Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring

The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.

The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancer

In triple-negative breast cancer (TNBC), stromal restriction of CD8+ T cells associates with poor clinical outcomes and lack of responsiveness to immune-checkpoint blockade (ICB). To identify mediators of T cell stromal restriction, we profiled murine breast tumors lacking the transcription factor Stat3, which is commonly hyperactive in breast cancers and promotes an immunosuppressive tumor microenvironment. Expression of the cytokine Chi3l1 was decreased in Stat3-/- tumors. CHI3L1 expression was elevated in human TNBCs and other solid tumors exhibiting T cell stromal restriction. Chi3l1 ablation in the polyoma virus middle T (PyMT) breast cancer model generated an anti-tumor immune response and delayed mammary tumor onset. These effects were associated with increased T cell tumor infiltration and improved response to ICB. Mechanistically, Chi3l1 promoted neutrophil recruitment and neutrophil extracellular trap formation, which blocked T cell infiltration. Our findings provide insight into the mechanism underlying stromal restriction of CD8+ T cells and suggest that targeting Chi3l1 may promote anti-tumor immunity in various tumor types.

DNA methylation-based depiction of the immune microenvironment and immune-associated long non-coding RNAs in oral cavity squamous cell carcinomas

Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). DNA methylation analysis was performed in 46 matched OSCC and normal adjacent tissue samples using a genome-wide platform (Infinium HumanMethylation450 BeadChip). Reference-based computational deconvolution (MethylCIBERSORT) was applied to infer the immune cell composition of the bulk samples. The expression levels of genes encoding immune markers and differentially methylated lncRNAs were investigated using The Cancer Genome Atlas dataset. OSCC specimens presented distinct immune cell composition, including the enrichment of monocyte lineage cells, natural killer cells, cytotoxic T-lymphocytes, regulatory T-lymphocytes, and neutrophils. In contrast, B-lymphocytes, effector T-lymphocytes, and fibroblasts were diminished in tumor samples. The hypomethylation of three immune-associated lncRNAs (MEG3, MIR155HG, and WFDC21P) at individual CpG sites was confirmed by bisulfite-pyrosequencing. Also, the upregulation of a set of immune markers (FOXP3, GZMB, IL10, IL2RA, TGFB, IFNG, TDO2, IDO1, and HIF1A) was detected. The immune cell composition, immune markers alteration, and dysregulation of immune-associated lncRNAs reinforce the impact of the immune microenvironment in OSCC. These concurrent factors contribute to tumor heterogeneity, suggesting that epi-immunotherapy could be an efficient alternative to treat OSCC.

HER2Δ16 Engages ENPP1 to Promote an Immune-Cold Microenvironment in Breast Cancer

The tumor-immune microenvironment (TIME) is a critical determinant of therapeutic response. However, the mechanisms regulating its modulation are not fully understood. HER2Δ16, an oncogenic splice variant of the HER2, has been implicated in breast cancer and other tumor types as a driver of tumorigenesis and metastasis. Nevertheless, the underlying mechanisms of HER2Δ16-mediated oncogenicity remain poorly understood. Here, we show that HER2∆16 expression is not exclusive to the clinically HER2+ subtype and associates with a poor clinical outcome in breast cancer. To understand how HER2 variants modulated the tumor microenvironment, we generated transgenic mouse models expressing either proto-oncogenic HER2 or HER2Δ16 in the mammary epithelium. We found that HER2∆16 tumors were immune cold, characterized by low immune infiltrate and an altered cytokine profile. Using an epithelial cell surface proteomic approach, we identified ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) as a functional regulator of the immune cold microenvironment. We generated a knock-in model of HER2Δ16 under the endogenous promoter to understand the role of Enpp1 in aggressive HER2+ breast cancer. Knockdown of Enpp1 in HER2Δ16-derived tumor cells resulted in decreased tumor growth, which correlated with increased T-cell infiltration. These findings suggest that HER2Δ16-dependent Enpp1 activation associates with aggressive HER2+ breast cancer through its immune modulatory function. Our study provides a better understanding of the mechanisms underlying HER2Δ16-mediated oncogenicity and highlights ENPP1 as a potential therapeutic target in aggressive HER2+ breast cancer.

Bioprinted Multicomponent Hydrogel Co-culture Tumor-Immune Model for Assessing and Simulating Tumor-Infiltrated Lymphocyte Migration and Functional Activation

The immune response against a tumor is characterized by the interplay among components of the immune system and neoplastic cells. Here, we bioprinted a model with two distinct regions containing gastric cancer patient-derived organoids (PDOs) and tumor-infiltrated lymphocytes (TILs). The initial cellular distribution allows for the longitudinal study of TIL migratory patterns concurrently with multiplexed cytokine analysis. The chemical properties of the bioink were designed to present physical barriers that immune T-cells must breech during infiltration and migration toward a tumor with the use of an alginate, gelatin, and basal membrane mix. TIL activity, degranulation, and regulation of proteolytic activity reveal insights into the time-dependent biochemical dynamics. Regulation of the sFas and sFas-ligand present on PDOs and TILs, respectively, and the perforin and granzyme longitudinal secretion confirms TIL activation when encountering PDO formations. TIL migratory profiles were used to create a deterministic reaction-advection diffusion model. The simulation provides insights that decouple passive from active cell migration mechanisms. The mechanisms used by TILs and other adoptive cell therapeutics as they infiltrate the tumor barrier are poorly understood. This study presents a pre-screening strategy for immune cells where motility and activation across ECM environments are crucial indicators of cellular fitness.

Abstract 1512: Evolution of large copy number variants in breast cancer through genetic network rewiring

Large chromosomal alterations are common in cancer and often show preferential gain or loss across many cancer types indicating their selective advantage. Triple negative breast cancer (TNBC) exhibits complex mutational spectrum without common oncogenic drivers yet displays consistent loss of large chromosomal regions. Here, we characterize selection pressures that maintain a recurrently deleted region of chromosome 4p in TNBC. We used bulk WGS phylogenetic analysis of TNCB PT/PDX panel to show that chr4p deletion is an early event in tumor evolution. We used scRNAseq gene expression and inferred copy number analysis to show that chr4p loss is associated with a proliferative state. This finding was confirmed by a combination of RNA in situ hybridization and immunofluorescence. We then tested the dosage sensitivity of genes residing within this region by individual and dual overexpression in TNBC PDX-derived cell lines and control normal cell line by assessing their effect on cell proliferation. The overexpression of genes within chr4p elicited a strong cell proliferation defect in cancer but not normal cell line models. We also characterized an unknown gene within chr4p region as a novel member of the STRIPAK complex. Genome-wide pooled ORFeome library screens identified a global pattern of background-specific dosage sensitive regions. Our study shows that large chromosomal deletions are maintained due to evolutionary early genetic network rewiring rendering multiple genes within such regions to be dosage sensitive. Ultimately, this work enhances our understanding of genetic events that modulate TNBC.

Citation Format: Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Tom Lesluyes, Toby Barker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Jiannis Ragoussis, Guillaume Bourque, Morag Park. Evolution of large copy number variants in breast cancer through genetic network rewiring [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1512.

Abstract P3-08-09: Development and molecular characterization of hard-to-treat breast cancer pre-clinical models to enhance precision medicine

Invasive breast carcinoma is a combination of heterogeneous diseases with distinct molecular and clinical features. Some subsets of breast cancer present major clinical challenges, including triple-negative, metastatic/recurrent disease and rare breast histologies. Previously, we developed a unique resource of 37 hard-to-treat breast cancer patient-derived xenografts (PDX). This set included mainly triple negative breast cancer (TNBC) patients that presented poor response to neoadjuvant chemotherapies (Savage et al. 2020 - PMID: 32546838). PDXs accurately reproduce the molecular heterogeneity of the primary tumors and show that multi-drug chemoresistance was retained upon xenotransplantation. Here, we present the characterization of PDX 3-dimensional cultures organoids (8) and PDX derived epithelial cell lines (11). Using single-cell RNAseq we showed that an organoid cultured for several passages (P8) maintained the heterogeneity of the matched PDX. Although in different proportions, all cancer cell populations found in the PDX were retained in matched organoids supporting that organoids are suitable models that recapitulates the tumor heterogeneity and are therefore a suitable model for drug screening. Among our new PDXs models (30), we have developed four PDXs from rare metaplastic breast cancers (MpBC), an aggressive subtype of breast cancer that present the poorest response to standard of care chemotherapy. We also developed one male breast cancer PDX with matched organoid. Omic analysis on our pre-clinical models and patient primary tumor and metastasis will inform development of therapeutic opportunities. This molecular information will guide selection of compounds that will be validated using our high throughput organoid drug screening pipeline. This will allow rapid screens of thousands of approved drugs, enhancing drug repurposing with potential for rapid clinical translation. The combined use of 3D tumor organoids and PDXs, is an important opportunity poised to transform identification of new therapeutic options for hard-to-treat lethal breast cancers.

Citation Format: Hellen Kuasne, Anne-Marie fortier, Sandrine Busque, Simon Mathien, Paul Savage, Constanza Martinez Ramirez, Anie Monast, Margarita Soleinova, Atilla Omeroglu, Jamil Asselah, Nathaniel Bouganim, Sarkis Meterissian, Mark Basik, Morag Park. Development and molecular characterization of hard-to-treat breast cancer pre-clinical models to enhance precision medicine [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-08-09.

Coordinated activation of c-Src and FOXM1 drives tumor cell proliferation and breast cancer progression

Activation of the tyrosine kinase c-Src promotes breast cancer progression and poor outcomes, yet the underlying mechanisms are incompletely understood. Here, we show that deleting c-Src abrogates the activity of Forkhead Box M1 (FOXM1), a master transcriptional regulator of the cell cycle, in a genetically engineered model mimicking the Luminal B molecular subtype of breast cancer. By phosphorylating it on two tyrosine residues, c-Src stimulates the nuclear localization of FOXM1 and the expression of its target genes, including key regulators of G2-M cell cycle progression as well as c-Src itself. This positive feedback loop drives proliferation in genetically engineered and patient-derived models of Luminal B-like breast cancer. Targeting this mechanism, including through novel compounds that destabilize the FOXM1 protein, induces G2-M cell cycle arrest and apoptosis, blocking tumor progression and impairing metastasis. We identify a positive correlation between FOXM1 and c-Src expression in human breast cancer and show that the expression of FOXM1 target genes predicts poor outcomes and associates with the Luminal B subtype, which responds poorly to approved therapies. These findings indicate that a regulatory network centered on c-Src and FOXM1 is a targetable vulnerability in aggressive luminal breast cancers.

Abstract A033: Identification of gemcitabine-resistant populations using scRNA-sequencing in triple negative breast cancer patient-derived xenograft

Despite major advances in the treatment of breast cancer (BC), it remains the most diagnosed and second most deadly cancer among American women. BC is a heterogeneous disease consisting of distinct subtypes, including hormone receptor-positive, HER2 receptor-positive and cancers that lack these receptors categorized as triple-negative breast cancers (TNBC). The TNBC subtype presents the worst outcome and the highest rates of recurrence and metastasis. The absence of targets prevents the use of established precision therapies in TNBC, and the standard of care remains neoadjuvant chemotherapy. While this is effective in some patients, about 50% develop resistance, leading to the development of metastasis. It is known that selective pressures exerted by chemotherapy treatment can promote the outgrowth of resistant tumor subclones. However, the diverse intra-tumoral population and the mechanisms that lead to chemotherapy resistance in TNBC are still poorly understood. We hypothesized that therapeutic regimens influence tumor plasticity by exerting selective pressures leading to the outgrowth of resistant subpopulations with the greatest survival advantage. To evaluate this hypothesis, we aimed to generate in vivo models of chemotherapy resistance and to investigate the plasticity of tumor cell subpopulations challenged with standard-of-care chemotherapies. To this end, we selected a multi-drug resistant (Doxorubicin, Cyclophosphamide, Cisplatin, and Paclitaxel) BC patient and developed a patient-derived xenograft (PDX) from the primary tumor and the lung metastasis. The metastasis PDX model was initially responsive to Gemcitabine (as observed in the BC patient) but eventually developed resistance. We challenged this metastasis PDX with several cycles of Gemcitabine and obtained residual, rebound, and resistant tumor samples. We performed single-cell RNA sequencing (scRNAseq) of these models using a droplet-based technology from 10X Genomics. This scRNAseq data was used to compare the changes in the proportions of cellular subpopulations in each model. Interestingly, our data shows that the rebound model presents greater similarity to the untreated metastasis, while the resistant model has significant differences in cell population expression profiles. We identified a hypoxic population in the primary tumor and its matched metastasis. This population was validated in these models by Nanostring GeoMx Digital Spatial Profiler. Our recent analyses have identified that this hypoxic population persists in the residual, rebound and resistant models. In addition, we have identified other populations that vary in these models. We are currently investigating their cellular mechanisms and gene expression patterns. Using scRNA-sequencing to understand the clonal expansion of resistant subpopulations following chemotherapy reveals distinctive resistant cell features enabling the identification of the vulnerabilities of these tumors.

Citation Format: Sandrine Busque, Constanza Martinez Ramirez, Hellen Kuasne, Paul Savage, Anne-Marie Fortier, Anie Monast, Atilla Omeroglu, Jamil Asselah, Nathaniel Bouganim, Sarkis Meterissian, Claudia Kleinman, Mark Basik, Morag Park. Identification of gemcitabine-resistant populations using scRNA-sequencing in triple negative breast cancer patient-derived xenograft [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A033.

Interplay Between Immune and Cancer-Associated Fibroblasts: A Path to Target Metalloproteinases in Penile Cancer

Extracellular matrix (ECM) remodeling and inflammation have been reported in penile carcinomas (PeCa). However, the cell types and cellular crosstalk involved in PeCa are unexplored. We aimed to characterize the complexity of cells and pathways involved in the tumor microenvironment (TME) in PeCa and propose target molecules associated with the TME. We first investigated the prognostic impact of cell types with a secretory profile to identify drug targets that modulate TME-enriched cells. The secretome analysis using the PeCa transcriptome revealed the enrichment of inflammation and extracellular matrix pathways. Twenty-three secreted factors were upregulated, mainly collagens and matrix metalloproteinases (MMPs). The deregulation of collagens and MMPs was confirmed by Quantitative reverse transcription - polymerase chain reaction (RT-qPCR). Further, the deconvolution method (digital cytometry) of the bulk samples revealed a high proportion of macrophages and dendritic cells (DCs) and B cells. Increased DCs and B cells were associated with better survival. A high proportion of cancer-associated fibroblasts (CAFs) was observed in low-survival patients. Patients with increased CAFs had decreased immune cell proportions. The treatment with the MMP inhibitor GM6001 in CAF cells derived from PeCa resulted in altered cell viability. We reported a crosstalk between immune cells and CAFs, and the proportion of these cell populations was associated with prognosis. We demonstrate that a drug targeting MMPs modulates CAFs, expanding the therapeutic options of PeCa.

Abstract 44: Evolution of large copy number variants in breast cancer through genetic network rewiring

Large chromosomal alterations are common in cancer and often show preferential gain or loss across many cancer types indicating their selective advantage. Triple negative breast cancer (TNBC) exhibits complex mutational spectrum without common oncogenic drivers yet displays consistent loss of large chromosomal regions. Here, we characterize selection pressures that maintain a recurrently deleted region of chromosome 4p in TNBC. We used single cell and bulk WGS phylogenetic analysis of TNCB PT/PDX panel to show that chr4p deletion is an early event in tumor evolution. We used scRNAseq gene expression and inferred copy number analysis to show that chr4p loss is associated with a proliferative state. This finding was confirmed by a combination of RNA in situ hybridization and immunofluorescence. We then tested the dosage sensitivity of genes residing within this region by individual and dual overexpression in TNBC PDX-derived cell lines and control normal cell line by assessing their effect on cell proliferation. The overexpression of genes within chr4p elicited a strong cell proliferation defect in cancer but not normal cell line models. We also characterized an unknown gene within chr4p region as a novel member of the STRIPAK complex. Genome-wide pooled ORFeome library screens identified a global pattern of background-specific dosage sensitive regions. Our study shows that large chromosomal deletions are maintained due to evolutionary early genetic network rewiring rendering multiple genes within such regions to be dosage sensitive. Ultimately, this work enhances our understanding of genetic events that modulate TNBC.

Citation Format: Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Jarry Barber, Tom Lesluyes, Toby Baker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Quaid Morris, Jiannis Ragoussis, Guillaume Bourque, Morag Park. Evolution of large copy number variants in breast cancer through genetic network rewiring [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 44.

Abstract 47: Identifying genetic vulnerabilities of chromosome 4p large copy number variants in triple negative breast cancer

Triple Negative Breast Cancer (TNBC) is characterized by the absence of common oncogenic drivers, limiting its treatment options; however, it exhibits recurrent large chromosomal deletions. We previously showed that chromosome 4p (chr4p) loss is a frequently observed large copy number variant in TNBC and is associated with poor prognosis. We also showed that chr4p deletion is an early event in tumor evolution and confers on cells a proliferative advantage. Here, we set out to uncover the genetic vulnerabilities associated with chr4p deletion in TNBC to identify novel therapeutic avenues for TNBC and enhance our understanding of the genetic mechanisms that maintain chr4p deletion in the genome. Whole genome sequence analysis of our TNBC Primary Tumor(PT)/Patient-Derived Xenograft (PDX) panel identified samples with copy neutral and deletion status of chr4p. These deletion regions span a large fraction of the chr4p arm. RNAseq analysis revealed that chr4p deletion is functionally significant since gene expression of ~80% of genes was reduced upon chr4p deletion. Chr4p deletion was associated with global transcriptomic changes and differentially expressed genes were enriched for proliferation, DNA replication, cell migration, activation of the innate immune response and protein translation. PDX-derived cell models from these samples showed lentiviral infectivity based on a control lentivirus expressing GFP. Additionally, these PDX cell models were shown to be editable using CRISPR-Cas9 through the targeting of core essential genes. We will use a pooled CRISPR-Cas9 approach to systematically screen for genetic vulnerabilities in TNBC PDX-derived cell models harbouring chr4p copy neutral or deletion state. To further investigate the genetic mechanisms buffering chr4p loss, we have leveraged publicly-available CRISPR-Cas9 genome-wide genetic screen data from the Cancer DepMap to identify putative synthetic lethal (pSL) partners with chr4p deletion in TNBC. This was accomplished by developing regression models and integrating them with results from established methods such as drugZ and MAGeCK. We identified pSL partners for chr4p at gene, segmental and arm levels. pSLs were enriched for mitochondrial, protein translation and proliferation pathways. We will validate the top candidates from these analyses in our cohort of chr4p deletion and chr4p copy neutral TNBC PDX-derived cell models and integrate them with the pooled CRISPR screens. Together, this work aims to reveal potential TNBC-specific therapeutic avenues for precision oncology.

Citation Format: Michael Schwartz, Rohan Dandage, Lynn Karam, Alain Pacis, Hellen Kuasne, Anne-Marie Fortier, Sidong Huang, Guillaume Bourque, Traver Hart, Elena Kuzmin, Morag Park. Identifying genetic vulnerabilities of chromosome 4p large copy number variants in triple negative breast cancer [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 47.

Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair

DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).

miR-22 and miR-205 Drive Tumor Aggressiveness of Mucoepidermoid Carcinomas of Salivary Glands

Objectives

To integrate mRNA and miRNA expression profiles of mucoepidermoid carcinomas (MECs) and normal salivary gland (NSGs) tissue samples and identify potential drivers.

Material and Methods

Gene and miRNA expression arrays were performed in 35 MECs and six NSGs.

Results

We found 46 differentially expressed (DE) miRNAs and 3,162 DE mRNAs. Supervised hierarchical clustering analysis of the DE transcripts revealed two clusters in both miRNA and mRNA profiles, which distinguished MEC from NSG samples. The integrative miRNA-mRNA analysis revealed a network comprising 696 negatively correlated interactions (44 miRNAs and 444 mRNAs) involving cell signaling, cell cycle, and cancer-related pathways. Increased expression levels of miR-205-5p and miR-224-5p and decreased expression levels of miR-139-3p, miR-145-3p, miR-148a-3p, miR-186-5p, miR-338-3p, miR-363-3p, and miR-4324 were significantly related to worse overall survival in MEC patients. Two overexpressed miRNAs in MEC (miR-22 and miR-205) were selected for inhibition by the CRISPR-Cas9 method. Cell viability, migration, and invasion assays were performed using an intermediate grade MEC cell line. Knockout of miR-205 reduced cell viability and enhanced ZEB2 expression, while miR-22 knockout reduced cell migration and invasion and enhanced ESR1 expression. Our results indicate a distinct transcriptomic profile of MEC compared to NSG, and the integrative analysis highlighted miRNA-mRNA interactions involving cancer-related pathways, including PTEN and PI3K/AKT.

Conclusion

The in vitro functional studies revealed that miR-22 and miR-205 deficiencies reduced the viability, migration, and invasion of the MEC cells suggesting they are potential oncogenic drivers in MEC.

Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler

Breast cancer is a heterogenous disease with variability in tumor cells and in the surrounding tumor microenvironment (TME). Understanding the molecular diversity in breast cancer is critical for improving prediction of therapeutic response and prognostication. High-plex spatial profiling of tumors enables characterization of heterogeneity in the breast TME, which can holistically illuminate the biology of tumor growth, dissemination and, ultimately, response to therapy. The GeoMx Digital Spatial Profiler (DSP) enables researchers to spatially resolve and quantify proteins and RNA transcripts from tissue sections. The platform is compatible with both formalin-fixed paraffin-embedded and frozen tissues. RNA profiling was developed at the whole transcriptome level for human and mouse samples and protein profiling of 100-plex for human samples. Tissue can be optically segmented for analysis of regions of interest or cell populations to study biology-directed tissue characterization. The GeoMx Breast Cancer Consortium (GBCC) is composed of breast cancer researchers who are developing innovative approaches for spatial profiling to accelerate biomarker discovery. Here, the GBCC presents best practices for GeoMx profiling to promote the collection of high-quality data, optimization of data analysis and integration of datasets to advance collaboration and meta-analyses. Although the capabilities of the platform are presented in the context of breast cancer research, they can be generalized to a variety of other tumor types that are characterized by high heterogeneity.

Tumour-associated macrophages drive stromal cell-dependent collagen crosslinking and stiffening to promote breast cancer aggression

Stromal stiffening accompanies malignancy, compromises treatment and promotes tumour aggression. Clarifying the molecular nature and the factors that regulate stromal stiffening in tumours should identify biomarkers to stratify patients for therapy and interventions to improve outcome. We profiled lysyl hydroxylase-mediated and lysyl oxidase-mediated collagen crosslinks and quantified the greatest abundance of total and complex collagen crosslinks in aggressive human breast cancer subtypes with the stiffest stroma. These tissues harbour the highest number of tumour-associated macrophages, whose therapeutic ablation in experimental models reduced metastasis, and decreased collagen crosslinks and stromal stiffening. Epithelial-targeted expression of the crosslinking enzyme, lysyl oxidase, had no impact on collagen crosslinking in PyMT mammary tumours, whereas stromal cell targeting did. Stromal cells in microdissected human tumours expressed the highest level of collagen crosslinking enzymes. Immunohistochemical analysis of biopsies from a cohort of patients with breast cancer revealed that stromal expression of lysyl hydroxylase 2, an enzyme that induces hydroxylysine aldehyde-derived collagen crosslinks and stromal stiffening, correlated significantly with disease specific mortality. The findings link tissue inflammation, stromal cell-mediated collagen crosslinking and stiffening to tumour aggression and identify lysyl hydroxylase 2 as a stromal biomarker.

Circulating let-7e-5p, miR-106a-5p, miR-28-3p, and miR-542-5p as a Promising microRNA Signature for the Detection of Colorectal Cancer

Simple Summary

The detection of early-stage colorectal cancer increases the chance to prevent tumor progression and death by the disease. Colonoscopy is one sensitive screening test to detect malignant or potentially malignant lesions in the intestines. However, it has some disadvantages, including sedation requirements, increased risk of colon perforation, and bleeding. Circulating microRNAs (miRNAs) in plasma or serum from cancer patients have been investigated and described as potential diagnostic or prognostic markers. We conducted an miRNAs screening test in plasma samples from colorectal cancer patients and subjects without cancer, aiming to identify markers for the early detection of the disease. We identified and validated four miRNAs capable of distinguishing cancer from non-cancer cases. Our non-invasive diagnostic biomarkers presented high performance and are easily applicable to clinical practice.

Abstract

Colorectal cancer (CRC) is a disease with high incidence and mortality. Colonoscopy is a gold standard among tests used for CRC traceability. However, serious complications, such as colon perforation, may occur. Non-invasive diagnostic procedures are an unmet need. We aimed to identify a plasma microRNA (miRNA) signature for CRC detection. Plasma samples were obtained from subjects (n = 109) at different stages of colorectal carcinogenesis. The patients were stratified into a non-cancer (27 healthy volunteers, 17 patients with hyperplastic polyps, 24 with adenomas), and a cancer group (20 CRC and 21 metastatic CRC). miRNAs (381) were screened by TaqMan Low-Density Array. A classifier based on four differentially expressed miRNAs (miR-28-3p, let-7e-5p, miR-106a-5p, and miR-542-5p) was able to discriminate cancer versus non-cancer cases. The overexpression of these miRNAs was confirmed by RT-qPCR, and a cross-study validation step was implemented using eight data series retrieved from Gene Expression Omnibus (GEO). In addition, another external data validation using CRC surgical specimens from The Cancer Genome Atlas (TCGA) was carried out. The predictive model’s performance in the validation set was 76.5% accuracy, 59.4% sensitivity, and 86.8% specificity (area under the curve, AUC = 0.716). The employment of our model in the independent publicly available datasets confirmed a good discrimination performance in five of eight datasets (median AUC = 0.823). Applying this algorithm to the TCGA cohort, we found 99.5% accuracy, 99.7% sensitivity, and 90.9% specificity (AUC = 0.998) when the model was applied to solid colorectal tissues. Overall, we suggest a novel signature of four circulating miRNAs, i.e., miR-28-3p, let-7e-5p, miR-106a-5p, and miR-542-5p, as a predictive tool for the detection of CRC.

Alginate-gelatin-Matrigel hydrogels enable the development and multigenerational passaging of patient-derived 3D bioprinted cancer spheroid models

Hydrogels consisting of controlled fractions of alginate, gelatin, and Matrigel enable the development of patient-derived bioprinted tissue models that support cancer spheroid growth and expansion. These engineered models can be dissociated to be then reintroduced to new hydrogel solutions and subsequently reprinted to generate multigenerational models. The process of harvesting cells from 3D bioprinted models is possible by chelating the ions that crosslink alginate, causing the gel to weaken. Inclusion of the gelatin and Matrigel fractions to the hydrogel increases the bioactivity by providing cell-matrix binding sites and promoting cross-talk between cancer cells and their microenvironment. Here we show that immortalized triple-negative breast cancer cells (MDA-MB-231) and patient-derived gastric adenocarcinoma cells can be reprinted for at least three 21 d culture cycles following bioprinting in the alginate/gelatin/Matrigel hydrogels. Our drug testing results suggest that our 3D bioprinted model can also be used to recapitulatein vivopatient drug response. Furthermore, our results show that iterative bioprinting techniques coupled with alginate biomaterials can be used to maintain and expand patient-derived cancer spheroid cultures for extended periods without compromising cell viability, altering division rates, or disrupting cancer spheroid formation.

Abstract SP112: Spatial variance signatures/Intra-tumor zonation in TNBC

It is increasingly clear that triple negative breast cancer (TNBC) is a heterogeneous disease with variable clinical presentation, histological features and response to therapy. While these differences have been partially explained by inter- and intra-tumoral heterogeneity, spatial heterogeneity represented by the tumor architecture plays a critical role in clonal evolution and displays a landscape for different compartment-specific processes and cell-to-cell specific interactions. To better understand the impact of spatial heterogeneity on gene-expression-defined cell populations, we have coupled single-cell RNA sequencing with multiplex immunofluorescence (IF). Multiplex immunofluorescence using specific markers for each cell cluster, integrated with computational image analyses and neighborhood maps, has revealed spatial zonation of single cell subpopulations. Zonation of single cell populations was coupled to hypoxia and overlayed distinct metabolic tumor zones and defined areas of differential stress and cell plasticity that give rise to tumor cells with enhanced fitness and aggressivity.

Citation Format: M Park, C Martínez Ramirez, Y Yang, A Blanchet-Cohen, H Kuasne, A Fortier, J Ragoussis, P Savage, A Omeroglou, S Meterissian, S Costantino, C Kleinman. Spatial variance signatures/Intra-tumor zonation in TNBC [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP112.

GLUT1 inhibition blocks growth of RB1-positive triple negative breast cancer

Triple negative breast cancer (TNBC) is a deadly form of breast cancer due to the development of resistance to chemotherapy affecting over 30% of patients. New therapeutics and companion biomarkers are urgently needed. Recognizing the elevated expression of glucose transporter 1 (GLUT1, encoded by SLC2A1) and associated metabolic dependencies in TNBC, we investigated the vulnerability of TNBC cell lines and patient-derived samples to GLUT1 inhibition. We report that genetic or pharmacological inhibition of GLUT1 with BAY-876 impairs the growth of a subset of TNBC cells displaying high glycolytic and lower oxidative phosphorylation (OXPHOS) rates. Pathway enrichment analysis of gene expression data suggests that the functionality of the E2F pathway may reflect to some extent OXPHOS activity. Furthermore, the protein levels of retinoblastoma tumor suppressor (RB1) strongly correlate with the degree of sensitivity to GLUT1 inhibition in TNBC, where RB1-negative cells are insensitive to GLUT1 inhibition. Collectively, our results highlight a strong and targetable RB1-GLUT1 metabolic axis in TNBC and warrant clinical evaluation of GLUT1 inhibition in TNBC patients stratified according to RB1 protein expression levels.

Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors

Subsets of breast tumors present major clinical challenges, including triple-negative, metastatic/recurrent disease and rare histologies. Here, we developed 37 patient-derived xenografts (PDX) from these difficult-to-treat cancers to interrogate their molecular composition and functional biology. Whole-genome and transcriptome sequencing and reverse-phase protein arrays revealed that PDXs conserve the molecular landscape of their corresponding patient tumors. Metastatic potential varied between PDXs, where low-penetrance lung micrometastases were most common, though a subset of models displayed high rates of dissemination in organotropic or diffuse patterns consistent with what was observed clinically. Chemosensitivity profiling was performed in vivo with standard-of-care agents, where multi-drug chemoresistance was retained upon xenotransplantation. Consolidating chemogenomic data identified actionable features in the majority of PDXs, and marked regressions were observed in a subset that was evaluated in vivo. Together, this clinically-annotated PDX library with comprehensive molecular and phenotypic profiling serves as a resource for preclinical studies on difficult-to-treat breast tumors.

Estrogen-related receptors are targetable ROS sensors

Excessive reactive oxygen species (ROS) can cause oxidative stress and consequently cell injury contributing to a wide range of diseases. Addressing the critical gaps in our understanding of the adaptive molecular events downstream ROS provocation holds promise for the identification of druggable metabolic vulnerabilities. Here, we unveil a direct molecular link between the activity of two estrogen-related receptor (ERR) isoforms and the control of glutamine utilization and glutathione antioxidant production. ERRα down-regulation restricts glutamine entry into the TCA cycle, while ERRγ up-regulation promotes glutamine-driven glutathione production. Notably, we identify increased ERRγ expression/activation as a hallmark of oxidative stress triggered by mitochondrial disruption or chemotherapy. Enhanced tumor antioxidant capacity is an underlying feature of human breast cancer (BCa) patients that respond poorly to treatment. We demonstrate that pharmacological inhibition of ERRγ with the selective inverse agonist GSK5182 increases antitumor efficacy of the chemotherapeutic paclitaxel on poor outcome BCa tumor organoids. Our findings thus underscore the ERRs as novel redox sensors and effectors of a ROS defense program and highlight the potential therapeutic advantage of exploiting ERRγ inhibitors for the treatment of BCa and other diseases where oxidative stress plays a central role.

E-Cadherin Downregulation is Mediated by Promoter Methylation in Canine Prostate Cancer

E-cadherin is a transmembrane glycoprotein responsible for cell-to-cell adhesion, and its loss has been associated with metastasis development. Although E-cadherin downregulation was previously reported in canine prostate cancer (PC), the mechanism involved in this process is unclear. It is well established that dogs, besides humans, spontaneously develop PC with high frequency; therefore, canine PC is an interesting model to study human PC. In human PC, CDH1 methylation has been associated with E-cadherin downregulation. However, no previous studies have described the methylation pattern of CDH1 promoter in canine PC. Herein, we evaluated the E-cadherin protein and gene expression in canine PC compared to normal tissues. DNA methylation pattern was investigated as a regulatory mechanism of CDH1 silencing. Our cohort is composed of 20 normal prostates, 20 proliferative inflammatory atrophy (PIA) lesions, 20 PC, and 11 metastases from 60 dogs. The E-cadherin protein expression was assessed by immunohistochemistry and western blotting and gene expression by qPCR. Bisulfite- pyrosequencing assay was performed to investigate the CDH1 promoter methylation pattern. Membranous E-cadherin expression was observed in all prostatic tissues. A higher number of E-cadherin negative cells was detected more frequently in PC compared to normal and PIA samples. High-grade PC showed a diffuse membranous positive immunostaining. Furthermore, PC patients with a higher number of E-cadherin negative cells presented shorter survival time and higher Gleason scores. Western blotting and qPCR assays confirmed the immunohistochemical results, showing lower E-cadherin protein and gene expression levels in PC compared to normal samples. We identified CDH1 promoter hypermethylation in PIA and PC samples. An in vitro assay with two canine prostate cancer cells (PC1 and PC2 cell lines) was performed to confirm the methylation as a regulatory mechanism of E-cadherin expression. PC1 cell line presented CDH1 hypermethylation and after 5-Aza-dC treatment, a decreased CDH1 methylation and increased gene expression levels were observed. Positive E-cadherin cells were massively found in metastases (mean of 90.6%). In conclusion, low levels of E-cadherin protein, gene downregulation and CDH1 hypermethylation was detected in canine PC. However, in metastatic foci occur E-cadherin re-expression confirming its relevance in these processes.

CD44 Promotes PD-L1 Expression and Its Tumor-Intrinsic Function in Breast and Lung Cancers

The PD-L1 (CD274) immune-checkpoint ligand is often upregulated in cancers to inhibit T cells and elicit immunosuppression. Independent of this activity, PD-L1 has recently been shown to also exert a cancer cell-intrinsic function promoting tumorigenesis. Here, we establish this tumor-intrinsic role of PD-L1 in triple-negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC). Using FACS-assisted shRNA screens, we identified the cell-surface adhesion receptor CD44 as a key positive regulator of PD-L1 expression in these cancers. Mechanistically, CD44 activated PD-L1 transcription in part through its cleaved intracytoplasmic domain (ICD), which bound to a regulatory region of the PD-L1 locus containing a consensus CD44-ICD binding site. Supporting this genetic interaction, CD44 positively correlated with PD-L1 expression at the mRNA and protein levels in primary tumor samples of TNBC and NSCLC patients. These data provide a novel basis for CD44 as a critical therapeutic target to suppress PD-L1 tumor-intrinsic function. SIGNIFICANCE: CD44 is a potential target to suppress PD-L1 function in TNBC. This finding has the potential to open a new area of therapy for TNBC.

DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions

Background: The differential diagnosis of thyroid nodules using fine-needle aspiration biopsy (FNAB) is challenging due to the inherent limitation of the cytology tests. The use of molecular markers has potential to complement the FNAB-based diagnosis and avoid unnecessary surgeries. In this study, we aimed to identify DNA methylation biomarkers and to develop a diagnostic tool useful for thyroid lesions. Methods: Genome-wide DNA methylation profiles (Illumina 450K) of papillary thyroid carcinoma (PTC = 60) and follicular thyroid carcinoma (FTC = 10) were compared with non-neoplastic thyroid tissue samples (NT = 50) and benign thyroid lesions (BTL = 17). The results were confirmed in publicly available databases from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) using the same DNA methylation platform. Two classifiers were trained to discriminate FTC and PTC from BTL. To increase the applicability of the method, six differentially methylated CpGs were selected and evaluated in 161 thyroid tumors and 69 BTL postsurgical specimens and 55 prospectively collected FNAB using bisulfite-pyrosequencing. Results: DNA methylation analysis revealed 2130 and 19 differentially methylated CpGs in PTC and FTC, respectively. The CpGs confirmed by GEO and TCGA databases showing high areas under the receiver operating characteristic curve in all sample sets were used to train our diagnostic classifier. The model based on six CpGs was able to differentiate benign from malignant thyroid lesions with 94.3% sensitivity and 82.4% specificity. A similar performance was found applying the algorithm to TCGA and GEO external data sets (91.3-97.4% sensitivity and 87.5% specificity). We successfully evaluated the classifiers using a bisulfite-pyrosequencing technique, achieving 90.7% sensitivity and 75.4% specificity in surgical specimens (five of six CpGs). The study comprising FNAB cytology materials corroborated the applicability and performance of the methodology, demonstrating 86.7% sensitivity and 89.5% specificity in confirmed malignant tumors, and 100% sensitivity and 89% specificity in cases with indeterminate cytology. Conclusions: A novel diagnostic tool with potential application in preoperative screening of thyroid nodules is reported here. The proposed protocol has the potential to avoid unnecessary thyroidectomies.

Circulating mRNA signature as a marker for high-risk prostate cancer

Prostate cancer (PCa) is the second most common cancer in men. The indolent course of the disease makes the treatment choice a challenge for physicians and patients. In this study, a minimally invasive method was used to evaluate the potential of molecular markers in identifying patients with aggressive disease. Cell-free plasma samples from 60 PCa patients collected before radical prostatectomy were used to evaluate the levels of expression of eight genes (AMACR, BCL2, NKX3-1, GOLM1, OR51E2, PCA3, SIM2 and TRPM8) by quantitative real-time PCR. Overexpression of AMACR, GOLM1, TRPM8 and NKX3-1 genes was significantly associated with aggressive disease characteristics, including extracapsular extension, tumor stage and vesicular seminal invasion. A trio of genes (GOLM1, NKX3-1 and TRPM8) was able to identify high-risk PCa cases (85% of sensitivity and 58% of specificity), yielding a better overall performance compared with the biopsy Gleason score and prostate-specific antigen, routinely used in the clinical practice. Although more studies are required, these circulating markers have the potential to be used as an additional test to improve the diagnosis and treatment decision of high-risk PCa patients.

Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity

Glioblastoma (GBM) is one of the most aggressive cancers, with median survival of less than 2 years. Despite of considerable advance in molecular classification of GBMs, no improvements in therapy have been described. The scenario is further complicated by tumor heterogeneity and the relationship among genetic, transcriptional and functional findings. Classically, gene expression has been evaluated by steady-state mRNA, however, this does not take translational control into consideration, which contributes considerably to the composition of the proteome. In this study, we evaluated the transcriptomic and translatomic signature of a GBM obtained from a single patient focusing in tumor heterogeneity. In a sampling of eight fragments, we investigated the translation rates, mTORC1 and ERK1/2 pathways and identified both total and polysome associated mRNAs. An increased translation rate was observed in fragments with high-grade histological features. High-grade histology was also associated with the expression of genes related to extracellular matrix (ECM) and angiogenesis, in both transcriptomes and translatomes. However, genes associated with epithelial to mesenchymal transition and stress response, were observed only in translatomes from high-grade fragments. Overall, our results demonstrate that isolation of translated mRNA can be used to identify biomarkers and reveal previously unrecognized determinants of heterogeneity in GBMs.

SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice

DNA double-strand breaks (DSBs) can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)-based approach, we identify 11 high-confidence REV7 interactors and elucidate the role of SHLD2 (previously annotated as FAM35A and RINN2) as an effector of REV7 in the NHEJ pathway. FAM35A depletion impairs NHEJ-mediated DNA repair and compromises antibody diversification by class switch recombination (CSR) in B cells. FAM35A accumulates at DSBs in a 53BP1-, RIF1-, and REV7-dependent manner and antagonizes HR by limiting DNA end resection. In fact, FAM35A is part of a larger complex composed of REV7 and SHLD1 (previously annotated as C20orf196 and RINN3), which promotes NHEJ and limits HR Together, these results establish SHLD2 as a novel effector of REV7 in controlling the decision-making process during DSB repair.

Nuclear loss and cytoplasmic expression of androgen receptor in penile carcinomas: role as a driver event and as a prognosis factor

Androgen receptor (AR) is a member of the steroid and nuclear family receptor that acts as transcription factor. AR signaling plays pivotal role in the development and progression of prostate cancer. However, the role of AR in penile cancer (PeCa) is poorly explored. Our previous molecular studies unveiled frequent AR mRNA loss in PeCa, which was further predicted as a major driver alteration in this neoplasm. Herein, we assessed the AR protein expression in 59 usual PeCa tissues and 42 surrounding normal tissues (SNT) by immunohistochemistry using a tissue microarray. In a paired analysis, we found a total absence of nuclear AR expression in PeCa while 95.2% of SNT samples presented strong nuclear AR expression (P < 0.001). Interestingly, 17 of 42 PeCa presented weak or moderate cytoplasmic AR staining, contrasting with 5 of 42 SNT (P = 0.008). Increased levels of AR cytoplasmic expression were related with poor prognosis features including advanced clinical staging (P = 0.044), compromised surgical margins (P = 0.005), and pathological inguinal node status (P = 0.047). Furthermore, AR cytoplasmic expression was also related with shorter overall survival (P = 0.032). In conclusion, the frequent loss of nuclear AR protein levels suggests a potential function in PeCa development. Based on this result, the androgen deprivation therapy is not indicated for PeCa patients. In addition, the AR cytoplasmic expression found in a significant number of cases (40.5%) showed prognostic value and pathways activated by the non-genomic AR signaling may represent a promising therapeutic strategy.

Abstract 2355: Penile cancer in vitro models useful for the identification of targeted therapies

Background: Penile carcinoma (PeCa) is a frequent disease in poor and developing countries showing high morbidity. Despite the recent progress in the molecular research of PeCa, the lack of well-characterized in vitro models precludes new advances in the knowledge of cellular processes and in preclinical tests for anticancer drugs' efficacy.

Material and Methods: Twenty PeCa were surgically removed, dissected and cultured in vitro (2D and 3D environment) using 3 KSFM: 1 DMEM/F12. We established five penile cancer cell cultures in vitro (passage 20), which were characterized by genomic (CytoScan HD - Affymetrix), translatomic (Clariom D Array - Affymetrix), epigenomic (Infinium Methylation EPIC BeadChip - Illumina) and proteomic profiles (Reverse phase protein array - RPPA). Chemosensitivity assay using cisplatin and EGFR inhibitors (Erbitux and Tarceva) was performed by MTT test.

Results: Two cell cultures presented typical epithelial cell morphology and epithelial markers expression such as cytokeratin and EpCAM and three were cancer-associated fibroblasts (CAFs). These cell cultures presented cancer behavior features including anchorage-independent growth, invasive potential, and capability to form tumor in nude mice. The genomic analysis revealed high similarity between the primary tumor and its derived cell culture. Transcriptomic and proteomic analysis revealed that the most relevant differentially expressed genes and proteins are components of key oncogenic pathways (MMPs, EGFR, STAT3, and PI3K/AKT/mTOR), supporting our previous data using PeCa fresh tissues. We also identified a set of genes potentially regulated by epigenetic modifications. A chemosensitivity investigation suggested that these cells are sensitive to cisplatin, a chemotherapy agent commonly used in advanced PeCa. One cell culture with EGFR overexpression was sensitive to anti-EGFR drugs (Tarceva and Erbitux).

Conclusion: In general, PeCa cell cultures recapitulated cancer behavior in vitro and showed the same dysregulated pathways than their corresponding primary tumors. These cells proved to be reliable in vitro models to dissect mechanisms promoting penile carcinogenesis and to test new targeted therapies. Our results support recent studies in which patients with advanced PeCa expressing EGFR can benefit from the treatment with EGFR-targeted therapies.

Citation Format: Hellen Kuasne, Mateus Barros-Filho, Juan Muñoz, Fabio Marchi, Cristovam Scapulatempo-Neto, Eliney Faria, Gustavo Guimarães, Ademar Lopes, Julia Mello, Maria Domingues, Sebastien Carréno, Silvia Rogatto. Penile cancer in vitro models useful for the identification of targeted therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2355.

Abstract 1044: Establishment and characterization of rare breast patient-derived xenograft models as a potential resource for personalized medicine

Breast cancer (BC) exhibits a wide range of morphologic phenotypes and gene expression profiles. Most of the studies that led to the identification of intrinsic molecular subtypes in BC were limited to invasive ductal carcinomas of the breast and did not take rare histopathologic subtypes into account. Rare histopathologic BC subtypes (collectively less than 2% of all breast cancer) have particular prognostic and clinical characteristics. There is no current established treatment that takes into account the specificity of rare BC subtypes. This is mainly due to the absence of clinical trials to determine the optimal management of these rare pathologies. The establishment of relevant preclinical models and molecular characterization of rare BC subtypes is essential for identifying directed and suitable therapeutic regimens for BC patients diagnosed with these rare histopathologic variants. Patient-derived xenograft (PDX) has been recognized as a valuable method to evaluate the clinical diversity of breast cancer. These models were shown to be predictive of clinical outcomes and are being used for preclinical drug evaluation, biomarker identification, and personalized medicine strategies. We developed a cohort of eight BC rare histopathologic subtypes, including four metaplastic, one adenoid cystic, one IDC pleomorphic, one neuroendocrine, and one mucinous BC subtype. These PDXs and their primary tumors were submitted to whole-genome sequencing (WGS) and RNA sequencing. We also evaluated a total of 255 proteins by reverse phase protein array (RPPA) in these PDX samples. We are currently performing conditional reprogramming experiments to generate cell lines from these rare BC PDXs. Our preliminary results indicate that pathways related to PI3K/AKT, ERK/MAPK, mTOR, HGF, ERBB, AMPK and IL3 signaling are disrupted in rare BC subtypes. Several genes belonging to these pathways are dysregulated in rare BC tumors, and therefore represent potential therapeutic targets for personalized treatment.

Citation Format: Hellen Kuasne, Paul Savage, Constanza Martinez Ramirez, Leah Liu, Valentina Muñoz-Ramos, Virginie Pilon, Anie Monast, Radia Johnson, Nicholas Bertos, Jamil Asselah, Nathaniel Bouganim, Kevin Petrecca, Sarkis Meterissian, Atilla Omeroglu, Mark Basik, Morag Park. Establishment and characterization of rare breast patient-derived xenograft models as a potential resource for personalized medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1044.

Abstract 4416: MiRNAs genes are regulated by methylation in papillary thyroid carcinomas

Background: Papillary thyroid cancer (PTC) is the most common thyroid malignancy. DNA methylation associated with microRNAs (miRNA) regulation is an effective epigenetic mechanism for controlling gene expression. This mechanism is poorly explored in PTC. Patients and Methods: To investigate miRNAs genes regulated by methylation, global DNA methylation (Infinium® Human Methylation450 BeadChip, Illumina) analysis was performed in 50 matched PTC and normal tissues (NT) and compared with those deposited in The Cancer Genome Atlas (TCGA) (515 PTC and 56 NT). An integrative analysis was performed in 510 cases evaluated by whole methylation and miRNA expression analysis (TCGA). Using these findings, three miRNAs were investigated by RT-qPCR and pyrosequencing in PTC (N=103), normal thyroid tissues (NT, N=40) and benign thyroid lesions (BTL, N=32). In addition, seven target genes of these miRNAs were evaluated by RT-qPCR (44PTC, 30BTL and 28NT). Functional assays using three PTC cell lines (TPC1, K1 and BCPAP) were used to investigate the role of methylation in the miRNAs expression. Results: We found 50 differentially methylated probes of which 42 (27 microRNA genes) were confirmed in the TCGA database. The miRNA expression data from TCGA presented 67 differentially expressed miRNAs in PTC. The integrative analysis revealed three miRNAs (hsa-miR-146b-5p, hsa-miR-146b-3p and hsa-miR-21-5p) as candidates to be regulated by methylation. A significant hypomethylation pattern in PTC compared to NT and BTL (thyroid benign lesions) was found for these three miRNAs. Increased expression levels of hsa-miR-21-5p and hsa-miR-146b-5p were detected in PTC compared to NT and BTL. Combining these two miRNAs expression values, 45/47 PTC were distinguished from 66/67 non-malignant tissues (96% sensitivity and 99% specificity). Similarly, the association of methylation and expression data distinguished 41/45 PTC from 55/60 non-malignant tissues (91% sensitivity and 92% specificity) for MIR21 gene and 45/47 PTC from 61/61 NT/BTL (96% sensitivity and 100% specificity) for MIR146B gene. Seven target genes (MPPED2, STXBP5L, MRO, FHL1, FLRT1, DOK6 and MOB3B) of these miRNAs were significantly down regulated in PTC compared to NT and BTL. The BRAFV600E mutation was significantly associated to hypomethylation and overexpression of hsa-miR-21-5p and hsa-miR-146b-5p. Methylation and expression data in these three cell lines revealed that MIR146B is putatively regulated by methylation. Conclusion: We provide evidences that MIR21 and MIR146B genes are regulated by methylation having control in the expression of target genes associated with PTC. These miRNAs have a strong potential to be used as diagnostic markers in the clinical practice.

Citation Format: Isabella Maria D. Ortiz, Mateus de Camargo Barros-Filho, Mariana B. dos Reis, Caroline Moraes Beltrami, Fabio Albuquerque Marchi, Hellen Kuasne, Clovis Pinto, Luiz Kowalski, Silvia Rogatto. MiRNAs genes are regulated by methylation in papillary thyroid carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4416.

Deregulation of E-cadherin, β-catenin, APC and Caveolin-1 expression occurs in canine prostate cancer and metastatic processes

Prostate cancer is a heterogeneous disease with high levels of clinical and gene heterogeneity, consequently offering several targets for therapy. Dogs with naturally occurring prostate cancer are useful models for molecular investigations and studying new treatment efficacy. Three genes and proteins associated with the WNT pathway (β-catenin, APC and E-cadherin) and Caveolin-1 (CAV-1) were evaluated in canine pre-neoplastic proliferative inflammatory atrophy (PIA), prostate cancer and metastatic disease. The APC gene methylation status was also investigated. As in human prostate cancer, cytoplasmic and nuclear β-catenin, which are fundamental for activating the canonical WNT pathway, were found in canine prostate cancer and metastasis. Membranous E-cadherin was also lost in these lesions, allowing cellular migration to the stroma and nuclear localization of β-catenin. In contrast to human prostate tumours, no APC downregulation or hypermethylation was found in canine prostate cancer. The CAV-1 gene and protein overexpression were found in canine prostate cancer, and as in humans, the highest levels were found in Gleason scores ≥8. In conclusion, as with human prostate cancer, β-catenin and E-cadherin in the WNT pathway, as well as Caveolin-1, are molecular drivers in canine prostate cancer. These findings provide additional evidence that dogs are useful models for studying new therapeutic targets in prostate cancer.

Estabelecimento e caracterização molecular de culturas celulares de câncer de pênis: Como análise em larga escala podem auxiliar na identificação de novas estratégias terapêuticas

O câncer de pênis (CaPe) apresenta distribuição geográfica disntinta sendo uma doença rara em países desenvolvidos e altamente frequente em países pobres e em desenvolvimento, como o Brasil. Apesar do seu comportamento imprevisível e tratamento agressivo, há um número muito limitado de dados sobre os mecanismos moleculares e epigenéticos envolvidos na doença. Nosso grupo tem utilizado estudos em larga escala (perfil de metilação do DNA, expressão de transcritos, miRNA e alterações genômicas) em CaPe, com o objetivo de caracterizar as alterações moleculares neste tipo tumoral assim como identificar marcadores moleculares envolvidos no desenvolvimento e progressão da doença. Nós também estabelecemos 5 linhagens celulares de CaPe e por metodologias de análises globais nós verificamos se as linhagens celulares recapitulam o tumor original. O uso de metodologias de análises globais é a principal etapa para a descoberta de marcadores que possam contribuir para o entendimento dos mecanismos genéticos e epigenéticos envolvidos no CaPe. Os resultados provenientes dessas análises forneceu subsídios para o teste de terapias alvo específicas e análises funcionais, abrindo novas estratégias de tratamento para CaPe.

Abstract A13: Gene body methylation could regulate the expression of genes associated to papillary thyroid carcinomas

Background: Papillary thyroid carcinoma (PTC) is the histological subtype more frequently reported among the endocrine malignancies. Deregulation of DNA methylation has been extensively reported in cancer with hypermethylation usually found in promoter and hypomethylation in nonpromoter regions. The methylation profile of PTC revealed altered genome regions; however, its impact on the gene expression remains poorly understood. DNA methylation profile in PTC patients was performed, aiming to investigate the role of novel genic and intergenic regions on the expression of genes.

Patients and Methods: The methylation profile of 41 patients diagnosed with PTC was evaluated using the Methylation 450 Human Infinium®BeadChip platform (Illumina). The data were normalized and analyzed using SVA, watermelon, and LIMMA packages. Delta beta of 0.15 and adjusted p-value &lt;0.05 were used to identify differentially methylated probes between PTC and non-neoplastic thyroid tissue (NT). An integrative analysis was performed using the expression data obtained in 34 matched-cases. The results were submitted to a cross-validation with The Cancer Genome Atlas (TCGA) database. An in silico analysis was performed using genes/probes showing negative correlation and confirmed by TCGA using the Ingenuity Pathways Analysis. ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5 were validated by pyrosequencing and RT-qPCR methods.

Results: Methylation analysis revealed 4,995 differentially methylated probes. A global hypomethylation was found in PTC samples (88% hypomethylated probes) mostly in nonpromoter regions (especially in gene body), distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes with negative and positive correlation, respectively. Genes showing negative correlation highlighted FGF and retinoic acid signaling as crucial pathways disrupted by DNA methylation in PTC. The selected genes were confirmed as altered in both methylation and expression levels. Interestingly, four of them (ERBB3, FGF1, GABRB2, and HMGA2) were mapped in gene body, suggesting that methylation in this region regulates the gene expression.

Conclusion: Loss of methylation was extensively observed in PTC, especially in nonpromoter, poor CGI, and enhancer-enriched regions. Gene body and promoter regions have the potential to influence the gene expression levels (both repressing and inducing). Genes potentially regulated by DNA methylation were identified from the integrative and cross-validation analyses. ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5 biomarkers are regulated by methylation in PTC samples.

Citation Format: Caroline Moraes Beltrami, Mateus Camargo Barros-Filho, Mariana Bisarro dos Reis, Fábio Albuquerque Marchi, Hellen Kuasne, Skirant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Silvia Regina Rogatto. Gene body methylation could regulate the expression of genes associated to papillary thyroid carcinomas [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A13.

Abstract B61: Evaluation of tumor heterogeneity through analysis of polysomal RNA

Glioblastoma is the most common primary brain malignancy in adults and one of the most aggressive cancers. The overall treatment outcome of this tumor type remains unsatisfactory even though advanced multimodal treatments including surgery, chemotherapy, and radiotherapy have been available for decades. The median survival of patients is typically less than 2 years. Insights into the genetic landscape of glioblatomas have been achieved by high-throughput studies and patterns of gene expression have been able to identify molecular subgroups with putative prognostic or predictive significance. However, this approach provides little information about protein expression levels, since the expression of mRNAs does not necessarily reflect the levels of proteins. In addition, the establishment of molecular subgroups is compounded by the endemic problem of tumor heterogeneity, since subtype classifiers are variably expressed across individual cells within a tumor and the impact of sampling bias has not been addressed. More importantly, the relationships between different sources of intratumoral heterogeneity---genetic, transcriptional and functional--–remain obscure. Thus, to evaluate such intratumoral heterogeneity is fundamental to demonstrate potential therapeutic targets, source of tumor recurrences, and potential prognostic implications. We evaluated a specific transcriptomic and translatomic signature of the glioblastoma heterogeneity at the single-patient level, with 3 different patients. We performed a sampling of 2 pieces from each glioblastoma tumor. The samples could be histologically classified as high or low grade and total and polysomal mRNA was isolated and identified by the microarray HTA (Human Transcriptome Array). By comparing histologically high- vs. low-grade tumors we were able to identify 106 differentially transcribed and 53 differentially translated genes in one of the tumors, 170 differentially transcribed and 235 differentially translated genes in the second tumor, and 1500 differentially transcribed and 942 differentially translated genes in the third sample. Thus, our results demonstrate that the isolation of mRNA engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches. In addition, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.

Citation Format: Fernanda Sulla Lupinacci, Hermano Bellato, Martin Roffé, Hellen Kuasne, Tiago Santos, Victor Piana de Andrade, Paulo Sanematsu, Vilma Regina Martins, Silvia Rogatto, Glaucia Hajj. Evaluation of tumor heterogeneity through analysis of polysomal RNA [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B61.

Oestrogen receptor beta isoform expression in sporadic colorectal cancer, familial adenomatous polyposis and progressive stages of colorectal cancer

Background

Among the sex hormones, oestrogen may play a role in colorectal cancer, particularly in conjunction with oestrogen receptor-β (ERβ). The expression of ERβ isoform variants and their correlations with familial adenomatous polyposis (FAP) syndrome and sporadic colorectal carcinomas are poorly described.

Methods

This study aimed to investigate the expression levels of the ERβ1, ERβ2, ERβ4 and ERβ5 isoform variants using quantitative RT-PCR (921 analyses) in FAP, normal mucosa, adenomatous polyps and sporadic colorectal carcinomas.

Results

Decreased expression of ERβ isoforms was identified in sporadic polyps and in sporadic colorectal cancer as well as in polyps from FAP syndrome patients compared with normal tissues (p < 0.001). In FAP patients, ERβ1 and ERβ5 isoforms showed significant down-expression in polyps (p < 0.001) compared with matched normal tissues. However, no differences were observed when sporadic colorectal carcinomas were compared to normal mucosa tissues. These findings suggest an association of the ERβ isoform variants in individuals affected by germline mutations of the APC gene. Progressively decreased expression of ERβ was found in polyps at early stages of low-grade dysplasia, followed by T1-T2 and T3-T4 tumours (p < 0.05). In sporadic colorectal cancer, the loss of expression was an independent predictor of recurrence, and ERβ1 and ERβ5 expression levels were associated with better disease-free survival (p = 0.002).

Conclusion

These findings may provide a better understanding of oestrogens and their potential preventive and therapeutic effects on sporadic colorectal cancer and cancers associated with FAP syndrome.

Electronic supplementary material

The online version of this article (10.1186/s12885-017-3688-4) contains supplementary material, which is available to authorized users.

Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors

Context

Even though the majority of well-differentiated thyroid carcinoma (WDTC) is indolent, a number of cases display an aggressive behavior. Cumulative evidence suggests that the deregulation of DNA methylation has the potential to point out molecular markers associated with worse prognosis.

Objective

To identify a prognostic epigenetic signature in thyroid cancer.

Design

Genome-wide DNA methylation assays (450k platform, Illumina) were performed in a cohort of 50 nonneoplastic thyroid tissues (NTs), 17 benign thyroid lesions (BTLs), and 74 thyroid carcinomas (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated, and 3 anaplastic). A prognostic classifier for WDTC was developed via diagonal linear discriminant analysis. The results were compared with The Cancer Genome Atlas (TCGA) database.

Results

A specific epigenetic profile was detected according to each histological subtype. BTLs and follicular carcinomas showed a greater number of methylated CpG in comparison with NTs, whereas hypomethylation was predominant in papillary and undifferentiated carcinomas. A prognostic classifier based on 21 DNA methylation probes was able to predict poor outcome in patients with WDTC (sensitivity 63%, specificity 92% for internal data; sensitivity 64%, specificity 88% for TCGA data). High-risk score based on the classifier was considered an independent factor of poor outcome (Cox regression, P < 0.001).

Conclusions

The methylation profile of thyroid lesions exhibited a specific signature according to the histological subtype. A meaningful algorithm composed of 21 probes was capable of predicting the recurrence in WDTC.

Circulating mRNAs and miRNAs as candidate markers for the diagnosis and prognosis of prostate cancer

Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples. The prediction analyses of target genes and integrative analysis of mRNA and miRNA expression revealed eleven genes and eight miRNAs which were validated by RT-qPCR in plasma samples from 102 untreated PCa patients and 50 cancer-free individuals. Two genes, OR51E2 and SIM2, and two miRNAs, miR-200c and miR-200b, showed significant association with PCa. Expression levels of these transcripts distinguished PCa patients from controls (67% sensitivity and 75% specificity). PCa patients and controls with prostate-specific antigen (PSA) ≤ 4.0 ng/mL were discriminated based on OR51E2 and SIM2 expression levels. The miR-200c expression showed association with Gleason score and miR-200b, with bone metastasis, bilateral tumor, and PSA > 10.0 ng/mL. The combination of circulating mRNA and miRNA was useful for the diagnosis and prognosis of PCa.

Integrative miRNA and mRNA analysis in penile carcinomas reveals markers and pathways with potential clinical impact

Penile carcinoma (PeCa) is an important public health issue in poor and developing countries, and has only recently been explored in terms of genetic and epigenetic studies. Integrative data analysis is a powerful method for the identification of molecular drivers involved in cancer development and progression. miRNA and mRNA expression profiles followed by integrative analysis were investigated in 23 PeCa and 12 non-neoplastic penile tissues (NPT). Expression levels of eight miRNAs and 10 mRNAs were evaluated in the same set of samples used for microarray and in a validation set of cases (PeCa = 36; NPT = 27). Eighty-one miRNAs and 2,697 mRNAs were identified as differentially expressed in PeCa. Integrative data analysis revealed 255 mRNAs potentially regulated by 68 miRNAs. Using RT-qPCR, eight miRNAs and nine transcripts were confirmed as altered in PeCa. We identified that MMP1, MMP12 and PPARG and hsa-miR-31-5p, hsa-miR-224-5p, and hsa-miR-223-3p were able to distinguish tumors from NPT with high sensitivity and specificity. Higher MMP1 expression was detected as a better predictor of lymph node metastasis than the clinical-pathological data. In addition, PPARG and EGFR were highlighted as potential pathways for targeted therapy in PeCa. The analysis based on HPV positivity (7 of 23 cases) revealed five miRNA and 13 mRNA differentially expressed. Although in a limited number of cases, HPV positive PeCa presented less aggressive phenotype in comparison with negative cases. Overall, an integrative analysis using mRNA and miRNA profiles revealed markers related with tumor development and progression. Furthermore, MMP1 expression level was a predictive marker for lymph node metastasis in patients with PeCa.

Multidimensional integrative analysis uncovers driver candidates and biomarkers in penile carcinoma

Molecular data generation and their combination in penile carcinomas (PeCa), a significant public health problem in poor and underdeveloped countries, remain virtually unexplored. An integrativemethodology combin ing genome-wide copy number alteration, DNA methylation, miRNA and mRNA expression analysis was performed in a set of 20 usual PeCa. The well-ranked 16 driver candidates harboring genomic alterations and regulated by a set of miRNAs, including hsa-miR-31, hsa-miR-34a and hsa-miR-130b, were significantly associated with over-represented pathways in cancer, such as immune-inflammatory system, apoptosis and cell cycle. Modules of co-expressed genes generated from expression matrix were associated with driver candidates and classified according to the over-representation of passengers, thus suggesting an alteration of the pathway dynamics during the carcinogenesis. This association resulted in 10 top driver candidates (AR, BIRC5, DNMT3B, ERBB4, FGFR1, PML, PPARG, RB1, TNFSF10 and STAT1) selected and confirmed as altered in an independent set of 33 PeCa samples. In addition to the potential driver genes herein described, shorter overall survival was associated with BIRC5 and DNMT3B overexpression (log-rank test, P = 0.026 and P = 0.002, respectively) highlighting its potential as novel prognostic marker for penile cancer.

Abstract 1476: Cell-free miR-141 as a molecular marker for prostate cancer metastasis

Prostate cancer is the second most commonly diagnosed neoplasia in men. Currently, there is no available non-invasive tool to assist in the identification of the aggressive form of this disease. Cell-free nucleic acid has been tested as a potential new molecular tool that can be useful in the diagnosis and prognosis of prostate cancer. MicroRNAs are a class of non-coding RNAs, that are shown to impact the development and progression of prostate cancer and their detection in plasma have been indicated as a promising non-invasive tool for disease screening and prognosis assessment. Among the several deregulated miRNAs that are observed in prostate cancer, the miRNA-141-3p was observed with upregulated expression levels in prostate cancer, particularly in the metastatic lesions. Therefore, the main aim of this study was to verify the diagnostic potential of miR-141 as a circulating tumor marker for prostate cancer and determine its functional role in modulating tumorigenesis in prostate cancer metastatic cell lines. MiR-141 expression analysis was performed in plasma samples of 102 prostate cancer patients without treatment and of 50 health controls by RT-qPCR. The experimental assays were performed by transfecting the PC3 cell line using miRNA-141 mimic/ inhibitor systems and directly accessing their effect in classical tumor phenotypes. Expression of the miR-141 were found significantly upregulated in the metastatic patients’ plasma specimens (FC=9.11, p=0.04; AUC=0.66) when compared to the patients without metastasis, showing its screening potential for prostate cancer metastasis. The in vitro ectopic expression of miR-141 in PC3 cell line showed a significant increased in cell proliferation, associated with changes in cell cycle (decreased number of cells in the G1 phase). Conversely, the inhibition of miR-141 showed an increase in the migratory ability, cell adhesion and in the Docetaxel cytotoxicity of the PC3 cells. Western-blot analysis showed that the inhibition of the miR-141 levels reduced the expression of the EMT inducers markers E-CADHERIN and CLAUDIN, and up-regulated the levels of ZEB-1, pAKT and VIMENTIN, consistent with their repression roles in the EMT process. These findings showed that miR-141 presents a direct function in controlling some of the in vitro metastatic phenotypes in prostate cancer, through the regulation of the epithelial-mesenchymal transition expression proteins. In conclusion, miR-141 presents a potential use as a minimally invasive molecular marker for prostate cancer diagnosis and can be used as a druggable target for therapy, particularly in the metastatic clinical setting.

Citation Format: Marilesia Ferreira de Souza, Ilce Mara de Syllos Cólus, Aline Simoneti Fonseca, Hellen Kuasne, Paulo Emilio Fuganti, Deepak Kumar, Silvia Regina Rogatto, Luciane Regina Cavalli. Cell-free miR-141 as a molecular marker for prostate cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1476. doi:10.1158/1538-7445.AM2017-1476

Abstract 3358: Epigenetic signatures associated with patient outcome in thyroid carcinoma

BACKGROUND: Thyroid cancer (TC) is the most frequent endocrine neoplasia composed essentially by well-differentiated tumors (90%). These tumors generally are indolent and the patients show a favorable outcome. However, a set of TC patients presents aggressive outcome. Global deregulation of DNA methylation has been described as involved in thyroid cancer (TC) development. In this study, DNA methylation profile was performed aiming to identify a prognostic signature in TC.

PATIENTS AND METHODS: The methylation profile of 50 non-neoplastic thyroid tissues (NT), 17 benign thyroid lesions and 74 TC (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated and 3 anaplastic thyroid carcinomas) were investigated using the Methylation 450 Human Infinium®BeadChip platform (Illumina). The data were normalized and analyzed using SVA, wateRmelon and LIMMA packages. The threshold delta beta of 0.2 and adjusted p-value &lt;0.05 were used to identify differentially methylated probes among the histological subtypes. The delta beta of 0.1 and adjusted p-value &lt;0.05 were used in the prognostic features analysis in WDTC (well differentiated thyroid cancer) cases. An epigenetic classifier according to WDTC was identified using diagonal linear discriminant analysis. The results were compared with The Cancer Genome Atlas (TCGA) database.

RESULTS: Methylation analyses revealed a specific epigenetic profile according to the histological subtypes. A global hypermethylation was observed in benign lesions and follicular carcinomas, while papillary and undifferentiated carcinomas were widely hypomethylated compared with NT. An epigenetic signature comprising 21 probes differentially methylated (delta beta 0.1) was able to predict poor outcome in WDTC patients. This classifier reveled 63% of sensitivity and 92% of specificity, which was confirmed by TCGA database (64% of sensitivity and 88% of specificity). Using the established signature, we were able to confirm the involvement of poor prognosis markers with high-risk scores (multivariable analysis; P&lt;0.001).

CONCLUSION: Thyroid tumors showed different methylation profile according to the histological subtypes. Genes regulated by methylation in TC and associated with the tumor development were identified and confirmed by TCGA. In addition, a meaningful algorithm was designed and confirmed as capable to predict recurrence in WDTC.

FINANCIAL SUPPORT: FAPESP (2015/20548-5) and National Institute of Science and Technology in Oncogenomics (FAPESP 2008/57887-9 and CNPq 573589/08-9), CNPq (302606/2011-4).

Note: This abstract was not presented at the meeting.

Citation Format: Mariana Bisarro dos Reis, Caroline Moraes Beltrami, Mateus Camargo Barros-Filho, Fabio Albuquerque Marchi, Hellen Kuasne, Skirant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Silvia Regina Rogatto. Epigenetic signatures associated with patient outcome in thyroid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3358. doi:10.1158/1538-7445.AM2017-3358

Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

BACKGROUND

Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related.

RESULTS

The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAFV600E-positive tumors. The methylation and expression pattern of six selected genes (ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5) were confirmed as altered by pyrosequencing and RT-qPCR.

CONCLUSIONS

DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC, especially in tumors harboring BRAFV600E. In addition to the promoter region, gene body and 3'UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). The integrative analysis revealed genes potentially regulated by DNA methylation pointing out potential drivers and biomarkers related to PTC development.

Abstract B38: Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs

Glioblastoma is the most common primary brain malignancy in adults and one of the most aggressive cancers. The overall treatment outcome of this tumor type remains unsatisfactory even though advanced multimodal treatments including surgery, chemotherapy, and radiotherapy have been available for decades. The median survival of patients is typically less than 2 years. Insights into the genetic landscape of glioblastomas have been achieved by high-throughput studies and patterns of gene expression have been able to identify molecular subgroups with putative prognostic or predictive significance. However, this approach provides little information about protein expression levels, since the expression of mRNAs do not necessarily reflect the levels of proteins. In addition, the establishment of molecular subgroups is compounded by the endemic problem of tumor heterogeneity, since subtype classifiers are variably expressed across individual cells within a tumor and the impact of sampling bias has not been addressed. More importantly, the relationships between different sources of intratumoral heterogeneity—genetic, transcriptional and functional—remain obscure. Thus, to evaluate such intratumoral heterogeneity is fundamental to demonstrate potential therapeutic targets, source of tumor recurrences and potential prognostic implications. Herein, we evaluated a specific transcriptomic and translatomic signature of the glioblastoma heterogeneity at the single-patient level. We performed a sampling of 8 pieces from a single glioblastoma tumor. The samples could be histologically classified as high or low grade and total and polysomal mRNA was isolated and identified by microarray. By comparing histologically high vs low grade tumors we were able to identify 42 differentially transcribed and 138 differentially translated genes. Among the differentially translated genes validated by qPCR there are many related to proliferation, development and cancer, such as FOXC1, HOXB5, SNAI2, LOX, WISP1, ITGA11 and COL5A2. Thus, our results demonstrate that the isolation of mRNA engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches. In addition, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.

Ethical approval: 1775/13. Funding support: FAPESP 2013/03315-2, 2014/15550-9

Citation Format: Fernanda C. S. Lupinacci, Hermano M. Bellato, Martin Roffe, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Jr., Vilma R. Martins, Silvia R. Rogatto, Glaucia N M Hajj. Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B38.

Abstract 2389: Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity

Glioblastoma is among the most aggressive tumor type and less responsive to chemotherapeutic agents, thus a better understanding of the behavior of these tumors may help to develop new treatments for this disease. Currently, many genome-wide projects attempt to define general patterns of gene expression based on deep sequencing or microarray data from total mRNA populations. However, this approach provides little information about the molecular mediators of tumor biology, because the expression levels of mRNAs do not necessarily reflect the levels of proteins. The identification of mRNAs target of translational alterations in tumors can show gene expression profiles that better reflect the population of proteins. In this work we were able to identify mRNAs differentially translated in a human glioblastoma that presented histologically different parts. The sample was divided in 8 pieces that were classified as high or low grade based on histological characteristics. Actively translating ribosomes and their associated mRNAs were isolated biochemically through a polysomal profile. Total and polysomal mRNA was then extracted and submitted to a microarray analysis. By comparing high vs low grade tumor pieces, we were able to identify more differentially translated genes (138 genes) than differentially expressed genes (43 genes). Among the differentially translated mRNAs, there are many related to proliferation, development and cancer. By Integrated Pathway Analysis, we identified the TGF-β pathway among the the most relevant for grade progression. Thus, the technique of isolating mRNAs engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches.

Citation Format: Glaucia N. Hajj, Fernanda S. Lupinacci, Martín Roffé, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Vilma R. Martins, Silvia R. Rogatto. Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2389.