tbuckley/cabot-search huggingface dataset:
Abstract 4266: Reproducible spheroid formation using functionalized hyaluronan 3D scaffolds
Authors: Pauline Pannetier, Fiona Louis, Zied Souguir, Agathe Devaux, Didier Le Cerf, Jean-Pierre Vannier, Elise Demange, Guillaume Vidal
Journal: Cancer Research (2016)

Abstract Extracellular matrix (ECM) characteristics, including stiffness, porosity, composition and spatial interaction with the surrounding cells and soluble factors are key components for cell growth in a tissue microenvironment. However, poor performance of 2D in vitro systems and animal models demands physiologically relevant well controlled 3D platforms for mechanistic assays, drug resistant phenotypes, new drug efficacy, toxicity assessment. Technical limitations in the current use of multicellular spheroids prevent their widespread use in cancer research and drug development. Existing systems for spheroid formation require lengthy processing times, and make simple tasks like media exchange, cell retrieval and microscopy analysis challenging. An ideal 3D cell culture system would form spheroids in an in vivo like microenvironment, while being easy to handle and compatible with all analytical methods. To address this unmet needs, we use a controlled hyaluronic acid-based scaffolds for spheroid formation. We have enriched 2 hyaluronan scaffolds with other components of the ECM such as collagen I, collagen IV, collagen VI, RGDs motif or galactosamine. Functionalised scaffolds overpass the 2D flat culture limitations by recreating cell/cell interactions and cell/matrix interaction to recreate a more physiologically authentic 3D architecture. The 2 functionalized scaffolds recapitulate the microenvironment for Hepatocyte and Adipocyte growth. Once formed, the spheroids can be cultured long-term, the scaffold is transparent allowing reproducible High Content Screening, the spheroids and the cells can be retrieve, avoiding the technical issues of other 3D systems to retain samples. Moreover, the scaffold is compatible with fluorescence/luminescent kit and immunofluorescent microscopy. We demonstrated this technology using cell lines, primary cells (adipocytes, hepatocytes). We assayed the spheroids over time using various endpoint spheroid morphology, growth and viability, resistance to anti-cancer drug, relevant cell organization formation and toxicity endpoint. Thus, this study introduces functionalized HA scaffold for the use of in vitro culture model as that represent native cell environments is ready to ready to use and compatible with HTS and all analytical methods for drug development and compound screening. Citation Format: Pauline Pannetier, Fiona Louis, Zied Souguir, Agathe Devaux, Didier Le Cerf, Jean-Pierre Vannier, Elise Demange, Guillaume Vidal. Reproducible spheroid formation using functionalized hyaluronan 3D scaffolds. [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 4266.
Estrogen Receptor α Promotes Breast Cancer by Reprogramming Choline Metabolism
Authors: Min Jia, Trygve Andreassen, Lasse Jensen, Tone Frost Bathen, Indranil Sinha, Hui Gao, Chunyan Zhao, Lars-Arne Haldosen, Yihai Cao, Leonard Girnita, Siver Andreas Moestue, Karin Dahlman-Wright
Journal: Cancer Research (2016)

Abstract Estrogen receptor α (ERα) is a key regulator of breast growth and breast cancer development. Here, we report how ERα impacts these processes by reprogramming metabolism in malignant breast cells. We employed an integrated approach, combining genome-wide mapping of chromatin-bound ERα with estrogen-induced transcript and metabolic profiling, to demonstrate that ERα reprograms metabolism upon estrogen stimulation, including changes in aerobic glycolysis, nucleotide and amino acid synthesis, and choline (Cho) metabolism. Cho phosphotransferase CHPT1, identified as a direct ERα-regulated gene, was required for estrogen-induced effects on Cho metabolism, including increased phosphatidylcholine synthesis. CHPT1 silencing inhibited anchorage-independent growth and cell proliferation, also suppressing early-stage metastasis of tamoxifen-resistant breast cancer cells in a zebrafish xenograft model. Our results showed that ERα promotes metabolic alterations in breast cancer cells mediated by its target CHPT1, which this study implicates as a candidate therapeutic target. Cancer Res; 76(19); 5634–46. ©2016 AACR.
Abstract 4338: Advanced neoplasia detection in colorectal cancer screening using multiple stool DNA markers and haemoglobin
Authors: Linda J.W. Bosch, Veerle Melotte, Sandra Mongera, Kathleen L.J. Daenen, Veerle H.M. Coupe, Sietze T. van Turenhout, Esther M. Stoop, Thomas R. de Wijkerslooth, Chris J.J. Mulder, Ernst J. Kuipers, Evelien Dekker, Michael Domanico, Graham P. Lidgard, Barry M. Berger, Beatriz Carvalho, Manon van Engeland, Gerrit A. Meijer
Journal: Cancer Research (2016)

Abstract Purpose of the study: Molecular tests have the potential to improve current non-invasive faecal immunochemical test (FIT) screening for colorectal cancer (CRC) and advanced precancerous lesions. We examined the performance of a panel of faecal DNA (sDNA) markers and FIT in archival samples from an invitational CRC screening population. Methods: Whole stool samples were prospectively collected from individuals participating an invitational primary colonoscopy-screening program (COCOS trial). Only participants that provided stool, performed FIT (OC-Sensor) and underwent colonoscopy were selected. The sDNA panel included quantitative molecular assays for KRAS mutations and for aberrant NDRG4 and BMP3 methylation. The performance of the sDNA plus FIT panel was compared to the FIT results alone, by Receiver Operator Characteristic (ROC) analyses. Results: A total of 1047 individuals (51% male) with a median age of 60 years (range 50-75) were included, of which 7 (0.7%) had colorectal cancer and 104 (9.9%) had advanced precancerous lesions (advanced adenomas or sessile serrated polyps ≥ 1 cm). The combination of sDNA and FIT was more sensitive than FIT alone for detecting advanced precancerous lesions (49% (50/102) and 25% (26/102), respectively). Specificities among individuals with non-advanced or negative findings (controls) were 89% and 96% for sDNA and FIT testing, respectively. ROC analysis of CRC and advanced precancerous lesions compared to controls revealed an Area Under the Curve (AUC) of 0.75 for the sDNA plus FIT test, compared to 0.68 for FIT alone. At an equal specificity of 95%, advanced precancerous lesions were detected with a higher sensitivity by the sDNA plus FIT test compared to FIT alone (36% vs 28%, p = 0.08). Conclusions: In an invitational colorectal cancer screening cohort, combining stool DNA markers with FIT detected more advanced neoplasia than FIT alone, primarily due to detecting more advanced adenomas. Citation Format: Linda J.W. Bosch, Veerle Melotte, Sandra Mongera, Kathleen L.J. Daenen, Veerle H.M. Coupe, Sietze T. van Turenhout, Esther M. Stoop, Thomas R. de Wijkerslooth, Chris J.J. Mulder, Ernst J. Kuipers, Evelien Dekker, Michael Domanico, Graham P. Lidgard, Barry M. Berger, Beatriz Carvalho, Manon van Engeland, Gerrit A. Meijer. Advanced neoplasia detection in colorectal cancer screening using multiple stool DNA markers and haemoglobin. [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 4338.
Prognostic value of programmed death-ligand 1 (PD-L1) expression in patients with stage III colorectal cancer.
Authors: Shigehiro Koganemaru, Naoko Inoshita, Yuji Miura, Yudai Fukui, Yukinori Ozaki, Kenji Tomizawa, Yutaka Hanaoka, Shigeo Toda, Koichi Suyama, Yuko Tanabe, Jin Moriyama, Takeshi Fujii, Shuichiro Matoba, Hiroya Kuroyanagi, Toshimi Takano
Journal: Journal of Clinical Oncology (2016)

3568 Background: The programmed death-1 (PD-1)/PD-L1 pathway is a negative feedback mechanism that suppresses the activity of T cells. PD-L1 was expressed on tumor cells (TCs) or tumor-infiltrating immune cells (ICs) in several malignancies. We previously reported that high PD-L1 expression on TCs and ICs were associated with poor and better prognosis in patients with stage IIIb colorectal cancer, respectively. We reported whether these findings were validated in patients with stage III colorectal cancer. Methods: Formalin-fixed paraffin-embedded (FFPE) blocks specimens were obtained from the patients with stage III colorectal cancer who underwent surgical resection and adjuvant chemotherapy at our institution between January 2009 and July 2012. We excluded patients who received radiotherapy or chemoradiotherapy before surgery. PD-L1 expression was evaluated by immunohistochemistry (IHC) on TCs and ICs. Specimens were scored as IHC low (L) or high (H), when < 5% or ≥ 5% of cells were PD-L1 positive, respectively. Results: Two hundred and thirty-five patients were included in this analysis. Median age was 63 years (range 32-84). One hundred and seventy-four and 61 patients received fluoropyrimidine and fluoropyrimidine combined with oxaliplatin as adjuvant chemotherapy, respectively. The number of patients with PD-L1 expression on TCs/ICs (H/H, H/L, L/H, and L/L) was 0, 19, 36, and 180, respectively. The median follow-up time of this study was 52.9 months. Patients with high PD-L1 expression on TCs had significantly shorter disease-free survival (DFS) than patients with low expression (hazard ratio [HR] 2.36; 95% confidence interval [CI], 1.21-4.62; p = 0.012). Meanwhile, patients with high PD-L1 expression on ICs were associated with longer DFS than patients with low expression (HR 0.40; 95% CI, 0.16-0.98; p = 0.046). Conclusions: High PD-L1 expression on TCs negatively affect the survival, whereas high PD-L1 expression on ICs is associated with favorable prognosis of patients with stage III colorectal cancer.
Abstract 4626: In-vitro growth inhibitory effects of diosmetin on human prostate cancer cells
Authors: Rebecca Pakradooni, Riddhi Patel, Janmejai K. Srivastava, Sanjeev Shukla
Journal: Cancer Research (2016)

Abstract Characterization of effective chemo-preventive agents for treatment of prostate cancer is an utmost priority. Diosmetin (5, 7-Trihydroxy-4′-methoxyflavone), a natural flavonoid present in citrus plant, has anti-mutagenic and anti-allergic properties. However, the anticancer properties of diosmetin have not been explored in prostate cancer. Present study demonstrates, cell growth inhibition and induction of apoptosis in human prostate carcinoma LNCaP (androgen-responsive) and PC-3 (androgen-refractory) cells by diosmetin, however, no significant growth inhibition observed in normal prostate epithelial cells (RWPE1). Cell growth is a fundamental biological process, where mTOR (mammalian target of rapamycin) pathway has its role, regulates cell growth by coordinating energy and nutrient signals with growth factor. mTOR protein kinase have two different complexes; complex-I contains major component raptor; a target of rapamycin and complex II; insensitive to rapamycin, has major component rictor. Rictor is important as it phosphorylates Ser-473 of Akt/PKB, which is essential for full Akt/PKB activation. We observed diosmetin treated prostate cancer cells was able to inhibit growth factor (IGF-1) and cytokine (IL-6) induced rictor expression. Furthermore, diosmetin (20μM) treatment to prostate cancer cells prevented rictor nuclear localization and subsequently inhibited phospho-Akt (Ser-473), which subsequently resulted in increased FOXO3a nuclear presence. Downstream pathway p70S6 kinase, which has a critical role in cell cycle, growth and survival, was also inhibited after diosmetin treatment. These effects were associated with a marked decrease in the protein expression of cyclin D1 and their activating partner, cyclin-dependent kinase (cdk) 2 and 4 with concomitant upregulation of KIP1/p27 and INK4a/p16. Additionally diosmetin treatment to these cells modulated cell survival machinery by down regulating key molecules viz., c-Myc, Survivin and XIAP (X-Linked Inhibitor of Apoptosis). Diosmetin treatment also resulted in alteration in Bax/Bcl2 ratio in favor of apoptosis, which was associated with an increase in cleaved caspase-3. Taken together, our studies demonstrate that diosmetin-mediated growth inhibition and induction of apoptosis in both LNCaP and PC-3 cells were due to deregulated levels of rictor and Akt signaling cascade and modulation of cell-cycle machinery. We are documenting these evidences for the first time that diosmetin acts against potential molecular targets to alter cellular events to elicit anticancer effects in prostate cancer cells. Citation Format: Rebecca Pakradooni, Riddhi Patel, Janmejai K. Srivastava, Sanjeev Shukla. In-vitro growth inhibitory effects of diosmetin on human 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 4626.
Abstract LB-246: Next generation sequencing (NGS) reveals high mutation rates in established and potentially novel cancer genes involved in triple-negative breast cancer
Authors: Vahid Bemanian, Torill Sauer, Joel Touma, Katja Vetvik, Ying Chen, Vessela Kristensen, Ida Bukholm, Jürgen Geisler
Journal: Cancer Research (2016)

Abstract Introduction. Following the development of novel targeted therapies for selected breast cancer (BC) patients (like HER-2 pos. BC), the subgroup of triple-negative breast cancer (TNBC) patients is still characterized by a poor prognosis and a lack of reliable tumor markers that might guide medical therapy. Methods. Genomic DNA was extracted from paraffin embedded formalin fixed (FFPE) tissue obtained from 77 consecutive patients diagnosed with a TNBC at our hospital. The DNA samples were analyzed by next-generation sequencing (NGS) using Human Breast Cancer GeneRead DNAseq Targeted Panel V2 (Qiagen). The panel consists of a collection of PCR primers for targeted enrichment of the coding region of 44 genes commonly mutated in breast cancer. Target enrichment and library construction was performed according to the GeneReader workflow (Qiagen) and paired end sequencing was performed on a NextSeq 500 sequencer (Illumina) running 2 × 150 bp chemistry Version 2. Data analysis including alignment to the reference genome hg19 and variant calling was performed using Qiagen's online Ingenuity Variant analysis. Results. The ingenuity variant analysis classified the genetic mutations according to their clinical significance into four groups: pathogenic, likely pathogenic, benign and likely benign. We present only mutations in genes that are characterized as pathogenic or likely pathogenic, where the term “likely pathogenic” indicates greater than 90% certainty of the mutation being pathogenic (as defined by the American College of Medical Genetics and Genomics). Genetic variations were mostly observed in a subset of 44 genes included in the breast cancer panel. The tumor suppressor genes TP53 as well as BRCA1 and BRCA2 represented the highest mutation rates (&amp;gt;5%) among all TNBC samples. Interestingly, additional genes probably playing a pivotal role in breast cancer biology like EP300 and FGFR-1 were also found to be mutated at a high rate in TNBC. Conclusion. Next generation sequencing of samples obtained from primary TNBC patients confirmed a high level of pathogenic or likely pathogenic mutations in well-described key cancer genes like TP53, BRCA1/2, ATM, EGFR, RB1 and PIK3CA and frequently mutated additional genes (EP300, FGFR1) that will be further investigated. Citation Format: Vahid Bemanian, Torill Sauer, Joel Touma, Katja Vetvik, Ying Chen, Vessela Kristensen, Ida Bukholm, Jürgen Geisler. Next generation sequencing (NGS) reveals high mutation rates in established and potentially novel cancer genes involved in 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 LB-246.
Effect of DNA-PK dependent phosphorylation of topo-I-S10 on its rate of proteasomal degradation and CPT response.
Authors: Ankur K. Shah, Vibhu Sachdew, Julian Taylor-Parker, Umit Tapan, Yara Hamade Tohme, Yevgeniya Malinkovich, Ben Tran, Peter Gibbs, Ravi Salgia, Forest M. White, Jeffrey Parvin, Ajit Bharti
Journal: Journal of Clinical Oncology (2015)

606 Background: Topoisomerase I (topo-I) degradation by ubiquitin proteasomal pathway (UPP), in response to camptothecins (CPTs) is linked to the CPT response. But the mechanism is not understood. Methods: Improvised GST pull down experiments were performed to isolate topo-I interacting proteins which were analyzed by SDS-PAGE and identified by mass spectrometry. DNA-PKcs mediated phosphorylation of GST-topo-I was analyzed by SDS-PAGE and autoradiography. Immunoblot analysis of anti-BRCA1 precipitates from HCT15 cell lines was performed. GST-topo-I phosphorylated by DNA-PKcs, was incubated with the BRCA1/BARD1 heterodimer in the presence of E1, UbCH5c and ATP in ubiquitination buffer. Four triple negative breast cancer cell lines were selected to compare the degree of topo-I degradation. Colorectal cancer (CRC) tissues were immunostained with 1C1.H5.H7 to determine topo-I-pS10 level and identify a correlation between the topo-I-pS10 level and CPT response. Results: We isolated a topo-I interacting protein complex and determined that Ku70/Ku80/DNA-PKcs complex associates with topo-I, and DNA-PKcs phosphorylates topo-I at Serine10. We showed that cells with higher topo-I-pS10 level rapidly degrade topo-I and are CPT resistant. The cells with non-detectable level of topo-I-pS10 fail to degrade topo-I and are CPT sensitive. Retrospective study with 48 CRC tissues immuno-stained with anti-topo-I-pS10 supported our cell line data. Percent DAB positive nuclei demonstrated statistically significant differential staining between CPT responders and non-responders, and ROC analysis confirmed that nearly all non-responders exhibit &gt;35% positive nuclei, indicating that topo-I-pS10 level determines topo-I degradation and a potential predictive biomarker for CPT response. Conclusions: Colorectal cancers are treated with topo-I inhibitors, but the response rate is low. We have shown that topo-I degradation rate is linked to CPT response. We have determined that high topo-I-pS10 level is indicative of rapid topoI degradation and can serve as a biomarker for CPT resistance.
Phase II Study of VEGF Inhibitor, PTK787/ZK222584, in Patients with Refractory or Relapsed Diffuse Large B-Cell Lymphoma
Authors: Danielle M. Brander, Anne W Beaven, Jon P. Gockerman, Louis F. Diehl, Cristina Gasparetto, Thomas C. Shea, Carlos deCastro, Joseph O. Moore, David A. Rizzieri
Journal: Blood (2012)
Studies on Erythropoiesis. XI. Reticulocyte Response of Transfusion-Induced Polycythemic Mice to Anemic Plasma from Nephrectomized Mice and to Plasma from Nephrectomized Rats Exposed to Low Oxygen
Authors: LEON O. JACOBSON, EDNA K. MARKS, EVELYN O. GASTON, EUGENE GOLDWASSER
Journal: Blood (1959)
Abstract 4874: Interleukin-12/FasTI: A novel bi-functional fusion protein for cancer immunotherapy
Authors: Xi Yang, Ashlee Tietje, Xianzhong Yu, Yanzhang Wei
Journal: Cancer Research (2016)

Abstract Whereas cancer immunotherapy with cytokines demonstrates effective in activating immune response against tumor cells, one major obstacle with the use of these cytokines is their severe side effects when delivered systemically at high doses. Another challenge is that advanced tumor cells often evade immunosurveillance of the immune system and block the Fas-mediated apoptosis by down-regulating its expression. In the present study, we report the design and preliminary evaluation of the antitumor activity of a novel fusion protein:mIL-12/FasTI, consisting of mIL-12 and the transmembrane and intracellular domains of Fas. The fusion construct (pmIL-12/FasTI) was transfected into mouse lung carcinoma cell line TC-1. Stable cell clones expressing the fusion protein were established as assayed by RT-PCR and immunohistochemistry. ELISA and cell proliferation analyses demonstrated that NK cells were effectively activated by the fusion protein with increased IFN-ã production and cytotoxicity. Enhanced caspase 3 activity of the clones when co-cultured with NK cells demonstrated that apoptosis was induced through Fas/FasL signaling pathway. The bifunctional protein is clearly more effective than IL-12 alone. It, therefore, represents a promising new therapeutic agent for cancer treatment when combined with tumor cell-specific gene delivery. Citation Format: Xi Yang, Ashlee Tietje, Xianzhong Yu, Yanzhang Wei. Interleukin-12/FasTI: A novel bi-functional fusion protein for cancer immunotherapy. [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 4874.
The Metastatic Breast Cancer Project: A national direct-to-patient initiative to accelerate genomics research.
Authors: Nikhil Wagle, Corrie Painter, Max Krevalin, Coyin Oh, Kristin Anderka, Katie Larkin, Niall Lennon, Deborah Dillon, Elizabeth Frank, Eric P. Winer, Eric Lander, Todd Golub
Journal: Journal of Clinical Oncology (2016)

LBA1519 Background: The challenge in studying tumors from patients (pts) with metastatic breast cancer (MBC) has been that most tumors are not available for research, largely because most pts are cared for in community settings where genomics studies are not conducted. To address this, we launched a nationwide study, The Metastatic Breast Cancer Project, which seeks to empower patients to accelerate research by sharing their samples and clinical information. Methods: In collaboration with pts and advocacy groups, we developed a website to allow MBC pts to participate across the U.S. Enrolled pts are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. We contact participants’ medical providers and obtain medical records and part of their tumor biopsy. Whole exome and transcriptome sequencing is performed on tumor and germline. Clinically annotated genomic data are used to identify mechanisms of response and resistance to therapies. The database is shared widely with researchers. Study updates and discoveries are shared with participants regularly. Results: In the first 3 months, 1227 MBC pts enrolled. 1178 (96%) completed the 16-question survey about their cancer and treatments. Median age was 54 years (yrs) (range 25-91). Median time between initial diagnosis (dx) of breast cancer and MBC was 2 yrs; 424 pts were dx’d with de novo MBC. 1022 (87%) reported having a biopsy at or following their dx of MBC. Median time since MBC dx was 3 yrs; 87 reported having MBC &gt;10 yrs. 436 (37%) reported being on a therapy for &gt;2 yrs; 672 (57%) reported an “extraordinary response” to a therapy. For example, 77 reported long and/or extraordinary responses to capecitabine ; 44 to platinums, and 20 to everolimus. Initial medical records, saliva, and tumors have been received. Conclusions: A direct-to-patient approach enabled rapid identification of large numbers of MBC pts willing to share tumors, saliva, and medical records. This includes many with rare phenotypes, a group that has been challenging to identify with traditional approaches. Genomic analysis of pts with extraordinary responses and with de novo MBC are underway. Pt reported data has also identified unanticipated research questions.