bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 738: Correlation between tumor infiltrating lymphocytes and CCL5 gene expression in chemotherapy-resistant triple negative breast cancer
Authors: Pinto Joseph A. , Morante Zaida D. , Salgado Roberto , Cardenas Nadezhda , Araujo Jhajaira , Ponce Jaime , Doimi Franco , Balko Justin , Gomez Henry
Published: July 2016

Background:

The presence of tumor infiltrating lymphocytes (TILs) have been associated with a better outcome in triple negative breast cancer (TNBC). In the other hand, we have found that CCL5, a chemokine involved in the recruitment of immune cells to the tumor microenvironment is an independent prognostic marker for distant-recurrence free survival (DFRS) in TNBC. The aim of this work was to evaluate the relationship between these two immunological prognostic markers in chemotherapy-resistant TNBC.

Material and Methods:

We evaluated a retrospective cohort (n = 74) of TNBC patients with residual disease after neoadjuvante chemotherapy. Residual tumors were profiled with Nanostring for genes previously related to TNBC aggressiveness. Gene expression values for CCL5 were log2 transformed and median centered. TIL count was performed according to the methods published by Salgado et al (2015). Values of TILs count were log2 transformed (values with 0% were removed from the cohort; n = 1). Spearman's rank correlation analysis and proportional hazards regression was used to investigate the relationship and impact in the outcome between these two markers.

Results: The median TIL count was 10% (interquartile range: 21.25). A total of 59.5% of cases had TILs <15%. There was a significant correlation between TILs and CCL5 (ñ = 0.345, P = 0.032). In univariate analysis (as continuous variable), TILs (HR = 0.968 per unit of change; 95%IC: 0.946-0.990; P = 0.006) and CCL5 (HR = 0.95 per unit of change; 95%IC: 0.635-0.996; P = 0.046) were both associated with outcome. After adjusting to CCL5 expression, TIL's count, was the only significant marker with a P-value = 0.007 (HR = 0.702 per unit of change; 95%IC: 0.54-0.909), in contrast to CCL5 (HR = 0.925, CI95%:0.717-1,194; P-value = 0.550).

Conclusions: TILs and CCL5 gene expression are significantly correlated in chemotherapy-resistant TNBC. However, although CCL5 expression is strongly associated with the progression of BC, particularly TNBC, TIL assessment remains the stronger and more significant prognostic immunological marker.

Citation Format: Joseph A. Pinto, Zaida D. Morante, Roberto Salgado, Nadezhda Cardenas, Jhajaira Araujo, Jaime Ponce, Franco Doimi, Justin Balko, Henry Gomez. Correlation between tumor infiltrating lymphocytes and CCL5 gene expression in chemotherapy-resistant triple negative 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 738.
Abstract 739: The role of obesity on inflammation markers in the prostate tumor microenvironment
Authors: Zeigler-Johnson Charnita M. , Morales Knashawn H. , Lal Priti , Rebbeck Timothy R. , Feldman Michael
Published: July 2016

Background: Obesity reflects a chronic inflammatory environment that may contribute to prostate cancer progression and poor treatment outcomes. However, it is not clear which mechanisms drive this association within the tumor microenvironment. The aim of this pilot study was to examine prostatic inflammation via tumor infiltrating lymphocytes and macrophages characterized by obesity and cancer severity.

Methods: We studied paraffin-embedded prostatectomy tissue from 99 participants (63 non-obese and 36 obese) from the Study of Clinical Outcomes, Risk and Ethnicity (University of Pennsylvania) Pathologists analyzed the tissue for type and count of lymphocytes and macrophages, including CD3, CD8, FOXP3, and CD68. Pathology data were linked to clinical and demographic variables. Statistical analyses included frequency tables, Kruskal-Wallis tests, Spearman correlations, and multivariable models.

Results: We observed positive univariate associations between the number of CD68 cells and tumor grade (p = 0.019), as well as biochemical failure (p = 0.033). In multivariable analysis, CD3 and CD8 counts were associated with time to biochemical failure (HR = 0.93, 95% CI = 0.88-0.99; HR = 1.08, 95% CI = 1.01-1.17, respectively.) Preliminary results suggested differences in lymphocytes by race. There were no differences in lymphocytes or macrophages by obesity status or BMI.

Conclusions: The number of lymphocytes and macrophages in the tumor microenvironment did not differ by obesity status. However, these inflammation markers were associated with poor prostate cancer outcomes. Further examination of underlying mechanisms that influence obesity-related effects on prostate cancer outcomes is warranted. Such research will guide immunotherapy protocols and weight management as they apply to diverse patient populations and phenotypes.

Citation Format: Charnita M. Zeigler-Johnson, Knashawn H. Morales, Priti Lal, Timothy R. Rebbeck, Michael Feldman. The role of obesity on inflammation markers in the prostate tumor microenvironment. [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 739.
Abstract 749: Betaglycan-mediated regulation of mesenchymal stromal cell behavior in the prostate tumor-bone microenvironment
Authors: Cook Leah M. , McGuire Jeremy J. , Lynch Conor C.
Published: July 2016

Prostate cancer frequently metastasizes to bone, resulting in increased risk of fractures and severe pain that significantly impacts patient quality of life. Bone metastatic prostate cancer is currently incurable with standard of care therapies being mainly palliative. In bone, prostate cancer generates extensive osteogenic lesions by promoting osteoblast activity. Osteoblasts are specialized bone forming cells derived from mesenchymal stem cells. In a bid to find new molecular targets through which prostate cancer induces osteogenesis, we incubated naïve MSCs with osteogenic bone metastatic prostate cancer cell line C4-2B conditioned media. Gene expression analysis revealed a 3-fold increase in expression of the TGFâ co-receptor, betaglycan. Given the critical role of TGFâ in the context of bone metastatic disease, we examined the role of betaglycan in MSC behavior. To this end, we utilized shRNA to knockdown betaglycan gene expression in mouse bone marrow-derived primary MSCs. Reduced betaglycan expression in knockdown (KD) MSCs had little to no impact on the expression of TGFâ signaling receptors, TGFâRI and TGFâRII, or pan-TGFâ ligand expression. However, using PAI promoter activity, a readout for TGFâ signaling, we observed a 3-fold increase in luminescence in KD-MSCs compared to controls. Likewise, phosphorylated Smad 2 was significantly increased in Betaglycan KD-MSCs in response to TGFâ treatment, collectively demonstrating increased TGFâ signaling in MSCs with reduced betaglycan expression. Using modified Boyden chamber assays, we found that 50% more Betaglycan-KD MSCs migrated towards recombinant TGFâ than controls (100 KD-MSCs cells migrated towards recombinant TGFâ vs. 50 control cells); this change was reversed with the addition of recombinant betaglycan. Using osteogenic differentiation assay, we found that Betaglycan KD-MSC differentiation was reduced by approximately 70% compared to control MSCs as measured by alizarin red staining. Addition of recombinant TGFâ further suppressed differentiation in both KD-MSCs and Control MSCs. This phenomenon was rescued by the addition of recombinant betaglycan, suggesting that MSC-derived betaglycan is critical for driving the osteogenic program. We are currently determining the impact of betaglycan on MSC behavior in the tumor bone microenvironment using in vivo models of bone metastatic prostate cancer. Collectively, these findings suggest that prostate cancer-induced MSC osteogenic programs are regulated in part via the induction of betaglycan.

Citation Format: Leah M. Cook, Jeremy J. McGuire, Conor C. Lynch. Betaglycan-mediated regulation of mesenchymal stromal cell behavior in the prostate tumor-bone microenvironment. [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 749.
Abstract 753: The use of proteomics to analyse whole tumors and identify unique stroma cell targets for antibody-based therapeutics
Authors: Ackroyd James , Allen Jason , Berry Jo , Roesch Lisa , Barnes Martin , Bisht Arnima , Rohlff Christian , Wilson Keith , Aud Dee , Boyd Robert
Published: July 2016

Solid tumors comprises of two distinct compartments: cancer cells and the stroma that the cancer cells induce and are dispersed in. This stroma contains stromal (Fibroblasts, endothelial and pericyte cells) and infiltrating immune cells (Lymphocytes, macrophages, granulocytes and myeloid derived suppressor cells). Recent oncology research has implicated these stroma cells as promoters of tumor progression and there is thus a strong need to profile the cell membrane proteins present on these cells. For tumors which do not contain infiltrating T cells (non-immunogenic tumors) it has been recognized that it will be necessary to employ therapeutic agents to disrupt the tumor micro-environment (TME); allowing the release and processing of tumor antigens by antigen presenting cells, entry and migration T cells into intrastromal sites and potent activation of T cell responses to tumor antigens.

We have conducted in-depth proteomic profiling of tumors from 14 different solid cancer indications with varying degrees of stroma involvement to characterize their immune and stromal cell composition. The data from this work was analyzed in OGAP®; a unique proteomic database that integrates information at the tissue, disease and protein isoform level across diseases, indications, and normal tissues to clarify membrane protein expression levels and profiles. It is one of the world's largest proprietary cell-membrane focused proteomic database, with data on over 5000 cancer membrane proteins. Purified stroma cell populations were also profiled to facilitate the interpretation of whole tumor proteomic data.

Cell membrane proteins present in tumors from different cancer indications were analyzed by mass spectrometry. We classified tumors as immunogenic or non-immunogenic using validated T cell markers (CD3, CD4, CD8 and CD69). We then profiled the non-immunogenic tumors for fibroblast, macrophage and B cell type markers to try and identify strong stroma cell expression patterns not detected in normal tissues. Importantly, most current antibody therapeutic stroma cell targets (CSF-1R, FAP and VEGF-A) were re-discovered. Several novel stroma cell therapeutic targets were identified which if targeted by a therapeutic antibody have the potential to enhance the T cell immune response in tumors resistant to current immunotherapy.

Citation Format: James Ackroyd, Jason Allen, Jo Berry, Lisa Roesch, Martin Barnes, Arnima Bisht, Christian Rohlff, Keith Wilson, Dee Aud, Robert Boyd. The use of proteomics to analyse whole tumors and identify unique stroma cell targets for antibody-based therapeutics. [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 753.
Abstract 757: p16INK4A negatively regulates Leptin through miR-141 and miR-146b-5p in breast stromal adipocytes
Authors: Alkhalaf Huda H. , Aboussekhra Abdelilah
Published: July 2016

Obesity, a disease linked to increased number of adipocytes in various tissues, is increasingly recognized as a risk factor for the development of breast cancer. Obesity has been reported to be associated with the occurrence of larger, more advanced tumors and aggressive cancer pathological features, including lymph node metastasis, advanced tumor stage, and high grade. Accumulating recent evidence highlights the tumor-surrounding adipose tissue as a key component of breast cancer progression. However, the molecular basis of adipocyte-related breast carcinogenesis remains elusive. To shed light on this important phenomenon, we investigated the autocrine and paracrine roles of the tumor suppressor p16 INK4A protein in adipocytes. We have found that down-regulation of p16INK4A by specific shRNA in breast adipocytes enhanced their migration/invasion abilities and increased the expression/secretion levels of various adipokines including leptin. In addition, we have shown that p16INK4A protein inhibits the pro-carcinogenic effects of breast stromal adipocytes in vitro and in tumor xenografts through repressing the expression/secretion of Leptin. Indeed, p16INK4A suppresses Leptin at the mRNA level. This effect is mediated trough miR-141 and miR-146b-5p, which inhibits Leptin expression through a specific sequence at the Leptin 3’UTR. In addition, we present clear evidence that down-regulation of p16INK4A is sufficient to trans-activate breast stromal adipocytes, which promote epithelial-to-mesenchymal-transition in normal breast luminal cells in a leptin-dependent manner.

These results provide the first indication that p16INK4A and miR-141 and miR-146b-5p represses Leptin and its procarcinogenic effects in breast stromal adipocytes. This indicates that p16 pathway has non-cell-autonomous tumor suppressor function.

Citation Format: Huda H. Alkhalaf, Abdelilah Aboussekhra. p16INK4A negatively regulates Leptin through miR-141 and miR-146b-5p in breast stromal adipocytes. [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 757.
Abstract 762: The interleukin-1 inflammatory cytokine family modulates p62/SQSTM1 accumulation in breast cancer cell lines
Authors: Fathima Nawas Afshan , Ramachandran Janani , Thomas Shayna , Ravichandran Jananisree , Delk Nikki
Published: July 2016

Tumors are likened to wounds that do not heal. Thus, not surprisingly, inflammatory cytokines are present in the primary and metastatic tumor microenvironments due, in part, to infiltrating bone-derived cells (e.g., macrophages). We previously discovered that a bone marrow stromal cell line that secretes the inflammatory cytokine, interleukin-1 beta (IL-1â), upregulates p62 mRNA and protein in prostate cancer cell lines and we showed that p62 can be cytoprotective for prostate cancer cells. p62/Sequestome-1 is a multifunctional scaffold protein that can be seen microscopically as subcellular “speckles” which serve as organizing centers for multiple different signaling cascades, ranging from autophagy-mediated degradation of ubiquitinated proteins to KEAP1-NRF2 antioxidant response. To determine if our previous discoveries might be cancer-type specific and to test our hypothesis that p62 promotes cancer cell survival in response to inflammatory cytokines, we expanded our studies to various breast cancer cell lines of varying receptor status, including ZR57-1, T47D, and MDA-MB-468 and determined cell response two interleukin-1 family members, alpha (á) and beta (â). We treated the breast cancer cells with IL-1á and/or IL-1â and analyzed p62 mRNA and protein levels, subcellular localization, and protein-protein interactions. IL-1á and IL-1â can induce p62 speckle accumulation that can be seen to co-localize with the autophagosome membrane protein, LC3B, suggesting an autophagy-dependent regulation and/or function for p62. In addition, p62 co-immunoprecipitates with KEAP1, suggesting a KEAP1-NRF2-dependent antioxidant function for p62. Taken together, our data implies that cancer cells usurp inflammatory cytokines, such as IL-1, present in the primary or metastatic tumor microenvironment to promote cell survival through proteins such as p62.

Citation Format: Afshan Fathima Nawas, Janani Ramachandran, Shayna Thomas, Jananisree Ravichandran, Nikki Delk. The interleukin-1 inflammatory cytokine family modulates p62/SQSTM1 accumulation in breast cancer cell lines. [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 762.
Abstract 763: Exosomal miR-6126 as a novel tumor suppressor in ovarian cancer
Authors: Kanlikilicer Pinar , Rashed Mohammed Mohammed H. S. , Bayraktar Recep , Mitra Rahul , Ivan Cristina , Aslan Burcu , Zhang Xinna , Cristian Rodriguez-Aguayo , Bayraktar Emine , Picher Martin , Ozpolat Bulent , Calin George A. , Sood Anil K. , Lopez-Berestein Gabriel
Published: July 2016

Tumor microenvironment has been known to play a key role in cancer by the development of drug resistance, epithelial-mesenchymal transition, metastasis and angiogenesis. There is emerging evidence that cancer originated exosomes may contribute to the tumor microenvironment to promote tumorigenesis. Exosomes are nano-sized vesicles that contain non-coding RNAs such as miRNAs or siRNAs. Non-coding RNAs are involved in the pathogenesis of the majority of cancer and reveals a new layer of complexity in the molecular architecture of tumorigenicity. The purpose of this study is to identify miRNA content of both sensitive and resistant ovarian cancer-cell derived exosomes for the identification of exosomal RNA-mediated tumorigenesis in ovarian cancer. Using miRNA microarray profiling, we identified differentially expressed exosomal miRNAs in three sensitive (Heya8, Skov3, A2780) and resistant (Heya8-MDR, Skov3-TR, A2780-CP20) isogenic ovarian cancer cell lines. miR-6126 was found to be only miRNA significantly up-regulated in all cancer cell exosomes released to tumor microenvironment. In vitro functional assays showed that miR-6126 act as a tumor suppressor by inhibiting proliferation, migration, invasion and tube formation. miR-6126 acts as a novel potential tumor suppressor through targeting integrin beta-1, leading to inhibition of PI3K/AKT and Ras/Raf signaling. In vivo experiments also demonstrated that administration of miR-6126 into the nude mice with established tumors inhibited tumor weight. Immunohistochemistry results showed that miR-6126 treatment inhibits many oncogenic functions such as proliferation and angiogenesis of ovarian cancer. We believe that these findings help the identification of exosomal RNA-mediated tumorigenesis in ovarian cancer.

Citation Format: Pinar Kanlikilicer, Mohammed Mohammed H. S. Rashed, Recep Bayraktar, Rahul Mitra, Cristina Ivan, Burcu Aslan, Xinna Zhang, Rodriguez-Aguayo Cristian, Emine Bayraktar, Martin Picher, Bulent Ozpolat, George A. Calin, Anil K. Sood, Gabriel Lopez-Berestein. Exosomal miR-6126 as a novel tumor suppressor in ovarian 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 763.
Abstract 764: LOX and LOXL2 inhibition as a treatment for ovarian cancer
Authors: Cho Angela , Hudson Amanda L. , Yuen Samuel , Tran Nham , Howell Viive M. , Colvin Emily K.
Published: July 2016

Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy in women. Despite advances in our understanding of the molecular biology of EOC, patient survival has not significantly improved in decades and new treatments are needed. There is increased interest in therapeutic targeting of the tumor microenvironment (TME). The lysyl oxidase (LOX) family of enzymes are involved in extracellular matrix remodelling through crosslinking of collagen and elastin. They have been shown to play an important role in the TME of other cancers and are regulated by hypoxia, however little is known about their role in EOC. Therefore we aimed to investigate the role of LOX and LOXL2 in EOC using in vitro models.

Tumor epithelial (n = 2) and matched cancer-associated fibroblast cell lines (n = 2) derived from an SV40-induced mouse model of EOC were generated. MTT assays were performed on all cell lines to assess the effect of LOX and LOXL2 inhibition on cell viability. The effect of LOX and LOXL2 inhibition on cancer cell migration and invasion towards cancer-associated fibroblast conditioned media was also investigated using transwell assays. RNA and protein were isolated and analysed from cells cultured in normoxic and hypoxic conditions to assess whether LOX and LOXL2 gene and protein expression is regulated by hypoxia.

Inhibition of LOX and LOXL2 did not affect cell viability. LOX and LOXL2 inhibition significantly reduced the migration and invasion of EOC cells towards cancer-associated fibroblast conditioned media in vitro (p<0.05). Gene expression analysis comparing Lox and Loxl2 expression in all cell lines demonstrated a significant increase in Lox and Loxl2 expression in cells cultured in hypoxia (p<0.05). Similarly, cellular and secreted LOX and LOXL2 protein expression was increased in cells cultured in hypoxic conditions, supporting hypoxia as a regulator of LOX and LOXL2 expression.

This study demonstrates a role for LOX and LOXL2 in promoting migration and invasion of EOC cells in vitro. The upregulation of LOX and LOXL2 in hypoxia suggests a role in facilitating tumor growth and progression within hypoxic tumors. These results provide support for the utility of LOX and LOXL2 inhibition as promising and novel therapeutic strategies in EOC.

Citation Format: Angela Cho, Amanda L. Hudson, Samuel Yuen, Nham Tran, Viive M. Howell, Emily K. Colvin. LOX and LOXL2 inhibition as a treatment for ovarian 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 764.
Abstract 767: TCR sequencing can identify and track tumor-specific T cell populations and is a predictive biomarker of response to DC vaccination in glioblastoma patients
Authors: Sedighim Shaina , Hsu Melody , Wang Tina , Everson Richard G. , Tucker Alex , Antonios Joseph P. , Du Lin , Emerson Ryan , Yusko Erik , Sanders Catherine , Robins Harlan , Yong William , Davidson Tom B. , Li Gang , Liau Linda M. , Prins Robert
Published: July 2016

While immunotherapeutic strategies are emerging adjunctive treatments for cancer, sensitive methods of monitoring the immune response after treatment remain to be established. We used a novel next generation sequencing (NGS) approach to determine whether quantitative assessments of tumor infiltrating lymphocyte (TIL) content and the degree of overlap of T cell receptor (TCR) sequences in brain tumors and peripheral blood were predictors of immune response and overall survival in glioblastoma (GBM) patients treated with autologous tumor lysate-pulsed dendritic cell (DC) immunotherapy. A significant correlation was found between a higher estimated TIL content and increased time to progression (TTP) and overall survival (OS). In addition, we were able to assess the proportion of shared TCR sequences between tumor and peripheral blood at time points before and after therapy, and found the level of TCR overlap to correlate with survival outcomes. Higher degrees of overlap, or the development of an increased overlap following immunotherapy, correlated with improved clinical outcome, and may provide insights into the successful, antigen-specific immune response.

Citation Format: Shaina Sedighim, Melody Hsu, Tina Wang, Richard G. Everson, Alex Tucker, Joseph P. Antonios, Lin Du, Ryan Emerson, Erik Yusko, Catherine Sanders, Harlan Robins, William Yong, Tom B. Davidson, Gang Li, Linda M. Liau, Robert Prins. TCR sequencing can identify and track tumor-specific T cell populations and is a predictive biomarker of response to DC vaccination in glioblastoma patients. [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 767.
Abstract 770: Negative regulation of the CCL22/CCR4 axis by TNFR1 improves melanoma outcome
Authors: Leite Caio Abner , Melo Paulo Henrique , Mota Jose Mauricio , Prado Douglas Silva , Viacava Paula Ramos , Cunha Fernando Queiroz , Alves Filho Jose Carlos
Published: July 2016

Purpose: Immunotherapy for melanoma skin cancer is mainly focused on preventing T cell deactivation through PD1 or CTLA4 inhibition. Another proposed mechanism to increase global T cell response is to prevent Treg immunossupressive function through TNFR1/TNF activation or CCR4/CCL22 inhibition. We aimed to evaluate the role of TNFR1 and CCR4 in an experimental model of melanoma.

Experimental procedures: C57/Bl6 WT, TNFR1 -/- or CCR4 -/- mice were subcutaneously inoculated with 30,000 B16-F10 cells for tumor growth measurement and survival analysis. In a different set of experiments, mice were euthanized fourteen days after inoculation (D14) for spleen, lymph nodes and tumor harvesting for Treg (CD4+CD25+FoxP3+) and TAM (CD45+F4/80+CD206+) quantification by flow cytometry. CCL22 concentrations were quantified in conditioned media from bone marrow-derived macrophages (BMDM) from WT, or TNFR1 -/- mice. Furthermore, TNFR1 and CCR4 gene expression in human melanoma was determined by data mining in deposited datasets (GSE46517).

Results: TNFR1-/- showed increased tumor volumes and reduced survival when compared to their WT counterparts. At D14, we detected increased Treg and TAM accumulation in TNFR1-/- tumor microenvironment. CCL22 concentrations were increased in conditioned media from M2-polarized BMDM from TNFR1-/- mice. CCR4 deficient mice presented reduced tumor volumes and increased survival, accompanied by a reduced Treg accumulation at D14. Data mining in GEO gene expression bank revealed that metastatic melanoma presented reduced TNFR1 and increased CCR4 expression.

Conclusions: CCR4 inhibition is a potential strategy to reduce Treg accumulation and improve outcomes in cancer patients. Further assessments are required to demonstrate the role of TNFR1 pathway in CCR4 activation.

Citation Format: Caio Abner Leite, Paulo Henrique Melo, Jose Mauricio Mota, Douglas Silva Prado, Paula Ramos Viacava, Fernando Queiroz Cunha, Jose Carlos Alves Filho. Negative regulation of the CCL22/CCR4 axis by TNFR1 improves melanoma outcome. [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 770.
Abstract 775: Combinatorial compound stratification based on integration of LINCS, TCGA and PubChem data
Authors: Stathias Vasileios , Allen Bryce , Clarke Jennifer , Ayad Nagi G. , Schürer Stephan
Published: July 2016

The purpose of this study is to leverage the large number of perturbation signatures from the NIH Library of Integrative Network-based Cellular Signatures (LINCS) and integrate them with patient data from The Cancer Genome Atlas (TCGA) and PubChem bioactivity data in an effort to prioritize compounds based on their synergistic effect in cancer treatment.

From the large number of LINCS L1000 transcriptional data capturing cellular responses after chemical or genetic perturbations, we extracted gene expression signatures that were indicative of specific LINCS compounds. Moreover, we compared the L1000 transcriptional profiles with ones from TCGA in order to identify characteristic signatures of major cancer types and prioritized small molecule compounds with discordant expression profiles to those cancer types. We then linked the above compounds to protein target annotations and therefore produced a compound-specific protein target profile. For this, we utilized biochemical data produced by the LINCS KinomeScan and KiNative assays and also biochemical data obtained through PubChem. Using the above information, we obtained pairs of compounds that would inhibit unlinked gene sub-networks that were produced through processing of the TCGA transcriptional data.

The above process can be used as a means to suggest compound combinations towards specific cancer types and to prioritize the development of compounds with targeted polypharmacology.

Citation Format: Vasileios Stathias, Bryce Allen, Jennifer Clarke, Nagi G. Ayad, Stephan Schürer. Combinatorial compound stratification based on integration of LINCS, TCGA and PubChem data. [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 775.
Abstract 785: The prepubertal mammary gland transcriptome suggests a role for the immune system in hormone-independent breast cancer
Authors: Stires Hillary , Crismale-Gann Catina , Belden William J. , Cohick Wendie S.
Published: July 2016

Identifying signaling pathways involved in mammary gland development has contributed to our understanding of breast cancer. While growth of the gland is isometric between birth and puberty, ductal expansion is significant and morphological changes such as terminal end bud formation occur during this developmental window. While estrogen receptor alpha (ERá) and progesterone receptor (PR) expression are evident during this time, pre-pubertal levels of free estradiol are low and growth is independent of ovarian hormones. Basal-like breast cancers represent a subset of breast cancers (10-15% of all women with breast cancer) that often lack ERá, PR and HER2 (i.e. triple negative), are ovarian hormone independent, and have a worse prognosis than other tumor subtypes. Animal models for basal-like breast cancer are limited. Therefore identifying gene changes during prepubertal mammary gland development may give insight into the mechanisms that drive these breast cancers. Offspring from individual Sprague Dawley dams were sacrificed on postnatal days (PND) 2, 10 and 20 (n = 5 to 6 for each PND) and the fourth inguinal glands were removed. RNA was isolated and sequenced by RNASeq using 25 million paired end reads. Bioinformatics analysis utilizing TopHat, Bowtie2, and CummeRbund revealed >7000 genes that changed during this time (alpha = 0.05). Analysis by DAVID/KEGG and Ingenuity Pathway Analysis demonstrated differences in immune pathways over time whereby immune genes increased from PND 2 to 10 to 20. Specifically, T Cell Receptor Signaling and B Cell Development were two of the most affected pathways. These results are interesting as recent studies have indicated that the immune system may influence basal-like breast cancers. Molecular signatures defining subtypes of basal-like breast cancer have been described and include basal-like immunosuppressed (BLIS) and basal-like immune activated (BLIA). A better understanding of the role of the immune system in prepubertal mammary gland development may help guide treatment strategies for hormone independent breast cancers.

Citation Format: Hillary Stires, Catina Crismale-Gann, William J. Belden, Wendie S. Cohick. The prepubertal mammary gland transcriptome suggests a role for the immune system in hormone-independent 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 785.
Abstract 786: Project Survival: Interrogative Biology® platform mediated discovery of molecular markers for detection, stratification and outcomes in pancreatic cancer
Authors: Narain Niven R. , Moser A James , Ramanathan Ramesh , Crowley John , Stoll-D’Astice Amy , Sun Yezhou , Rodrigues Leonardo O. , Grund Eric M. , Chen Emily , Vishnudas Vivek K. , Kiebish Michael A. , Akmaev Viatcheslav R. , Sarangarajan Rangaprasad
Published: July 2016

Pancreatic adenocarcinoma generally presents with a poor prognosis and an extremely low response rate to first line therapies. There is a critical unmet need to discover and implement effective diagnostic panels to stratify outcomes and tailor treatment strategies to improve survival. The BERG Interrogative Biology® platform utilizes Artificial Intelligence to analyze and integrate multi-omic profiles with clinical annotation to define novel biomarkers and improve treatment interventions. Herein, we analyzed the serum proteome, signaling lipidome, structural lipidome, and metabolome of 163patients at multiple timepoints (pancreatic cancer: 115; pancreatitis: 15; and age-matched healthy controls: 33). Utilizing the power of the Bayesian Network learner, bAIcis™ (BERG Artificial Intelligence Clinical Information System), multi-omic profiles were aligned to the longitudinal clinical information and subjected to AI-algorithms to infer probabilistic cause-and-effect relationships among molecular and clinical variables explicitly explaining pancreatic cancer status, cancer progression, and survival, and defining the interconnectivity of molecular features with clinical phenotype. Network features linking into clinical endpoints and key network pressure points were identified as molecular drivers. The drivers of clinical endpoints were analyzed to rank potential biomarkers. Novel biomarkers were discovered that demonstrate diagnostic potential for pancreatic cancer detection, disease prognosis including metastatic disease progression, patient stratification associated with survival, and response to standard chemotherapy agents like Gemcitibine. A prospective study is underway to validate the biomarkers and discover additional diagnostic and therapeutic molecules to improve the outcomes for patients affected by adenocarcinoma of the pancreas.

Citation Format: Niven R. Narain, A James Moser, Ramesh Ramanathan, John Crowley, Amy Stoll-D’Astice, Yezhou Sun, Leonardo O. Rodrigues, Eric M. Grund, Emily Chen, Vivek K. Vishnudas, Michael A. Kiebish, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan. Project Survival: Interrogative Biology® platform mediated discovery of molecular markers for detection, stratification and outcomes 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 786.
Abstract 792: Super-transactivation TP53 variant in the germline of a family with Li-Fraumeni variant
Authors: Id Said Badr , Kim Han , Tran James , Novokmet Ana , Malkin David
Published: July 2016

Li-Fraumeni Syndrome (LFS) is a rare autosomal dominant familial cancer syndrome, characterized by multiple malignancies and frequent germline alterations in TP53. In this study, we highlight four unclassified exonic p53 variants detected in patients with a suspected diagnosis of LFS. We report for the first time the discovery of two novel functional variants in codons 191(c.572C>G; p.P191R) and 360 (c.1079G>T; p.G360V), located, respectively, in the DNA binding domain and in a linker region near the tetramerization domain of TP53. Our data revealed that while the P191R variant decreased the transactivation levels of several p53 targets, it failed to segregate with the disease state. The G360V variant, on the other hand, behaved in a paradoxical fashion by causing a stark upregulation in the activity of several p53 response elements. This tumor suppressive effect was also observed at the level of colony formation and c-Caspase 3 activation. While unlikely to be disease-causing, we propose that these variants may represent novel p53 polymorphisms and potential phenotypic modifiers in LFS. In the future, the enhanced transactivation effects of G360V-p53 may also prove useful in designing more efficacious p53-based gene therapies.

Citation Format: Badr Id Said, Han Kim, James Tran, Ana Novokmet, David Malkin. Super-transactivation TP53 variant in the germline of a family with Li-Fraumeni variant. [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 792.
Abstract 82: Genomic profiling of PDX models across 14 tumor types reveals novel targeted therapeutic opportunities
Authors: Dong Hua , Zhang Zhixiang , Zhang Baoyuan , Tang Xuzhen , Qiang Xiangnan , Qin Yuxin , Yang Shuqun , Yan Yunbiao , Zhang Norman , Gu Qingyang , Ji Qunsheng
Published: July 2016

Introduction: Large efforts have been made to detect somatic alterations and corresponding transcriptome changes in cancer patients, which are expected to bring about significant improvements in precision cancer medicine. Here we report a comprehensive list of driver genes and new targets identified in a large pan-cancer cohort of 550 Patient Derived Xenograft (PDX) models across 14 tumor types.

Material and methods: For each PDX model with passages 2-4, we performed comprehensive genomic analyses, including whole exome sequencing (WES), SNP6.0 array, and RNASeq (or microarray). The genomic data were used for extrapolating genomic SNV, CNV, mRNA expression levels, and for identifying gene fusions. Genomic profiling data were generated in internal and analyzed by in-house validated pipelines.

Results: 220 PDXs were identified to have actionable driver gene mutations /and/or amplifications among 550 models. We identified novel genomic alterations in a number of the PDX models. Significant portion of the models were validated with targeted therapeutic agents (TKI, Abs etc.) and certain cytotoxic agents. All processed data could be accessed via OncoWuXi database: http://onco.wuxiapptec.com and corresponding OncoWuXi APP (App store or onco.wuxiapptec.com/oncowuxi.apk

Conclusions:

We have established a large panel of PDX models with comprehensive genomic annotation and identified novel targets, with open access database and App. These models could serve as a platform for Mouse Clinical Trial and for pre-clinical development of next generation targeted therapeutic drugs.

Citation Format: Hua Dong, Zhixiang Zhang, Baoyuan Zhang, Xuzhen Tang, Xiangnan Qiang, Yuxin Qin, Shuqun Yang, Yunbiao Yan, Norman Zhang, Qingyang Gu, Qunsheng Ji. Genomic profiling of PDX models across 14 tumor types reveals novel targeted therapeutic opportunities. [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 82.
Abstract 820: Molecular epidemiological studies of germinal center-associated nuclear protein (ganp) in the development of human sporadic breast cancers
Authors: Kuwahara Kazuhiko , Ito Hidemi , Kuzushima Kiyotaka , Iwata Hiroji , Tanaka Hideo , Matsuo Keitaro
Published: July 2016

[Introduction]

The altered expression of germinal center-associated nuclear protein (GANP), a member of mammalian TREX2 complex, has been observed in various tumors. Previously, we demonstrated that deficiency of GANP developed mammary gland tumors resembling human breast cancers in two mouse models. In addition, we showed that decreased expression of GANP was an independent prognostic factor of human breast cancer in a retrospective cohort study. These results suggested that GANP might be associated with breast cancer development. Although a little is know about functional significance of ganp polymorphisms, we explored possible association.

[Methods]

We conducted a case-control study to examine association between ganp polymorphisms and risk of breast cancer among Japanese population within the framework of the Hospital-based Epidemiologic Research Program at Aichi Cancer Center (HERPACC). Cases are 694 incident cases who had been diagnosed as breast cancer at Aichi Cancer Center Hospital (ACCH) during 2001-2005. A total of 1,376 non-cancer controls were patients who visited ACCH at same period as cases and were confirmed to have no evidence of cancer. Controls were individually matched for age and menopausal status with cases. ganp polymorphisms were assessed by iCOGS chip (Reference: Michailidou K et al. Nat. Genet. 2013;45:353-361). Multivariable conditional logistic regression models were applied to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for each locus.

[Results]

Ten out of 13 polymorphisms, in high linkage disequilibrium, showed statistically significant associations with breast cancer risk. For instance, in rs2839186, the OR for those with AA alleles compared with those with GG alleles is 0.41 (95% CI, 0.23-0.72, p = 0.002) in genotype model. As compared with those with G allele, the OR for those without was 0.40 (95% CI, 0.23-0.71, p = 0.002) in recessive model. On the other hand, in dominant model, the OR for those with A allele was 0.95 (95% CI, 0.78-1.16, p = 0.635) in comparison to those without that.

[Conclusion]

In this study, we clearly show that mutant SNPs in rs2839186 decrease breast cancer risk. We are currently analyzing if the ganp SNPs affect the prognosis of breast cancer patients.

Citation Format: Kazuhiko Kuwahara, Hidemi Ito, Kiyotaka Kuzushima, Hiroji Iwata, Hideo Tanaka, Keitaro Matsuo. Molecular epidemiological studies of germinal center-associated nuclear protein (ganp) in the development of human sporadic breast cancers. [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 820.
Abstract 825: Myc-nick promotes efferocytosis through M2 macrophage polarization
Authors: Zhong Xiancai , Lee Ha-Na , Surh Young-Joon
Published: July 2016

Resolution of inflammation is an active process which is important for maintaining or restoring homeostasis in response to inflammatory insult. Failure in resolution results in persistent and chronic inflammation which increases the risk of cancer development. Efferocytosis, an essential part of resolution of inflammation, is defined as phagocytic removal of apoptotic cells, especially neutrophils, at the inflamed site, thereby preventing exposure of tissue to toxic intracellular components. It is carried out by a distinct group of phagocytes including anti-inflammatory macrophages (M2 type). Therefore, M2 macrophages represent a key component of the cellular proresolving mechanism and a potential factor for prevention of inflammation-associated cancer. Dysregulation, often overexpression, of c-Myc drives dedifferentiation of cancer cells to acquire capacity for self-renewal and metastasis, which accounts for poor prognosis in cancer patients. A cytoplasmic N-terminal part of full length c-Myc, termed Myc-nick, has been reported to promote differentiation of myoblasts. In the present study, we investigated whether Myc-nick is involved in M2 macrophage polarization and promotion of efferocytosis. We found that ectopic expression of Myc-nick in mouse bone marrow derived macrophages (BMDM) promoted the M2 macrophage polarization through upregulation of interleukin 10 (IL-10) and peroxisome proliferator activated receptor gamma (PPARγ). Furthermore, overexpression of exogenous Myc-nick in BMDM increased capture of apoptotic cells by BMDM through upregulation of a class of phosphatidyl serine (PS) receptors including T-cell immunoglobulin and mucin domain containing 4 (Timd4). PS constitutes one of ‘eat-me’ signals carried by apoptotic cells. PS receptors present on the surface of macrophages are important to recognize, engulf and finally clear apoptotic cells via phagocytosis. In addition, Myc-nick-induced efferocytosis was found to be tightly associated with K (lysine) acetyltransferase 2A (Kat2a/Gcn5). This may lead to the acetylation of transcription factors that regulate expression of PS receptor proteins. In conclusion, activation of M2 macrophages by Myc-nick facilitates efferocytosis and hence resolution of inflammation, and this may suppress inflammation-associated cancer progression.

Citation Format: Xiancai Zhong, Ha-Na Lee, Young-Joon Surh. Myc-nick promotes efferocytosis through M2 macrophage polarization. [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 825.
Abstract 83: MicroRNAs associated with the p53 tumor suppressor signaling network are differentially expressed in triple negative breast cancer cell lines
Authors: Moses Malcolm M. , Godfrey Sherette S. , Lusk Niageria Q. , Rorie Checo J.
Published: July 2016

“Triple-negative” breast cancer (TNBC) is an aggressive subtype of breast cancer that appears prevalently in African American women below the age of 35, and has no known biomarker that can be targeted for drug therapy. This aggressive breast cancer phenotype is due to its high mitotic index and high metastatic potential, and may be due to the fact that up to 80% of TNBC has a mutation in the p53 tumor suppressor gene. The p53 tumor suppressor gene signaling pathway can be mediated by microRNAs (miRNAs) which are short sequences of RNA (∼22nt) that target protein coding mRNA and mark them for degradation. Characterization of the miRNA profiles in TNBC cells compared to normal breast cell lines may provide potential targets in treating TNBC. In this study, microarray analysis was performed on TNBC cell lines HCC1806, HCC70, and MB157 and the normal breast cells AG11132. The expression levels of miRNAs found to play a role in the p53 tumor suppressor gene signaling pathway were compared between the normal and TNBC cell lines. The miRNAs let-7b, let-7a, miR-29a, miR-100, let-7f, miR-34a, miR-15b, miR-21, miR-16, and miR-22 displayed the greatest differences in expression levels between the normal and TNBC cell lines, thereby implicating them as potential biomarkers for TNBC and potential drug treatment targets. These miRNAs can be studied further to determine their role in mediating the p53 tumor suppressor gene signaling pathway in these cells for their potential use in the diagnosis and treatment of TNBC.

Citation Format: Malcolm M. Moses, Sherette S. Godfrey, Niageria Q. Lusk, Checo J. Rorie. MicroRNAs associated with the p53 tumor suppressor signaling network are differentially expressed in triple negative breast cancer cell lines. [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 83.