tbuckley/cabot-search huggingface dataset:
Abstract 2548: Oncogenic function and molecular mechanism of H19 noncoding RNA in colorectal cancer
Authors: Hui Ling, Masahisa Ohtsuka, Cristina Ivan, Martin Pichler, Meng Chen, Ondrej Slaby, Ajay Goel, Milan Radovich, George Calin
Journal: Cancer Research (2017)

Abstract The clinical significance of long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) remains largely unknown. We analyzed a large panel of cancer-associated lncRNAs in 483 TCGA CRC cases, and identified that H19 correlates most significantly with overall survival and disease-free survival, independent of stage and other clinical parameters. We validated the TCGA findings with two additional CRC cohorts. As one of the “oldest” lncRNAs, diverse activities of H19 including interaction with epigenetic regulators, regulation of microRNAs as competing endogenous RNA (ceRNA), and production of miR-675 as a primary transcript have been reported. However, an unbiased study to clarify the essential mechanisms of H19 is lacking. To decipher the functional involvement of H19 in CRC, we used an integrative approach combining unbiased microarray analysis, experimental validation, and bioinformatic analysis of clinical data. With such approach, we revealed not only previously reported mechanisms such as let-7 and MYC regulation by H19, but also several novel mechanisms that have not been appreciated before. We discovered a mechanism of H19 on regulating RB-E2F signaling and accordingly controlling cell cycle progression. We also identified for the first time that H19 regulates CDK8, an oncogenic driver in CRC pathogenesis, and consequently affects β-catenin activity (Firestein et al., Nature, 2008). We further identified an interaction of H19 with macroH2A, a histone variant reported to repress CDK8 transcription (Kapoor et al., Nature, 2010). Importantly, expression correlation analysis with clinical samples strongly supported the above-identified mechanisms. Combined analysis of H19 with its targets showed strong independent prediction power for CRC survival. These data indicate the clinical relevance of Rb-E2F and CDK8/β-catenin signaling in mediating H19’s oncogenic activity in CRC. Citation Format: Hui Ling, Masahisa Ohtsuka, Cristina Ivan, Martin Pichler, Meng Chen, Ondrej Slaby, Ajay Goel, Milan Radovich, George Calin. Oncogenic function and molecular mechanism of H19 noncoding RNA in colorectal cancer [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 2548. doi:10.1158/1538-7445.AM2017-2548
Abstract 2606: Accelerating clinical research using cloud technology
Authors: Arun Apte, Shonali Paul, Aditi Gade, Carolyn Compton
Journal: Cancer Research (2017)

Abstract Introduction: Existing protocols for clinical trials are typically slow and error-prone due to lack of informatics tools for sharing and accessing clinical data in real time. There is an increasing pressure on clinical trial laboratories to change the way clinical research is performed so as to minimize costs and speed up R&amp;D, which in turn will produce better and faster outcomes. Cloud-based technologies are emerging as one of the most viable options for streamlining the heavily regulated clinical research processes. Description: Cloud-based software tools such as laboratory information management systems (LIMS) are much more capable than traditional paper-based or desktop tools for accelerating a clinical trial life cycle. Cloud-based LIMS enhance collaboration between sponsors and investigators, enabling more timely and accurate sharing of information with pharmaceutical companies. Summary: Many sponsors are now adopting cloud-based LIMS for conducting clinical trials. The onus is on service providers to keep pace with the demands of the industry, comply with the regulatory framework and at the same time deliver value to CROs and testing labs by reducing costs and maintaining efficiency. Conclusion: CloudLIMS.com has developed a cloud based software called CloudLIMS Lite for managing clinical research workflows to provide a cost effective solution to the clinical research industry. Being on the cloud, CloudLIMS Lite facilitates users to access and share data in real time, across multiple laboratories in different geographical locations and adhere to the regulatory framework. This in turn improves their operational efficiency. CloudLIMS Lite uses 256-bit AES encryption SSL protocol, thereby enabling secure data transmission. CloudLIMS Lite deploys a separate database layer for each of its customers making it impossible for any third party to view or access data. Citation Format: Arun Apte, Shonali Paul, Aditi Gade, Carolyn Compton. Accelerating clinical research using cloud technology [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 2606. doi:10.1158/1538-7445.AM2017-2606
Abstract LB-223: Whole genome sequencing of rhabdomyosarcoma germline cohort identifies low frequency of pathogenic mutations
Authors: Nicholas Light, Philip Lupo, Javed Khan, Joshua Schiffman, Douglas Hawkins, Adam Shlien, David Malkin
Journal: Cancer Research (2017)

Abstract Introduction: Rhabdomyosarcoma (RMS) is among the most frequently occurring tumors in Li-Fraumeni syndrome patients and is often observed in patients with a strong family history of cancer. Recent studies suggest that at least 10% of children with cancer harbor an underlying pathogenic germline mutation, although the frequency in children with RMS is not well characterized. In this study we sought to determine the rate of likely pathogenic germline mutations in rhabdomyosarcoma patients, unselected for family history. Methods: Of 275 RMS patients enrolled on one clinical trial (COG ARST0531), whole-genome sequencing was performed on blood-derived DNA of an initial set of 50 using the Illumina HiseqX to an average sequencing depth of 44.9X [34.2-58.4]. Single nucleotide variants (SNVs) and Indels were called and filtered to select only those occurring in exons or splicing regions. Variants were further filtered to include only those with a frequency of &amp;lt;0.5% in the ExAC database and lying in one of 99 genes identified as a cancer predisposition gene in the COSMIC Cancer Gene census. Nonsynonymous SNVs were required to be predicted as deleterious by one or more of Polyphen, mutation assessor or sift. Results: Across the 50 initial samples, a total of 290 variants ([0-17], median of 5) passed the described filters. Notably, no point mutations were identified in TP53 in the initial 50 samples. Two samples contained variants annotated as pathogenic in ClinVar - a frameshift deletion in CHEK2 and a rare SNP in MUTYH. Also notable was a potentially pathogenic frameshift deletion in MSH6 that lacked previous annotation. Conclusions: Our preliminary analysis suggests a lower incidence of causative TP53 mutations in RMS than previously suggested. Whole genome sequencing of the remaining samples in the cohort along with analysis of copy number and structural variants is ongoing. Statistical analysis of the entire cohort of 275 patient samples will allow for the most complete characterization of the germline genomic landscape of rhabdomyosarcoma to date. This information will better inform clinical surveillance and management parameters for RMS patients and families. Citation Format: Nicholas Light, Philip Lupo, Javed Khan, Joshua Schiffman, Douglas Hawkins, Adam Shlien, David Malkin. Whole genome sequencing of rhabdomyosarcoma germline cohort identifies low frequency of pathogenic mutations [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-223. doi:10.1158/1538-7445.AM2017-LB-223
Abstract 4030: Celsee™ SingleCell Chip can retrieve rare single cells with 100% efficiency for genetic analysis
Authors: Kalyan Handique, Priya Gogoi, William Chow, Kyle Gleason, Auston Payne, Vishal Premdev Sharma, Yixin Wang
Journal: Cancer Research (2017)

Abstract Tumors are comprised of heterogeneous cells. Only a specific or rare population of tumor cells is capable of metastasizing through blood. While mapping out the genome of cancer cells, gene expression variations indicative of more aggressive cancer cells might be missed among the noise. Therefore, single cell gene expression and mutation analysis provide a more comprehensive and most precise information about the heterogeneity of cancer progression and metastasis. Although there has been a surge in technologies used for selection and analysis of single cells, single cell analysis of rare cells such as circulating tumor cells (CTCs) is fraught with technical challenges. Among many used techniques to isolate single cells, the most common cell separation method is cell sorting by flow cytometry, which requires cell labeling. The numerous steps involved in cell labelling and centrifugation result in significant cell loss and changes in gene expression. In addition, centrifugation may also cause shear-induced gene expression changes in viable cells. For other single cell analysis platforms, there is a minimum input of cells ranging from 200 - 1000 cells. Rare cells like CTCs are found in the range of 1-10 per mL of blood. Another challenge is that the input volume required for these systems is very low usually in microliters. Here, we introduce a novel microfluidic chip with 250,000 microwells which captures cells at 100% efficiency down to one cell with a dynamic range over 5 logs. The underlying principle of this technology is that the geometric pattern of the microfluidic chip captures a single cell from an initial volume of up to 1 mL of fluid due to cell settling. The unique microwell structure promotes easy fluid exchange without perturbing the cells from their captured locations, thereby eliminating cell loss during multistep downstream processing. Preliminary tests have shown that single or cluster of spiked cancer cells in blood can be immunostained, both live or fixed and can also be retrieved very efficiently from this chip using a micro capillary. The retrieved single cells can further be used for several single cell genetic analysis. We will present data describing cancer gene expression and gene mutation analysis in isolated single cells. Citation Format: Kalyan Handique, Priya Gogoi, William Chow, Kyle Gleason, Auston Payne, Vishal Premdev Sharma, Yixin Wang. Celsee™ SingleCell Chip can retrieve rare single cells with 100% efficiency for genetic analysis [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 4030. doi:10.1158/1538-7445.AM2017-4030
Abstract 4578: Does poor prognosis in African Americans with MSI-H colorectal cancer associate with altered immune markers
Authors: Umamaheshwari Golconda, Lena Sokol, Babak Shokrani, Edward Lee, Donna Hansel, Oluwole Fadare, Sandip Patel, Mehdi Nouraie, Hooman Soleimani, Zaki Sharif, Ali Afsari, Fareed Daremipouran, Hassan Brim, Hassan Ashktorab
Journal: Cancer Research (2017)

Abstract BACKGROUND: Microsatellite instability high (MSI-H) of sporadic colorectal carcinomas (CRC) is usually associated with improved prognosis and a high density of tumor-infiltrating lymphocytes. However, African Americans with MSI-H have poor prognosis. AIM: To evaluate whether or not expression of different immune and tumor markers individually or in combination in African American MSI-H CRC associate with the prognosis status. METHODS: Tissues Microarray (TMA) were prepared by microdissection from FFPE (Formalin Fixed Paraffin Embedded) blocks of 15 MSI-H patients. Immune markers (CD8+, Granzymes, Perforins, CD4+, STAT1, IRF1 and IRF5) and PD-L1 status were analyzed by immunohistochemistry (IHC). Demography and clinical data including TNM, tumor grading (WHO standard), histological type of the tumor, date of diagnosis, date of the last follow-up examination, treatment, comorbidities, metastasis, recurrence, 5-year disease-free survival and death were collected. RESULTS: There were 4 patients with improved prognosis (27%) with relatively high CD4 density (2 with &amp;gt;50% and 2 with 11-50%) regardless of PD-L1 status (3+/1-), stage (II,III), and other immune markers (CD8, CD4, Granzymes, Perforins, IRF1, IRF5 and STAT1). One of the improved prognosis patients with KRAS mutation has elevated expression of all considered immune markers besides CD4. There were 9 patients (6 dead, 3 alive) with poor prognosis, with different immune and tumor markers level (3 were PD-L1+ and 5 have relatively high CD4 count; but with low level of STAT1. There were also 2 patients with expected improved prognosis based on their immune markers level (stage II), however, they died within the 5 year period post-diagnosis, due to their age (98 and 87 years old). Conclusion: MSI-H Colorectal cancer from African American patients has poor prognosis which may correlate with the nature of tumor-associated immune response. Other factors such as MSH3 defects might cancel the positive prognosis of MSI-H status. Nonetheless, low STAT1 and low CD4 may be indicators of poorer prognosis. Citation Format: Umamaheshwari Golconda, Lena Sokol, Babak Shokrani, Edward Lee, Donna Hansel, Oluwole Fadare, Sandip Patel, Mehdi Nouraie, Hooman Soleimani, Zaki Sharif, Ali Afsari, Fareed Daremipouran, Hassan Brim, Hassan Ashktorab. Does poor prognosis in African Americans with MSI-H colorectal cancer associate with altered immune markers [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 4578. doi:10.1158/1538-7445.AM2017-4578
Abstract 5261: Tocopherols inhibit the estrogen-stimulated expansion of cancer stem cells via down-regulation of OCT4 and NFκB
Authors: Min Ji Bak
Journal: Cancer Research (2017)

Abstract Cancer stem cells have been suggested to play a role in tumor initiation, maintenance, resistance, and metastasis. Breast cancer stem cells are defined as CD44+/CD24- cell populations that have the properties of tumor-initiating ability, self-renewal and differentiation. Although the importance of estrogen in breast cancer is well established, the effects of estrogen on breast cancer stem cells are not fully understood. Vitamin E, which is consisted of different forms of tocopherols and tocotrienols, has anti-tumor effects in various cancers, including breast cancer. In the present study, we examined the effects of α-, γ-, and δ-tocopherol against estrogen-stimulated expansion of cancer stem cells. To determine the effects of tocopherols on breast cancer stem cells, the MCF-7 tumorsphere cell culture system, which enriches for mammary progenitor cells and putative breast cancer stem cells, was utilized. Treatment of MCF-7 tumorsphere with estrogen for four days resulted in an increase in CD44+/CD24- stem cell populations in tumorspheres as well as the number and size of tumorspheres. Tocopherols at 1 and 10 μM inhibited formation of estrogen-induced stem cell enriched tumorspheres, indicating that tocopherols reversed estrogen-induced expansion of breast cancer stem cells. Tocopherols decreased the expression of estrogen-related genes such as TFF/pS2, cathepsin D, progesterone receptor and SerpinA1 in estrogen-stimulated tumorspheres. In addition, the mRNA levels of stem cell markers, including OCT4, NFκB, SOX-2 and CD44, were upregulated by estrogen, which were downregulated by the treatment with tocopherols. Our results suggest that tocopherols repress the expansion of breast cancer stem cell population by regulating OCT4 and NFκB signaling. Tocopherols could be effective natural agents for the prevention and treatment of estrogen-induced breast cancer. (This work was supported in part by the National Institutes of Health grant R01 AT007036.) Citation Format: Min Ji Bak. Tocopherols inhibit the estrogen-stimulated expansion of cancer stem cells via down-regulation of OCT4 and NFκB [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 5261. doi:10.1158/1538-7445.AM2017-5261
Abstract 1032: Identification of Ran binding protein 6 as a novel negative regulator of EGFR and candidate tumor suppressor in glioblastoma
Authors: Wan-Ying Hsieh, Barbara Oldrini, Hediye Erdjument-Bromage, Paolo Codega, Maria S. Carro, Igor Vivanco, Dan Rohle, Carl Campos, Craig Bielski, Barry Taylor, Paul Tempst, Massimo Squatrito, Ingo K. Mellinghoff
Journal: Cancer Research (2017)

Abstract Amplification and overexpression of the epidermal growth factor receptor (EGFR) are common in glioblastoma (GBM) and frequently associated with silencing of the phosphatase and tensin homologue (PTEN) tumor suppressor. PTEN silencing has been associated with clinical resistance to EGFR tyrosine kinase inhibitors, in part by raising EGFR levels. Here, we investigated the effect of PTEN on the EGFR signaling complex by EGFR affinity immunopurification and mass spectrometry with and without PTEN knockdown. We identified Ran binding protein 6 (RanBP6), a 125-kDa protein of previously unknown functions, as EGFR interacting protein in PTEN expressing, but not PTEN knockdown cells. Further studies of the effect of RanBP6 on EGFR revealed that RanBP6 depletion by shRNA or CRISPR/Cas9-mediated gene silencing resulted in increased EGFR mRNA levels and upregulation of EGFR promoter activity. Consistent with a model of a negative EGFR regulation by RanBP6, we observed an inverse correlation between RanBP6 and EGFR mRNA levels in PTEN wildtype but not PTEN altered cancer cells in a large panel of human cancer cell lines (Cancer Cell Line Encyclopedia). To further understand the mechanism of how RanBP6 negatively regulates EGFR mRNA level, we found that RanBP6 interacted with nuclear Ran-GTPase and repressed EGFR transcription by promoting nuclear import of Signal transducer and activator of transcription 3 (STAT3). Lastly, RanBP6 appeared to be frequently deleted on chromosome 9p in GBM. We showed that RanBP6 silencing raised EGFR levels and signal output and accelerated in-vivo glioma growth. Our results establish a novel function of RanBP6 as a link between EGFR signaling and the Ran-mediated nuclear import pathway, and identify RanBP6 as candidate tumor suppressor on chromosome 9p. Citation Format: Wan-Ying Hsieh, Barbara Oldrini, Hediye Erdjument-Bromage, Paolo Codega, Maria S. Carro, Igor Vivanco, Dan Rohle, Carl Campos, Craig Bielski, Barry Taylor, Paul Tempst, Massimo Squatrito, Ingo K. Mellinghoff. Identification of Ran binding protein 6 as a novel negative regulator of EGFR and candidate tumor suppressor in glioblastoma [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 1032. doi:10.1158/1538-7445.AM2017-1032
Abstract 5576: BPM 31510, a clinical stage candidate demonstrates potent anti-tumor effect in an immune-competent syngeneic pancreatic cancer model
Authors: Shiva Kazerounian, Aishwarya Sarma, Nidhi Gaur, Maria D. Nastke, Tulin Dadali, Anne R. Diers, Stephane Gesta, Vivek K. Vishnudas, Rangaprasad Sarangarajan, Niven R. Narain
Journal: Cancer Research (2017)

Abstract BPM 31510, a clinical stage nanodispersion of ubidecarenone, demonstrates anti-tumor effects by eliciting an anti-Warburg metabolic switch in cancer. Previous studies in an immune compromised PaCa2 xenograft model has unequivocally demonstrated significant efficacy of BPM 31510 on tumor volume and survival. The fundamental property of BPM 31510 to influence mitochondrial bioenergetics and the recognized interplay between T cell metabolism and maturation prompted investigation into the effects of BPM 31510 on T lymphocyte functions in eliciting anti-cancer effects. In this study BPM 31510 selectively influenced activation and maturation of T cells in murine peripheral blood mononuclear cells (PBMCs). Moreover, in addition to determining changes in the CD3+ population, changes in surface expression of PD-1 and CTLA4 along with the IFN-γ secretion were examined. Murine cancer cell lines exposed to BPM 31510 were associated with variable sensitivity with highly metabolic tumor types being most sensitive. Next, the anti-cancer activity of BPM 31510 in an in vivo immunocompetent syngeneic Pan02 rodent model was investigated. Murine Pan02 pancreatic cancer cells were implanted subcutaneously into C57BL/6 mice. Tumors with mean volume of 80 mm3 were treated twice a day with vehicle control or BPM 31510 at 25, 50, 100 mg/kg, administered intraperitoneal. Tumor volumes were measured every 4 days. At day 21 post treatment, tumors were harvested and analyzed for the level of infiltrating immune cells by immunofluorescent staining with CD8+ for T cells and F4/80 for tumor macrophages. These results demonstrate a dose-dependent reduction in tumor volume following 21 days of BPM 31510 treatment. In summary, BPM 31510 exerts potent anti-tumor effects through its dual function of modulating tumor cell metabolism and potentially influencing immune check-point to improve overall survival outcomes. Citation Format: Shiva Kazerounian, Aishwarya Sarma, Nidhi Gaur, Maria D. Nastke, Tulin Dadali, Anne R. Diers, Stephane Gesta, Vivek K. Vishnudas, Rangaprasad Sarangarajan, Niven R. Narain. BPM 31510, a clinical stage candidate demonstrates potent anti-tumor effect in an immune-competent syngeneic pancreatic cancer model [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 5576. doi:10.1158/1538-7445.AM2017-5576
68Ga-PSMA Uptake in an Incidentally Detected Gastrointestinal Stromal Tumor in a Case of Suspected Carcinoma Prostate
Authors: Arun Sasikumar, Ajith Joy, MRA Pillai, Bindu S, Sudin SR
Journal: Clinical Nuclear Medicine (2017)

A 74-year-old man with suspected prostate cancer and a previously negative transrectal ultrasound–guided prostate biopsy underwent 68Ga-PSMA PET/CT. Scan showed no abnormal tracer concentration in enlarged prostate gland to suggest prostate cancer. Note was made of an incidentally detected well defined soft tissue lesion in the greater curvature of the stomach with moderate tracer concentration in its intraluminal portion. Biopsy of the lesion revealed gastrointestinal stromal tumor.