bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4214: Antitumoral effects of orexins and their receptors OX1R in pancreatic ductal adenocarcinomas (PDAC)
Authors: Voisin Thierry , Speisky Daniela , Couvelard Anne , Couvineau Alain
Published: May 2015

Orexins A and B were identified as hypothalamic ligands for two serpentine G protein-coupled receptors, OX1R and OX2R. Aberrant expression of OX1R was detected in colonic cancer cells and hepatic metastasis. Orexins induce apoptosis in human colon cancer cell lines and in mice models, resulting in massive reduction of tumor cell growth. Pancreatic ductal adenocarcinomas (PDAC) are highly malignant neoplasms with poor prognosis. Chemotherapy treatment shows a poor response rate. Our previous data suggested the expression of OX1R in 98% of tested PDAC.

The aims of this study were 1) to investigate the presence of OX1R in human PDAC cell lines and to analyse orexin-A (OX-A) effects in relation to apoptosis and 2) to develop an in vivo heterotopic xenografted model from the cell lines expressing OX1R, for the study of tumor growth in response to OX-A.

The expression of OX1R was studied at mRNA (RT-PCR), proteins (immunocytochemistry) and functional levels (number of viable cells after OX-A treatment), in 3 PDAC cell lines (AsPC-1, HPAF-II and SW 1990). The development of an animal model (heterotopic xenograft) from the cell line expressing OX1R, has allowed studying the effect of OX-A in tumor growth. Resected tumors were analyzed by immunohistochemistry.

Only AsPC-1 cell line expresses OX1R. The treatment with OX-A promoted a 32% cell growth inhibition. OX-A injection in nude mice xenografted with AsPC-1 cells, has declined 49% of tumor progression in treated cases. This effect was dose-dependent and more important in weekly or twice-weekly treatments. All the tumors corresponded to poorly differentiated adenocarcinomas expressing OX1R. Induction of apoptosis was observed in OX-A treated tumors (activated caspase-3). To generalize further the role of OX1R in inhibition of cell growth and induction of apoptosis, we considered HPAF-II cells expressing the recombinant hOX1R. Orexin-A strongly inhibited HPAF-II/OX1R cell growth in vitro and tumor growth in vivo, whereas no effect of orexins could be detected in the parental HPAF-II cell line. The role of OX1R in controlling apoptosis is directly demonstrated by the expression of recombinant OX1R in HPAF-II cells that confers the ability of orexins to promote apoptosis in this cell line.

This work has demonstrated the antitumor and proapoptotic effect of orexins in PDAC, using in vitro and in vivo models. In this context, orexines receptors may establish a new therapeutic target in pancreatic antineoplastic therapies.

Citation Format: Thierry Voisin, Daniela Speisky, Anne Couvelard, Alain Couvineau. Antitumoral effects of orexins and their receptors OX1R in pancreatic ductal adenocarcinomas (PDAC). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4214. doi:10.1158/1538-7445.AM2014-4214
Abstract 4221: HSP90 as a therapeutic target in colorectal cancer
Authors: Nagaraju Ganji Purnachandra , Willingham Field F. , Woods Kevin E. , Sullivan Patrick , Landry Jerome C. , Diaz Roberto , El-Rayes Bassel F.
Published: May 2015

Purpose/Objectives: Activation of PI3K /Akt/ NF-κB and MAPK signaling pathway contributes to colorectal cancer cell growth, survival and resistance to therapy. HSP90 is required for PI3K/Akt and MAPK stability, folding and trafficking. Ganetespib is a potent functional inhibitor of HSP90 currently under evaluation in clinical trials. We tested the hypothesis that HSP90 functional inhibition by ganetespib can inhibit PI3K/Akt/ NF-κB and MAPK signaling pathways in colorectal cell lines.

Methods: Two colorectal cancer (CRC) cell lines were used, HCT-116 and HT-29. Cells were either untreated (control) or treated with ganetespib at 50nM for 24 hours. Western blot and RT-PCR analyses were carried out to determine the effect of ganetespib on protein molecules involved in cell survival and proliferation. Electrophoretic mobility shift assay (EMSA) was performed in CRC cells to evaluate the effects of ganetespib on NF-κB activity. A subcutaneous xenograft mouse model was used to evaluate the in vivo effects of ganetespib.

Results: Treatment of HCT-116 and HT-29 CRC cell lines with ganetespib inhibited survival signaling (PI3K/Akt) and proliferative signaling (MAPK) at the transcriptional and translational level. As validation, HSP90 knockdown similarly inhibited PI3K/Akt and MAPK protein and mRNA levels in both cell lines. Functional inhibition of HSP90 resulted in inhibition of PI3K/Akt and MAPK transcription. Functional inhibition or down regulation of HSP90 was associated with inhibition of NF-κB trafficking (downregulation of NF-κB in nucleus). Ganetespib sensitized colon cancer cell lines to the effects of oxaliplatin and 5FU. Similar effects were also observed in tumors from animals treated with ganetespib. Conclusion: In this study, we present in vitro and animal data supporting the targeting of HSP90 as a method to inhibit the PI3K/Akt/ NF-κB and MAPK signaling pathways in colorectal cancer. We demonstrate that inhibition of HSP90 downregulates PI3K/Akt/ NF-κB and MAPK leading to a decrease in colon cancer cell survival and proliferation, as well as sensitization to chemotherapy. Combining HSP90 inhibitors with chemotherapy is a rational approach for future drug development in colorectal cancer.

Citation Format: Ganji Purnachandra Nagaraju, Field F. Willingham, Kevin E. Woods, Patrick Sullivan, Jerome C. Landry, Roberto Diaz, Bassel F. El-Rayes. HSP90 as a therapeutic target in colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4221. doi:10.1158/1538-7445.AM2014-4221
Abstract 4226: B-thujaplicin suppressed estrogen dependent breast cancer via regulating estrogen receptor signaling
Authors: Ko Jiwon , Bao Cheng , Lee Jaehoo , Park Hyun-Chang , Lee Hong Jin
Published: May 2015

B-thujaplicin (Hinokitiol), a natural monoterpenoid found in the family of Chamaecyparis obtusa, has been demonstrated to exert anti-fungal, anti-bacterial, and anti-oxidant properties. However, the role of β-thujaplicin in mammary carcinogenesis has not been extensively studied. Here, we investigated the effect of β-thujaplicin on cell proliferation and underlying mechanisms in estrogen-dependent MCF-7 breast cancer cells and N-nitroso methy urea (NMU)-induced animal model. We first found that β-thujaplicin inhibited cell proliferation in a dose dependent manner, where the IC50 was 7.5 μM. The protein and mRNA expression of estrogen receptor (ER)-α was suppressed by β-thujaplicin, without affecting the level of ER-β. One of the target genes of estrogen signaling, cyclin D1 was also significantly inhibited by β-thujaplicin treatment. In animal study of NMU-induced breast cancer model, β-thujaplicin at 7.5mg/kg body weight significantly suppressed tumor growth and tumor multiplicity from 3.1 g in the control to 1.8 g in the β-thujaplicin treatment group, and from 2.9 tumor/rat to 1.7 tumor/rat, respectively. The ER-α expression and cyclin D1 in tumor tissues were also reduced by β-thujaplicin treatment. Taken together, β-thujaplicin suppressed ER-positive breast carcinogenesis through suppressing the ER-α expression and its target gene cyclin D1, and it suggests that β-thujaplicin may be a potent phytochemical in inhibiting breast cancer development.

Citation Format: Jiwon Ko, Cheng Bao, Jaehoo Lee, Hyun-Chang Park, Hong Jin Lee. B-thujaplicin suppressed estrogen dependent breast cancer via regulating estrogen receptor signaling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4226. doi:10.1158/1538-7445.AM2014-4226
Abstract 4235: Anti-proliferative effect of (19Z)-halichondramide from the sponge Chondrosia corticata via G2/M cell cycle arrest and suppression of mTOR signaling in human lung cancer cells
Authors: Bae Song Y. , Song Jayoung , Shin Yoonho , Kim Won Kyung , Oh Jedo , Choi Tae Joon , Jeong Eun Ju , Park So Hyun , Jang Eun Jeong , Kang Ji In , Park Hyen Joo , Hong Ji-Young , Kim Gi Dae , Jeon Ju-eun , Shin Jongheon , Lee Sang Kook
Published: May 2015

Five oxazole-containing macrolides isolated from the marine sponge Chondrosia corticata were evaluated for their anti-proliferative activity in a panel of human solid cancer cell lines. (19Z)-Halichondramide ((19Z)-HCA), a novel trisoxazole-containing macrolide, exhibited the highest potency among the macrolides, with IC50 values in the submicro-molar ranges. Prompted by the high potency of growth inhibition of cancer cells, we investigated the mechanism of action of the anti-proliferative activity of (19Z)-HCA in human A549 lung cancer cells. (19Z)-HCA induced cell cycle arrest in the G2/M phase, and this event was highly correlated with the expression of checkpoint proteins, including the up-regulation of p53 and GADD45α and the down-regulation of cyclin B1, cyclin A, CDC2, and CDC25C. In addition, the growth inhibition by (19Z)-HCA was associated with the suppression of mTOR and its downstream effector molecules 4EBP1 and p70S6K. The modulation of mTOR signaling by (19Z)-HCA was found to be mediated by the regulation of upstream proteins, including the down-regulation of Akt and p38 MAPK and the up-regulation of AMPK. These data suggest the potential of (19Z)-HCA to serve as a candidate for cancer chemotherapeutic agents derived from marine organisms by virtue of arresting the cell cycle in the G2/M phase and the modulation of mTOR/AMPK signaling pathways. [Acknowledgements: This work was supported by the MarineBio Research Program (NRF-2013045101) of the National Research Foundation of Korea (NRF) Grant funded by the Korean Government (MEST).]

Citation Format: Song Yi Bae, Jayoung Song, Yoonho Shin, Won Kyung Kim, Jedo Oh, Tae Joon Choi, Eun Ju Jeong, So Hyun Park, Eun Jeong Jang, Ji In Kang, Hyen Joo Park, Ji-Young Hong, Gi Dae Kim, Ju-eun Jeon, Jongheon Shin, Sang Kook Lee. Anti-proliferative effect of (19Z)-halichondramide from the sponge Chondrosia corticata via G2/M cell cycle arrest and suppression of mTOR signaling in human lung cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4235. doi:10.1158/1538-7445.AM2014-4235
Abstract 425: Methylation, copy number, and LOH analysis of Chr1q21.3 for discovery of ovarian and breast cancer biomarkers
Authors: Poulin Matthew L. , Meyer Ann , Alexander Jessica , Xu Jessica , Yan Liying
Published: May 2015

The association of genetic abnormalities and specific cancers is leading to an increasing number of biomarkers that can be used for early detection of cancers, determination of treatment protocols and predicted prognoses. Additionally, the methylation state of an increasing number of genes is also producing possible predictive biomarkers for specific cancers and stages of cancer as well. To this end, we have analyzed both breast and ovarian cancers and their normal adjacent tissue using both DNA methylation analysis and genome wide array screening for LOH and copy number variations. The combination of these two methods has yielded several groupings of markers that are cancer specific as well as showing specificity for the specific tumor type. Specifically, there are increased copies in the chr1q21.3 region in both ovarian and breast tumor DNA and differences in the methylation when one compares breast tumor to ovarian tumor DNA's. Interestingly, in ovarian tumor samples where there is no amplification of the region, the hypomethylation is greater than in tumor samples in which there is amplification in the region. This suggests that a greater degree of demethylation is needed to potentially activate this region of the genome, where this may not be necessary in regions where an increase in gene copy number may cause increased expression.

Citation Format: Matthew L. Poulin, Ann Meyer, Jessica Alexander, Jessica Xu, Liying Yan. Methylation, copy number, and LOH analysis of Chr1q21.3 for discovery of ovarian and breast cancer biomarkers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 425. doi:10.1158/1538-7445.AM2014-425
Abstract 4255: Rational targeting of the Androgen receptor interactome in prostate cancer
Authors: Ravindranathan Preethi , Tilley Wayne , Raj Ganesh V.
Published: May 2015

Background: The Androgen receptor (AR) is the central driver of prostate cancer and AR signaling is intact across all stages of disease. The interaction of AR with protein cofactors is critical for its signaling: targeted disruption of these interactions may enable shutdown of AR signaling.

Methods: Using known crystal structure, modeled structure and imputed structure based models, peptide agents were rationally designed to block the interface between AR and critical cofactors in its interactome and tested for physiologic activity using prostate cancer cell lines, xenografts and primary tumor explants.

Results: Knowledge of the protein cofactors, their interacting motifs and structure of the interface are needed for optimal targeting of protein-protein interactions. Using an iterative rational design approach, we have been able to successfully disrupt three classes of the AR interactome:

1. Interactions where the protein cofactor, the motifs and the structure of the interface is known, (targeting AR-PELP1 interface through a helical LxxLL motif)

2. Interactions where the protein cofactor is known but the motifs and the structure of the interface is not known, (targeting AR-FoxA1 interaction) and

3. Interactions where the motif is known, but neither the protein cofactor nor the structure of the interface are known (only known is a critical motif on AR).

The design of initial compounds targeting the interactions in Class 1 was based on crystal structures, while those for Class 2 and Class 3 were based on either predicted or imputed (motif in different context) structures. The interaction between AR and proteins in each of these classes is disrupted by a targeted agent as evidenced by co-immunoprecipitation of endogenous protein cofactors and AR. The functional utility of these agents blocking the AR interactome on AR driven gene expression and proliferation has been validated for agents in Class 1, but is being validated for agents in Classes 2 and 3. In each case, using significant structural modeling, active agents were synthesized with a minimal use of synthesis of analogues.

Conclusions: The rational targeting of the AR interactome is feasible and may be a useful complement to traditional screening campaigns. We have demonstrated the utility of this approach to blocking the interface in three distinct classes of protein-protein interactions. Further validation/optimization of these drugs is needed prior to their clinical implementation.

Citation Format: Preethi Ravindranathan, Wayne Tilley, Ganesh V. Raj. Rational targeting of the Androgen receptor interactome in prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4255. doi:10.1158/1538-7445.AM2014-4255
Abstract 4256: Characterization of the cellular inhibitor of apoptosis 1 (cIAP1) IRES trans-acting factors and their contribution to apoptotic resistance in rhabdomyosarcomas
Authors: Faye Mame Daro , Graber Tyson E. , Beug Shawn , Xiang Xiao , Wild Benjamin , Langlois Stephanie , Cowan Kyle N. , Korneluk Robert G. , Holcik Martin
Published: May 2015

The cellular inhibitor of apoptosis protein 1 (cIAP1) is a key regulator of the NFκB signaling pathway and of caspase-8 mediated cell death in mammalian cells. cIAP1 expression is regulated at the translation level via an internal ribosome entry site (IRES). We have previously identified and characterized two IRES trans-acting factors - NF45 and IGF2BP1 - that bind specifically to the cIAP1 IRES and regulates its activity in the context of cell division and apoptosis.

In this study, we characterized the minimal requirement of the cIAP1 IRES for these IRES trans-acting factors as well as other canonical translation factors. We also studied the contribution of cIAP1 expression regulation by these IRES trans-acting factors on the apoptotic resistance of rhabdomyosarcoma cancer cells. In particular, we show that the IRES trans-acting factor IGF2BP1 is overexpressed in a panel of rhabdomyosarcoma primary tumors and cell lines where it drives cIAP1 IRES-mediated translation, contributing to increased resistance to cell death. We also show that targeting cIAP1 by either IGF2BP1 knock-down or IAP antagonists delay RMS tumour growth in the presence of TNFα and improve survival in mice.

Citation Format: Mame Daro Faye, Tyson E. Graber, Shawn Beug, Xiao Xiang, Benjamin Wild, Stephanie Langlois, Kyle N. Cowan, Robert G. Korneluk, Martin Holcik. Characterization of the cellular inhibitor of apoptosis 1 (cIAP1) IRES trans-acting factors and their contribution to apoptotic resistance in rhabdomyosarcomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4256. doi:10.1158/1538-7445.AM2014-4256
Abstract 4270: The use of mutational signatures in identifying carcinogen exposure
Authors: Poon Song Ling , Pang See-Tong , McPherson John R. , Rozen Steven G. , Tan Patrick , Teh Bin Tean
Published: May 2015

Aristolochic acid (AA), a natural product of Aristolochia plants found in herbal remedies and health supplements, is a Group 1 carcinogen that can cause nephrotoxicity and upper urinary tract urothelial cell carcinoma (UCC). Whole genome and exome analysis of 9 AA-associated UCCs revealed a strikingly high somatic mutation rate (150 mutations/Mb), exceeding smoking-associated lung cancer (8 mutations/Mb) and ultraviolet radiation-associated melanoma (111 mutations/Mb). The AA-UCC mutational signature was characterized by A:T to T:A transversions at the sequence motif A[C|T]AGG, located primarily on non-transcribed strands. AA-induced mutations were also significantly enriched at splice sites, suggesting a role for splice site mutations in UCC pathogenesis. RNA sequencing of AA-UCC confirmed a general up-regulation of nonsense-mediated decay machinery components and aberrant splicing events associated with splice site mutations. We observed a high frequency of somatic mutations in chromatin modifiers, particularly KDM6A, in AA-UCC, and demonstrated the sufficiency of AA to induce renal dysplasia in mice and reproduced the AA mutational signature in experimentally treated human renal tubular cells. Finally, exploring other malignancies not previously associated with AA, we screened 93 hepatocellular carcinoma genomes/exomes and identified AA-like mutational signatures in eleven. Our study highlights a unique genome-wide AA mutational signature, and the potential use of mutation signatures as “molecular fingerprints” for interrogating high-throughput cancer genome data, to infer previous carcinogen exposures.

Citation Format: Song Ling Poon, See-Tong Pang, John R. McPherson, Steven G. Rozen, Patrick Tan, Bin Tean Teh. The use of mutational signatures in identifying carcinogen exposure. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4270. doi:10.1158/1538-7445.AM2014-4270
Abstract 4271: The cBioPortal for Cancer Genomics as a clinical decision support tool
Authors: Gao JianJiong , Aksoy B. Arman , Gross Benjamin , Dresdner Gideon , Sun Yichao , Sumer S. Onur , Sander Chris , Schultz Nikolaus
Published: May 2015

As sequencing of tumor samples is entering clinical practice, there is an urgent need for new tools that facilitate the interpretation of sequence data so that they can effectively inform treatment decisions. To this end, we are evolving the cBioPortal for Cancer Genomics into a clinical decision support tool. The cBioPortal is a web-based visualization and analysis engine that makes complex cancer genomics data accessible to a wide range of cancer researchers and clinicians.

To transition the cBioPortal towards use in clinical practice, we have recently developed the following new functions:

1. Filtering of oncogenic mutations: By using information about the known or likely oncogenic effects of specific mutations, the portal can now filter out passenger events and highlight known and potentially druggable drivers.

2. Clinical timelines: Compact and interactive visualization of a patient's clinical and treatment history

3. Image support: Interactive visualization of histology images

4. Support for multiple tumor samples from a single patient: The portal can display genomic differences and similarities of different samples (e.g. multiple sites of the same tumor, recurrence, metastasis, post-treatment) in the context of a patient's treatment history.

5. Tumor clonality: Assessment of a tumor's purity and clonality / heterogeneity

6. Targeted treatment suggestions: The portal matches drugs to drug targets that are altered in the patient's tumor.

7. Clinical trial matching: Based on a patient's clinical history and the genomic alterations found in the tumor, the cBioPortal will identify relevant clinical trials.

By making complex genomic data easily interpretable and linking it to information about drugs and clinical trials, the system has the potential to facilitate the proper use of genomic data in clinical decision making. We are constantly improving the software and will initially focus most strongly on the matching of patients to clinical trials. We are sharing the software with other hospitals, where it can be used by oncologists and tumor boards.

Citation Format: JianJiong Gao, B. Arman Aksoy, Benjamin Gross, Gideon Dresdner, Yichao Sun, S. Onur Sumer, Chris Sander, Nikolaus Schultz. The cBioPortal for Cancer Genomics as a clinical decision support tool. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4271. doi:10.1158/1538-7445.AM2014-4271
Abstract 428: HIC-1: A gene silenced in cancer stem cells of glioma
Authors: Bhagat Mohita , Sinha Subrata , Chattopadhyay Parthaprasad
Published: May 2015

Background : According to the cancer stem cell hypothesis, tumors contain and are driven by a minority cellular population which has retained or re-established key stem-cell properties. Studies have demonstrated frequent hypermethylation of the HIC-1 locus in human cancers and recent work has demonstrated hypermethylation of HIC-1 in ES cells. Targeted methylation of HIC-1 has been shown to transform mesenchymal stem cells into cancer stem/initiating cells. However, so far no study has established the epigenetic role/status of HIC-1 in cancer stem cells.

Methods and Results: U87MG, a glioblastoma cell line, showed a consistent decrease of HIC-1 expression in gliomaspheres obtained in Stem cell media compared to same tumor cells grown in normal media. To examine for the role of HIC-1 in regulating stemness (Sox-2, Oct-4, Nanog), we established a U87 cell line with dominant negative p53 (dn-U87) expressing low HIC-1 levels. Increase in expression of stemness markers was observed in dn-U87 compared to wt-U87.Moreover,effect of hypoxia in increasing stemness was more pronounced in the dn-U87 cell line.

Knockdown of HIC-1 in U87MG grown in normal or stem cell media exhibited an increase in expression of stemness markers (Sox2, Oct4, Nanog and Nestin) under both conditions compared to Mock and control, further confirming role of HIC-1 in modulating stemness expression . Also, gliomaspheres were obtained much earlier (i.e. on Day 4) in HIC-1 knockdown samples grown in stem cell media compared to both Mock and Control (Day7).

To look for the difference in epigenetic signature of HIC-1 gene between gliomaspheres and tumor cells, we checked for changes in methylation and chromatin accessibility in the two cell populations. MNAse assay ascertained heterochromatization of the HIC-1 promoter in gliomaspheres compared to normal U87 cells, while bisulfite sequencing or High Resolution Melt PCR could not detect any change in methylation pattern of the HIC-1 promoter in the two cell populations studied.

Interpretation and Conclusion: Down-regulation of HIC-1, by i) epigenetic changes or ii) knockdown by siRNA or iii) using mutant p53 cell line, may be responsible for contributing to stem cell-like properties to tumor cells. Since HIC-1 is a tumor suppressor gene silenced in many cancers as a result of promoter hypermethylation, it could by itself be a new target for epigenetic therapy. Moreover, increase in stemness on knockdown of HIC-1 could provide new insights into the behavior of cancer-initiating stem cells.

Citation Format: Mohita Bhagat, Subrata Sinha, Parthaprasad Chattopadhyay. HIC-1: A gene silenced in cancer stem cells of glioma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 428. doi:10.1158/1538-7445.AM2014-428
Abstract 4280: Integrative analyses of multi-omics sequencing data to guide treatment decisions in a patient with double malignancy
Authors: Zhu Wei , Huang Jiaqi , Higgs Brandon W. , Brohawn Philip , Dai Shujun , Richman Laura , Jallal Bahija , Jiang Liyan , Yao Yihong
Published: May 2015

Multiple primary malignancies are becoming common. The number of second or higher-order cancers is burgeoning and accounted for about 16% of incident cancers. Double malignancy cases pose the problem of finding the best treatment for the patient. Next generation sequencing (NGS) was used in this study to characterize the genetic and genomic composition in a patient with multiple cancer syndromes. A lung adenocarcinoma brain metastasis sample (FFPE) naïve to any tumor therapy, and relapsed primary lung adenocarcinoma and ovarian serous carcinoma tumor biopsies (fresh frozen) were procured from a 51-year old Chinese female never-smoker. The primary lung and ovarian cancer samples were post to the treatments with both first line and EGFR-TKI targeted therapy. Multiple NGS approaches were conducted on the patient biopsies, including DNA whole genome/exome sequencing, RNA sequencing, and microRNA sequencing. Integrative analyses of the comprehensive NGS data indicated EGFR exon 19 deletions in-frame, which encode part of the kinase domain presented in both primary lung cancer and its brain metastases. EGFR T790M mutation which accounts for the resistance of lung tumor to the EGFR-TKI therapy was identified in the relapsed lung sample but not in the brain malignancy. These results were well aligned with the clinical response to EGFR-TKI treatment in the patient. Furthermore, we uncovered frequent occurrences of somatic copy number variations in both lung and ovarian tumors. A somatic non-sense mutation (COSMIC ID: 307331) in TP53 was uniquely identified in the ovarian tumor biopsy, suggesting a different mechanism driving tumorigenesis than that in the lung. Besides, we also identified a heterozygous insertion in DUSP16 and a stop code gained mutation in MAP3K15 in the patient's germline DNA, a potential predisposition of multiple cancer syndromes and early onset of tumor in this patient. Finally, structural variation and gene fusion, gene interaction, pathway analysis of the affected genes were integrated and evaluated. Overall, NGS approaches shed insights into the molecular phenotypes of tumors and thus have the potential to provide the physician key scientific rationale to design targeted therapeutic approaches in the treatment course.

Citation Format: Wei Zhu, Jiaqi Huang, Brandon W. Higgs, Philip Brohawn, Shujun Dai, Laura Richman, Bahija Jallal, Liyan Jiang, Yihong Yao. Integrative analyses of multi-omics sequencing data to guide treatment decisions in a patient with double malignancy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4280. doi:10.1158/1538-7445.AM2014-4280
Abstract 4281: Targeted or whole genome sequencing of formalin-fixed tissue samples
Authors: Munchel Sarah , Hoang Yen , Zhao Yue , Cottrell Joseph , Klotzle Brandy , Godwin Andrew , Noel Janelle , Fridley Brooke , Beyerlein Peter , Fan Jian-Bing , Bibikova Marina , Chien Jeremy R.
Published: May 2015

Background: To provide a systematic analysis of formalin fixation artifacts on Illumina sequencing libraries and results, we generated two complementary sequencing libraries (target enrichment sequencing and whole exome sequencing) from 11 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tumor samples and two pairs of matched FFPE and FF germline samples. We also generated whole genome sequencing data from a single pair of FF/FFPE tumor samples.

Results: The results indicate minimal variations in library fragment size, coverage, and PCR duplicates within FF/FFPE paired samples that are less than 1 year old; whereas, a large variation in these parameters were observed in FF/FFPE pairs in samples that are approximately 2 years old. No significant increase in global mismatch rates and C•G>T•A substitutions were observed in FFPE samples from the former group; whereas, a discernible increase in mismatch rates and C•G>T•A substitutions were observed in FFPE samples from the latter group. However, over 99.7% and 99.5% of concordant calls were observed between matched FF and FFPE pairs at reference and non-reference positions within the targeted regions, respectively. Although an increased rate of global mismatches and C•G>T•A substitutions were observed in some FFPE samples, discordant rates were low (<0.26) in all samples because most of the FFPE artifacts were filtered out using GATK workflow. Consistent with this analysis, C•G>T•A substitutions are comparable in non-reference positions in paired FF and FFPE samples.

Conclusions: We developed upfront quality assessment and library preparation method that use low input DNA from FFPE samples to perform next-generation sequencing. The results from our studies indicate the suitability of FFPE samples in sequencing studies.

Citation Format: Sarah Munchel, Yen Hoang, Yue Zhao, Joseph Cottrell, Brandy Klotzle, Andrew Godwin, Janelle Noel, Brooke Fridley, Peter Beyerlein, Jian-Bing Fan, Marina Bibikova, Jeremy R. Chien. Targeted or whole genome sequencing of formalin-fixed tissue samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4281. doi:10.1158/1538-7445.AM2014-4281
Abstract 4282: High content multiparametric functional screen for regulators of epithelial-mesenchymal transition identifies genes associated with chemoresistance
Authors: Williams Elizabeth D. , Said Nur Akmarina , Gould Cathryn M. , Thompson Erik W. , Simpson Kaylene J.
Published: May 2015

Metastasis accounts for the majority of treatment-refractory cancers and poor prognosis of the disease. The phenotypic transition of non-motile epithelial tumor cells to migratory and invasive ‘mesenchymal’ cells enables the escape of cancer cells from the primary tumor into the circulation. Morphological changes from cobblestone epithelial cells to elongated and spindle-shaped cells is a key feature of this process. This transition is also marked by upregulation of vimentin, an intermediate filament found in mesenchymal cells. We have previously developed a bladder cancer model with a step-wise enhancement in the metastatic cascade that we have used to interrogate the role of tumor cell plasticity in metastasis (1). Given the need to elucidate pathways and assign functions to particular genes involved in this process, we conducted a high content screening assay across genome wide siRNA, miRNA and kinase inhibitor (131 compounds) libraries to systematically identify modulators of EMT/MET. We identified candidate gene regulators of EMT in TSU-Pr1-B1 bladder cancer cells using the readouts of morphological change (cells stained with CMFDA) and a vimentin promoter activity (dsRed reporter construct). Following integration of the predicted target genes for miRNA hits and kinase inhibitors with siRNA hits, initial validation using a siRNA deconvolution strategy was performed for 400 targets. 221 siRNAs were classified as inducing statistically significant effects on cell shape and/or vimentin promoter reporter activity (defined as at least 2/4 duplexes inducing the effect for a given target). Gene ontology and pathway analyses feature cell cycle and various developmental pathways. Furthermore, the validated gene list was associated with bladder cancer histology and drug sensitivity in clinical specimens in multiple cancer types (Oncomine). Molecules identified in this assay will be further analysed using functional assays to determine their role in maintaining the epithelial phenotype and as regulators of chemoresistance.

(1) Chaffer et al. (2005) Clin Exp Metastasis 22: 115-25.

Citation Format: Elizabeth D. Williams, Nur Akmarina Said, Cathryn M. Gould, Erik W. Thompson, Kaylene J. Simpson. High content multiparametric functional screen for regulators of epithelial-mesenchymal transition identifies genes associated with chemoresistance. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4282. doi:10.1158/1538-7445.AM2014-4282
Abstract 4294: Addressing the limitations of thyroid biopsies: Using elastic scattering spectroscopy to improve the assessment of indeterminate nodules
Authors: Rosen Jennifer E. , Giordano Nicholas J. , Rodriguez-Diaz Eladio , A'Amar Ousama M. , Bigio Irving J. , Lee Stephanie L.
Published: May 2015

Thyroid cancer is the most common endocrine tumor. The gold standard, fine-needle aspiration biopsy, yields 10-25% indeterminate results necessitating diagnostic surgery. Using the real-time imaging technique of elastic scattering spectroscopy (ESS), a pair of fiber optics are inserted through the lumen of a biopsy needle and placed in contact with the thyroid nodule moments before cell collection occurs. Our research focuses on utilizing this optical-biopsy technique to measure tissue in vivo with broadband light during biopsy. In this study we demonstrate the potential our novel ESS-integrated optical biopsy syringe can have on cancer diagnostics. Spectra from 148 patients were collected. Additional time during biopsy to perform ESS measurements was less than 20 seconds. Cytology results for enrolled patients were as follows: 37 indeterminate, 6 insufficient, 5 malignant and 100 benign. Correlating ESS measurements with cytology, we identified changes in spectra when fiber optics were placed in contact with malignant versus benign tissue. From our enrolled benign and malignant patients, we trained an algorithm to diagnose indeterminate nodules based off of ESS spectra and compared to pathology. Preliminary analysis of spectra show ESS has a NPV of 0.99, a sensitivity of 0.92 and a specificity of 0.85. This data suggests that elastic scattering spectroscopy may improve the reliability, speed, and cost of cancer diagnostics.

Citation Format: Jennifer E. Rosen, Nicholas J. Giordano, Eladio Rodriguez-Diaz, Ousama M. A'Amar, Irving J. Bigio, Stephanie L. Lee. Addressing the limitations of thyroid biopsies: Using elastic scattering spectroscopy to improve the assessment of indeterminate nodules. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4294. doi:10.1158/1538-7445.AM2014-4294
Abstract 4301: Detection and characterization of regions of hypoxia within orthotopic pancreatic tumors using multispectral optoacoustic tomography
Authors: Hudson Shanice V. , Kimbrough Charles , Egger Michael , Khanal Anil , Smith Michelle E. , Grizzle William E. , McNally Lacey R.
Published: May 2015

Optical imaging is a vital tool in cancer research for visualization of tumors in preclinical models. However, resolution for bioluminescence and fluorescence modalities is restricted to a depth of five millimeters, as light is attenuated at increased depth and autofluorescence can create background noise. Light propagation becomes diffuse at only a few millimeters, resulting in light scattering and absorption. To improve imaging resolution and acquisition in real-time, multispectral optoacoustic tomography (MSOT) was utilized to visualize molecular phenomena such as the tissue oxygenation of characteristically hypoxic aggressive pancreatic tumors. SCID mice were orthotopically implanted with S2VP10L and MIA PaCa-2 pancreatic cancer cells that highly express the epidermal growth factor receptor (EGFR), which exhibits extracellular domain binding of the epidermal growth factor (EGF) ligand.

Cohorts were then intravenously injected with fluorescent EGF ligand probes and imaged semiweekly to follow tumor growth and morphology. Medical Grade Air levels were set to 0.9 L and oxygen at 0.1 L to assess the correlation of increased hypoxia with tumor growth and progression. Pancreatic tumor cells were imaged concurrently with evaluating levels of oxygenated and deoxygenated hemoglobin, providing a distinct picture of the tumor and its vascularization. Use of MSOT to detect regions of hypoxia within tumor was validated using pimonidazole immunohistochemical staining of tumor tissue. For the first time, our data demonstrate regions of tumor hypoxia in living subjects, at depth, and noninvasively, via optoacoustic tomography. Dynamic assessment of tumor microenvironment, especially regions of tumor hypoxia, is essential to effectively target and treat tumors that are otherwise resistant to treatment.

Citation Format: Shanice V. Hudson, Charles Kimbrough, Michael Egger, Anil Khanal, Michelle E. Smith, William E. Grizzle, Lacey R. McNally. Detection and characterization of regions of hypoxia within orthotopic pancreatic tumors using multispectral optoacoustic tomography. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4301. doi:10.1158/1538-7445.AM2014-4301
Abstract 4308: 3D nuclear telomeric signatures define circulating tumor cells (CTCs) and characterize CTC subpopulations in intermediate risk prostate cancer patients
Authors: Julius Awe A. , Yan Adam , Shah Nidhi , Ludger Klewes , Kuzyk Alexandra , Xu Michael , Boles Ramy , Saranchuk Jeff , Drachenberg Darrel , Mai Sabine
Published: May 2015

Intermediate risk prostate cancer is a current medical challenge since the patients in this group can either be stable or progress, and there is no predictor for individual risk. Stratifying these patients would spare the patients unnecessary treatment or indicate the start of treatment immediately without losing precious time. Currently, prostate specific antigen (PSA) is used as evidence for biochemical progression. A more sensitive biomarker is needed to detect disease progression earlier and more reliably.

We have isolated circulating tumor cells (CTCs) using a filtration-based device (ScreenCell). We subsequently performed the genetic characterization of the captured CTCs on a single cell basis. Using three-dimensional (3D) nuclear telomere imaging and quantitative analysis of 3D telomeric signatures of CTCs, we have characterized CTCs in the blood of the patients and have identified patient subgroups with one or more groups of CTCs. 380 samples of intermediate risk prostate cancer all revealed the presence of CTCs. However, the CTCs found were not genetically identical. Marked heterogeneity was seen, and three main groups of CTC profiles were defined based on TeloView software our group developed earlier. Repeat samples taken 6 months intervals define stable, mildly changing and significantly altered 3D profiles indicative of disease stability vs. progression.

Citation Format: Awe A. Julius, Adam Yan, Nidhi Shah, Klewes Ludger, Alexandra Kuzyk, Michael Xu, Ramy Boles, Jeff Saranchuk, Darrel Drachenberg, Sabine Mai. 3D nuclear telomeric signatures define circulating tumor cells (CTCs) and characterize CTC subpopulations in intermediate risk prostate cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4308. doi:10.1158/1538-7445.AM2014-4308
Abstract 4318: Mycoplasma arginini infection shifts the energy catabolism ratio of metastatic macrophages towards fermentation and is associated with an increase in primary tumor size, metastasis and malignancy
Authors: Flores Roberto , Brown Ashley K. , Akgoc Zeynep , Seyfried Thomas N.
Published: May 2015

Mycoplasma are the smallest self-replicating prokaryotes and are burdened by their notoriety. It is widely unknown that mycoplasma are readily detected in many primary human cancer tissues and can influence tumorigenesis. Some mycoplasma species such as M. fermentans and M. hyorhinis can transform normal murine and human cell lines into tumorigenic cells. Mycoplasma infection can inactivate tumor suppressor genes and activate oncogenes. These observations suggest that mycoplasma can be both carcinogenic and or onco-modulators. We found that M. arginini was present in the metastatic macrophage cell line VM-M3 (referred to as M3myco+). Antibiotic was used to eradicate M. arginini (verified by mycoplasmal 16S rDNA PCR amplification) from the M3 cells (M3myco- cells). Oxygen consumption rate was higher in the than the M3myco- cells than in the M3myco+ cells, whereas lactate production was similar in both the M3myco+ and M3myco- cells. Glucose suppressed oxygen consumption in both cell lines indicating a Crabtree effect. The in-vitro proliferation rate was similar in both cell lines when seeded at low density, but was higher in the M3myco+ cells than in the M3myco- cells at higher cell densities. Tumor size at the primary inoculation site in flank was notably smaller and systemic metastasis in the syngeneic inbred VM mouse host was qualitatively less for the M3myco- cells than for the M3myco + cells, respectively. Survival was also longer in VM mice inoculated with the M3myco- cells compared to the M3myco+ cells. Our data indicate that M. arginini is an onco-modulator that might influence tumor growth through an effect tumor cell energy metabolism. (Supported by Boston College Research Expense fund).

Citation Format: Roberto Flores, Ashley K. Brown, Zeynep Akgoc, Thomas N. Seyfried. Mycoplasma arginini infection shifts the energy catabolism ratio of metastatic macrophages towards fermentation and is associated with an increase in primary tumor size, metastasis and malignancy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4318. doi:10.1158/1538-7445.AM2014-4318
Abstract 432: BIN3 is a novel 8p21 tumor suppressor gene that regulates the attachment checkpoint in epithelial cells
Authors: Marshall Netonia , Sanchez Felix , Llobet David , Barrueco Ruth Rodriguez , Castro Veronica , Kotlia Dylan , Pires Maira , Villagrasa Patricia , Putcha Preeti , Parsons Ramon , Pe'er Dana , Silva Jose
Published: May 2015

An important characteristic of multicellular organisms is the control that the tissue architecture exerts on the fate of individual cells. Epithelial cells sense their location through interactions with the extracellular matrix (ECM) and remove themselves by programmed cell death (anoikis) when those interactions are disturbed. Importantly, anoikis is a line of defense that has to be circumvented by cancerous epithelial cells to be able to leave their home environment and establish long distance metastases. Here, by combining a genome-wide RNAi screen and a novel algorithm to study copy number alterations (ISAR-DEL), we identify the Bridging Integrator-3 (BIN3) as a novel 8p21 tumor suppressor gene whose inactivation promotes escape from anoikis in epithelial cancers. Mechanistically, we link the tumor suppression function of BIN3 to its ability to relocate to the cell membrane after cell detachment and to induce a proapoptotic cascade. This death signaling is mediated by CDC42 activation of the P38-α stress pathway and the consequent accumulation of the apoptotic facilitator BimEL. Our results identify BIN3 as a novel epithelial tumor suppressor gene, provide novel insights on the mechanisms of attachment tumor suppressor checkpoint and highlight the importance of anoikis escape in driving cell transformation and metastasis in human cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Netonia Marshall, Felix Sanchez, David Llobet, Ruth Rodriguez Barrueco, Veronica Castro, Dylan Kotlia, Maira Pires, Patricia Villagrasa, Preeti Putcha, Ramon Parsons, Dana Pe'er, Jose Silva. BIN3 is a novel 8p21 tumor suppressor gene that regulates the attachment checkpoint in epithelial cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 432. doi:10.1158/1538-7445.AM2014-432