Suppressor T helper type 17 cell responses in intestinal transplant recipients with allograft rejection

BACKGROUND

Intestinal transplant (ITx) rejection is associated with memory T helper type 17 cell (Th17) infiltration of grafted tissues. Modulation of Th17 effector cell response is facilitated by T regulatory (Treg) cells, but a phenotypic characterization of this process is lacking in the context of allograft rejection.

METHODS

Flow cytometry was performed to examine the expression of surface receptors, cytokines, and transcription factors in Th17 and Treg cells in ITx control (n = 34) and rejection patients (n = 23). To elucidate key pathways guiding the rejection biology, we utilized RNA sequencing (RNAseq) and assessed epigenetic stability through pyrosequencing of the Treg-specific demethylated region (TSDR).

RESULTS

We found that intestinal allograft rejection is characterized by Treg cellular infiltrates, which are polarized toward Th17-type chemokine receptor, ROR-γt transcription factor expression, and cytokine production. These Treg cell subsets have maintained epigenetic stability, as defined by FoxP3-TSDR methylation status, but displayed upregulation of functional Treg and purinergic signaling genes by RNAseq analysis such as CD39, in keeping with suppressor Th17 properties.

CONCLUSION

We show that ITx rejection is associated with increased polarized cells that express a Th17-like phenotype concurrent with regulatory purinergic markers.

Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review

Translational bioinformatics and data science play a crucial role in biomarker discovery as it enables translational research and helps to bridge the gap between the bench research and the bedside clinical applications. Thanks to newer and faster molecular profiling technologies and reducing costs, there are many opportunities for researchers to explore the molecular and physiological mechanisms of diseases. Biomarker discovery enables researchers to better characterize patients, enables early detection and intervention/prevention and predicts treatment responses. Due to increasing prevalence and rising treatment costs, mental health (MH) disorders have become an important venue for biomarker discovery with the goal of improved patient diagnostics, treatment and care. Exploration of underlying biological mechanisms is the key to the understanding of pathogenesis and pathophysiology of MH disorders. In an effort to better understand the underlying mechanisms of MH disorders, we reviewed the major accomplishments in the MH space from a bioinformatics and data science perspective, summarized existing knowledge derived from molecular and cellular data and described challenges and areas of opportunities in this space.

Lymphocyte antigen 6K signaling to aurora kinase promotes advancement of the cell cycle and the growth of cancer cells, which is inhibited by LY6K-NSC243928 interaction

Lymphocyte antigen 6K (LY6K) is a small GPI-linked protein that is normally expressed in testes. Increased expression of LY6K is significantly associated with poor survival outcomes in many solid cancers, including cancers of the breast, ovary, gastrointestinal tract, head and neck, brain, bladder, and lung. LY6K is required for ERK-AKT and TGF-β pathways in cancer cells and is required for in vivo tumor growth. In this report, we describe a novel role for LY6K in mitosis and cytokinesis through aurora B kinase and its substrate histone H3 signaling axis. Further, we describe the structural basis of the molecular interaction of small molecule NSC243928 with LY6K protein and the disruption of LY6K-aurora B signaling in cell cycle progression due to LY6K-NSC243928 interaction. Overall, disruption of LY6K function via NSC243928 led to failed cytokinesis, multinucleated cells, DNA damage, senescence, and apoptosis of cancer cells. LY6K is not required for vital organ function, thus inhibition of LY6K signaling is an ideal therapeutic approach for hard-to-treat cancers that lack targeted therapy such as triple-negative breast cancer.

Federated learning enables big data for rare cancer boundary detection

Although machine learning (ML) has shown promise across disciplines, out-of-sample generalizability is concerning. This is currently addressed by sharing multi-site data, but such centralization is challenging/infeasible to scale due to various limitations. Federated ML (FL) provides an alternative paradigm for accurate and generalizable ML, by only sharing numerical model updates. Here we present the largest FL study to-date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature (n = 6, 314). We demonstrate a 33% delineation improvement for the surgically targetable tumor, and 23% for the complete tumor extent, over a publicly trained model. We anticipate our study to: 1) enable more healthcare studies informed by large diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further analyses for glioblastoma by releasing our consensus model, and 3) demonstrate the FL effectiveness at such scale and task-complexity as a paradigm shift for multi-site collaborations, alleviating the need for data-sharing.

StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit

Target prioritization is essential for drug discovery and repositioning. Applying computational methods to analyze and process multi-omics data to find new drug targets is a practical approach for achieving this. Despite an increasing number of methods for generating datasets such as genomics, phenomics, and proteomics, attempts to integrate and mine such datasets remain limited in scope. Developing hybrid intelligence solutions that combine human intelligence in the scientific domain and disease biology with the ability to mine multiple databases simultaneously may help augment drug target discovery and identify novel drug-indication associations. We believe that integrating different data sources using a singular numerical scoring system in a hybrid intelligent framework could help to bridge these different omics layers and facilitate rapid drug target prioritization for studies in drug discovery, development or repositioning. Herein, we describe our prototype of the StarGazer pipeline which combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits, and is available via https://github.com/AstraZeneca/StarGazer.

Molecular predictors of response to pembrolizumab in thymic carcinoma

Thymic carcinoma is rare and has a poorer prognosis than thymomas. The treatment options are limited after failure of platinum-based chemotherapy. We previously performed a single-center phase II study of pembrolizumab in patients with advanced thymic carcinoma, showing a 22.5% response rate. Here, we characterize the genomic and transcriptomic profile of thymic carcinoma samples from 10 patients (5 non-responders versus 5 responders) in this cohort, with the main aim of identifying potential predictors of response to immunotherapy. We find that expression of PDL1 and alterations in genes or pathways that correlated with PD-L1 expression (CYLD and BAP1) could be potential predictors for response or resistance to immunotherapy in patients with advanced thymic carcinoma. Our study provides insights into potential predictive markers/pathways to select patients with thymic carcinoma for anti-PD-1 immunotherapy.

Rejection of intestinal allotransplants is driven by memory T helper type 17 immunity and responds to infliximab

Intestinal transplantation (ITx) can be life-saving for patients with advanced intestinal failure experiencing complications of parenteral nutrition. New surgical techniques and conventional immunosuppression have enabled some success, but outcomes post-ITx remain disappointing. Refractory cellular immune responses, immunosuppression-linked infections, and posttransplant malignancies have precluded widespread ITx application. To shed light on the dynamics of ITx allograft rejection and treatment resistance, peripheral blood samples and intestinal allograft biopsies from 51 ITx patients with severe rejection, alongside 37 stable controls, were analyzed using immunohistochemistry, polychromatic flow cytometry, and reverse transcription-PCR. Our findings inform both immunomonitoring and treatment. In terms of immunomonitoring, we found that while ITx rejection is associated with proinflammatory and activated effector memory T cells in the blood, evidence of treatment efficacy can only be found in the allograft itself, meaning that blood-based monitoring may be insufficient. In terms of treatment, we found that the prominence of intra-graft memory TNF-α and IL-17 double-positive T helper type 17 (Th17) cells is a leading feature of refractory rejection. Anti-TNF-α therapies appear to provide novel and safer treatment strategies for refractory ITx rejection; with responses in 14 of 14 patients. Clinical protocols targeting TNF-α, IL-17, and Th17 warrant further testing.

SPTBN1 inhibits inflammatory responses and hepatocarcinogenesis via the stabilization of SOCS1 and downregulation of p65 in hepatocellular carcinoma

Background: Spectrin, beta, non-erythrocytic 1 (SPTBN1), an adapter protein for transforming growth factor beta (TGF-β) signaling, is recognized as a tumor suppressor in the development of hepatocellular carcinoma (HCC); however, the underlying molecular mechanisms of this tumor suppression remain obscure.

Methods: The effects on expression of pro-inflammatory cytokines upon the inhibition or impairment of SPTBN1 in HCC cell lines and liver tissues of Sptbn1^+/- and wild-type (WT) mice were assessed by analyses of quantitative real-time reverse-transcription polymerase chain reaction (QRT-PCR), enzyme linked immunosorbent assay (ELISA), Western blotting and gene array databases from HCC patients. We investigated the detailed molecular mechanisms underlying the inflammatory responses by immunoprecipitation-Western blotting, luciferase reporter assay, chromatin immunoprecipitation quantitative real time PCR (ChIP-qPCR), immunohistochemistry (IHC) and electrophoretic mobility shift assay (EMSA). The proportion of myeloid-derived suppressor cells in liver, spleen, bone marrow and peripheral blood samples from WT and Sptbn1^+/- mice were measured by fluorescence-activated cell sorting (FACS) analysis. Further, the hepatocacinogenesis and its correlation with inflammatory microenvironment by loss of SPTBN1/SOCS1 and induction of p65 were analyzed by treating WT and Sptbn1^+/- mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC).

Results: Loss of SPTBN1 in HCC cells upregulated the expression of pro-inflammatory cytokines including interleukin-1α (IL-1α), IL-1β, and IL-6, and enhanced NF-κB transcriptional activation. Mechanistic analyses revealed that knockdown of SPTBN1 by siRNA downregulated the expression of suppressor of cytokine signaling 1 (SOCS1), an E3 ligase of p65, and subsequently upregulated p65 accumulation in the nucleus of HCC cells. Restoration of SOCS1 abrogated this SPTBN1 loss-associated elevation of p65 in HCC cells. In human HCC tissues, SPTBN1 gene expression was inversely correlated with gene expression of IL-1α, IL-1β and IL-6. Furthermore, a decrease in the levels of SPTBN1 gene, as well as an increase in the gene expression of IL-1β or IL-6 predicted shorter relapse free survival in HCC patients, and that HCC patients with low expression of SPTBN1 or SOCS1 protein is associated with poor survival. Heterozygous loss of SPTBN1 (Sptbn1^+/-) in mice markedly upregulated hepatic expression of IL-1α, IL-1β and IL-6, and elevated the proportion of myeloid-derived suppressor cells (MDSCs) and CD4⁺CD25⁺Foxp3⁺ regulatory T cells (Foxp3⁺Treg) cells in the liver, promoting hepatocarcinogenesis of mouse fed by DDC.

Conclusions: Our findings provided evidence that loss of SPTBN1 in HCC cells increases p65 protein stability via the inhibition of SOCS1 and enhances NF-κB activation, stimulating the release of inflammatory cytokines, which are critical molecular mechanisms for the loss of SPTBN1-induced liver cancer formation. Reduced SPTBN1 and SOCS1 predict poor outcome in HCC patients.

Type 3 innate lymphoid cells are associated with a successful intestinal transplant

Although innate lymphoid cells (ILCs) play fundamental roles in mucosal barrier functionality and tissue homeostasis, ILC-related mechanisms underlying intestinal barrier function, homeostatic regulation, and graft rejection in intestinal transplantation (ITx) patients have yet to be thoroughly defined. We found protective type 3 NKp44⁺ ILCs (ILC3s) to be significantly diminished in newly transplanted allografts, compared to allografts at 6 months, whereas proinflammatory type 1 NKp44^- ILCs (ILC1s) were higher. Moreover, serial immunomonitoring revealed that in healthy allografts, protective ILC3s repopulate by 2-4 weeks postoperatively, but in rejecting allografts they remain diminished. Intracellular cytokine staining confirmed that NKp44⁺ ILC3 produced protective interleukin-22 (IL-22), whereas ILC1s produced proinflammatory interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α). Our findings about the paucity of protective ILC3s immediately following transplant and their repopulation in healthy allografts during the first month following transplant were confirmed by RNA-sequencing analyses of serial ITx biopsies. Overall, our findings show that ILCs may play a key role in regulating ITx graft homeostasis and could serve as sentinels for early recognition of allograft rejection and be targets for future therapies.

The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling

BACKGROUND & AIMS

Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic.

METHODS

We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients.

RESULTS

High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients.

CONCLUSIONS

We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.

Integrated copy number and miRNA expression analysis in triple negative breast cancer of Latin American patients

Triple negative breast cancer (TNBC), a clinically aggressive breast cancer subtype, affects 15–35% of women from Latin America. Using an approach of direct integration of copy number and global miRNA profiling data, performed simultaneously in the same tumor specimens, we identified a panel of 17 miRNAs specifically associated with TNBC of ancestrally characterized patients from Latin America, Brazil. This panel was differentially expressed between the TNBC and non-TNBC subtypes studied (p ≤ 0.05, FDR ≤ 0.25), with their expression levels concordant with the patterns of copy number alterations (CNAs), present mostly frequent at 8q21.3-q24.3, 3q24-29, 6p25.3-p12.2, 1q21.1-q44, 5q11.1-q22.1, 11p13-p11.2, 13q12.11-q14.3, 17q24.2-q25.3 and Xp22.33-p11.21. The combined 17 miRNAs presented a high power (AUC = 0.953 (0.78–0.99);95% CI) in discriminating between the TNBC and non-TNBC subtypes of the patients studied. In addition, the expression of 14 and 15 of the 17miRNAs was significantly associated with tumor subtype when adjusted for tumor stage and grade, respectively. In conclusion, the panel of miRNAs identified demonstrated the impact of CNAs in miRNA expression levels and identified miRNA target genes potentially affected by both CNAs and miRNA deregulation. These targets, involved in critical signaling pathways and biological functions associated specifically with the TNBC transcriptome of Latina patients, can provide biological insights into the observed differences in the TNBC clinical outcome among racial/ethnic groups, taking into consideration their genetic ancestry.

Abstract 4764: A global transcriptome analysis of pancreatic cancer cells distinguishes between acute and acquired PARP inhibitor resistance mechanisms

Pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer related deaths in the U.S. Recent advances in understanding RNA biology in PDAC have shed light on post-transcriptional regulation of genes and pathways through RNA binding proteins (RBP). Our lab has demonstrated that HuR, an RBP, is overexpressed in PDAC cells and stabilizes pro-survival mRNAs. Additionally, our work and others have demonstrated that this level of gene regulation can support drug resistance in PDAC cells. A synthetic lethal strategy employing Poly-ADP ribose polymerase inhibitors (PARPi) in a subset of patients with DNA repair deficient pancreatic cancers has been gaining interest. However, the success of PARPi is often hindered by the emergence of drug resistance in patients who initially respond. We have published that short-term PARPi treatment of PDAC cells causes activation of HuR where it stabilizes a DNA repair enzyme, PAR-glycohydrolase, and mediates acute PARPi resistance. In this study, we generated olaparib acquired resistant pancreatic cancer cells in vitro and acquired pancreatic patient derived xenograft cell lines (pre- and post PARPi) to understand acute versus acquired resistant mechanism(s). In characterising the acquired resistant model of PARPi resistance, we found that these cells are >20 fold more resistant to olaparib and platinums and >5 fold resistant to other PARPi like rucaparib and veliparib, compared to parental cells. No cross resistance was seen with other chemotherapeutics like gemcitabine. Additionally, we also found acquired resistant cells lost PARP-1 protein expression compared to parental cells. Bioinformatic analyses on HuR-RNA immunoprecipitation-microarray (RIP-microarray) data from acutely treated olaparib cells show enrichment of pro-survival mRNAs. Interestingly, these mRNAs are significantly downregulated in acquired resistant cells compared to control cells (i.e., negative log2 fold changes, p<0.001) in differential expression of HuR and HuR established targets. Interestingly, upregulated gene transcripts in these samples belong to pathways that negatively regulate biosynthetic and metabolic processes, and hence may represent pathways to target. Further, in vitro analyses show that parental PDAC cells are sensitive to combined inhibition of PARP and HuR but acquired resistant cells fail to respond to HuR inhibition. In conclusion, HuR mediates acute resistance to PARPi in PDAC cells and HuR inhibitor therapy could enhance PARPi therapy immediately, yet is most likely not useful in the setting of acquired- resistance. Future studies will explore genetic alterations and novel HuR-independent pathways in PARPi acquired resistant cells. Finally, we have begun a line of investigation of combining PARPi therapy with HuR inhibitors in an effort to optimize upfront therapeutic efficacy

Citation Format: Aditi Jain, Matthew McCoy, Lebaron A. Agostini, Yuriy Gusev, Subha Madhavan, Michael Pishvaian, Sankar Addya, Eric Londin, Maria R. Gurevich, Chani Stossel, Talia Golan, Charles J. Yeo, Jonathan R. Brody. A global transcriptome analysis of pancreatic cancer cells distinguishes between acute and acquired PARP inhibitor resistance mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4764.

Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients

BACKGROUND

Osteosarcoma is the most common malignant bone tumor in children. Survival remains poor among histologically poor responders, and there is a need to identify them at diagnosis to avoid delivering ineffective therapy. Genetic variation contributes to a wide range of response and toxicity related to chemotherapy. The aim of this study is to use sequencing of blood cells to identify germline haplotypes strongly associated with drug resistance in osteosarcoma patients.

METHODS

We used sequencing data from two patient datasets, from Inova Hospital and the NCI TARGET. We explored the effect of mutation hotspots, in the form of haplotypes, associated with relapse outcome. We then mapped the single nucleotide polymorphisms (SNPs) in these haplotypes to genes and pathways. We also performed a targeted analysis of mutations in Drug Metabolizing Enzymes and Transporter (DMET) genes associated with tumor necrosis and survival.

RESULTS

We found intronic and intergenic hotspot regions from 26 genes common to both the TARGET and INOVA datasets significantly associated with relapse outcome. Among significant results were mutations in genes belonging to AKR enzyme family, cell-cell adhesion biological process and the PI3K pathways; as well as variants in SLC22 family associated with both tumor necrosis and overall survival. The SNPs from our results were confirmed using Sanger sequencing. Our results included known as well as novel SNPs and haplotypes in genes associated with drug resistance.

CONCLUSION

We show that combining next generation sequencing data from multiple datasets and defined clinical data can better identify relevant pathway associations and clinically actionable variants, as well as provide insights into drug response mechanisms.

Abstract 496: The synergistic role of miR-150-5p and miR-661 in regulating epithelial mesenchymal transition in triple negative breast cancer

MiRNA dysregulation has been linked to cancer initiation and progression, through their control in multiple cancer associated signaling pathways. MiRNA low specificity of target interaction confer them the ability to cooperatively regulate a single biological process. Epithelial mesenchymal transition (EMT) plays pivotal roles in cancer progression and metastasis, through the regulation of transcription factors and proteins, such as E-cadherin, Slug, Snail, Twist and Zeb1. This process is also controlled post-transcriptionally by a complex and regulated network of miRNAs. We have shown that miR-150-5p and miR-661, up-regulated in triple negative breast cancer (TNBC) when compared to normal tissue and other breast cancer subtypes, exert an oncogenic action and modulate cell proliferation, clonogenicity, migration and cytotoxic response in in vitro TNBC models. The main objective of this study was to determine whether the modulation of these phenotypes were due to the regulation of their corresponding gene targets associated with EMT. By conducting an integrated computational and experimental analysis, in which miR-150-5p and miR-661 were suppressed or ectopically expressed in transfected MDA-MB-231 cells, we showed that they present common regulatory roles in cell adhesion and motility signaling networks, including those involved in EMT. Gene expression analysis in a targeted panel of 770 genes with primary functional annotations in EMT, cell adhesion and motility and metastasis, revealed that: i. the suppression of miR-150-5p and miR-661, affected the expression of 160 and 123 genes, respectively; 18% of these genes were commonly affected by both miRNAs, including ACVR1C (ALK-7), CHAD, GIMAP6, SFRCL1, SPARCL1 and TBX1; ii. the ectopic expression of miR-150-5p and miR-661, affected the expression of 283 and 267 genes, respectively; 27% of which commonly affected by both miRNAs, including AKT1, DCL1, MAPK2, MMP1, SFRP1 and TPM2. iii. 26 genes were inversely affected by the suppression and ectopic expression of miR-150-5p and miR-661 (consistent with the general post-transcriptional regulation of miRNA/mRNA targets); 73% of these genes were predicted to be miRs150-5p and 661 direct or indirect targets. In summary, based on the computational and experimental data presented, we provide evidences that strongly suggest that miRNA-150-5p and miR-661 modulate the aggressive tumor phenotype in TNBC cells by regulating common gene targets associated with the EMT process. Further functional studies in TNBC experimental models will allow us to dissect the mechanisms by which they contribute to the TNBC aggressive phenotypes by synergistically regulating EMT.

Funding: Partially funded by Georgetown University Center of Excellence in Regulatory Science and Innovation (CERSI U01FD004319), CNPq, Capes-Brazil (scholarship to PMMO, BMS, ASF).

Citation Format: Patricia MM Ozawa, Bruna M. Sugita, Aline S. Fonseca, Yara Rodriguez, Yuriy Gusev, Paolo Fadda, Deepak Kumar, Luciane R. Cavalli. The synergistic role of miR-150-5p and miR-661 in regulating epithelial mesenchymal transition in triple negative breast cancer [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 496.

viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors

An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge, there are no publicly available pipelines or packages that would provide this type of complete analysis in one open source package. In this paper, we applied the viGEN pipeline to two case studies. We first demonstrate the working of our pipeline on a large public dataset, the TCGA cervical cancer cohort. In the second case study, we performed an in-depth analysis on a small focused study of TCGA liver cancer patients. In the latter cohort, we performed viral-gene quantification, viral-variant extraction and survival analysis. This allowed us to find differentially expressed viral-transcripts and viral-variants between the groups of patients, and connect them to clinical outcome. From our analyses, we show that we were able to successfully detect the human papilloma virus among the TCGA cervical cancer patients. We compared the viGEN pipeline with two metagenomics tools and demonstrate similar sensitivity/specificity. We were also able to quantify viral-transcripts and extract viral-variants using the liver cancer dataset. The results presented corresponded with published literature in terms of rate of detection, and impact of several known variants of HBV genome. This pipeline is generalizable, and can be used to provide novel biological insights into microbial infections in complex diseases and tumorigeneses. Our viral pipeline could be used in conjunction with additional type of immuno-oncology analysis based on RNA-seq data of host RNA for cancer immunology applications. The source code, with example data and tutorial is available at: https://github.com/ICBI/viGEN/.

Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women

Triple Negative Breast Cancer (TNBC), a clinically aggressive subtype of breast cancer, disproportionately affects African American (AA) women when compared to non-Hispanic Whites (NHW). MiRNAs(miRNAs) play a critical role in these tumors, through the regulation of cancer driver genes. In this study, our goal was to characterize and compare the patterns of miRNA expression in TNBC of AA (n = 27) and NHW women (n = 30). A total of 256 miRNAs were differentially expressed between these groups, and distinct from the ones observed in their respective non-TNBC subtypes. Fifty-five of these miRNAs were mapped in cytobands carrying copy number alterations (CNAs); 26 of them presented expression levels concordant with the observed CNAs. Receiving operating characteristic (ROC) analysis showed a good power (AUC ≥ 0.80; 95% CI) for over 65% of the individual miRNAs and a high combined power with superior sensitivity and specificity (AUC = 0.88 (0.78−0.99); 95% CI) of the 26 miRNA panel in discriminating TNBC between these populations. Subsequent miRNA target analysis revealed their involvement in the interconnected PI3K/AKT, MAPK and insulin signaling pathways. Additionally, three miRNAs of this panel were associated with early age at diagnosis. Altogether, these findings indicated that there are different patterns of miRNA expression between TNBC of AA and NHW women and that their mapping in genomic regions with high levels of CNAs is not merely physical, but biologically relevant to the TNBC phenotype. Once validated in distinct cohorts of AA women, this panel can potentially represent their intrinsic TNBC genome signature.

Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma

Transcribed ultraconserved regions (T-UCRs) are a class of non-coding RNAs with 100% sequence conservation among human, rat and mouse genomes. T-UCRs are differentially expressed in several cancers, however their expression in pancreatic adenocarcinoma (PDAC) has not been studied. We used a qPCR array to profile all 481 T-UCRs in pancreatic cancer specimens, pancreatic cancer cell lines, during experimental pancreatic desmoplasia and in the pancreases of P48^Cre/wt; Kras^LSL-G12D/wt mice. Fourteen, 57 and 29% of the detectable T-UCRs were differentially expressed in the cell lines, human tumors and transgenic mouse pancreases, respectively. The vast majority of the differentially expressed T-UCRs had increased expression in the cancer. T-UCRs were monitored using an in vitro model of the desmoplastic reaction. Twenty-five % of the expressed T-UCRs were increased in the HPDE cells cultured on PANC-1 cellular matrix. UC.190, UC.233 and UC.270 were increased in all three human data sets. siRNA knockdown of each of these three T-UCRs reduced the proliferation of MIA PaCa-2 cells up to 60%. The expression pattern among many T-UCRs in the human and mouse pancreases closely correlated with one another, suggesting that groups of T-UCRs are co-activated in PDAC. Successful knockout of the transcription factor EGR1 in PANC-1 cells caused a reduction in the expression of a subset of T-UCRs suggesting that EGR1 may control T-UCR expression in PDAC. We report a global increase in expression of T-UCRs in both human and mouse PDAC. Commonalties in their expression pattern suggest a similar mechanism of transcriptional upregulation for T-UCRs in PDAC.

CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data

The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways. This enables in-depth systems biology-based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes. This package was successfully applied to analysis of DNA copy number data in colorectal cancer as a part of multi-omics integrative study as well as for analysis of several other cancer types. The source code, along with an end-to-end tutorial, and example data are freely available in Bioconductor at http://bioconductor.org/packages/CINdex/.

Distinct lymphocyte antigens 6 (Ly6) family members Ly6D, Ly6E, Ly6K and Ly6H drive tumorigenesis and clinical outcome

Stem cell antigen-1 (Sca-1) is used to isolate and characterize tumor initiating cell populations from tumors of various murine models [1]. Sca-1 induced disruption of TGF-β signaling is required in vivo tumorigenesis in breast cancer models [2, 3-5]. The role of human Ly6 gene family is only beginning to be appreciated in recent literature [6-9]. To study the significance of Ly6 gene family members, we have visualized one hundred thirty gene expression omnibus (GEO) dataset using Oncomine (Invitrogen) and Georgetown Database of Cancer (G-DOC). This analysis showed that four different members Ly6D, Ly6E, Ly6H or Ly6K have increased gene expressed in bladder, brain and CNS, breast, colorectal, cervical, ovarian, lung, head and neck, pancreatic and prostate cancer than their normal counter part tissues. Increased expression of Ly6D, Ly6E, Ly6H or Ly6K was observed in sub-set of cancer type. The increased expression of Ly6D, Ly6E, Ly6H and Ly6K was found to be associated with poor outcome in ovarian, colorectal, gastric, breast, lung, bladder or brain and CNS as observed by KM plotter and PROGgeneV2 platform. The remarkable findings of increased expression of Ly6 family members and its positive correlation with poor outcome on patient survival in multiple cancer type indicate that Ly6 family members Ly6D, Ly6E, Ly6K and Ly6H will be an important targets in clinical practice as marker of poor prognosis and for developing novel therapeutics in multiple cancer type.

Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors

Conditionally reprogrammed cells (CRCs) are epithelial cells that are directly isolated from patients' specimens and propagated in vitro with feeder cells and a Rho kinase inhibitor. A number of these cells have been generated from biopsies of breast cancer patients, including ductal carcinoma in situ and invasive carcinomas. The characterization of their genomic signatures is essential to determine their ability to reflect the natural biology of their tumors of origin. In this study, we performed the genomic characterization of six newly established invasive breast cancer CRC cultures in comparison to the original patients' primary breast tumors (PBT) from which they derived. The CRCs and corresponding PBTs were simultaneously profiled by genome-wide array-CGH, targeted next generation sequencing and global miRNA expression to determine their molecular similarities in the patterns of copy number alterations (CNAs), gene mutations and miRNA expression levels, respectively. The CRCs' epithelial cells content and ploidy levels were also evaluated by flow cytometry. A similar level of CNAs was observed in the pairs of CRCs/PBTs analyzed by array-CGH, with >95% of overlap for the most frequently affected cytobands. Consistently, targeted next generation sequencing analysis showed the retention of specific somatic variants in the CRCs as present in their original PBTs. Global miRNA profiling closely clustered the CRCs with their PBTs (Pearson Correlation, ANOVA paired test, P<0.05), indicating also similarity at the miRNA expression level; the retention of tumor-specific alterations in a subset of miRNAs in the CRCs was further confirmed by qRT-PCR. These data demonstrated that the human breast cancer CRCs of this study maintained at early passages the overall copy number, gene mutations and miRNA expression patterns of their original tumors. The further characterization of these cells by other molecular and cellular phenotypes at late cell passages, are required to further expand their use as a unique and representative ex-vivo tumor model for basic science and translational breast cancer studies.

Abstract 2585: viGEN: An open source bioinformatics pipeline for viral RNA detection and quantification in human tumor samples

We present a novel pipeline for viral RNA detection and quantification in human RNA-seq data. Our pipeline has been tested on the TCGA liver cancer cohort, can not only detect the presence of a viral species, but also provide gene level read counts for individual viral species and extract viral-variants.

Introduction Approximately 20% of human cancer types are associated with viral infection that is routinely detected in blood samples. However the extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using existing Human RNA-seq data from tumor samples. We have developed a bioinformatics pipeline viGEN combining existing and novel RNAseq tools that allows for detection and quantification of viral RNA in human RNAseq data.

Methods The pipeline includes 4 major modules: The first module allows to align and filter out human RNA sequences; second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module calculates quantitate read counts at the individual viral genes level thus allowing for downstream differential expression analysis of viral genes between experimental and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge there are no publicly available pipelines or packages that would provide this type of complete analysis in one package. Customized solutions have been reported in the literature however were not made public.

Results We used this pipeline to examine viruses present in RNA-seq data from 75 liver cancer patients in the TCGA data collection. Our pipeline allows conducting quantitative analysis at the gene level for visualization and detection of statistically significant differentially expressed viral genes between groups of patients known to be infected with both HBV and various subtypes of HCV. Once the viral genomes are detected at the genome level, we examine the differences between “Dead” and “Alive” samples at the viral-transcript level, and at the viral-variant level.

Conclusion Our results show that it is possible to detect viral sequences from whole-transcriptome (RNA-seq) data in humans. We were able to not only quantify them at a viral-gene/CDS level, but also extract variants from the 75-sample dataset from TCGA. The results presented here are in correspondence with published literature and are a proof of concept of our pipeline. This pipeline can be used on cancer and non-cancer human RNA-seq or other NGS data to provide additional insights into the biological significance of viral infection in complex diseases, tumorigeneses and cancer immunology.

Citation Format: Krithika Bhuvaneshwar, Lei Song, Yuriy Gusev. viGEN: An open source bioinformatics pipeline for viral RNA detection and quantification in human tumor samples [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 2585. doi:10.1158/1538-7445.AM2017-2585

Abstract 3568: Variant analysis of LY6 genes in TCGA ovarian cancer

Background Human Ly6 gene family has been associated with stem cell marker Sca-1 in murine cancer. Sca-1 is known to regulate TGF-b signaling, Wnt signaling & it is important in cancer progression and metastasis in mouse models. Human Ly6 genes are associated with poor clinical outcome in human cancers. Previous studies have shown that this family of genes is highly expressed in Ovarian & Breast cancer compared to normal tissues. Overexpression of these genes was found to be correlated with poor outcome in overall and metastasis free survival. Recent studies have also shown that human Ly6 genes are associated with tumor immune escape & drug resistance. In this poster, we explore the variants in Ly6 and related genes in the TCGA Ovarian Cancer (OV) data collection.

Materials and Methods We first downloaded RNA-seq data of primary tumor tissues from 21 TCGA OV patients from CGHUB (https://cghub.ucsc.edu/), and after quality control, aligned to human reference genome using tool RSEM on the Globus Genomics platform. The BAM file was sorted and PCR duplicates were removed. Variant calling was done on BAM files based on Genome Analysis Toolkit (GATK)’s best practices, to obtain a multi sample variant call file (VCF). After getting the multi sample VCF file, we used SnpEff and Annovar software to annotate and predict the functional effects of variants on genes. SnpSift toolbox was used to filter out variants by extracting only variant of Ly6 genes (and other genes of interest) that passed the quality check, and categorized the output into 4 different groups according to the impact (High, Moderate, Modifier, Low). To see if these variants were germline or somatic, DNA-seq from a second set of 22 TCGA Ovarian cancer samples (tumor tissue and normal blood samples) were used. BAM files were downloaded and variants were called using the Seven Bridges system. The same filtering steps were applied as above.

Results In Set 1, we found variants in CD59, LY6E and LYPD6 mutated in all the 21 cases. We found two stop-loss mutations in CD59 gene, which is responsible for regulating the immune response, tumor cell growth and apoptosis. We found a total of 3794 unique variants short-listed in Set 1, and a total of 8879 unique variants short-listed in Set 2. It was expected to see more variants from the DNA-seq data compared to the RNA-seq data. Among these, 103 unique variants were common to both Set 1 and Set 2. Variants in ESR1, CD44 and LYPD6 family were mutated in most samples in both Set 1 and Set 2. We also performed survival analysis on variants present in RNA but not in DNA, and found variants in LY6E, PINLYP, LYPD5, ZNF283 significant w.r.t overall survival.

Conclusion We found a total of 3794 unique variants (from short-listed set) in Set 1 (TCGA OV RNAseq data), and a total of 8879 unique variants (from short-listed set) in Set 2 (TCGA OV DNAseq). There were total of 103 unique variants common to Set 1 and Set 2. We see evidence of LY6 variants in non-coding regions of RNA (not in DNA) to be significantly associated with overall survival.

Citation Format: Krithika Bhuvaneshwar, Midrar Al Hossiny, Yuriy Gusev, Subha Madhavan, Geeta Upadhyay. Variant analysis of LY6 genes in TCGA ovarian cancer [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 3568. doi:10.1158/1538-7445.AM2017-3568

Abstract 548: RNAseq analysis of infiltrating immune cells in liver cancer

Hepatocellular carcinoma (HCC) has emerged as second most common cause of cancer deaths worldwide. During the last 10 years, there has been a clear delineation of landscape of genetic alterations in HCC and deregulated pathways in HCC. However, the treatment for patients with advanced HCC is limited despite of great effort developing therapeutic targeting the deregulated pathways in HCC. Recent studies reveal a direct causal relationship between cancer & immune dysfunction, whereby tumor cells and their microenvironment are able to evade immune attack by exploiting various immunoregulatory mechanisms in a process termed cancer immune editing.

Methods In this poster, the objective is to perform exploratory analysis of TCGA liver cancer data to see if immune infiltrates matter, and if they offer anti-tumor immunity to a cell. For this purpose, we analyzed RNA-seq data for a cohort of 75 liver cancer samples from TCGA collection. We obtained the gene expression data from a pre-selected group of specific markers for infiltrating lymphocytes (several subtypes), and explored the association of expression of these markers with clinical outcome.We downloaded raw RNA-seq data from the TCGA Liver cancer collection from 75 patients. These included 25 patients who had Hepatitis B virus (HBV), 25 patients who had Hepatitis C virus (HCV) and 25 patients who had both viruses. After processing of raw data, we extracted isoform expression (TPM values) from specific markers for infiltrating lymphocytes. This data was stratified into ‘high’ and ‘low’ expression based on median cutoff.We compared the ‘high’ and ‘low’ expression groups of patients by performing differential expression & pathway analysis, to see if the differentially expressed results were linked to immune pathways. We then performed survival analysis tests (Log rank, Cox regression) and Kaplan Meier (KM) survival graphs to explore the association with overall survival outcome.

Results We found 14 of 75 HCC cases expressed CD8B isoform, while 61 of 75 HCC cases did not express CD8B isoform. The Log Rank survival test showed a significant association between the expression of CD8B isoform and overall survival (Chisq= 5.2 on 1 degrees of freedom, p= 0.0222). The survival test using a Cox model on the same CDBB isoform, showed that samples that expressed CD8B isoform were at higher risk of event compared to those that did not express the isoform. Other markers that showed good separation of survival curves included CD3 & CD8A.

Conclusion Additional immune cell subtype specific transcripts are being tested. Based on our preliminary analysis, we saw that most of the affected pathways were highly relevant to lymphocyte signaling & immune response and infiltration. Hence, exploring infiltrating lymphocytes can give evidence of immune surveillance against HCC. Testing immune cell specific transcript in tumor samples may service as predictor to treatment targeting immune evasion in cancer patients.

Citation Format: Krithika Bhuvaneshwar, Coleman I. Smith, Alexander H. Kroemer, Aiwu Ruth He, Yuriy Gusev. RNAseq analysis of infiltrating immune cells in liver cancer [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 548. doi:10.1158/1538-7445.AM2017-548

Abstract 2604: The Georgetown Database of Cancer (G-DOC): A web-based data sharing platform for precision medicine

Introduction An overarching goal of biomedical research is to improve the use and dissemination of rapidly growing biomedical datasets to support precision medicine. Individualized molecular profiling and the identification of predictive biomarkers can powerfully inform the choice of therapies for cancer patients. However, both require integration of extensive molecular, clinical, and pharmacological data, often from disparate and diverse sources. The Georgetown Database of Cancer (G-DOC) was designed and engineered to be a unique multi-omics data analysis platform to enable translational research and precision medicine.

Methods G-DOC is home to 61 datasets that contain data from over 10,000 patients across 14 diseases (10 cancers and 4 non-cancers). 1700+ researchers from over 48 different countries worldwide currently use the platform. The data and tools in the G-DOC system have enabled over 40 research publications. G-DOC has the largest public collection of brain cancer patients from NCI Rembrandt dataset (671 patients).G-DOC integrates clinical, transcriptomic, metabolomic, microRNA, next generation sequencing (NGS) data, and MRI medical images with systems-level analysis tools into a single, user-friendly platform. The “Variant Search” feature in G-DOC currently enables exploratory analysis of mutations based on genes, chromosomes, and functional location. A researcher can use this feature to 1) identify clinically actionable mutations in their dataset 2) identify pathways that may be affected by these mutations, and 3) identify novel mutations in their dataset and explore their potential impact on protein function.

Results and Conclusion We are currently working on developing features to support the import, integration, search, and retrieval of CLIA/CAP-certified cancer molecular diagnostic (molDx) data. This will enhance G-DOC’s interoperability with clinical and patient molecular profiling data that may be already stored in other databases. Our vision is to continuously improve and expand G-DOC with the long-term vision of supporting integration of informatics techniques into everyday research and practice.

Citation Format: Krithika Bhuvaneshwar, Anas Belouali, Shruti Rao, Adil Alaoui, Yuriy Gusev, Robert Clarke, Louis M. Weiner, Subha Madhavan. The Georgetown Database of Cancer (G-DOC): A web-based data sharing platform for precision medicine [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 2604. doi:10.1158/1538-7445.AM2017-2604

Abstract 3431: The oncogenic role of miR-150-5p in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that confers disease recurrence, treatment resistance and high mortality rates. MicroRNAs are a class of noncoding RNAs, that when dysregulated, impact tumorigenesis through the control of the expression of multiple mRNA targets involved in critical cancer signaling pathways. MiR-150-5p has been shown to control the expression of several driver oncogenes and/or tumor suppressor genes involved in these critical pathways. Its pattern of expression varies according to the cancer type; it has been observed mostly downregulated in hematological diseases and GI cancers, and upregulated in hormonal dependent cancers, such as prostate and breast cancer. The main objective of this study was to assess the patterns of expression of miR-150-5p in TNBC and determine its functional role in affecting the tumor phenotype. Archived paraffin samples of 113 patients with ductal breast carcinoma (56 of the TNBC and 57 of the non-TNBC subtype) and 49 adjacent normal tissue (ANT), obtained from the the pathology tumor bank of Lombardi Comprehensive Cancer Center, Washington DC, were profiled for miRNA using the wide-genome Nanostring platform and a Taqman specific miRNA-150-5p assay. Significant overexpression levels of miRNA-150-5p were observed in the tumor tissues when compared to the ANT and in the TNBC cases when compared to the non-TNBC cases, demonstrating its tumor and TNBC subtype specificity, respectively. Overexpressed levels of miRNA-150-5p were also preferentially observed in the TNBC cases from patients that presented with LN metastasis and breast cancer recurrence, indicating its association with poor prognosis. Interestingly, the TNBC of African-American patients, which is the ethnic group mostly affected by this cancer subtype, presented overexpression levels of this miRNA when compared to the Non-Hispanic White patients. Functional analysis performed in the TNBC cell lines, MDA-MB-231 and HCC1806, showed after transfection with miR-150-5p inhibitor, reduced levels on cell proliferation, clonogenicity, migration, drug resistance and expression of the EMT promoter markers, SLUG and SNAIL. These findings, indicate an oncogenic type of action of miRNA-150-5p in TNBC. In summary, miRNA-150-5p is upregulated in TNBC clinical cases in association with poor prognostic parameters and its functional inhibition, directly confers to the cells a reduction of their tumorigenic phenotype.

Funding: This project was supported by the Georgetown University Center of Excellence in Regulatory Science and Innovation (CERSI U01FD004319), a collaborative effort between the university and the U.S. Food and Drug Administration to promote regulatory science through innovative research and education. This research does not necessarily reflect the views of the FDA. Scholarship to B.S. was provided by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).

Citation Format: Bruna M. Sugita, Yara Zabala, Aline Fonseca, Rodrigo Almeida, Yuriy Gusev, Simina Boca, Iglenir J. Cavalli, Enilze M. Ribeiro, Luciane R. Cavalli. The oncogenic role of miR-150-5p in triple-negative breast cancer [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 3431. doi:10.1158/1538-7445.AM2017-3431

EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer

About 70% of all breast cancers are estrogen receptor alpha positive (ER+; ESR1). Many are treated with antiestrogens. Unfortunately, de novo and acquired resistance to antiestrogens is common but the underlying mechanisms remain unclear. Since growth of cancer cells is dependent on adequate energy and metabolites, the metabolomic profile of endocrine resistant breast cancers likely contains features that are deterministic of cell fate. Thus, we integrated data from metabolomic and transcriptomic analyses of ER+ MCF7-derived breast cancer cells that are antiestrogen sensitive (LCC1) or resistant (LCC9) that resulted in a gene-metabolite network associated with EGR1 (early growth response 1). In human ER+ breast tumors treated with endocrine therapy, higher EGR1 expression was associated with a more favorable prognosis. Mechanistic studies showed that knockdown of EGR1 inhibited cell growth in both cells and EGR1 overexpression did not affect antiestrogen sensitivity. Comparing metabolite profiles in LCC9 cells following perturbation of EGR1 showed interruption of lipid metabolism. Tolfenamic acid, an anti-inflammatory drug, decreased EGR1 protein levels and synergized with antiestrogens in inhibiting cell proliferation in LCC9 cells. Collectively, these findings indicate that EGR1 is an important regulator of breast cancer cell metabolism and is a promising target to prevent or reverse endocrine resistance.

Immune cell surface proteins from tumor samples to predict patient clinical outcome

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Background: The incidence and mortality of Hepatocellular carcinoma (HCC) are rapidly increasing in the US. Treatments for advanced HCC are limited despite best efforts to develop therapeutics that target the deregulated pathways of HCC. Recent studies reveal a direct causal relationship between cancer and immune dysfunction, whereby tumor cells and their microenvironment can evade immune attack by exploiting various immunoregulatory mechanisms in a process termed “cancer immune editing”. The objective is to determine the relationship between immune cell surface protein transcripts from tumor samples and the clinical outcome of pts by performing exploratory analyses of liver cancer data from the cancer genome atlas (TCGA). Methods: We analyzed RNAseq data from a cohort of 75 HCC samples in the TCGA collection. We explored the association of expression of a group of specific markers for infiltrating lymphocytes (several subtypes) with overall survival (OS) and these results were confirmed by IHC analysis of the same cell subtypes in HCC samples from patients at GUH. Results: Among the 75 HCC cases analyzed, 25 pts had Hepatitis C (HCV), 25 had Hepatitis B (HBV), and 25 had HCV and HBV co-infection. Fourteen of the 75 cases were found to express the CD8B isoform. The LOG RANK survival test showed a significant association between CD8B levels and OS (ChiSq = 5.2, 1df; p = 0.0222), as did the Cox proportional hazard model for survival. The latter test showed that pts with HCC that did not express CD8B were at a higher risk of death compared with those who had CD8B-expressing HCC. Additional immune cell subtype specific transcripts are being tested. Based on analysis of differentially expressed gene differences between immune cell subtype ‘low’ vs. ‘high’ groups, pathways highly relevant to lymphocyte signaling and immune response and infiltration were identified. Thus, 5 tumor-infiltrating immune cell subtypes were found to have wide variability among patients. Using IHC, these cell subtypes were assessed in HCC samples from patients and correlated to clinical outcome. Conclusions: Immune cell specific transcripts in tumor samples may serve as a predictor of response to treatments that target immune evasion in cancer patients.

Transcripts of immune cell surface proteins from tumor samples to predict patient clinical outcome

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Background: Hepatocellular carcinoma (HCC) is the second most common cause of cancer death worldwide, and its incidence and mortality are rapidly increasing in the US. Treatments for advanced HCC are limited despite best efforts to develop therapeutics that target the deregulated pathways of HCC. Recent studies reveal a direct causal relationship between cancer and immune dysfunction, whereby tumor cells and their microenvironment can evade immune attack by exploiting various immunoregulatory mechanisms in a process termed cancer immune editing. This study objective is to determine the relationship between immune cell surface protein transcripts from tumor samples and the clinical outcome of pts by performing exploratory analyses of liver cancer data from the cancer genome atlas (TCGA). Methods: We analyzed RNAseq data from a cohort of 75 HCC samples in the TCGA collection. We explored the association of expression of a group of specific markers for infiltrating lymphocytes (several subtypes) with overall survival (OS) and tumor immune infiltrates (IHC data). Results: Among the 75 HCC cases analyzed, 25 pts had Hepatitis C (HCV), 25 had Hepatitis B (HBV), and 25 had HCV and HBV co-infection. Fourteen of the 75 cases were found to express the CD8B isoform. The LOG RANK survival test showed a significant association between CD8B level and OS (ChiSq = 5.2, 1df; p= 0.0222), as did the Cox proportional hazard model for survival. The latter test showed that pts who’s HCC did not express the CD8B were at higher risk of death compared with those who did. Additional immune cell subtype specific transcripts are being tested. Based on analysis of differentially expressed genes between immune cell subtype "Low" and vs. "High" groups, pathways highly relevant to lymphocyte signaling and immune response and infiltration are identified. Conclusions: Immune cell specific transcripts in tumor samples may serve as a predictor of response to treatments that target immune evasion in cancer pts.

G-DOC Plus - an integrative bioinformatics platform for precision medicine

BACKGROUND

G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information.

RESULTS

G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability.

CONCLUSION

G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available at: https://gdoc.georgetown.edu .

Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance

Stem cell antigen Sca-1 is implicated in murine cancer stem cell biology and breast cancer models, but the role of its human homologs Ly6K and Ly6E in breast cancer are not established. Here we report increased expression of Ly6K/E in human breast cancer specimens correlates with poor overall survival, with an additional specific role for Ly6E in poor therapeutic outcomes. Increased expression of Ly6K/E also correlated with increased expression of the immune checkpoint molecules PDL1 and CTLA4, increased tumor-infiltrating T regulatory cells, and decreased natural killer (NK) cell activation. Mechanistically, Ly6K/E was required for TGFβ signaling and proliferation in breast cancer cells, where they contributed to phosphorylation of Smad1/5 and Smad2/3. Furthermore, Ly6K/E promoted cytokine-induced PDL1 expression and activation and binding of NK cells to cancer cells. Finally, we found that Ly6K/E promoted drug resistance and facilitated immune escape in this setting. Overall, our results establish a pivotal role for a Ly6K/E signaling axis involving TGFβ in breast cancer pathophysiology and drug response, and highlight this signaling axis as a compelling realm for therapeutic invention. Cancer Res; 76(11); 3376-86. ©2016 AACR.

MicroRNA analysis of breast ductal fluid in breast cancer patients

Recent studies suggest that microRNAs show promise as excellent biomarkers for breast cancer; however there is still a high degree of variability between studies making the findings difficult to interpret. In addition to blood, ductal lavage (DL) and nipple aspirate fluids represent an excellent opportunity for biomarker detection because they can be obtained in a less invasive manner than biopsies and circumvent the limitations of evaluating blood biomarkers with regards to tissue of origin specificity. In this study, we have investigated for the first time, through a real-time PCR array, the expression of 742 miRNAs in the ductal lavage fluid collected from 22 women with unilateral breast tumors. We identified 17 differentially expressed miRNAs between tumor and paired normal samples from patients with ductal breast carcinoma. Most of these miRNAs have various roles in breast cancer tumorigenesis, invasion and metastasis, therapeutic response, or are associated with several clinical and pathological characteristics of breast tumors. Moreover, some miRNAs were also detected in other biological fluids of breast cancer patients such as serum (miR-23b, -133b, -181a, 338-3p, -625), plasma (miR-200a), and breast milk (miR-181a). A systems biology analysis of these differentially expressed miRNAs points out possible pathways and cellular processes previously described as having an important role in breast cancer such as Wnt, ErbB, MAPK, TGF-β, mTOR, PI3K-Akt, p53 signaling pathways. We also observed a difference in the miRNA expression with respect to the histological type of the tumors. In conclusion, our findings suggest that miRNA analysis of breast ductal fluid is feasible and potentially very useful for the detection of breast cancer.

Abstract B1-44: G-DOC Plus: A cloud based next-generation systems medicine platform for precision medicine

Systems medicine leverages complex computational tools and high dimensional data offering the potential for effective individualized diagnosis, prognosis and treatment options. Our flagship web platform, the Georgetown Database of Cancer (G-DOC), was deployed with the goal of enabling translational research by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. With the goal of improving health outcomes through genomics research, we present G-DOC Plus, our enhanced web platform offering precision medicine, translational research and population genetics workflows. This enhanced platform takes advantage of cloud computing to handle next generation sequencing (NGS) data so that they can be analyzed in the full context of other omics and clinical information.

G-DOC Plus uses cloud computing and other advanced computational tools to enable analysis of NGS and medical images in the full context of other omics and clinical information. It allows translational science researchers to explore data one sample at a time, as a sub-cohort of samples; or as a population as a whole, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer to support detection of prognostic markers for relapse in colorectal cancer samples, and to detect key metabolites related to disease severity; hypothesis generation; biomarker detection and multi-omic analysis, in-silico and population genetics analysis; and to explore somatic mutation and breast cancer MRI images. The long-term vision of G-DOC Plus is to extend this systems medicine platform to hospital networks to provide clinical decision support using multi-omics and relevant clinical information to support personalized patient care. G-DOC Plus was released in October 2014, and is available at: https://gdoc.georgetown.edu.

Citation Format: Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M. Johnson, Lei Song, Adil Alaoui, Michael Harris, Yuriy Gusev, Robert Clarke, Subha Madhavan. G-DOC Plus: A cloud based next-generation systems medicine platform for precision medicine. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-44.

Abstract B1-23: Early growth response (EGR1) is a critical regulator of cellular metabolism and predicts increased responsiveness to antiestrogens in breast cancer

Breast cancer is the most commonly diagnosed cancer in women and about 1 million new cases per year are diagnosed worldwide. About 70% of all breast cancers are estrogen receptor alpha positive (ER+). Antiestrogens (e.g., Tamoxifen or Faslodex) or aromatase inhibitors (e.g., Letrozole) are often used to treat ER+ breast cancers. However, resistance to these therapies (endocrine resistance) is prevalent in the clinic and the underlying mechanisms remain unclear. We have recently shown that the oncogene MYC is overexpressed in ER+ breast cancer and up-regulates glucose and glutamine uptake in endocrine resistant breast cancer cells, which suggests that the metabolomic profile of endocrine resistant breast cancer cells may contain features that are distinct from sensitive cells. In this study, to identify the biochemical pathways that are differentially regulated in endocrine resistance in breast cancer cells, we have analyzed gene expression data and untargeted metabolite profiles of ER+ MCF7-derived breast cancer cells that are antiestrogen sensitive (LCC1) or antiestrogen resistant (LCC9) under basal conditions. Glycolysis and glutamine-dependent pathways were increased in endocrine resistant cells. Integration of the transcriptomics and metabolomics data predicted an essential role for a gene-metabolite network associated with early growth response (EGR1) and glutamine metabolism in endocrine resistant cells. EGR1 is an immediate-early gene induced by E2, growth factors, or stress signals, and has been reported to exhibit both tumor suppressor and promoter activities, based on cellular context. While EGR1 mediated signaling is important for the normal development of female reproductive organs, its precise role in breast cancer remains unknown. EGR1 gene expression and protein levels were significantly higher in LCC1 cells compared with LCC9 cells. Kaplan-Meier survival curves with gene expression data obtained from ER+ human breast tumors treated with endocrine therapy show that higher EGR1 expression is associated with a more favorable prognosis: GSE17705 [HR=0.38 (0.21-0.69); p=0.00083], GSE6532 (ER+ samples on GPL96 platform) [HR=0.55 (0.34-0.9); p=0.017]. In GSE20181, pre-treatment vs 90 days post-treatment comparisons show significantly increased levels of EGR1 expression (p&lt;0.0001) only in the responder group. Interestingly, in both LCC1 and LCC9 cells, EGR1 overexpression increased ER protein levels and cell proliferation while EGR1 knockdown decreased ER protein levels and cell proliferation. Therefore, to understand the precise role of down-regulated EGR1 in regulating cellular metabolism and survival in endocrine resistance, we compared metabolite profiles in LCC9 cells following knockdown or overexpression of EGR1. Several major biochemical pathways such as glycolysis, lipid metabolism, glutathione, and polyamine metabolism were shown to be regulated by EGR1 in LCC9 cells. Collectively, these findings indicate that down-regulated EGR1 is an important regulator of the aberrant cellular metabolic pathways specific to endocrine resistance. Furthermore, high levels of EGR1 may serve as a favorable prognostic marker in endocrine treatment strategies in breast cancer.

Citation Format: Ayesha N. Shajahan-Haq, Lu Jin, Amrita K. Cheema, Simina M. Boca, Yuriy Gusev, Krithika Bhuvaneshwar, Diane M. Demas, Habtom Ressom, Ryan Michalek, Xi Chen, Jianhua Xuan, Subha Madhavan, Robert Clarke. Early growth response (EGR1) is a critical regulator of cellular metabolism and predicts increased responsiveness to antiestrogens in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-23.

ERRγ target genes are poor prognostic factors in Tamoxifen-treated breast cancer

Background

One-third of estrogen (ER+) and/or progesterone receptor-positive (PGR+) breast tumors treated with Tamoxifen (TAM) do not respond to initial treatment, and the remaining 70% are at risk to relapse in the future. Estrogen-related receptor gamma (ESRRG, ERRγ) is an orphan nuclear receptor with broad, structural similarities to classical ER that is widely implicated in the transcriptional regulation of energy homeostasis. We have previously demonstrated that ERRγ induces resistance to TAM in ER+ breast cancer models, and that the receptor’s transcriptional activity is modified by activation of the ERK/MAPK pathway. We hypothesize that hyper-activation or over-expression of ERRγ induces a pro-survival transcriptional program that impairs the ability of TAM to inhibit the growth of ER+ breast cancer. The goal of the present study is to determine whether ERRγ target genes are associated with reduced distant metastasis-free survival (DMFS) in ER+ breast cancer treated with TAM.

Methods

Raw gene expression data was obtained from 3 publicly available breast cancer clinical studies of women with ER+ breast cancer who received TAM as their sole endocrine therapy. ERRγ target genes were selected from 2 studies that published validated chromatin immunoprecipitation (ChIP) analyses of ERRγ promoter occupancy. Kaplan-Meier estimation was used to determine the association of ERRγ target genes with DMFS, and selected genes were validated in ER+, MCF7 breast cancer cells that express exogenous ERRγ.

Results

Thirty-seven validated receptor target genes were statistically significantly altered in women who experienced a DM within 5 years, and could classify several independent studies into poor vs. good DMFS. Two genes (EEF1A2 and PPIF) could similarly separate ER+, TAM-treated breast tumors by DMFS, and their protein levels were measured in an ER+ breast cancer cell line model with exogenous ERRγ. Finally, expression of ERRγ and these two target genes are elevated in models of ER+ breast cancer with hyperactivation of ERK/MAPK.

Conclusions

ERRγ signaling is associated with poor DMFS in ER+, TAM-treated breast cancer, and ESRRG, EEF1A2, and PPIF comprise a 3-gene signaling node that may contribute to TAM resistance in the context of an active ERK/MAPK pathway.

βII-Spectrin (SPTBN1) suppresses progression of hepatocellular carcinoma and Wnt signaling by regulation of Wnt inhibitor kallistatin

βII-Spectrin (SPTBN1) is an adapter protein for Smad3/Smad4 complex formation during transforming growth factor beta (TGF-β) signal transduction. Forty percent of SPTBN1(+/-) mice spontaneously develop hepatocellular carcinoma (HCC), and most cases of human HCC have significant reductions in SPTBN1 expression. In this study, we investigated the possible mechanisms by which loss of SPTBN1 may contribute to tumorigenesis. Livers of SPTBN1(+/-) mice, compared to wild-type mouse livers, display a significant increase in epithelial cell adhesion molecule-positive (EpCAM(+)) cells and overall EpCAM expression. Inhibition of SPTBN1 in human HCC cell lines increased the expression of stem cell markers EpCAM, Claudin7, and Oct4, as well as decreased E-cadherin expression and increased expression of vimentin and c-Myc, suggesting reversion of these cells to a less differentiated state. HCC cells with decreased SPTBN1 also demonstrate increased sphere formation, xenograft tumor development, and invasion. Here we investigate possible mechanisms by which SPTBN1 may influence the stem cell traits and aggressive behavior of HCC cell lines. We found that HCC cells with decreased SPTBN1 express much less of the Wnt inhibitor kallistatin and exhibit decreased β-catenin phosphorylation and increased β-catenin nuclear localization, indicating Wnt signaling activation. Restoration of kallistatin expression in these cells reversed the observed Wnt activation.

CONCLUSION

SPTBN1 expression in human HCC tissues is positively correlated with E-cadherin and kallistatin levels, and decreased SPTBN1 and kallistatin gene expression is associated with decreased relapse-free survival. Our data suggest that loss of SPTBN1 activates Wnt signaling, which promotes acquisition of stem cell-like features, and ultimately contributes to malignant tumor progression.

A high density of tumor infiltrating CD3 and CD8 cells to predict recurrence free survival in patient with hepatocellular carcinoma

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Background: The ability to define risk of hepatocellular carcinoma (HCC) recurrence after resection could improve the clinical management of patients. The pathological factors currently indicative of tumor invasiveness, such as vascular invasion, elevated AFP and advanced pTNM stage, are the established risk factors for recurrence. It has been suggested that immune cells that infiltrate a tumor are a prognostic factor in predicting patient outcome. In this study, the prognostic significance of tumor immune infiltration, as defined by the Immunoscore methodology, was assessed in patients with HCC. Methods: The influence of immune infiltration on clinical outcome was evaluated in patients who had undergone resection of HCC. The density of intratumoral immune infiltrates were measured in the center of the tumor (CT) and in the invasive margin (IM) of 45 stage I to IV HCC tissue specimens from a single cohort. The density of total (CD3+) and cytotoxic (CD8+) T lymphocytes in the CT and IM were obtained by immunohistochemistry and quantified using a Nuance FX Multiplex Biomarker Imaging system in tandem with ImageJ image processing software. Immune cell density in the CT and IM was converted to a binary score (0 as Low, 1 as High), with a cutoff threshold determined by the median density of CD3+ and CD8+ cells (273 cells/mm² and 217.5 cells/mm², respectively). The Immunoscore values were correlated with tumor recurrence and recurrence-free survival. Results: High densities of both CD3+ and CD8+ T lymphocytes in the CT and IM, along with a corresponding Immunoscore of 3+ (on a scale from 0 to 4), were significantly correlated with a low rate of recurrence (p-value = 0.0004). High densities of CD3+ lymphocytes alone were correlated with a prolonged recurrence-free survival (p-value = 0.0005). High densities of CD8+ lymphocytes alone were also correlated with a prolonged recurrence-free survival (p-value = 0.0031). Conclusions: The Immunoscore is a useful prognostic marker in patients with HCC who have received primary tumor resection. To better characterize the immune landscape of HCC tumors, the correlation between the Immunoscore and additional immune biomarkers are being evaluated.

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the "Globus Genomics" system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

Abstract 1545: Identification of microRNA targets in triple-negative breast cancer

Introduction: Triple negative breast cancers (TNBC) are clinically aggressive tumors that lack the expression of ER, PR and HER2 receptors, and therefore do not respond effectively to the available target therapies. The study of the molecular alterations that are present in these tumors can lead to the identification of potential therapeutic targets that can improve patient's outcome. MicroRNAs (miRNAs) are short non-coding sequences that play a role in breast tumorigenesis regulating the expression of cancer-associated genes. In the present study, we investigated miRNAs expression profile in TNBC and non-TNBC tumors and integrated the data with DNA copy number changes (array-CGH) obtained from the same samples, to obtain the most relevant miRNA targets that may be involved in the pathogenesis of TNBC.

Methods: Formalin-fixed paraffin-embedded samples from 43 TNBC and 16 non-TNBC cases were profiled for miRNA using the Nanostring system. Significant differentially expressed miRNAs (with at least 2 fold differences and p≤0.05) between the lesions were calculated by the comparative Ct method (ΔΔCt). DNA copy number analysis from the same samples was performed using an Agilent array-CGH platform. The miRNA data was directly integrated with the array-CGH data from the same cases. Combinatorial target predicted algorithms in conjunction with functional and pathway annotation enrichment systems (Ingenuity Pathway, Pathway Studio) were performed to identify predicted target functions.

Results: The miRNA profiling revealed 89 miRNAs significant differentially expressed between the TNBC and non-TNBC lesions. Using miRBase and MiRDB target prediction databases we identified 3,378 target genes of upregulated miRNAs and 823 for downregulated miRNAs. A number of 15 miRNAs (out of the 89) presented concomintant genomic gains or losses and miRNA increase or decrease expression, respectively. This direct integration of the data reduced the number of miRNA targets to 1,242. Ingenuity pathway analysis on these predicted targets function, identified canonical pathways, including p53, IL-8 and Rac signaling. Gene expression profiling analysis is underway to confirm the regulatory effect of the selected miRNAs on the targets identified.

Conclusions: We have observed significant differentially expressed miRNAs in the analysis of TNBC cases in comparison with non-TNBC cases. The integration analysis with DNA copy number data let us to select the miRNAs with concomitant changes in copy number and gene expression and predicted target algorithms identified key pathways that may be related to the TNBC phenotype. The functional validation of these targets, by in vitro and in vivo experimental models, through the assessment of miRNA-mRNA interaction and/or modulation of miRNA expression will allow us to identify the most relevant miRNAs that are mechanistically involved in the pathogenesis of TNBC.

Note: This abstract was not presented at the meeting.

Citation Format: Mandeep Gill, Bruna Sugita, Silma R. Pereira, Catalin Marian, Xi Li, Yuriy Gusev, Enilze MSF Ribeiro, Iglenir J. Cavalli, Luciane R. Cavalli. Identification of microRNA targets in triple-negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1545. doi:10.1158/1538-7445.AM2014-1545

Transcriptional regulation of STAT3 by SPTBN1 and SMAD3 in HCC through cAMP-response element-binding proteins ATF3 and CREB2

The cytoskeletal protein Spectrin, beta, non-erythrocytic 1 (SPTBN1), an adapter protein to SMAD3 in TGF-β signaling, may prevent hepatocellular carcinoma (HCC) development by downregulating the expression of signal transducer and activator of transcription 3 (STAT3). To elucidate the as yet undefined mechanisms that regulate this process, we demonstrate that higher levels of STAT3 transcription are found in livers of heterozygous SPTBN1(+/-) mice as compared to that of wild type mice. We also found increased levels of STAT3 mRNA, STAT3 protein, and p-STAT3 in human HCC cell-lines after knockdown of SPTBN1 or SMAD3, which promoted cell colony formation. Inhibition of STAT3 overrode the increase in cell colony formation due to knockdown of SPTBN1 or SMAD3. We also found that inhibition of SPTBN1 or SMAD3 upregulated STAT3 promoter activity in HCC cell-lines, which is dependent upon the cAMP-response element (CRE) and STAT-binding element (SBE) sites of the STAT3 promoter. Mechanistically, suppression of SPTBN1 and SMAD3 augmented the transcription of STAT3 by upregulating the CRE-binding proteins ATF3 and CREB2 and augmented the binding of those proteins to the regions within or upstream of the CRE site of the STAT3 promoter. Finally, in human HCC tissues, SPTBN1 expression correlated negatively with expression levels of STAT3, ATF3, and CREB2; SMAD3 expression correlated negatively with STAT3 expression; and the level of phosphorylated SMAD3 (p-SMAD3) correlated negatively with ATF3 and CREB2 protein levels. SPTBN1 and SMAD3 collaborate with CRE-binding transcription factors to inhibit STAT3, thereby preventing HCC development.

Increased copy number of the DLX4 homeobox gene in breast axillary lymph node metastasis

DLX4 is a homeobox gene strongly implicated in breast tumor progression and invasion. Our main objective was to determine the DLX4 copy number status in sentinel lymph node (SLN) metastasis to assess its involvement in the initial stages of the axillary metastatic process. A total of 37 paired samples of SLN metastasis and primary breast tumors (PBT) were evaluated by fluorescence in situ hybridization, quantitative polymerase chain reaction and array comparative genomic hybridization assays. DLX4 increased copy number was observed in 21.6% of the PBT and 24.3% of the SLN metastasis; regression analysis demonstrated that the DLX4 alterations observed in the SLN metastasis were dependent on the ones in the PBT, indicating that they occur in the primary tumor cell populations and are maintained in the early axillary metastatic site. In addition, regression analysis demonstrated that DLX4 alterations (and other DLX and HOXB family members) occurred independently of the ones in the HER2/NEU gene, the main amplification driver on the 17q region. Additional studies evaluating DLX4 copy number in non-SLN axillary lymph nodes and/or distant breast cancer metastasis are necessary to determine if these alterations are carried on and maintained during more advanced stages of tumor progression and if could be used as a predictive marker for axillary involvement.

Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse

The use and benefit of adjuvant chemotherapy to treat stage II colorectal cancer (CRC) patients is not well understood since the majority of these patients are cured by surgery alone. Identification of biological markers of relapse is a critical challenge to effectively target treatments to the ~20% of patients destined to relapse. We have integrated molecular profiling results of several “omics” data types to determine the most reliable prognostic biomarkers for relapse in CRC using data from 40 stage I and II CRC patients. We identified 31 multi-omics features that highly correlate with relapse. The data types were integrated using multi-step analytical approach with consecutive elimination of redundant molecular features. For each data type a systems biology analysis was performed to identify pathways biological processes and disease categories most affected in relapse. The biomarkers detected in tumors urine and blood of patients indicated a strong association with immune processes including aberrant regulation of T-cell and B-cell activation that could lead to overall differences in lymphocyte recruitment for tumor infiltration and markers indicating likelihood of future relapse. The immune response was the biologically most coherent signature that emerged from our analyses among several other biological processes and corroborates other studies showing a strong immune response in patients less likely to relapse.

Tumor suppressive function of mir-205 in breast cancer is linked to HMGB3 regulation

Identifying targets of dysregulated microRNAs (miRNAs) will enhance our understanding of how altered miRNA expression contributes to the malignant phenotype of breast cancer. The expression of miR-205 was reduced in four breast cancer cell lines compared to the normal-like epithelial cell line MCF10A and in tumor and metastatic tissues compared to adjacent benign breast tissue. Two predicted binding sites for miR-205 were identified in the 3’ untranslated region of the high mobility group box 3 gene, HMGB3. Both dual-luciferase reporter assay and Western blotting confirmed that miR-205 binds to and regulates HMGB3. To further explore miR-205 targeting of HMGB3, WST-1 proliferation and in vitro invasion assays were performed in MDA-MB-231 and BT549 cells transiently transfected with precursor miR-205 oligonucleotide or HMGB3 small interfering RNA (siRNA). Both treatments reduced the proliferation and invasion of the cancer cells. The mRNA and protein levels of HMGB3 were higher in the tumor compared to adjacent benign specimens and there was an indirect correlation between the expression of HMGB3 mRNA and patient survival. Treatment of breast cancer cells with 5-Aza/TSA derepressed miR-205 and reduced HMGB3 mRNA while knockdown of the transcriptional repressor NRSF/REST, reduced miR-205 and increased HMGB3. In conclusion, regulation of HMGB3 by miR-205 reduced both proliferation and invasion of breast cancer cells. Our findings suggest that modulating miR-205 and/or targeting HMGB3 are potential therapies for advanced breast cancer.

Abstract 3570: Phospho-dependent regulation of ERRγ expression, transcriptional activity, and Tamoxifen resistance in ER+ breast cancer

Selective estrogen receptor modulators (SERMs) such as Tamoxifen (TAM) can significantly improve breast cancer-specific survival for women with ER-positive (ER+) disease. However, resistance to TAM remains a major clinical problem. Estrogen-related receptor gamma (ERRγ) is an orphan nuclear receptor with broad, structural similarities to classical ER that is widely implicated in the transcriptional regulation of energy homeostasis. We previously reported that ERRγ is upregulated during the acquisition of TAM resistance in ER+ breast cancer cell lines, exogenous expression of ERRγ is sufficient to induce TAM resistance, and ERRγ mRNA is significantly increased in tumor samples from women with ER+ breast cancer who relapse following TAM treatment.

Because ERRγ has no known ligand, our recent studies have focused on understanding how the expression and activity of this orphan nuclear receptor is regulated, and how this contributes to the TAM resistant phenotype. We have found that TAM-resistant breast cancer cells in which endogenous ERRγ is upregulated show a concomitant hyper activation of p44/p42 ERK. Furthermore, ERK activity (but not that of JNK or p38 MAPK) directly enhances ERRγ protein stability via Serines 57, 81, and/or 219 of the receptor. Phospho-deficient ERRγ is impaired in its ability to induce TAM resistance, and this is associated with a significant reduction in transcriptional activity at the estrogen-related response element (ERRE) half-site, in particular.

This led us to hypothesize that ERRγ action at ERREs is most relevant to the development of TAM resistance. We examined a meta-list of validated, ERRE-containing ERR target genes in association with distant metastasis-free survival (DMFS) within 5 years of primary diagnosis in each of 3 publicly available clinical datasets comprised of ER+ breast cancer patients treated with TAM, and obtained a list of 37 differentially expressed targets. The proximal promoter regions of these 37 genes are enriched for binding sites for ELK1, a well-known ERK substrate. Sub-network analysis reveals enrichment of genes whose protein products regulate the mitochondrial unfolded protein response (UPRmito). We also performed differential dependency network (DDN) analysis in an independent dataset using the full meta-list of ERRγ target genes and also identified genes associated with UPRmito. These data suggest a potentially novel role for ERK-mediated regulation of ERRγ in mitochondrial protein folding in TAM-resistant breast cancer.

Citation Format: Rebecca B. Riggins, Mary M. Heckler, Hemang Thakor, Cara C. Schafer, Salendra Singh, Ye Tian, Yuriy Gusev, Subha Madhavan, Yue Wang. Phospho-dependent regulation of ERRγ expression, transcriptional activity, and Tamoxifen resistance in ER+ breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3570. doi:10.1158/1538-7445.AM2013-3570

Abstract 5333: Identification of miRNA targets in axillary breast cancer metastases

Introduction: MicroRNAs (miRNAs) are a class of non-coding endogenous RNA molecules that play a role in the invasion and metastatic breast cancer process. Correlation of miRNA alterations and lymph node (LN) breast cancer metastasis status are described, however most of the data are in advanced metastatic cancer cell lines and/or mouse mammary models. There are limited miRNA analysis that are conducted directly in axillary LN specimens and to our knowledge, there are no analysis performed specifically in sentinel lymph nodes (SLN), the first axillary metastatic site. Therefore our main objective is to identify the miRNA profile and its corresponding miRNA targets in paired samples of primary breast tumors (PBT) and SLN metastatic lesions. We hypothesize that these changes will represent the ones that occur in early stages of the axillary breast cancer metastatic process, before distant metastasis occurs. Methods: RNA was isolated from microdissected 50μm tumor sections of formalin-fixed paraffin-embedded from 30 paired samples of PBT and SLN metastasis. MiRNA profiling was performed using the Nanostring miRNA system and significantly differentially expressed miRNAs (with at least 2 fold difference and p≤0.05) between the lesions were calculated by the comparative Ct method (ΔΔCt). The miRNA data was integrated with previous array-CGH data from the same cases, to select for targets with concomitant copy number and miRNA expression alterations. Combinatorial target predicted algorithms in conjunction with functional and pathway annotation enrichment systems were performed to identify predicted target functions. Results: The miRNA profiling of the paired PBT and SLN metastasis, revealed 25 miRNAs significantly differently expressed between these lesions. Among the significant miRNAs observed, were the miR-24-3p, miR-221-3p and miR-99a-5p, which are involved in epithelial-mesenchymal transition (EMT) of metastatic cells. Using miRBase and MiRDB target prediction databases we identified 4691 target genes of deregulated miRNAs, that were reduced to 41 after integration with DNA copy number data from the same cases. Ingenuity pathway analysis on these predicted targets function, identified 73 canonical pathways, including the cyclin D1 cell cycle regulation, p53 and cAMP-mediated signaling. Conclusions: The miRNA profiling in our set of paired PBT and SLN metastasis revealed significant differently expressed miRNAs between these lesions. The selection of the most relevant miRNA targets in the pathways identified with a role in tumor invasion/progression are underway and will be evaluated for its co-expression with the corresponding miRNAs. Finally, the direct functional validation of these targets, by in vitro and in vivo experimental models, will allow us to identify the most relevant ones that are mechanistically involved in the initial stages of axillary breast cancer metastases.

Citation Format: Mandeep Gill, Catalin Marian, Clarissa Torresan, Enilze Ribeiro, Iglenir J. Cavalli, Yuriy Gusev, Xi (James) Li, Luciane R. Cavalli. Identification of miRNA targets in axillary breast cancer metastases. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5333. doi:10.1158/1538-7445.AM2013-5333

Platform for Personalized Oncology: Integrative analyses reveal novel molecular signatures associated with colorectal cancer relapse

Approximately 80% of Stage II colon cancer patients are cured by appropriate surgery. However, 20% relapse, and virtually all of these people will die due to metastatic disease. Adjuvant chemotherapy has little or no impact on relapse or survival in Stage II colon cancer, and can only add toxicity without benefit for 80% of the target population that has been cured by surgery. Despite much effort, it is difficult to identify clinical or molecular determinants of outcome in Stage II colon cancer, defeating attempts to target treatments to the 20% of individuals who are destined to relapse. We hypothesized that a multidimensional molecular analysis will identify a combination of factors that serve as prognostic biomarkers in Stage II adenocarcinoma of the colon. The Georgetown informatics team generated and analyzed multi-omics profiling datasets in stage II CRC patients with or without relapse to identify molecular signatures in CRC that may serve both as prognostic markers of recurrence, and also allow for identification of the subgroup of patients who might benefit from adjuvant chemotherapy. The datasets were loaded to GDOC® (Georgetown Database of Cancer) for further mining and analysis. The G-DOC web portal (http://gdoc.georgetown.edu) includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major "omics" types: DNA, mRNA, microRNA, and metabolites. Through technology re-use, the G-DOC infrastructure will accelerate progress for a variety of ongoing programs in need of integrative multi-omics analysis, and advance our opportunities to practice effective personalized oncology in the near future.

In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers

The aim of this study was to perform comparative analysis of multiple public datasets of gene expression in order to identify common genes as potential prognostic biomarkers. Additionally, the study sought to identify biological processes and pathways that are most significantly associated with early distant metastases (<5 years) in women with estrogen receptor-positive (ER+) breast tumors. Datasets from three published studies were selected for in silico analysis of gene expression profiles of ER+ breast cancer, using time to distant metastasis as the clinical endpoint. A subset of 44 differently expressed genes (DEGs) was found common to all three studies and characterized by mitotic checkpoint genes and pathways that regulate mitotic spindle and chromosome dynamics. DEG promoter regions were enriched with NFY binding sites. Analysis of miRNA target sites identified significant enrichment of miR-192, miR-193B, and miR-16-1 targets. Aberrant mitotic regulation could drive increased genomic instability leading to a progression towards an early onset metastatic phenotype. The relative importance of mitotic instability may reflect the clinical utility of mitotic poisons in metastatic breast cancer, including poisons such as the taxanes, epothilones, and vinca alkaloids.

Preclinical magnetic resonance imaging and systems biology in cancer research: current applications and challenges

Biologically accurate mouse models of human cancer have become important tools for the study of human disease. The anatomical location of various target organs, such as brain, pancreas, and prostate, makes determination of disease status difficult. Imaging modalities, such as magnetic resonance imaging, can greatly enhance diagnosis, and longitudinal imaging of tumor progression is an important source of experimental data. Even in models where the tumors arise in areas that permit visual determination of tumorigenesis, longitudinal anatomical and functional imaging can enhance the scope of studies by facilitating the assessment of biological alterations, (such as changes in angiogenesis, metabolism, cellular invasion) as well as tissue perfusion and diffusion. One of the challenges in preclinical imaging is the development of infrastructural platforms required for integrating in vivo imaging and therapeutic response data with ex vivo pathological and molecular data using a more systems-based multiscale modeling approach. Further challenges exist in integrating these data for computational modeling to better understand the pathobiology of cancer and to better affect its cure. We review the current applications of preclinical imaging and discuss the implications of applying functional imaging to visualize cancer progression and treatment. Finally, we provide new data from an ongoing preclinical drug study demonstrating how multiscale modeling can lead to a more comprehensive understanding of cancer biology and therapy.