bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1474: A novel oncolytic adenovirus expressing tumor microenvironment modulators that activates myeloid cells, lymphocytes and endothelial cells
Authors: Loskog Angelica , Eriksson Emma , Milenova Ioanna , Moreno Rafael , Alemany Ramon
Published: July 2016

Immunotherapy is becoming a cornerstone in cancer treatment of many indications. So far, pancreatic cancer has shown little response to so called checkpoint blockade antibodies. However, animal data suggests that activating immunotherapies releases the effect of checkpoint blockade also in pancreatic cancer. The tumor microenvironment (TEM) supports the growth of the tumor cells and consists of stroma cells, fibroblasts, blood vessels and immune cells. In some tumor lesions, such as those in pancreatic cancer, the TEM is dense and comprises most of the lesion. The TEM regulates immune activity via its high content of M2 macrophages, myeloid derived suppressor cells and T regulatory cells. Further, the dysfunctional blood vessels in lesions are not optimal for recruiting lymphocytes. With these aspects in mind, LOAd703 was developed. LOAd703 is an oncolytic adenovirus carrying TEM modulators.

LOAd703 was constructed from the ICOVIR system of oncolytic adenoviruses in which replication depends on a dysfunctional, hyperphosphorylated retinoblastoma pathway. The genome was further altered by removing E3-6.7K and gp19K, changing the serotype 5 fiber to a serotype 35 fiber to target CD46 expressed by most tumors, as well as by adding a CMV-driven transgene cassette with the human transgenes for TMZ-CD40L and 4-1BBL. Hence, the transgenes will be expressed in both tumor and stroma while oncolysis is initiated in the tumor cells. We demonstrate herein that LOAd703 infection of a panel of pancreatic cancer cell lines efficiently induced tumor cell death within 48-72 hrs post infection while LOAd703 infection of dendritic cells demonstrated an increased maturation of myeloid cells including dendritic cells (DCs). These DCs could in turn potently activate and promote expansion of both T- and NK cells. Further, LOAd703 infection of endothelial cells (HUVEC) induced upregulation of molecules involved in lymphocyte attachment, rolling and transmigration. In conclusion, LOAd703 is a novel oncolytic virus that targets both the tumor and its TME and a clinical trial is underway to elucidate its effect in pancreatic cancer.

Citation Format: Angelica Loskog, Emma Eriksson, Ioanna Milenova, Rafael Moreno, Ramon Alemany. A novel oncolytic adenovirus expressing tumor microenvironment modulators that activates myeloid cells, lymphocytes and endothelial cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1474.
Abstract 1475: Local immune activation resulting in tumor growth inhibition with MEDI9197 - an intratumorally administered TLR7/8 agonist
Authors: Mullins Stefanie , Grigsby Iwen , Harrison Lester I. , Ren Song , Soukharev Serguei , Young Lesley , Elvecrog James M. , Wilkinson Robert W. , Tomai Mark A. , Herbst Ronald , Vasilakos John P. , Leishman Andrew J.
Published: July 2016

MEDI9197 (formerly 3M-052) is a sustained-release imidazoquinoline toll like receptor (TLR) TLR7/8 agonist designed with a lipid tail that, when injected, is retained within the tumor. This has been shown in pharmacokinetic studies in mice and rats injected with MEDI9197 via the subcutaneous (SC) or intratumoral (IT, mouse only) routes. Stimulation of TLR7 and TLR8 in primary human dendritic cells induces the release of interferon-alpha (IFN-a) from plasmacytoid dendritic cells (pDCs) and interleukin 12 (IL-12) from myeloid dendritic cells (mDCs). Intratumoral administration of MEDI9197 induces a local immune response characterized by upregulation of genes involved in activation of innate and adaptive immunity both from the injected tumor and tumor draining lymph node. Furthermore, flow cytometric analysis of tumor infiltrating lymphocytes (TILs) show increased expression of activation markers, such as CD69, on natural killer (NK) cells and CD8 cytotoxic T cells. This local stimulation of immune cells with MEDI9197 results in tumor growth inhibition as shown in the B16F10 luc syngeneic mouse tumor model using in vivo imaging system (IVIS) equipment. Additionally, combination of MEDI9197 with immune checkpoint inhibitors enhances the efficacy observed in syngeneic mouse tumor models. The data presented shows intratumoral administration of MEDI9197 induces local immune activation leading to tumor growth inhibition in preclinical models of cancer. MEDI9197 is currently being evaluated as a monotherapy for safety and efficacy in human clinical trials.

Citation Format: Stefanie Mullins, Iwen Grigsby, Lester I. Harrison, Song Ren, Serguei Soukharev, Lesley Young, James M. Elvecrog, Robert W. Wilkinson, Mark A. Tomai, Ronald Herbst, John P. Vasilakos, Andrew J. Leishman. Local immune activation resulting in tumor growth inhibition with MEDI9197 - an intratumorally administered TLR7/8 agonist. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1475.
Abstract 1486: Pharmacodynamic response to HER2/CD3 bispecific antibody (HER2-TDB): evidence of T-cell recruitment and further rationale for combination treatment with anti-PD-L1
Authors: Li Ji , Hristopoulos Maria , Clark Robyn , Johnston Jennifer , Slaga Dion , Wang Bu-Er , Cubas Rafael , Totpal Klara , Junttila Melissa R. , Junttila Teemu T.
Published: July 2016

Based on the recent clinical success of tumor immunotherapies that block immune suppressive mechanisms to restore T cell function, there is a profound interest in the clinical development of T cell targeted therapies. We have produced a trastuzumab-based HER2 T cell dependent bispecific antibody (HER2/CD3; HER2-TDB; Junttila et al Cancer Res 2014, 74:5561) that conditionally activates T cells resulting in lysis of HER2 expressing cancer cells at low picomolar concentrations. In vivo, HER2/CD3 can inhibit growth of established mammary tumors in mice at doses as low as 0,01 mg/kg. Due to its unique mechanism of action, which is unrelated to HER2 signaling or sensitivity to chemotherapeutic agents, HER2/CD3 can eliminate cells refractory to currently approved HER2 therapies and inhibit growth of Kadcyla insensitive mammary tumor models. Treatment with HER2-TDBs also results in tumor regression as a second line treatment for Kadcyla relapsed mammary tumors in mice.

Spontaneous mammary tumors arising in MMTV-huHER2 transgenic animals are poorly immunogenic or “immunological deserts” due to their low mutational load and low T cell infiltration. Despite these attributes, HER2/CD3 shows remarkable activity in this model characterized by a robust increase in the number of infiltrating lymphocytes and CD8+ T cells as well as a significant enhancement of tumor CD8+ cytotoxic effector function as measured by increased IFNg production. In addition to inducing T cell proliferation, we further show that HER2/CD3 strongly recruits new T cells from the periphery and this leads to significantly increased T cell numbers in the mammary tumor tissue. Another notable feature of the response to HER2/CD3 treatment is a significant upregulation of PD-1 expression on tumor infiltrating CD8+ T cells. This observation adds a strong rationale for combining HER2/CD3 with anti-PDL1 treatment. Our in vitro experiments further demonstrate that PD-1/PD-L1 signaling can inhibit killing mediated by CD3 bispecific antibodies and that combining two immune therapies - direct polyclonal recruitment of T cell activity together with inhibiting the T cell suppressive PD-1/PD-L1 axis results in enhanced and durable long term responses in vivo.

Citation Format: Ji Li, Maria Hristopoulos, Robyn Clark, Jennifer Johnston, Dion Slaga, Bu-Er Wang, Rafael Cubas, Klara Totpal, Melissa R. Junttila, Teemu T. Junttila. Pharmacodynamic response to HER2/CD3 bispecific antibody (HER2-TDB): evidence of T-cell recruitment and further rationale for combination treatment with anti-PD-L1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1486.
Abstract 1497: Development of a novel TCR-like bi-specific T-cell engager targeting endogenous PR1/HLA-A2 leukemia antigen
Authors: Herrmann Amanda Cernosek , Im Jin S. , Lu Sijie , Sergueeva Anna , Molldrem Jeffrey
Published: July 2016

PR1 (VLQELNVTV) is a HLA-A2 restricted peptide derived from endogenous tumor associated antigens proteinase-3 and neutrophil elastase that are aberrantly expressed in myeloid leukemia blasts. Previously, we have developed a high affinity T-cell receptor-like monoclonal antibody (h8F4) specific for PR1/HLA-A2, and demonstrated the effective killing of myeloid leukemia blasts via antibody dependent cellular cytotoxicity (ADCC). To improve the therapeutic efficacy of h8F4, we adopted a novel antibody engineering strategy, bi-specific T-cell engaging (BiTE) antibody that can bring T cells in close proximity to leukemia blasts through the binding of both PR1/HLA-A2 and CD3, resulting in T-cell mediated cytolysis of leukemia blasts. Here we successfully generated h8F4-BiTE proteins using a eukaryotic expression system and investigated binding characteristics, target specificities, and subsequent T-cell activation with the h8F4-BiTE. The h8F4 BiTE showed binding affinities in the nM range for PR1/HLA-A2 and CD3 moiety of T cells. Within 18 hours of h8F4-BiTE engagement with PR1 pulsed T2 cells, polyclonal T cells from healthy donors up-regulated surface expression of CD69 and down-regulated CD3 in a PR1/HLA-A2 specific and concentration dependent manner, suggesting successful T-cell activation. In conclusion, we developed a novel h8F4 BiTE antibody that recognizes both the CD3 on T cells and endogenous PR1/HLA-A2 complexes on myeloid leukemia, and demonstrated high affinity bindings and subsequent T cell activation. We envision our novel TCR-like BiTE antibody will provide a safer and more potent treatment option for patients with aggressive myeloid leukemias that will improve upon currently available highly toxic standard therapies.

Citation Format: Amanda Cernosek Herrmann, Jin S. Im, Sijie Lu, Anna Sergueeva, Jeffrey Molldrem. Development of a novel TCR-like bi-specific T-cell engager targeting endogenous PR1/HLA-A2 leukemia antigen. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1497.
Abstract 1500: How K-Ras4B attaches to the membrane and forms a dimer: A new paradigm
Authors: Jang Hyunbum , Nussinov Ruth
Published: July 2016

Ras is a small GTPase, controlling signal transduction pathways and promoting cell proliferation and survival. KRAS is frequently mutated in cancer. Ras consists of highly homologous catalytic domains (G-domains) and flexible C-terminal hypervariable regions (HVRs) that differ significantly across Ras isoforms. Recent nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations discovered that the HVR of K-Ras4B in the GDP-bound state extensively interacts with the catalytic domain. However, it weakly interacts with the catalytic domain in the GTP-bound state. Here, using MD simulations we modeled K-Ras4B membrane interaction and dimerization. Membrane binding of K-Ras4B through the anchoring of the positively charged HVR is thought to be critical to its function as an oncogene and initiates signaling events. At the membrane, the catalytic domain takes on multiple orientations, including perpendicular and parallel alignments of the allosteric helices with respect to the membrane normal. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with the farnesyl anchored into the membrane and the HVR unrestrained, the catalytic domain fluctuates reinlessly, exposing its effector binding site. Notably, we also observe HVR-autoinhibited K-Ras4B-GTP states that display GDP-bound-like orientations of the helices. We thus propose that GDP/GTP nucleotide exchange may not be sufficient for K-Ras4B activation; composite mechanisms including HVR sequestration, farnesyl insertion, and orientation/localization of the catalytic domain on the membrane can determine the functional state of K-Ras4B. Remarkably, K-Ras4B-GTP, but not GDP-bound, is able to form stable homodimers with different dimer interfaces, suggesting that the nucleotide-dependent dimerization with various dimer interfaces can resolve nanoclustering and cluster reorganization accomplishment with Raf's activation. Ras was believed to function as a monomer; however, since Raf dimerizes, it has been suspected that Ras can also dimerize. Dimerization and clustering could rein the fluctuations producing more productive pre-organized conformations. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261200800001E.

Citation Format: Hyunbum Jang, Ruth Nussinov. How K-Ras4B attaches to the membrane and forms a dimer: A new paradigm. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1500.
Abstract 1508: Integration of transcriptomic and metabolomic data reveals a central role for EGR1 in regulating survival and cellular metabolism in endocrine-resistant breast cancer
Authors: Shajahan-Haq Ayesha N. , Cheema Amrita , Jin Lu , Boca Simina , Gusev Yuriy , Bhuvaneshwar Krithika , Demas Diane , Raghavan Kristopher , Madhavan Subha , Clarke Robert
Published: July 2016

Breast cancer is the most commonly diagnosed cancer in women. About 70% of all breast cancers are estrogen receptor alpha positive (ER+) and are treated with antiestrogens. However, endocrine resistance is prevalent in the clinic and the underlying mechanisms remain unclear. MYC is overexpressed in endocrine resistant ER+ breast cancers, which suggests that the metabolomic profile of endocrine resistant breast cancers may contain features that are distinct from sensitive cells. We integrated data from transcriptomics and metabolomics analysis of ER+ MCF7-derived breast cancer cells that are antiestrogen sensitive (LCC1) or resistant (LCC9; resistant to ICI182,780). To validate our model, we tested a gene-metabolite network associated with EGR1 (early growth response 1), which was significantly higher in LCC1 cells compared with LCC9 cells. In ER+ human breast tumors treated with endocrine therapy, higher EGR1 expression was associated with a more favorable prognosis. In both LCC1 and LCC9 cell lines, compared to respective controls, knockdown of EGR1 decreased cell proliferation, ERα and MYC protein levels while overexpression of EGR1 did not change these. Comparison of metabolite profiles in LCC9 cells following knockdown or overexpression of EGR1 showed interruption of several biochemical pathways such as glycolysis, lipid metabolism, glutathione, and polyamine metabolism. Treatment with tolfenamic acid (TOL), a nonsteroidal anti-inflammatory drug (NSAID) known to target EGR1, decreased EGR1 protein levels and had an additive effect with ICI182,780 in inhibiting cell proliferation 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, and targeting EGR1 may be an effective therapeutic approach in inhibiting growth of these tumors. Furthermore, high levels of EGR1 may serve as a favorable prognostic marker in some endocrine resistant tumors.

Citation Format: Ayesha N. Shajahan-Haq, Amrita Cheema, Lu Jin, Simina Boca, Yuriy Gusev, Krithika Bhuvaneshwar, Diane Demas, Kristopher Raghavan, Subha Madhavan, Robert Clarke. Integration of transcriptomic and metabolomic data reveals a central role for EGR1 in regulating survival and cellular metabolism in endocrine-resistant breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1508.
Abstract 1511: Mutational signatures from RNA-seq data distinguish HPV(+) and HPV(-) HNSCC
Authors: Hall Pelle , Virani Shama , Warden Charles , Zhang Yanxiao , Koneva Lada , Rentschler Katie M. , Virani Alisha , Rozek Laura S. , Sartor Maureen A. ,   The UM Head and Neck SPORE Investigators
Published: July 2016

IntroductionHead and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide, and an increasing percentage of HNSCC cases are associated with human papillomavirus (HPV) which have improved prognosis compared to HPV(-) HNSCC. Identifying distinctions between HPV(+) and HPV(-) HNSCC may lead to improved prognosis or new treatments, such as determining mutagen(s) that are driving accumulation of genetic variants in each tumor. A recent approach uses the fact that different mutagens cause different types of mutations, referred to as a mutagen's signature. By comparing the mutations in a tumor sample with the mutagen signatures, the mutagens responsible for most of the mutations in the tumor can be identified. We hypothesized that mutational signatures could distinguish HPV(+) from HPV(-) HNSCC tumors.

Materials and Methods

We performed RNA-sequencing on 18 HPV(+) and 18 HPV(-) tumor samples collected from HNSCC patients by the University of Michigan Head and Neck SPORE. Variant calling was performed on each sample using a GATK best practices for RNA-seq pipeline. These variants were then filtered to include only variants that were both rare (<5%) and predicted to have a functional effect. The bases 5’ and 3’ of each variant were extracted to identify its sequence context. The observed mutations in each sample were then approximated by a non-negative linear combination of previously reported mutagen signatures. Certain signatures are associated with dysregulation of particular pathways; this dysregulation was validated with expression and mutation analysis of the RNA data.

Results

In the studied HNSCC tumors, signatures related to aging and impaired DNA repair were responsible for the largest proportion of the mutations found. The signatures that were significantly different between HPV(+) and HPV(-) tumors were associated with APOBEC editing and defective DNA mismatch repair. Expression and mutational analysis validated that APOBEC is more active in HPV(+) than HPV(-) tumors. Interestingly, signatures associated with smoking were not among the most relevant.

Conclusion

The evaluation of mutational signatures in HNSCC tumors identified the main sources of mutations for HNSCC. The differences in mutational signatures between HPV(+) and HPV(-) identify distinct methods of carcinogenesis for these two subtypes of HNSCC.

Citation Format: Pelle Hall, Shama Virani, Charles Warden, Yanxiao Zhang, Lada Koneva, Katie M. Rentschler, Alisha Virani, Laura S. Rozek, Maureen A. Sartor, The UM Head and Neck SPORE Investigators. Mutational signatures from RNA-seq data distinguish HPV(+) and HPV(-) HNSCC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1511.
Abstract 1512: Functional validation of microRNA activity inferred by ActMiR in bladder cancer
Authors: Castillo-Martin Mireia , Collazo Lorduy Ana , Li EunJee , Zhu Jun
Published: July 2016

Background: MicroRNAs (miRs) play a key role in cancer, both in tumorigenesis and tumor progression. In the past years, miR expression signatures have been reported as prognostic biomarkers in different tumor types including bladder cancer (BC). However, miR's expression does not always correlate with activity. We recently developed a novel computational method, named ActMiR, for explicitly inferring the activity of miRs based on the changes in expression levels of target genes. The main objective of this study was to validate the inferred miRs’ activity using BC as a model.

Design: We applied ActMiR in 405 BC cases from The Cancer Genome Atlas (TCGA) database for which information from both mRNA and miR expression was available. Different BC cell lines (5637 and HT1376 for basal BC, SW780 and HT1197 for p53-like BC, and RT4 and RT112 for luminal BC) as well as the immortalized urothelial cell line [Human Urothelium cell (HUC)] were used to perform the in vitro functional validation. RNA was extracted from these cells basally and after inhibition of miR106-5p with specific anti-miR inhibitor (Taqman, Life Technologies); miR and target genes’ expression was assessed by qRT-PCR.

Results: ActMir analyses revealed that a subset of 306 out of 1044 miRNAs were differentially expressed between tumor and normal samples at p-value<10-4. More importantly, at p-value<10-4, 155 out of 556 miRNAs were functionally active. From these, only four (miR106b, miR532, mir556, and mir134) were significantly differentially expressed, functionally active and showed prognostic significance. We chose to further analyze mir106b because it showed the biggest and most significant difference in activity between normal and cancer cells (p-value<2*10-11). As inferred by ActMir, mir106-5p was significantly overexpressed in all cancer cells when compared to HUC. Basal cells showed the highest fold increase (mean of 39; range: 31-47), followed by luminal (mean of 19; range: 5-32) and p53-like cells (mean of 8; range: 3-13). Inhibition of mir106b-5p was performed to assess whether the predicted target genes were consequently upregulated.

Conclusion: Our results underscore the value of ActMir for inferring miR activity in BC from a systems biology perspective. It endorses ActMir as a promising tool for studying casual effects of miR activity on target genes, and ultimately for determining survival outcomes of BC patients.

Citation Format: Mireia Castillo-Martin, Ana Collazo Lorduy, EunJee Li, Jun Zhu. Functional validation of microRNA activity inferred by ActMiR in bladder cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1512.
Abstract 1513: Pan-cancer analysis of alternative splicing patterns and association to genomic aberrations
Authors: Häyrynen Sergei , Nykter Matti
Published: July 2016

Alternative splicing of pre-messenger RNA is responsible for the diversity of transcriptome and proteome, with the majority of multi exon genes producing multiple transcripts. Aberrations in regulative factors of alternative splicing are known to produce transcript isoforms associated with cancer progression and prognosis. Both mutations in the proximity of spliced regions and mutations in and regulation of previously identified splicing factor genes are known to alter splicing patterns.

In this study, we utilized publicly available TCGA data to study association patterns between alternative splicing and its regulatory elements across multiple cancer tissue types. We collected evidence of splicing patterns of annotated isoforms in addition to novel patterns identified using our previously developed tools using RNA-seq data. We mined for associations between somatic mutations and changes of splicing patterns as well as genome and transcriptome level changes in splicing factors. Selective transcriptome assembly was done in loci with differentially expressed patterns and novel patterns with sufficient evidence to identify transcript isoforms and quantify isoform specific expression.

In our study we compiled a catalogue of splicing patterns and their changes across multiple cancer types. Integration of this comprehensive set of quantified splicing patterns with data on proximal mutations and aberrations in splicing factors resulted in statistically relevant associations with clinical phenotypes. Our analysis enables identification of mechanisms behind splicing aberrations common to all cancers and cancer specific splicing patterns.

Citation Format: Sergei Häyrynen, Matti Nykter. Pan-cancer analysis of alternative splicing patterns and association to genomic aberrations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1513.
Abstract 1516: Biomedical informatics applied to the analysis of colon cancer genome: looking for a mutational pattern associated to infectious-origin cancer
Authors: Machicado Claudia , Machicado Enrique
Published: July 2016

Colon carcinoma, one of the most common malignancies globally, is the fourth cause of death due to cancer in Peru. Number of diagnosed cases have increased notably in the latest 5 years, which can be partially explained due to eating habits and environmental factors. In the present work we investigated the presence, in colon cancer genome, of genetic mutations reported in infectious-related cancer. Since most of gastric cancer is associated with chronic infection by Helicobacter pylori and Epstein-Barr virus (EBV), we investigated if the mutational pattern of gastric cancer caused by such infectious agents was similar to the colon carcinoma. Biomedical informatics tools were used to analyze the genomes of both gastric and colon carcinoma. Taken the 20 most frequently mutated genes both in gastric and colon cancer, a total of 8 genes in common resulted broadly mutated in both malignancies including p53, ATM, PIK3CA, ARID1A, CREBBP, KMT2D, KMT2C, and TRRAP. From such list, PIK3CA gene has been associated with gastric cancer caused by H. pylori and the mutational profile matched with that found in colon carcinoma. The point mutations of the oncoprotein PIK3CA identified equally in gastric and colon carcinoma were K111E, M1043I and E545G, all of them associated with gastric cancer caused by infection. Further screening of the gastric cancer genome allowed us to identify a point mutation of the oncoprotein β-catenin reported in infective-origin gastric cancer (D32N). Gene amplifications reported in infection-caused gastric cancer were also identified in the colon carcinoma genome in JAK2, CD274 and PDCD1LG2 genes. Finally downregulation of the tumor supresor gene FOXD3 associated to gastric cancer caused by pathogens was also found in colon carcinoma. Given that the origin of such genetic mutations have not been determined in colon cancer, our study brings evidence that colon carcinoma contain genetic mutations associated to infectious-related cancer. Further experimental studies will be required to verify the existence of mutations induced by parasites in colon carcinoma.

Citation Format: Claudia Machicado, Enrique Machicado. Biomedical informatics applied to the analysis of colon cancer genome: looking for a mutational pattern associated to infectious-origin cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1516.
Abstract 1519: Myb-regulated gene networks and signaling pathways in pancreatic cancer
Authors: Azim Shafquat , Srivastava Sanjeev K. , Bhardwaj Arun , Zubair Haseeb , Khan Mohammad Aslam , Singh Seema , Singh Ajay P.
Published: July 2016

The MYB proto-oncogene (a cellular progenitor of v-Myb oncogene) encodes an oncogenic transcription factor that regulates the expression of a wide array of genes responsible for different cellular functions. We have recently identified MYB as a key driver of pancreatic cancer (PC) pathogenesis. Our findings demonstrated that MYB was overexpressed in majority of PC tissues and cell lines, while remained undetectable in normal pancreatic cells. In addition, MYB overexpression was shown to be associated with pancreatic tumor growth and metastasis. To gain further insight into the molecular mechanisms involved in MYB-potentiated effects in PC cells, we conducted Next-Generation Sequencing of transcriptome of control and MYB-silenced MiaPaCa cells on an Illumina HiSeq 2500 platform. By keeping a cut-off of fold change > 1.5 and p ≤ 0.05, we identified a total of 774 genes to be differentially expressed in MYB-altered MiaPaCa cells. Out of these, 485 genes were downregulated, while 289 genes exhibited upregulated expression. The differentially-regulated genes were subsequently analyzed for functions and cellular pathways alterations using Ingenuity Pathway Analysis (IPA) software. The top three networks to be affected in MYB knockdown PC cells included i) RNA post-transcriptional modifications, molecular transport, RNA trafficking, ii) cellular assembly and organization, cancer, and, iii) cell cycle, DNA replication, recombination and repair. These networks are centered on splicing factors, EGFR and NF-κB complex, respectively. IPA predicted pancreatic adenocarcinoma signaling as one of the most significantly affected canonical pathway upon MYB-silencing. Altogether, our findings identify novel MYB-regulated gene networks and signaling pathways in PC and thus suggest potential molecular mechanisms involved in mediating MYB action in pancreatic tumorigenesis.

Citation Format: Shafquat Azim, Sanjeev K. Srivastava, Arun Bhardwaj, Haseeb Zubair, Mohammad Aslam Khan, Seema Singh, Ajay P. Singh. Myb-regulated gene networks and signaling pathways in pancreatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1519.
Abstract 1552: Nucleotide excision repair gene expression in childhood acute lymphocytic leukemia is a predictor of early relapse
Authors: Ibrahim Omar , As Sobeai Homood , Grant Stephen G. , Latimer Jean J.
Published: July 2016

Double strand break repair and its relationship with genomic instability have been well studied in Acute Lymphocytic Leukemia (ALL). In contrast, base repair mechanisms, such as Nucleotide Excision Repair (NER) have not been well characterized in ALL. The NER pathway addresses base damage resulting in helix distortion and replication stalling, making it important for all types of cancer. Since increased NER is a known mechanism of chemotherapeutic drug resistance, we hypothesize that there will be an increase in the expression of the NER genes at the time of relapse in ALL patients. We have studied the role of NER in ALL by secondary analysis of 2 independent gene expression microarray studies performed by Staal et al. (Set A, GSE18497) and Hogan et al. (Set B, GSE28460). Both studies analyzed matched samples of ALL patients at diagnosis and relapse (41 and 49 pairs, respectively). In Set A we found that 17/20 NER genes have higher expression at the time of relapse, than at the time of diagnosis. 4 of these genes were individually significant. However, in a subset analysis of these data sets, based on the time to relapse, patients who have early (<3 years) vs. late (>3 years) relapse gave distinct results. In Set A, 18/20 NER genes were upregulated at the time of diagnosis in the early relapse group vs. the late relapse group. 4 genes were individually significantly increased. In set B, NER gene expression at the time of diagnosis of patients in the early relapse group was increased in all 20 NER genes when compared to the late relapse group. 7 genes showed individually significant increases in expression. In addition patients in the late relapse group showed an increase in expression of many of the NER genes at time of relapse when compared to time of diagnosis. In conclusion, there are two types of ALL. Early relapsing ALL manifests high NER gene expression at diagnosis with little change at relapse. Late relapsing ALL manifests low NER gene expression at diagnosis with substantial increase at the time of relapse. NER gene expression at the time of diagnosis may allow us to predict which patients are at greatest risk for earlier relapse. This will allow pharmacogenomic targeting of each type of ALL.

Citation Format: Omar Ibrahim, Homood As Sobeai, Stephen G. Grant, Jean J. Latimer. Nucleotide excision repair gene expression in childhood acute lymphocytic leukemia is a predictor of early relapse. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1552.
Abstract 1557: Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of prometastatic TAMs
Authors: Rabe Daniel C. , Frankenberger Casey , Bainer Russell , Sankarasharma Devipriya , Chada Kiran , Krausz Thomas , Gilad Yoav , Becker Lev , Rosner Marsha R.
Published: July 2016

Triple-negative breast cancer (TNBC) patients have the highest risk of recurrence and metastasis. Because they cannot be treated with targeted therapies, and many do not respond to chemotherapy, they represent a clinically underserved group. While physiological inhibitors of metastasis (metastasis suppressors) play key roles in regulating tumor growth, invasion and metastasis, their role in regulating the tumor microenvironment and immune system is unknown. We hypothesized that the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) regulates stromal cells, which then affect tumor invasiveness.

Using species-specific RNAseq we determined that expression of RKIP in tumors markedly reduces the number and metastatic potential of infiltrating TAMs. While TAMs isolated from TNBC xenografts drive in vitro invasion, RKIP+ derived TAMs did not drive invasion and had decreased secretion of pro-metastatic factors including SLPI, OPN, MMP-12, Galectin-3, VEGF-A, VEGF-D, TNFR2, and PGRN. We determined that RKIP regulates TAM recruitment by blocking HMGA2, which activates CCL5 expression. CCL5 rescued pro-metastatic TAM infiltration as well as tumor intravasation. We additionally showed that factors decreased in RKIP-derived TAMs were restored in CCL5-derived TAMs. CCL5 derived TAMs were also able to promote metastasis when co-injected with MDA-MB-231 tumors. These tumor cells demonstrated permanent increases in both growth and invasive potential after co-injection with highly pro-metastatic CCL5 derived TAMs.

To determine the clinical utility of these TAM genes we combined their expression with RKIP signaling in the tumor to create a signature that strikingly separates TNBC patients based on outcome. Our results demonstrate for the first time that metastasis suppressors can regulate the microenvironment, regulating invasion through TAMs. Our results also suggest aggressive triple negative breast cancers could be controlled by attacking CCL5 derived TAMs crucial for promoting metastasis.

Funded by: GM087630, CA184494, and CA192780

Citation Format: Daniel C. Rabe, Casey Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Lev Becker, Marsha R. Rosner. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of prometastatic TAMs. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1557.
Abstract 1562: miRNAs in exosomes from prostate cancer cells modify normal fibroblasts and osteoblasts favoring tumor spread and metastasis
Authors: Andahur Eliana , Castellon Enrique A. , Ramos Chistian , Fulla Juan A. , Sanchez Catherine A.
Published: July 2016

Introduction: Exosomes from bulk and cancer stem cells (CSCs) from prostate cancer primary cultures present a differential pattern of miRNAs. The most abundant miRNA in all exosomes is miR-100, while miR-21 and miR-139 were the most abundant differentially expressed miRNAs in bulk and CSCs exosomes, respectively. Bioinformatics analysis suggested that these miRNAs were related with tumor progression. The functional effect of these miRNAs on targets related with changes at primary and pre-metastatic microenvironment was evaluated in prostatic stromal cells and osteoblasts.

Methods: Normal human undifferentiated osteoblasts (hFOB1.19) and prostate fibroblasts (WPMY-1) cell lines were transfected, by separated, with 25 nM of the following miRNas: miR-100-5p, miR-21-5p, miR-139-5p. let7c was included as transfection control. After 48 hours, changes in the expression of metalloproteinases (MMP)-2, -9 and-13, RANKL, OPG and IL-8 at mRNAs and protein levels were evaluated by qPCR and western blot, respectively. As transfection control, expression of specific targets previously described for each miRNA was evaluated. Besides, the effect of miRNAs in fibroblast migration was evaluated by transwell assay.

Results: In fibroblasts, transfection with miR-21, -100 and -139 increased significantly expression of RANKL, IL8 and all MMPs, with a higher effect in MMP-9. Besides, miR-21 increased fibroblast migration. In osteoblasts, transfection with miRNAs changed the balance that triggers vicious circle at the bone, increasing RANKL and diminishing OPG expression. miRNAs also increased MMPs expression. The greater effect was observed with miR-21 transfection.

Conclusions: Through exosomes, prostate cancer cells recruit normal cells to favor their growth and spread. miRNAs in exosomes increase expression of proteins (in particular, MMPs and RANKL) and cell migration of fibroblasts that create a favorable microenvironment for tumor progression at the primary niche. Besides, through bloodstream, tumoral exosomes can reach the bone, preparing the premetastatic niche. miRNAs from these exosomes change the balance RANKL/OPG that triggers osteoclast recruitment facilitating metastases by activation of the bone vicious circle. miR-21, overexpressed in bulk cells, the main cellular component of tumor, has the higher effect in modify microenvironment, being a potential therapeutic target. (FONDECYT 11121525 and 1140417).

Citation Format: Eliana Andahur, Enrique A. Castellon, Chistian Ramos, Juan A. Fulla, Catherine A. Sanchez. miRNAs in exosomes from prostate cancer cells modify normal fibroblasts and osteoblasts favoring tumor spread and metastasis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1562.
Abstract 1567: Prostate cancer-derived exosomes alter the metabolic microenvironment of bone marrow pre-metastatic niche through PKM2 to promote bone metastasis
Authors: Dai Jinlu , Lu Yi , Zhang Jian , Keller Evan
Published: July 2016

Tumor-derived exosomes are emerging mediators of tumor progression. We explored the role of prostate cancer (PCa)-derived exosomes (Ex) in PCa bone metastasis. Systemic pre-treatment of mice with PCa-Ex increased PCa tumor growth in bone, this was associated with increased early PCa cell seeding into the bone marrow. PCa-Ex had no direct impact on PCa growth or invasive ability in vitro; whereas, conditioned-media (CM) from PCa-Ex-treated stromal cells increased PCa cell growth, invasion and epithelial mesenchymal transition (EMT). PCa-Ex preferentially targeted bone marrow versus lung or liver stroma when injected IV. Proteomic analysis of PCa-Ex-treated cells revealed that PCa-Ex increased pyruvate kinase M2 (PKM2) protein expression in both ST2 stromal cells and primary bone marrow stromal cells, although PKM2 mRNA expression was not altered. PKM2 protein expression correlated with aggressiveness of PCa cell lines and was highest in serum of PCa patients with metastases compared to those with primary tumors. PCa-Ex induced both autophagy and β-hydroxybutarate (BHB) production from stromal cells. Knockdown of PKM2 in PCa cells resulted in production of PCa-Ex with low PKM2. The low PKM2 PCa-Ex had diminished ability to induce PCa cell growth, autophagy and BHB production. IV PCa-Ex and orthotopic tumors increased bone marrow BHB levels. PCa-Ex treatment of stromal cells induced the CM to (1) increase in oxygen consumption rate (OCR) by 80%; (2) extracellular acidification rate (ECAR) by 25%; and (3) increase ATP production in PCa cells. BHB induced OCR, but not ECAR in a dose responsive fashion. BHB administration induced a dose-responsive increase in intratibial tumor growth in mice. Our experiments indicate that primary tumor PCa-Ex can target the bone marrow microenvironment and educate stromal cells to promote PCa progression through increasing PKM2 expression in stromal cells resulting in ketone production that supports metastatic growth. Overall this demonstrates that primary tumor exosomes modulate the metabolic status of the distant pre-metastatic niche to promote metastasis.

Citation Format: Jinlu Dai, Yi Lu, Jian Zhang, Evan Keller. Prostate cancer-derived exosomes alter the metabolic microenvironment of bone marrow pre-metastatic niche through PKM2 to promote bone metastasis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1567.
Abstract 1574: Neuropilin 2 regulates lung disseminated tumor cell escape from dormancy and progression into metastasis
Authors: Bragado Domingo Paloma , Alonso Raul , Fuster Gemma , Mancino Mario , Fernandez-Nogueira Patricia , Aguirre-Ghiso Julio , Gascon Pere
Published: July 2016

Despite considerable advances in the treatment of cancer, about 50% of patients will still eventually develop metastatic disease which remains the main cause of cancer-related death. Disseminated tumor cells (DTCs) are the precursors of metastasis and understanding their biology is one of the most important challenges for the future of cancer research. Our previous studies have shown that TGFβ2 through binding to TGFβR3 regulates DTCs quiescence through the activation of p38αMAPK and induction of the dormant genes DEC2 and p27. However, these DTCs dormancy may be reversed when micro-environmental conditions shift to support DTCs expansion. Nerve fibers and neural mediators are present in organs that serve as key targets for breast and head and neck cancer metastasis, including lungs and bone. In addition, neuropeptides and neurotransmitters receptors are expressed by both, nerve and cancer cells, which suggests that neurotrophic factors can act as messengers between the nervous system and DTCs and influence metastasis progression. Therefore, we hypothesized that in situations of chronic stress or inflammation, neural mediators might influence DTCs fate at secondary organs. Using bioinformatics tools we have found that the semaphorins receptor Neuropilin 2 (NRP2), a co-receptor for TGFβ ligands, is overexpressed in basal and HER2+ breast cancer patient samples and its expression in primary tumors correlate with worst prognosis. In basal breast cancer cell lines, NRP2 expression correlates with lower levels of DEC2 and p27 dormancy genes. Furthermore, we have found that NRP2 is downregulated in dormant cells and overexpressed in proliferative lung DTCs derived cell lines that express low levels of P-p38, DEC2 and p27 dormancy markers. Our results show that in lung DTCs derived cell lines, NRP2 inhibits TGFβR3 expression favoring TGFβ1 signaling and promoting DTCs growth. In agreement with this, breast cancer lung metastasis express higher levels of NRP2 than quiescence lung DTCs in vivo, suggesting that NRP2 might play a role in lung DTCs proliferation. Therefore, we conclude that NRP2 can regulate breast cancer lung DTCs progression from a dormant state to a proliferative state and promote metastasis formation.

Citation Format: Paloma Bragado Domingo, Raul Alonso, Gemma Fuster, Mario Mancino, Patricia Fernandez-Nogueira, Julio Aguirre-Ghiso, Pere Gascon. Neuropilin 2 regulates lung disseminated tumor cell escape from dormancy and progression into metastasis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1574.
Abstract 1580: Cancer-associated fibroblasts potentiates tumor relapse after radiotherapy
Authors: Mi Jun , Wang Yongbin , Gan Guifang , Zhao Jiangmin
Published: July 2016

Cancer-associated fibroblasts (CAFs) are a major component of cancer stromal cells, about 40∼50% of total cell population in cancer. Our data show that CAFs are distributed into larger area than tumor image revealed by MRI or CT since MRI- or CT- images only represent the core region containing cancer cells. Although the image-guided stereotactic body radiation therapy (SBRT) can precisely deliver radiation does to cancers and decreases radiation side effects, compared to the conventional external beam radiotherapy (EBRT), the data from our retrospective study showed that cancer recurrence including local and remote in patients with conventional EBRT was more frequent than patients with SBRT, and the survival time of patients with EBRT was also longer than patients with SBRT. We also demonstrated that CAFs could promote cancer cells recovery from radiation-induced damage through secreting cytokines/chemokines and exporting intermediate metabolites, which induce cancer cell dormancy and enhance DNA damage repair capacity.

Citation Format: Jun Mi, Yongbin Wang, Guifang Gan, Jiangmin Zhao. Cancer-associated fibroblasts potentiates tumor relapse after radiotherapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1580.
Abstract 1581: Crosstalk of androgen sensitive prostate cancer cells and insensitive prostate cancer cells
Authors: Takezawa Yuta , Mizokami Atsushi , Machioka Kazuaki , Izumi Kouji , Iwamoto Hiroaki , Aerken Maolake , Ariunbold Natsagdorg , Namiki Mikio
Published: July 2016

[Background] The mechanisms that prostate cancer (PCa) progresses to castration-resistant PCa (CRPC) are adaptation and clonal selection. We hypothesized that PCa proliferated while each mechanism cooperated when PCa recurred.

[Materials and Methods] After LNCaP cells were transfected with luciferase reporter driven by PSA promoter, LNCaP were cocultured with androgen-insensitive DU145 or PC-3. Then DHEA or DHT were added to the medium and luciferase assay was performed. Also, we added DHEA or DHT in the medium and measured various androgens level by LC-MS/MS. As for proliferation, LNCaP were cocultured with DU145 or PC -3 in 2-layer chamber and number of LNCaP were counted. DU145 and PC-3 were also cocultured with LNCaP cells for 4 days. We also checked migration by using 2-layer chamber and migrated cells were counted.

[Results] Whereas DHEA was converted into DHT in DU145 and induced PSA promoter activity in LNCaP, the effect was not found in PC-3. Moreover, DU145 elevated DHT-induced PSA promoter activity. DU145 promoted LNCaP proliferation stimulated by DHT and DHEA, but PC-3 did not. LNCaP also promoted proliferation of DU145 and PC-3. LNCaP promoted migration of PC-3, but not DU145.

[Conclusion] Cross-talk between androgen-sensitive PCa cells and androgen-insensitive PCa cells might regulate progression of CRPC.

Citation Format: Yuta Takezawa, Atsushi Mizokami, Kazuaki Machioka, Kouji Izumi, Hiroaki Iwamoto, Maolake Aerken, Natsagdorg Ariunbold, Mikio Namiki. Crosstalk of androgen sensitive prostate cancer cells and insensitive prostate cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1581.