a clearly inferior outcome in EFS, PFS and OS (Figure 1 a-c). This result could be independently reproduced in the seven clinical trials named above, thus clearly depicting the robustness of the signature. Multivariate analysis revealed that high expression of the stromal signature is a prognostic risk factor independent of the IPI factors in EFS (HR 1.7, 95 % CI 1.2-2.4, p-value =0.001), PFS (HR 1.8, 95 % CI 1.2-2.5, p-value =0.001) and OS (HR1.8, 95 % CI 1.3-2.7, p-value =0.001). Combining stromal signature count with IPI-score led to the identification of a high-risk cohort (Fig. 1 d-f). Of importance, additional multivariate analyses adjusted for the IPI factors performed within selected trials showed that the stromal signature provides prognostic information independent of the COO status, MYC and dual MYC/BCL2 rearrangements, TP53 mutations and the MYC/BCL2 double expresser status.In summary, our data from prospectively randomized trials of the DSHNHL underline the importance of the microenvironment in the prognostic stratification of DLBCL patients and suggest that the composition and quality of the tumor stroma is an independent risk factor in DLBCL. Analysis of stromal features, therefore, may provide a rationale for targeted treatment approaches, e.g. with immunomodulatory substances (IMIDs), in patients at risk. [Display omitted] DisclosuresKlapper:Regeneron: Honoraria, Research Funding; HTG Molecular Diagnostics, Inc.: Research Funding; F.Hoffman-La Roche: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Takeda: Honoraria, Research Funding. Richter:HTG Molecular Diagnostics, Inc.: Research Funding. Poeschel:Roche: Other: Travel grants; Amgen: Other: Travel grants. Held:BMS: Consultancy, Other: Travel grants, Research Funding; Spectrum: Research Funding; Roche: Consultancy, Other: Travel grants, Research Funding; Amgen: Research Funding; MSD: Consultancy.

ColXα1 is a stromal component that colocalizes with elastin in the breast tumor extracellular matrix.

The tumor microenvironment regulates tissue development and homeostasis, and its dysregulation contributes to neoplastic progression. Increased expression of type X collagen α‐1 (ColXα1) in tumor‐associated stroma correlates with poor pathologic response to neoadjuvant chemotherapy in estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2)‐positive breast cancers. Evaluation of ColXα1 expression patterns suggests a potential connection with elastin fibers. To investigate the possible interaction between ColXα1 and elastin, we evaluated the expression of ColXα1 in relation to elastin fibers in normal breast tissue, ductal carcinoma in situ, and invasive breast carcinomas at cellular and subcellular levels. Our findings demonstrate that ColXα1 colocalizes with elastin in invasive breast cancer‐associated stroma by immunohistochemistry, immunofluorescence, and electron microscopy. In 212 invasive breast carcinomas, this complex was aberrantly and selectively expressed in tumor extracellular matrix in 79% of ER+/HER2−, 80% of ER+/HER2+, 76% of ER−/HER2+, and 58% of triple negative breast cancers. In contrast, ColXα1 was generally absent, while elastin was present perivascularly in normal breast tissue. ColXα1 and elastin were coexpressed in 58% of ductal carcinoma in situ (DCIS) in periductal areas. In mass‐forming DCIS with desmoplastic stroma, the complex was intensely expressed in periductal areas as well as within the tumor‐associated stroma in all cases. Our data suggest that the breast carcinoma neoplastic process may involve aberrant expression of ColXα1 and elastin in the tumor microenvironment emerging early at the DCIS stage. Enrichment of these complexes in tumor‐associated stroma may represent a stromal signature indicative of intrinsic differences between breast cancers. These findings shed light on investigation into the role of aberrant collagen complex expression in tumorigenesis and tumor progression which may be leveraged in therapeutic and theranostic applications.

A genomic ruler to assess oncogenic transition between breast tumor and stroma.

BackgroundCancers induce gene expression alterations in stroma surrounding tumors that supports cancer progression. However, it is actually not at all known the extent of altered stromal gene expression enacted by tumors nor the extent to which altered stromal gene expression penetrates the stromal tissue. Presently, post-surgical “tumor-free” stromal tissue is determined to be cancer-free based on solely on morphological normality—a criteria that has not changed in more than 100 years despite the existence of sophisticated gene expression data to the contrary. We therefore investigated the extent to which breast tumors alter stromal gene expression in three dimensions in women undergoing mastectomy with the intent of providing a genomic determination for development of future risk of recurrence criteria, and to inform the need for adjuvant full-breast irradiation.Methods and findingsGenome-wide gene expression changes were determined in histopathologically normal breast tissue in 33 women undergoing mastectomy for stage II and III primary invasive ductal carcinoma at serial distances in three dimensions from the tumor. Gene expression was determined by genome-wide mRNA analysis and subjected to metagene mRNA characterization. Tumor-like gene expression signatures in stroma were identified that surprisingly transitioned to a plastic, normalizing homeostatic signature with distance from tumor. Stroma closest to tumor displayed a pronounced tumor-like signature enriched in cancer-promoting pathways involved in disruption of basement membrane, cell migration and invasion, WNT signaling and angiogenesis. By 2 cm from tumor in all dimensions, stromal tissues were in transition, displaying homeostatic and tumor suppressing gene activity, while also expressing cancer supporting pathways.ConclusionsThe dynamics of gene expression in the post-tumor breast stroma likely co-determines disease outcome: reversion to normality or transition to transformation in morphologically normal tissue. Our stromal genomic signature may be important for personalizing surgical and adjuvant therapeutic decisions and risk of recurrence.

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2

BackgroundGene expression-based profiling of colorectal cancer (CRC) can be used to identify four molecularly homogeneous consensus molecular subtype (CMS) groups with unique biologic features. However, its applicability to colorectal premalignant lesions remains unknown. Patients and methodsWe assembled the largest transcriptomic premalignancy dataset by integrating different public and proprietary cohorts of adenomatous and serrated polyps from sporadic (N=311) and hereditary (N=78) patient populations and carried out a comprehensive analysis of carcinogenesis pathways using the CMS random forest (RF) classifier. ResultsOverall, transcriptomic subtyping of sporadic and hereditary polyps revealed CMS2 and CMS1 subgroups as the predominant molecular subtypes in premalignancy. Pathway enrichment analysis showed that adenomatous polyps from sporadic or hereditary cases (including Lynch syndrome) displayed a CMS2-like phenotype with WNT and MYC activation, whereas hyperplastic and serrated polyps with CMS1-like phenotype harbored prominent immune activation. Rare adenomas with CMS4-like phenotype showed significant enrichment for stromal signatures along with transforming growth factor-β activation. There was a strong association of CMS1-like polyps with serrated pathology, right-sided anatomic location and BRAF mutations. ConclusionsBased on our observations made in premalignancy, we propose a model of pathway activation associated with CMS classification in colorectal carcinogenesis. Specifically, while adenomatous polyps are largely CMS2, most hyperplastic and serrated polyps are CMS1 and may transition into other CMS groups during evolution into carcinomas. Our findings shed light on the transcriptional landscape of premalignant colonic polyps and may help guide the development of future biomarkers or preventive treatments for CRC.

A Paradoxical Correlation of Cancer-Associated Fibroblasts With Survival Outcomes in B-Cell Lymphomas and Carcinomas.

The tumor microenvironment is increasingly recognized as an active participant in tumor progression. A recent pan-cancer genomic profile analysis has revealed that gene signatures representing components of the tumor microenvironment are robust predictors of survival. A stromal gene signature representing fibroblasts and extracellular matrix components has been associated with good survival in diffuse large B-cell lymphoma (DLBCL). Paradoxically, a closely related gene signature has been shown to correlate with poor survival in carcinomas, including breast, ovarian, pancreatic, and colorectal cancer. To date, there has been no explanation for this paradoxical inverse correlation with survival outcomes in DLBCL and carcinomas. Using public gene data sets, we confirm that the DLBCL stromal gene signature is associated with good survival in DLBCL and several other B-cell lymphomas while it is associated with poor survival in ovarian cancer and several other solid tumors. We show that the DLBCL stromal gene signature is enriched in lymphoid fibroblasts in normal lymph nodes and in cancer-associated fibroblasts (CAFs) in ovarian cancer. Based on these findings, we propose several possible mechanisms by which CAFs may contribute to opposite survival outcomes in B-cell lymphomas and carcinomas.

Immune Cell and Stromal Signature Associated With Progression-Free Survival of Patients With Resected Pancreatic Ductal Adenocarcinoma

Changes to the microenvironment ofpancreatic ductal adenocarcinomas (PDACs) have been associated with poor outcomes of patients. We studied the associations between composition of the pancreatic stroma (fibrogenic, inert, dormant, or fibrolytic stroma) and infiltration by inflammatory cells and times of progression-free survival (PFS) of patients with PDACs after resection. We obtained 1824 tissue microarray specimens from 385 patients included in the European Study Group for Pancreatic Cancer trial 1 and 3 and performed immunohistochemistry to detect alpha smooth muscle actin, type 1 collagen, CD3, CD4, CD8, CD68, CD206, and neutrophils. Tumors that expressed high andlow levels of these markers were compared with patient outcomes using Kaplan-Meier curves and multivariable recursive partitioning for discrete-time survival tree analysis. Prognostic index was delineated by a multivariable Cox proportional hazards model of immune cell and stromal markers and PFS. Findings were validated using 279 tissue microarray specimens from 93 patients in a separate cohort. Levels of CD3, CD4, CD8, CD68, and CD206 were independently associated with tumor recurrence. Recursive partitioning for discrete-time survival tree analysis identified a high level of CD3 as the strongest independent predictor for longer PFS. Tumors with levels of CD3 and high levels of CD206 associated with a median PFS time of 16.6 months and a median prognostic index of -0.32 (95% confidence interval [CI] -0.35 to -0.31), whereas tumors with low level of CD3 cell and low level of CD8 and high level of CD68 associated with a median PFS time of 7.9 months and a prognostic index of 0.32 (95% CI 0.050-0.32); we called these patterns histologic signatures. Stroma composition, when unassociated with inflammatory cellmarkers, did not associate significantly with PFS. In thevalidation cohort, the histologic signature resulted in an error matrix accuracy of predicted response of 0.75 (95% CI 0.64-0.83; accuracy P < .001). In an analysis of PDAC tissue microarray specimens, we identified and validated a histologic signature, based on leukocyte and stromal factors, that associates with PFS times of patients with resected PDACs. Immune cells might affect the composition of the pancreatic stroma to affect progression of PDAC. These findings provide new insights into the immune response to PDAC.

PO-512 Gene expression signature comprising distinct stromal and tumor-intrinsic signals predicts response to combined anti-PD1 and anti-CTLA4 checkpoint inhibition

IntroductionInnovations in both targeted and immunotherapy (IT) of metastatic melanoma have led to improved responses in a considerable number of patients. For both types of therapies, resistance remains a formidable challenge. For IT, knowledge on the mechanisms behind resistance is an urgent and unmet need for better patient stratification. Gene expression signatures to predict response in baseline samples could help to better stratify patients. It is expected that both tumour cell intrinsic signals and stromal signals play a role. However, gene expression signatures are typically derived from RNA-sequencing data from patients’ tumours, where the distinction between stromal and tumour signals cannot be made. Here, we take advantage of our melanoma PDX platform [Kemper et al. Cell Reports 2016] to dissect the stromal and tumour cell intrinsic signals and relate these to the response to immune checkpoint blockade.Material and methodsRNA sequencing was performed on 95 PDX tumours derived from metastatic melanoma [Kemper et al. Cell Reports 2016]. Gene expression data and clinical information of patients treated with anti-PD1 and anti-CTLA4 were downloaded [Hugo et al. 2016 & Van Allen, 2015]. Additionally, we performed RNA sequencing on samples of patients treated with the combination of anti-CTLA4 and anti-PD1 [Blank et al. submitted].Results and discussionsWe found that tumour cell-intrinsic and stromal gene expression signatures differentially predicted response to anti-PD1 and anti-CTLA4 immune checkpoint inhibition. Furthermore, a combination of signatures predicts response in patients treated with the combination of anti-PD1 and anti-CTLA4.ConclusionOur PDX platform provided the possibility to computationally dissect the gene expression signals from tumour cells and stromal tissue. These stromal and tumour intrinsic gene expression signatures differentially predict response to anti-PD1 and anti-CTLA4 in baseline samples which can be used for better patient stratification.