tbuckley/cabot-search huggingface dataset:
Abstract 4260: Increased mutation burden in normal-appearing lung tissues with high cancer risk
Authors: Emi Kubo, Hideyuki Takeshima, Noriko Motoi, Toshikazu Ushijima
Journal: Cancer Research (2017)

Abstract Background: Genetic alterations are considered to be accumulated in normal tissues at extremely low levels by exposure to various carcinogenic factors, and the degree of accumulated alterations, namely mutation burden, is likely to be associated with cancer risk. In lung tissues, smoking is a well-known carcinogenic factor, and is considered to be involved in accumulation of mutation burden. However, due to the limitation of detection methods of such extremely low frequency mutations, the presence of mutation burden in normal human lung tissues has been unclear. To overcome this limitation, we recently developed a new method to detect mutations with extremely low frequency by sequencing 100 DNA molecules using a next generation sequencer[Yamashita, submitted]. Aim: We aimed to reveal 1) the presence of mutation burden in normal lung tissues, and 2) its association with cancer risk. Methods and results: The presence of somatic mutations was analyzed in 55 cancer-related genes (totally 15,724 bp) in normal lung tissues (n = 11) obtained from background tissues of lung metastasis of cancer patients, without smoking history, other than those with lung cancers (''entirely normal lung tissues'') and non-cancerous lung tissues (n = 11) of lung cancer patients with smoking history (''smoking-exposed normal tissues''). The mutation frequency in smoking-exposed normal tissues (2.7 ± 0.8×10-5/bases) was significantly higher than that in entirely normal tissues (1.8 ± 0.5×10-5/bases) (p= 0.0189). C to T transition was most frequent in both smoking-exposed normal tissues (60% of detected base substitutions) and entirely normal tissues (61%), but the fractions were not different between the two groups. In contrast, C to A transversion, the signature mutation of smoking, was more frequent in smoking-exposed normal tissues (4%) than in entirely normal tissues (2%). Accumulation of somatic mutations tended to be associated with cancer risk [OR = 3.75 (95% CI = 0.54-26.046)]. Conclusion: It was shown, for the first time, that somatic mutations were accumulated in normal lung tissues with high cancer risk, possibly by exposure to tobacco smoking. Citation Format: Emi Kubo, Hideyuki Takeshima, Noriko Motoi, Toshikazu Ushijima. Increased mutation burden in normal-appearing lung tissues with high cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4260. doi:10.1158/1538-7445.AM2017-4260
Freeze‐Drying as a Novel Biofabrication Method for Achieving a Controlled Microarchitecture within Large, Complex Natural Biomaterial Scaffolds
Authors: Claire M. Brougham, Tanya J. Levingstone, Nian Shen, Gerard M. Cooney, Stefan Jockenhoevel, Thomas C. Flanagan, Fergal J. O'Brien
Journal: Advanced Healthcare Materials (2017)

Abstract The biofabrication of large natural biomaterial scaffolds into complex 3D shapes which have a controlled microarchitecture remains a major challenge. Freeze‐drying (or lyophilization) is a technique used to generate scaffolds in planar 3D geometries. Here we report the development of a new biofabrication process to form a collagen‐based scaffold into a large, complex geometry which has a large height to width ratio, and a controlled porous microarchitecture. This biofabrication process is validated through the successful development of a heart valve shaped scaffold, fabricated from a collagen‐glycosaminoglycan co‐polymer. Notably, despite the significant challenges in using freeze‐drying to create such a structure, the resultant scaffold has a uniform, homogenous pore architecture throughout. This is achieved through optimization of the freeze‐drying mold and the freezing parameters. We believe this to be the first demonstration of using freeze‐drying to create a large, complex scaffold geometry with a controlled, porous architecture for natural biomaterials. This study validates the potential of using freeze‐drying for development of organ‐specific scaffold geometries for tissue engineering applications, which up until now might not have been considered feasible.
Abstract 5265: Breast cancer stem cell inhibition by benzyl isothiocyanate is hampered by induction of Kruppel-like factor 4
Authors: Su-Hyeong Kim, Yong Wan, Shivendra V. Singh
Journal: Cancer Research (2017)

Abstract Breast cancer is a leading cause of cancer-related deaths among women in the United States. Over the last decade, breast cancer stem cells (bCSC) have been identified and characterized as a key player in breast cancer progression and recurrence. Benzyl isothiocyanate (BITC) is a highly promising cancer chemopreventive constituent of edible cruciferous vegetables such as garden cress. We have shown previously that BITC inhibits bCSC in cultured breast cancer cells (MCF-7 and SUM159 cells) and in spontaneous tumors of mouse mammary tumor virus-neu (MMTV-neu) mice in vivo. Krüppel-like factor 4 (KLF4), a zinc finger transcription factor, is known as both oncogene and tumor suppressor in various types of human cancers and plays an important role in reprogramming differentiated somatic cells into induced pluripotent stem cells. The present study demonstrates that KLF4 impedes bCSC inhibition by BITC. Exposure of breast cancer cells (MCF-7, MDA-MB-231, and SUM159) to pharmacological concentrations of BITC (2.5 and 5 µM) resulted in induction of KLF4 protein, which was accompanied by increase of its transcription. In addition, BITC treatment increased nuclear level of KLF4 in breast cancer cells. KLF4 protein expression was also higher in tumors form BITC-treated MMTV-neu mice compared with the control group. Ectopic expression of KLF4 in MCF-7 cells conferred marked protection against BITC-mediated inhibition of bCSC as evidenced by aldehyde dehydrogenase 1 (ALDH1) activity. Consistent with these observations, BITC-mediated inhibition of bCSC in MCF-7, MDA-MB-231 and SUM159 cells was significantly augmented by RNA interference of KLF4 as evidenced by ALDH1 activity and frequency of mammospheres. KLF4 overexpression also increased cell migration capacity of MCF-7 cells. Furthermore knockdown of KLF4 augmented BITC-mediated inhibition of cell migration in SUM159 cells. These results suggest that anticancer activity of BITC may be enhanced by KLF4 inhibition or knockdown in breast cancer cells. This study was supported by the grant RO1 CA129347-09 awarded by the National Cancer Institute. Citation Format: Su-Hyeong Kim, Yong Wan, Shivendra V. Singh. Breast cancer stem cell inhibition by benzyl isothiocyanate is hampered by induction of Kruppel-like factor 4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5265. doi:10.1158/1538-7445.AM2017-5265
Abstract 4302: Disulfiram possesses antitumor activity and inhibits cancer stem-like properties via inhibition of STAT3 activation in triple-negative breast cancer cells
Authors: Yoon-Jae Kim, Nahyun Lee, Eunhye Oh, Daeil Sung, Tae-Min Cho, Ji Young Kim, Jae Hong Seo
Journal: Cancer Research (2017)

Abstract Disulfiram (DSF), a clinically used treatment for alcohol dependence, is considered as a potential anti-cancer agent due to its cytotoxicity in many cancer cell types on copper (Cu)-dependent processes. However, the molecular mechanisms underlying DSF-induced antitumor activity in triple-negative breast cancer (TNBC) are still poorly understood. Here, we hypothesized that DSF induces antitumor effects by targeting cancer stem cells (CSCs) and STAT3 signaling in TNBC. We then examined the effects of DSF in combination with Cu on the cell viability and apoptosis, cell proliferation and survival, as well as CSC-like properties in MDA-MB-231 and 4T1 TNBC cell lines. DSF/Cu effectively induced cytotoxicity and apoptotic cell death, concomitant with caspase-3 activation and PARP cleavage. DSF/Cu also significantly suppressed cell migration and mammosphere formation, which are accompanied by a remarkable decrease in the CD44+/CD24- (or CD49f+/CD24+ in mouse 4T1 cells) stem-like population and ALDH1 activity. These effects were functionally associated with the inhibition of STAT3 phosphorylation (Tyr705). Furthermore, DSF/Cu treatment resulted in the downregulation of cyclin D1 and survivin expression, which are downstream targets of STAT3 signaling. Interestingly, phosphorylated STAT3 and STAT3 downstream signaling were highly upregulated in the mammospheres, and these upregulated molecules were significantly decreased by DSF/Cu treatment. In MDA-MB-231-derived xenograft model, DSF administration elicited a significant reduction in tumor growth with a noticeable downregulation of CD44, ALDH1 and phosphorylated STAT3 levels. Taken together, our results suggest that therapeutic treatment to DSF can effectively manifest antitumor activity by reducing CSC-like properties, and that STAT3 could be a key molecule of aggressive TNBC that is targeted by DSF. Note: This abstract was not presented at the meeting. Citation Format: Yoon-Jae Kim, Nahyun Lee, Eunhye Oh, Daeil Sung, Tae-Min Cho, Ji Young Kim, Jae Hong Seo. Disulfiram possesses antitumor activity and inhibits cancer stem-like properties via inhibition of STAT3 activation in triple-negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4302. doi:10.1158/1538-7445.AM2017-4302
Abstract 5396: An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers
Authors: Dalia Dhingra, Richard Chien, Jian Gu, Dumitru Brinza, Ruchi Chaudhary, Kunal Banjara, Yanchun Li, Efren Ballesteros-Villagrana, Kelli Bramlett
Journal: Cancer Research (2017)

Abstract Noninvasive detection of rare mutations in blood could allow tumor monitoring for research purposes. Research studies have suggested that cfDNA contains DNA from tumor cells with somatic mutations that could inform on tumor progression and therapeutic resistance. Here, we demonstrate a complete workflow from a single tube of blood through data analysis for research samples down to a 0.1% allelic frequency. The low abundance tumor mutations found in cfDNA requires sensitive and accurate mutation detection. We have developed two panels that utilize an amplification-based assay that generates tagged DNA copies, which allows detection of low abundance tumor mutations found in cfDNA. The two panels allow multiplex interrogation of primary driver and resistance mutations specific to ctDNA from breast and colon cancer. The Oncomine Colon cfDNA panel targets 236 hotspots within 14 genes while the Oncomine Breast cfDNA panel covers 157 hotspot mutations in 10 genes. This workflow was validated from matched single blood tubes, Streck and K2EDTA. Additionally, the utility for cancer research was demonstrated with concordance studies using matched FFPE and plasma from oncology samples. To further characterize these panels we have developed an oncology control for cfDNA with nucleosome fragment sizing and minimal sonication damage. This engineered control contains SNPs and indels at 0.1% allelic frequencies, orthogonally confirmed with TaqMan based Rare Mutation assays. With this control, the Oncomine Breast cfDNA panel had over 81% sensitivity and 99.9% specificity. The Oncomine Colon cfDNA panel had over 85% sensitivity and 100% specificity. The Oncomine Breast cfDNA panel and Oncomine Colon cfDNA panel integrated into a complete workflow starting from a single tube of blood can advance oncology research with the ability to detect blood based cancer biomarkers present at 0.1%. Citation Format: Dalia Dhingra, Richard Chien, Jian Gu, Dumitru Brinza, Ruchi Chaudhary, Kunal Banjara, Yanchun Li, Efren Ballesteros-Villagrana, Kelli Bramlett. An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5396. doi:10.1158/1538-7445.AM2017-5396
Abstract 5823: Modulation of the Hippo pathway protein YAP as a mechanism of resistance to MEK inhibition in MAPK hyperactivated neuroblastoma
Authors: Grace E. Coggins, Lori S. Hart, Jimmy Elias, John M. Maris
Journal: Cancer Research (2017)

Abstract Background: Current therapies for high-risk neuroblastoma are highly toxic and ineffective, as a majority of patients will face therapy-resistant relapses. Our recent whole genome sequencing analysis revealed that a majority of relapsed tumors had mutations causing RAS-MAPK pathway activation. Recent studies have implicated the Hippo pathway transcriptional coactivator protein YAP in relapsed neuroblastoma as well as resistance to MEK inhibition in other cancer models. Based on these findings, we hypothesized that YAP activity may lead to acquired resistance to MEK inhibition, and that dual inhibition of these two pathways may have synergistic therapeutic efficacy. Methods: We selected the cell line NLF from a panel of NB cell lines due to its high YAP expression and NF1 loss. NLF cells were treated with MEK inhibitor trametinib (20 nM) over a 72-hour period and whole cell lysates and nuclear lysates were collected for immunoblot. Effects of YAP knockdown via siRNA transfection with and without trametinib co-treatment on survival were assessed by CellTiter-Glo and RT-CES. Cell signaling analyses of tumor lysates from mouse SKNAS (NRAS Q61K) xenografts treated with vehicle, 0.3 mg/kg, 1 mg/kg, or 3 mg/kg for YAP, ERK, and apoptosis pathways were performed via immunoblot. Results: Immunoblots of 72-hour time course treatments of trametinib in NLF showed decreased pYAP, the cytosolic inactive form of the YAP protein, indicating increased YAP capable of translocating to the nucleus, which was confirmed by analyses of nuclear extracts. siRNA-mediated knockdown of YAP alone in NLF cells had a modest effect on survival, while combinatorial inhibition of MEK and YAP signaling caused a significant reduction in cellular proliferation and survival. Immunoblotting of trametinib-treated SKNAS xenografts indicated decreased pYAP and pERK in response to increasing trametinib dose, while total YAP levels remained constant. Conclusion: Our results demonstrate that prolonged trametinib exposure causes a marked nuclear enrichment of unphosphorylated YAP and co-inhibition of MEK and YAP in neuroblastoma models effectively reduces proliferation and survival. We are currently investigating the effects of MEK inhibition on the expression of YAP target genes and on cellular proliferation upon modulation of YAP protein expression. Note: This abstract was not presented at the meeting. Citation Format: Grace E. Coggins, Lori S. Hart, Jimmy Elias, John M. Maris. Modulation of the Hippo pathway protein YAP as a mechanism of resistance to MEK inhibition in MAPK hyperactivated neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5823. doi:10.1158/1538-7445.AM2017-5823
Abstract 3914: KLF4-dependent perivascular plasticity enhances pre-metastatic niche formation and metastasis
Authors: Meera Murgai, Wei Ju, Matthew Eason, Jessica Kline, Rosandra N. Kaplan
Journal: Cancer Research (2017)

Abstract Metastasis causes most cancer deaths, and new therapies that are based on a deeper understanding of this process are required to improve patient survival. Metastatic tumor cell colonization and growth is facilitated by a pre-metastatic niche microenvironment composed of hematopoietic cells, stromal cells, and extracellular matrix that support tumor survival and growth. Perivascular cells, including vascular smooth muscle cells (vSMCs) and pericytes, are a key cell population involved in new vessel formation critical to primary tumor development. Given the well-described plasticity of perivascular cells, we sought to determine whether perivascular cells regulate tumor cell survival and proliferation at metastatic sites. Using perivascular cell-specific and pericyte-specific lineage tracing models, we demonstrated that perivascular cells lose traditional vSMC/pericyte marker expression in response to tumor-secreted factors, and exhibit increased proliferation, migration and extracellular matrix (ECM) synthesis. Expression of the pluripotency gene Klf4 is increased and is critical for this phenotypic transition to a less differentiated state characterized by increased proliferation and ECM production. Genetic inactivation of Klf4 specifically in perivascular cells decreases pre-metastatic perivascular cell proliferation and consequently integrin-fibronectin dependent tumor metastasis. Our data reveal a previously unidentified role for perivascular cells in pre-metastatic niche formation, and suggest that modulation of stromal cell plasticity may provide a novel strategy for limiting metastasis. Citation Format: Meera Murgai, Wei Ju, Matthew Eason, Jessica Kline, Rosandra N. Kaplan. KLF4-dependent perivascular plasticity enhances pre-metastatic niche formation and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3914. doi:10.1158/1538-7445.AM2017-3914
Abstract 2124: Differentiation of myeloid and multiple myeloma cell lines by inecalcitol involves a marked decrease in CD44 and CD49d cell surface labeling
Authors: Susan Benjamin, Cecile Planquette, Remi Delansorne
Journal: Cancer Research (2017)

Abstract Inecalcitol is a vitamin D receptor (VDR) agonist characterized by a high antiproliferative activity on various cancer cell lines (Okamoto et al., 2012; Ma et al., 2013) and a low calcemic potential as demonstrated by the high maximal tolerated oral daily dose of 4 mg in human patients (Medioni et al., 2014). On myeloid cells, inhibition of proliferation by vitamin D derivatives is paralleled by induction of differentiation into a monocyte/macrophage phenotype, mostly described as gain of functions (increase in lysozyme activity, phagocytosis and cell motility; Abe et al., 1981) and of the cell surface CD11b and CD14 biomarkers. The stimulation of the secretion of cathelicidin, a natural human antimicrobial peptide, is another specific activity of vitamin D and its derivatives (Wang et al., 2004). During a screening of 48 CD biomarkers on 4 human myeloid cell lines (HL-60, U-937, MOLM-13 and THP1) and 4 human multiple myeloma cell lines (MM.1R, MM.1S, L-363 and RPMI-8226) treated for 72 hours at 10 nM, we recently discovered that inecalcitol reproducibly induces CD38 expression (Benjamin et al., 2016), another gain of function. We now report the decrease in CD44 and CD49d cell surface labeling in all 8 cell lines (except CD44 in L-363 cells). This loss of functions reached -60% to -70% in MOLM-13 and HL-60 cells. We have then determined the EC50 (mean ± SEM; n = 3 or 4) of inecalcitol for several differentiation parameters on HL-60 cells. The most sensitive gains or loss of functions were the secretion of cathelicidin (0.2 ± 0.1 nM), the induction of CD38 (0.3 ± 0.1 nM) and the decrease in CD44 (0.8 ± 0.4 nM). Inhibition of proliferation (1.9 ± 0.8 nM) was exactly parallel to induction of CD11b (1.8 ± 0.8 nM). Decrease in CD49d (6.6 ± 1.1 nM) and increase in CD14 (8.0 ± 0.5 nM) occurred as final markers of differentiation by inecalcitol. CD44 is the receptor for hyaluronic acid; it is found on the surface of acute myeloid leukemia stem cells and suspected to favor the spread and relapse of the disease. CD49d is the integrin α4-subunit involved in the interactions of tumor cells with their microenvironment resulting in their “hiding” and survival. Therefore, decreasing both CD44 and CD49d represents newly identified potential beneficial pro-differentiation effects of inecalcitol. Citation Format: Susan Benjamin, Cecile Planquette, Remi Delansorne. Differentiation of myeloid and multiple myeloma cell lines by inecalcitol involves a marked decrease in CD44 and CD49d cell surface labeling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2124. doi:10.1158/1538-7445.AM2017-2124
Abstract LB-087: Stage specific re-calibration of E2F1 function after RB loss
Authors: Amy C. Mandigo, Christopher McNair, Kexin Xu, Fugen Li, Matthew J. Schiewer, Myles Brown, Karen E. Knudsen
Journal: Cancer Research (2017)

Abstract Prostate cancer (PCa) is the most frequently diagnosed non-cutaneous malignancy, and the third leading cause of cancer death in males in the United States. The development of the disease is reliant on the activity of the androgen receptor (AR), which promotes proliferation and is required for cell growth and survival. Deregulation of AR leads to the progression of PCa to the incurable form of disease termed castration-resistant prostate cancer (CRPC). One of the underlying mechanisms of AR deregulation is the loss of function of the retinoblastoma (RB) tumor suppressor protein. RB loss is almost exclusively seen in CRPC and is sufficient to induce a CRPC phenotype in primary PCa models. However, RB function is only lost in roughly 30% of tumors. The remaining 70% of tumors that progress to CRPC do so via other mechanisms and retain RB function. A subset of RB positive CRPC tumors progress to lose RB function even in this post-CRPC transition stage of disease. Biological assessment performed in isogenic RB knockdown, both hormone-sensitive and CRPC models, identified distinct functional consequences of RB loss depending on disease state. Transcriptome analysis identified opposing regulated gene signatures between disease stages. Further investigation of the E2F1 cistrome revealed differential E2F1 binding with RB loss in hormone sensitive and CRPC models, identifying distinct roles of E2F1, in the absence of RB, in different disease states. Data to be discussed reveal the stage-specific molecular pathways driven by E2F1 upon RB loss with the potential to promote disease progression. Citation Format: Amy C. Mandigo, Christopher McNair, Kexin Xu, Fugen Li, Matthew J. Schiewer, Myles Brown, Karen E. Knudsen. Stage specific re-calibration of E2F1 function after RB loss [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-087. doi:10.1158/1538-7445.AM2017-LB-087