bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2276: Efficient curation and ontology mapping of clinical and phenotypic data
Authors: Edgren Henrik , Mano Beatriz , Laaksonen Maria
Published: August 2018

Heterogeneity within and between data sets is one of the primary impediments to sound and efficient data analysis. This heterogeneity can arise from many sources: data collection practices can change over time, even within the same study; rigorous standards for data encoding may be missing, leading to inter-individual heterogeneity in data encoding; or the data may originally have been collected for a different purpose (e.g. EHR data). Additionally, narrative text, such as medical statements, are inherently unstructured and require curation before analysis.

No matter which source(s) heterogeneity derives from, curation of the data is necessary for efficient, accurate and reproducible data analysis. This not only includes correcting errors and standardizing encoding, but also extends to enriching the data through mapping it to relevant medical ontologies, such as SNOMED CT, or other standardized terminologies, such as Research Resource Identifiers.

To solve the most common issues in clinical and phenotypic data curation, we have developed the AccurateTM data curation and ontology mapping solution. It combines an intuitive web-based user interface for data cleaning with efficient solutions for semi-automated ontology mapping of both structured data and narrative text. For structured data, tokenized and stemmed data items are mapped against ontologies indexed in Elasticsearch. Term names, their synonyms and the local ontology structure are then used to query the target ontology, with a list of best matches returned along with a quality score for the mapping. Ontology tagging of narrative text is based on a sentence-based deep learning approach, analyzing sentences to classify and ontology map identified text units. In practice, combining a bidirectional long short term memory network with a conditional random field model into a named entity recognition system (bio-NER). Preliminary benchmarking of the bio-NER system on the MIMIC III data set suggests good specificity and sensitivity for identification of biomedically relevant concepts.

In summary, we here present an intuitive and highly efficient solution for curating clinical and phenotypic data, as well as enriching it using ontology mapping of both structured and narrative data.

Citation Format: Henrik Edgren, Beatriz Mano, Maria Laaksonen. Efficient curation and ontology mapping of clinical and phenotypic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2276.
Abstract 2285: Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer
Authors: Feng Yang-Yang , Ramu Avinash , Skidmore Zachary L. , Kunisaki Jason , Cotto Kelsy C. , Griffith Obi L. , Griffith Malachi
Published: August 2018

The interpretation of variants in cancer is frequently focused on direct protein coding alterations. However, most somatic mutations are in noncoding regions of the genome, and even exonic mutations may have unidentified noncoding consequences. Here we present Regtools, a software package designed to efficiently identify variants that may cause aberrant splicing in tumors. Our tool integrates variant calls from genomic data with junctions extracted from transcriptomic data in order to examine potential cis alterations to splicing near a somatic variant. Based on user-defined parameters and position relative to known exons, variants are first annotated as splicing relevant or not. Splicing junctions are inferred from transcriptomic sequencing data, and comparison of junctions to a reference transcriptome allows for identification and annotation of novel junctions and nearby regulatory or splicing motifs. From there, mutations are associated with junctions that overlap with a flanking region. In order to evaluate Regtools, we used it to analyze the transcriptional output of tumor-sequencing data from two cohorts of cancer patients, one of hepatocellular carcinoma and one of small cell lung cancer with 28 and 21 samples, respectively. We performed whole-exome and RNA sequencing on each sample. Somatic variants were called on whole-exome alignment data. For each cohort, we compared the junctional profiles between tumors and identified numerous examples of variants for which there are elevated levels of proximal novel or known junctions. Moreover, out of 754 (153 in HCC; 601 in SCLC) variants identified as splicing relevant by our approach, only 165 (20 in HCC; 145 in SCLC) were annotated as splicing relevant by Ensembl's Variant Effect Predictor, using the recommended “per_gene” option. This preliminary analysis illustrates the importance of an efficient, user-friendly computational tool for identifying important noncoding variants that would otherwise be undervalued or perhaps even completely ignored by traditional methods and annotators. Regtools is freely available and open source (https://github.com/griffithlab/regtools).

Citation Format: Yang-Yang Feng, Avinash Ramu, Zachary L. Skidmore, Jason Kunisaki, Kelsy C. Cotto, Obi L. Griffith, Malachi Griffith. Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2285.
Abstract 2292: Comparison of Q Path and Aperio Image Analysis System for quantification of ER and PR by IHC in breast carcinoma TMAs
Authors: Jacobsen Max Henry , Temm Constance , Sandusky George
Published: August 2018

According to the Centers for Disease Control and Prevention, breast cancer is still one of the most common cancer in women, and top one or two in cancer mortality rates for all races of women. Novel drug treatments are needed to develop new treatments and clinical validation with IHC are common in research. Some common methods of validations are using Tissue MicroArrays (TMAs). In this study 5 TMAs containing approximately 100 cores each were stained with Estrogen Receptor (ER) and Progesterone Receptor (PR). Paraffin-embedded tissue blocks were obtained from the Indiana University Heath Pathology Laboratory under IRB approved protocols. Immunostainings with ER and PR antibodies (DAKO) were preformed using the DAKO-flex platform system at the IU Health Pathology Laboratory. The slides were digitally imaged using the Aperio Digital Imaging System. The SVS digital images were quantified using two different image analysis systems. One imaging system was the Aperio TMALab software, the other was Q Path image analysis software. Both systems were compared not only on the basis of performance, but among other parameters such as user friendliness and the ability to use a SVS image file type. When comparing the systems, the algorithm of Q Path was altered to closely match the algorithm of the standard Aperio positive pixel algorithm. Two measurements of antibody quantification were compared, one being positive pixel percentage, the other being an H Score. A regression line was used to show correlation between systems. Standard deviations were used to compare data against a standard pathology hand count of 0, 1, 2, and 3. The results show a strong correlation (R-squared value at or greater than 0.85) between the two imaging systems for both the positive pixel algorithm and H Score. The tightness may be due to consistent and rigorously explored in the past 20 years with both of these nuclear antibodies. Further studies should help distinguish any other possible errors using novel biomarkers and also delineate any discrepancies between a nuclear expressions against both a cytoplasmic and/or cell membranous expressions. In conclusion, Aperio Imaging analysis systems and Q path image analysis systems were in strong correlation, and therefore interchangeable in scientific research.

Citation Format: Max Henry Jacobsen, Constance Temm, George Sandusky. Comparison of Q Path and Aperio Image Analysis System for quantification of ER and PR by IHC in breast carcinoma TMAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2292.
Abstract 2310: Targeting transcription-associated CDKs is an effective way to combat glioblastoma and medulloblastoma with minimal effect on primary neurons
Authors: Bhutada Isha , Chellappan Srikumar , Padmanabhan Jaya
Published: August 2018

Glioblastoma multiforme (GBM) is the most prevalent and malignant brain tumor in adults. Currently there are no effective therapies to manage the disease efficiently. Medulloblastoma is the most common type of pediatric tumor and accounts for approximately 15% of all pediatric brain tumors. We aimed to determine if targeting the transcription-associated cyclin-dependent kinases, cdk7 and cdk9, using specific inhibitors, could interfere with the growth and metastatic properties of glioblastoma and medulloblastoma cell lines. We tested the effectiveness of Flavopiridol, a known inhibitor of cdk4, cdk6, pTEFb and cdk9; THZ1, a cdk7 inhibitor; and SNS032, which is known to inhibit cdk2, cdk7 and cdk9, on U87 and SNB19 glioblastoma, H4 neuroglioma and Daoy medullobastoma cells. Treatment with these pharmacological agents showed very strong cytotoxic effects on these cancer cells as measured by MTT (3-(4, 5-dimethylthiazol-2yl)-2, 5-diphenyl tetrazolium bromide) assay. Among these agents the cdk7 inhibitor was most effective and showed efficacy at nanomolar concentrations. Additionally, the inhibitors interfered with the cancer cell migration, as measured by wound healing assay, and anchorage independent growth, as measured by soft agar colony formation. In stark contrast, the inhibitors had no cytotoxic effects on primary neurons. Mechanistically, western blot analysis showed that the tumor cells treated with the inhibitors had reduced levels of Pol II C-terminal domain phosphorylation, indicative of its inhibition and suppression of transcription. Furthermore, inhibitor treatment resulted in a significant reduction in p70S6 kinase phosphorylation, suggesting that in addition to the transcriptional machinery, the translational machinery is also affected upon treatment with the aforementioned cdk inhibitors. Immunostaining analysis of the cells showed a marked reduction in the levels of P-Pol II and P-p70S6 kinase upon inhibitor treatment, confirming that the cdk inhibitors indeed interfere with both transcription and translation. These inhibitors appear to be working in a p53-dependent fashion. These novel findings shed light on potential mechanisms that can be targeted to combat both glioblastoma and medulloblastoma effectively. More specifically, our studies imply that cdk7 and cdk9 inhibitors may serve as potential therapies for effective management of brain tumor.

Citation Format: Isha Bhutada, Srikumar Chellappan, Jaya Padmanabhan. Targeting transcription-associated CDKs is an effective way to combat glioblastoma and medulloblastoma with minimal effect on primary neurons [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2310.
Abstract 2353: Analysis of noncoding mutations in cancer revealed novel potentially pathogenic recurrent mutations
Authors: Koyama Takahiko , Parida Laxmi
Published: August 2018

Introduction:

98% of mutations are non-coding mutations. Thus far, most non-coding mutations are ignored or merely classified as variant of unknown significance with a few exceptions, despite the fact that non-coding region plays significant role in regulations and other important biological processes. Although they would not be directly druggable, these non-coding mutations might be important for cancer etiology, response to treatments and prognosis assessments.

Method:

Mutations in non-coding genes, intron, upstream and downstream, and intergenic regions are collected from COSMIC and TCGA as defined in Ensemble GRCh37.75 gene definition and hg19 RefSeq. Over 15 million non-coding mutations are analyzed for recurrence over 10 samples. Mutations in neighborhood of IG genes and dbSNP150 polymorphisms are removed from further investigation. We analyzed remaining mutations for possible super enhancer and transcription factor binding.

Result:

911 distinct recurrent mutations are identified. Promoter mutations in protein coding genes like MPRS31, NUDFB9, SZT2, WASF3 in addition to TERT are discovered. Intronic mutations of well-known cancer genes such as HIF1A, NF1, KMT2C, and ATR are discovered with their associated cancer type specificity. As for non-coding RNA's, lincRNA CROCCP2, LINC00969 and miRNA MIR4477 appear frequently. Only 182 mutations are reluctantly classified as intergenic; intergenic loci RP11-96F8.1-KSR1P1, MLLT10P1-DEFB115, and bP-21201H5.1-IGHV1OR21-1 contain unusually high recurrent mutations.

Conclusion:

Many non-coding mutations worth further investigation are found. Still, it is quite possible that many of these mutations might be artifacts resulting from paralogous alignments, gene definition compatibility and other technical issues. Importantly, we discovered novel intronic mutations in genes already associated with treatments. Mutations in intergenic regions might be involved in regulatory mechanisms and chromosomal structures. Understanding these non-coding mutations will further refine our understanding of biology as well as cancer.

Citation Format: Takahiko Koyama, Laxmi Parida. Analysis of noncoding mutations in cancer revealed novel potentially pathogenic recurrent mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2353.
Abstract 2374: Oncogenic kinases-induced PKM2 tyrosine 105 phosphorylation converts nononcogenic PKM2 to a tumor promoter and induces cancer stem-like cells
Authors: Zhang Lin , Zhou Zhifen , Li Min , Yu Dihua
Published: August 2018

The role of pyruvate kinase M2 isoform (PKM2) in tumor progression has been controversial. Previous studies showed that PKM2 promoted tumor growth in xenograft models; however, depletion of PKM2 in the Brca1-loss-driven mammary tumor mouse model accelerated tumor formation. Since oncogenic kinases are frequently activated in tumors and PKM2 phosphorylation promotes tumor growth, we hypothesized that PKM2 phosphorylation by activated kinases in tumor cells confers PKM2 oncogenic function, whereas non-phosphorylated PKM2 is non-oncogenic. Indeed, we found that PKM2 was phosphorylated at tyrosine 105 (Y105) in MDA-MB-231 breast cancer cells; whereas PKM2 was largely unphosphorylated in non-transformed MCF10A cells. Multiple kinases that are frequently activated in different cancer types were identified to phosphorylate PKM2-Y105 in our tyrosine kinase screening. Introducing the PKM2-Y105D phospho-mimetic mutant into MCF10A cells induced colony formation and the CD44hi/CD24neg cancer stem-like cell population partly by increasing YAP protein nuclear localization. ErbB2, a strong inducer of PKM2-Y105 phosphorylation, boosted YAP nuclear localization and cancer stem-like cell population. Lapatinib, an ErbB2 kinase inhibitor, decreased PKM2-Y105 phosphorylation and cancer stem-like cells, impeding PKM2 tumor-promoting function. Taken together, in non-transformed cells, unphosphorylated PKM2 is non-oncogenic; but in tumor cells, phosphorylated PKM2-Y105 by activated kinases gains oncogenic functions partly by activating YAP downstream signaling to increase cancer stem-like cell properties.

Citation Format: Lin Zhang, Zhifen Zhou, Min Li, Dihua Yu. Oncogenic kinases-induced PKM2 tyrosine 105 phosphorylation converts nononcogenic PKM2 to a tumor promoter and induces cancer stem-like cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2374.
Abstract 2397: Intracellular cholesterol regulates the DNA damage response in inflammatory breast cancer
Authors: Stecklein Shane R. , Wolfe Adam R. , Debeb Bisrat G. , Larson Richard A. , Woodward Wendy A.
Published: August 2018

Purpose: Inflammatory breast cancer (IBC) is a highly aggressive form of breast cancer, and patients with IBC remain at high risk of locoregional recurrence after radiotherapy. We previously demonstrated that depleting intracellular cholesterol induces radiosensitivity in IBC cells in vitro, and that IBC patients with high levels of high-density lipoprotein (HDL) and those taking a statin, which inhibits de novo cholesterol biosynthesis, have improved locoregional control after radiotherapy. These results suggest that targeting cholesterol metabolism may improve the radiotherapeutic management of IBC. Here, we aimed to understand the molecular mechanism(s) linking cholesterol metabolism and radiation-induced DNA damage and DNA repair and to evaluate statin pharmacotherapy as a DNA repair inhibitor and radiotherapeutic adjunct in an in vivo pre-clinical model of IBC.

Methods: KPL4, SUM149, SUM190, and IBC3 IBC cell lines were used to examine the effect(s) of simvastatin and human serum lipoproteins on radiation-induced DNA damage induction, DNA damage signaling, DNA damage-associated G1, intra-S, and G2/M cell cycle checkpoint activation, and DNA double strand break (DSB) repair by homologous recombination (HR) and non-homologous end joining (NHEJ).

Results: We have generated multiple IBC cells lines with an integrated Traffic Light Reporter (TLR) that is capable of measuring HR and NHEJ, and demonstrate that depletion of intracellular cholesterol abrogates HR-mediated repair of DNA DSBs. We also show that intracellular cholesterol has pleiotropic effects on cell cycle distribution and DNA damage-associated cell cycle checkpoints. We also report a novel polycistronic dual bioluminescence reporter system that can robustly visualize and quantitate DNA DSB induction and repair in vitro and in vivo.

Conclusions: Cholesterol is an important determinant of intrinsic radiosensitivity in IBC, and appears to regulate repair of radiation-induced DNA DSBs. Targeting cholesterol metabolism is a potential strategy to overcome IBC radioresistance and improve the prognosis for this aggressive disease.

Citation Format: Shane R. Stecklein, Adam R. Wolfe, Bisrat G. Debeb, Richard A. Larson, Wendy A. Woodward. Intracellular cholesterol regulates the DNA damage response in inflammatory breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2397.
Abstract 2471: Clinical significance of noncoding circHIPK3 RNA in human hepatocellular carcinoma
Authors: Kim Gyeonghwa , Yoon Jun Sik , Jang Se Young , Park Soo Young , Tak Won Young , Kweon Young-Oh , Hur Keun
Published: August 2018

Background and Aim: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, with poor prognosis and high risk of recurrence. Previous studies have shown that various microRNAs (miRNAs) are frequently dysregulated in HCC, which contributes to cancer development and progression. Nonetheless, the regulation mechanism of miRNAs is still unclear. Circular noncoding RNA (circRNA) is highly conserved and stable covalently closed RNA circles with gene-regulatory potential. Recently, one abundant circRNA from HIPK3 gene, circHIPK3, has been identified, and its function has been elucidated as multiple miRNAs sponge. Thus, we aimed to investigate the clinical relevance of circHIPK3 in HCC.

Materials and Methods: We analyzed clinical specimens from 152 pairs of HCC and corresponding normal liver (NL) tissues. Total RNAs were isolated from clinical tissues using Qiagen kit. CircHIPK3 expression levels were determined by quantitative real-time PCR (qRT-PCR), and its expression was normalized with GAPDH. In addition, we analyzed the correlation between circHIPK3 expression and various clinicopathologic features of HCC patients.

Results: CircHIPK3 expression was significantly downregulated in HCC tissues compared to corresponding NL tissues (P=0.036). In HCC patients, circHIPK3 expression was strongly suppressed in more advanced tumors (P<0.001). Further correlation analysis showed that circHIPK3 expression was significantly associated with T stage (P<0.001), TNM stage (P<0.001), BCLC stage (P<0.001), and alpha-fetoprotein (AFP) expression (P=0.033).

Conclusions: We have determined clinical significances of circHIPK3 expression in HCC, which may provide clinical evidence for the potential of circHIPK3 as novel markers for diagnosis and predicting prognosis in HCC patients.

Citation Format: Gyeonghwa Kim, Jun Sik Yoon, Se Young Jang, Soo Young Park, Won Young Tak, Young-Oh Kweon, Keun Hur. Clinical significance of noncoding circHIPK3 RNA in human hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2471.
Abstract 2498: Over-expression of dual-specificity phosphatase 4 (DUSP4) in multiple myeloma
Authors: Xia Tian , Lau Kin-Mang , Cheng Chi Keung , Chan Nelson CN , Ng Margaret H. L.
Published: August 2018

Super-enhancers are unique genomic domains with dense binding of transcription factors (TFs)/cofactors that drive expression of genes defining cell identity. They also contribute to over-expression of oncogenes. The abundance of multiple TFs and coactivators at the super-enhancers favors their cooperative binding and synergistic gene activation. Thus, super-enhancers are more sensitive to perturbation of TF levels than typical enhancers, providing a therapeutic window for preferential targeting oncogenic expression in cancer cells. Recently, a list of super-enhancer associated genes (SEAG) was identified in a multiple myeloma (MM) cell line MM1S and inhibition of transcriptional coactivator BRD4 by JQ1 selectively repressed MYC oncogene expression through reduction of BRD4 binding at the associated super-enhancer. Significances of SEAG other than MYC in myeloma cells remains unclear. By unsupervised hierarchical clustering analysis of expression of 682 identified SEAG in 74 MM, 28 relapsed MM and 15 normal plasma cells (NPC) (GSE6477), distinct expression pattern of SEAG was associated with MM as compared to NPC, indicating their importance in MM. Among the upregulated genes, DUSP4 (Dual Specificity Phosphatase 4), an inducible phosphatase of MAPK (Mitogen-Activated Protein Kinases), was significantly overexpressed in MM and further upregulated in the relapsed MM. High expression was associated with inferior patient outcomes. The overexpression was confirmed in our patient cohort which includes CD138-immunosorted myeloma cells from 30 untreated and 3 relapsed MM patients, 6 smoldering MM patients and 5 MGUS patients, 5 sorted normal plasma cells (NPC) and 7 MM cell lines. Using the cutoff for over-expression as higher than the mean level of NPC plus 2X Standard Deviation, 10 out of 30 MM and all the 3 relapsed samples showed significant DUSP4 over-expression. Functional significance of DUSP4 in MM was explored by siRNA knockdown and the knockdown inhibited myeloma cell growth, implying an oncogenic role of DUSP4 in MM. To study the significances of super-enhancer in regulation of DUSP4 expression, JQ1 was used and inhibition of BRD4 by JQ1 in MM1S, L363 and OPM2 repressed both DUSP4 expression and MM cell growth. By ChIP-PCR, we demonstrated BRD4 specifically bound onto the proximal region of DUSP4 promoter and the binding was blocked by JQ1. Taken together, the oncogenic role of DUSP4 as SEAG in MM was revealed and the preferential targeting SEAG by BRD4 inhibitor could provide insights into further developments of effective therapeutic approaches for MM patients.

Citation Format: Tian Xia, Kin-Mang Lau, Chi Keung Cheng, Nelson CN Chan, Margaret H. L. Ng. Over-expression of dual-specificity phosphatase 4 (DUSP4) in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2498.
Abstract 2523: Cooperativity of HOXA5 and STAT3 is critical for HDAC8 inhibition-mediated transcriptional activation of PD-L1 in human melanoma cells
Authors: Jiang Chen Chen , Wang Yu Fang , Sherwin Simonne , Farrelly Margaret , Liu Fen , Yan Xu Guang , Croft Amanda , Liu Tao , Jin Lei , Zhang Xu Dong
Published: August 2018

While the expression of programmed death-ligand 1 (PD-L1) is an important mechanism by which cancer cells evade the immune system, PD-L1 expression in cancer cells are commonly associated with patients' responses to treatment with anti-PD-1/PD-L1 antibodies. However, how PD-L1 expression is regulated in melanoma cells remains to be fully elucidated. Here we report that the class I histone deacetylase (HDAC) HDAC8 controls transcriptional activation of PD-L1 by a transcription complex consisting of transcription factors homeobox A5 (HOXA5) and signal transducer and activator of transcription 3 (STAT3). Inhibition of HDAC8 upregulated PD-L1 in melanoma cells. This was due to an increase in the activity of a fragment of the PD-L1 gene promoter that is enriched with binding sites for both HOXA5 and STAT3. Indeed, knockdown of HOXA5 or STAT3 abolished upregulation of PD-L1 by HDAC8 inhibition. Moreover, HOXA5 and STAT3

were physically associated and appeared interdependent in activating PD-L1 transcription. Functional studies showed that HDAC8-mediated regulation of PD-L1 expression participated in modulating anti-melanoma T cell responses. Collectively, these results identify HDAC8 as an important epigenetic regulator of PD-L1 expression, with implications for better understanding of the interaction between melanoma cells and the immune system.

Citation Format: Chen Chen Jiang, Yu Fang Wang, Simonne Sherwin, Margaret Farrelly, Fen Liu, Xu Guang Yan, Amanda Croft, Tao Liu, Lei Jin, Xu Dong Zhang. Cooperativity of HOXA5 and STAT3 is critical for HDAC8 inhibition-mediated transcriptional activation of PD-L1 in human melanoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2523.
Abstract 260: Apigenin nanoparticle suppresses sphere formation in CD133+/ALDH1high prostate cancer stem cells through downregulation of stem cell markers
Authors: Kanwal Rajnee , Shukla Sanjeev , Exner Agata A. , Tzakos Andreas G. , Gupta Sanjay
Published: August 2018

The recurrence of prostate cancer after definitive treatment(s) is thought to be due to the potential of rare cancer stem cells (CSCs) to withstand therapy and initiate tumor formation. CSCs are a subpopulation of cancer cells capable of self-renewal and plastic adaptation mediating tumorigenesis, metastasis, and therapy resistance. CSCs are associated with cancer progression and clinical outcome in cancer patients. In the present study, we isolated CSCs from various human prostate cancer 22Rv1, DU145 and PC-3 cells by applying selection of cluster of differentiation 133 cell surface marker and high ALDH1 activity (CD133+/ALDH1high). Next we aimed to identify CD133+/ALDH1high CSCs isolated from human prostate cancer cells and compare their profiles with non-CSCs as bulk counterparts of the population. Subsequently, the CSC population continued to grow in the three-dimensional multicellular spheroids. Differentiation investigated with stem cell-related genomic characteristics exhibited significant increase in genes viz. CD44, Nanog, β-catenin, c-Myc, SOX2 and Oct4 in CSCs at the message level. In further studies we determine the effect of natural plant flavone apigenin on CSC population. Apigenin is abundantly present in common fruits and vegetables and possess remarkable anticancer, anti-angiogenic and anti-metastatic properties. Apigenin loaded polyethylene glycol nanoparticles (Ap-NP) was characterized for particle size, morphology, zeta potential, drug release and encapsulation. Cellular entry and intracellular localization of Ap-NP were assessed by transmission electron microscopy. Treatment of CD133+/ALDH1high CSCs with Ap-NP inhibited cell viability and sphere formation at higher extent in time dependent manner, compared to the non-CSCs counterparts. Furthermore, Ap-NP exposure resulted in the downregulation of Nanog, β-catenin, c-Myc, SOX2 and Oct4 in the CSCs. Taken together, our study demonstrate overexpression of potential CSC markers and the ability to target these CSCs by the use of non-toxic agent apigenin killing this rare population that may lead to the total abolition of tumor recurrence and/or metastasis.

Citation Format: Rajnee Kanwal, Sanjeev Shukla, Agata A. Exner, Andreas G. Tzakos, Sanjay Gupta. Apigenin nanoparticle suppresses sphere formation in CD133+/ALDH1high prostate cancer stem cells through downregulation of stem cell markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 260.
Abstract 2698: Phosphoproteomics-guided anticancer drug combination design with a novel small-molecule PP2A activator
Authors: Wiredja Danica D. , Liao Peter , Sangodkar Jaya , Schlatzer Daniela , Chance Mark R. , Narla Goutham
Published: August 2018

Significance: Phosphatases are cellular antagonists of kinase signaling and have a diverse range of substrates, many of which are ideal targets for small molecule-based anticancer treatment. Our lab and collaborators have generated a novel series of compounds that bind to and activate the serine/threonine protein phosphatase 2A (PP2A), and these small-molecule activators of PP2A (SMAPs) induce apoptosis and inhibit tumor growth in numerous cancer models. Based on these findings, this project aimed to identify drug combinations with our SMAP that could drive optimal anticancer activity.

Methods: We first turned to global shotgun phosphoproteomics to compare the signaling response signatures of our SMAP against a combination of a MEK inhibitor (MEKi) and an AKT inhibitor (AKTi). We then applied Kinase-Substrate Enrichment Analysis (KSEA) to extract key diverging biologic patterns between these two arms, with the goal of identifying distinct pathways that are inhibited in each condition. These results, in turn, could provide insight to differences between phosphatase activation versus kinase inhibition.

Results: KSEA profiling revealed distinct signaling responses between the two arms. Notably, the kinase inhibitors caused robust downregulation of the MAPK signaling pathway, whereas SMAP treatment showed limited involvement of that cascade. Thus, we hypothesized that a combination of SMAP + MEKi would yield enhanced anticancer response compared to either single agent. Subsequent murine xenograft testing demonstrated superior tumor response with SMAP + MEKi versus either compound alone.

Conclusion: This project offers a phosphoproteomics-level glimpse to the signaling effects between phosphatase activation compared to kinase inhibition. The data, in turn, could be used for rational drug combination design to improve antitumor therapy.

Citation Format: Danica D. Wiredja, Peter Liao, Jaya Sangodkar, Daniela Schlatzer, Mark R. Chance, Goutham Narla. Phosphoproteomics-guided anticancer drug combination design with a novel small-molecule PP2A activator [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2698.
Abstract 2735: Cancer immunotherapy with agonistic anti-4-1BB scFv producing and secreting Bifidobacterium in syngeneic mouse model
Authors: Matsumura Tomio , Shioya Koichiro , Kanari Yasuyoshi , Shimatani Yuko , Kataoka Shiro , Taniguchi Shun'ichiro , Nakamura Takaaki
Published: August 2018

Agonistic antibodies against immune checkpoint molecules, such as 4-1BB, reportedly demonstrate antitumor effects at the early clinical phase, whereas immune-related adverse events hamper further development. A single chain variable fragment (scFv), which is expected to have better penetration into tissues, is clinically being investigated, however, poor distribution into tumor tissues due to rapid clearance is a serious issue.

In order to improve drug delivery and decrease adverse events, we have developed in situ Delivery and Production System (i-DPS) by genetically engineering a non-pathogenic anaerobic Bifidobacterium. We previously reported that the modified Bifidobacteria localized and proliferated only in the hypoxic area of the tumor engrafted in the mouse post i.v. injection, thus producing anti-tumor molecules persistently and selectively at the tumor site (AACR2010).

Here we present i-DPS with agonistic anti-murine 4-1BB scFv. We created a recombinant Bifidobacterium producing and secreting anti-murine 4-1BB scFv. The anti-murine 4-1BB scFv increased IFN-γ production by 171% over the control group (PBS(-)) in the mouse splenocytes activated by ant-CD3 antibody in vitro. Anti-tumor effects of Bifidobacteria producing the anti-murine 4-1BB scFv were demonstrated in the syngeneic model of CT-26 in Balb/c mouse (61.7% tumor growth inhibition (TGI) at 1×109 cfu/mouse, i.v. on day 14). We further evaluated the anti-tumor effects of i-DPS for anti-murine 4-1BB scFv (1×109 cfu/mouse, i.v.) in combination with PD-1 antibody (i.p.), and confirmed that the combination therapy significantly suppressed the tumor growth on day 21 (TGI: combination, 60.7%; anti-murine 4-1BB scFv, 38.8%; anti-mPD-1 mAb, 8.9%). In conclusion, i-DPS for anti-4-1BB scFv will provide a new promising modality for the immune-therapy targeting hypoxic solid tumors.

Citation Format: Tomio Matsumura, Koichiro Shioya, Yasuyoshi Kanari, Yuko Shimatani, Shiro Kataoka, Shun'ichiro Taniguchi, Takaaki Nakamura. Cancer immunotherapy with agonistic anti-4-1BB scFv producing and secreting Bifidobacterium in syngeneic mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2735.
Abstract 2895: Verteporfin targets p62 in prostate cancer therapeutics
Authors: Wang Lei , Kim Donghern , Wise James , Shi Xianglin , Zhang Zhuo , DiPaola Robert S.
Published: August 2018

To test the hypothesis that p62 is an optimal target for autophagy inhibition and Verteporfin, a clinically available drug approved by FDA to treat macular degeneration that inhibits autophagy by targeting p62 protein, can be developed clinically to improve therapy for advanced prostate cancer. Results showed that Verteporfin inhibited cell growth and colony formation in PC-3 cells. Verteporfin generated crosslinked p62 oligomers, resulting in inhibition of autophagy and constitutive activation of Nrf2 as well as its target proteins, Bcl-2 and TNF-α. In normal prostate epithelial cells, forced expression of p62 caused constitutive Nrf2 activation and development of apoptosis resistance and Verteporfin treatment exhibited inhibitory effects. Verteporfin treatments also inhibited starvation-induced autophagic influx of these cells. Verteporfin inhibited tumorigenesis of both normal prostate epithelial cells with p62 expression and prostate cancer cells and decreased p62, constitutive Nrf2, and Bcl-xL in xenograft tumor tissues, indicating that p62 can be developed as a drug target against prostate cancer. So p62 has a high potential to be developed as a therapeutic target. Verteporfin represents a prototypical agent with therapeutic potential against prostate cancer through inhibition of autophagy by a novel mechanism of p62 inhibition.

Citation Format: Lei Wang, Donghern Kim, James Wise, Xianglin Shi, Zhuo Zhang, Robert S. DiPaola. Verteporfin targets p62 in prostate cancer therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2895.
Abstract 3061: The clinicopathologic roles of SOX2 and Oct4 expressions in stage 1 and 2 oral squamous cell carcinoma
Authors: Tamatani Tetsuya , Takamaru Natsumi , Ohe Go , Nakagawa Takayuki , Kurio Naito , Kudou Keiko , Yamamura Yoshiko , Mano Takamitsu , Miyamoto Youji
Published: August 2018

[Background] Cancer stem cells (CSCs) exhibit self-replication, self-differentiation, drug resistance, and immune evasion activities. Recently, CSC has become increasingly important in the treatment of malignant tumors. Cancer stem cells express specific molecules termed CSC marker, including sex determining region Y-box2 (SOX2), and octamer-binding transcription factor 4 (Oct4), and their expression has been reported to be the potential prognostic values. However, the prognostic values of SOX2 and Oct4 expression in patients with stage I and II oral cancer are less understood.

[Purpose] The aims of present study were to evaluate the expression of SOX2 and Oct4 in stage I and II oral squamous cell carcinoma (OSCC) and to elucidate the relationships among the CSC marker expression, clinical stages, histological differentiation, classification of invasion mode, cerebral lymph node metastasis, distant metastasis, and disease-free survival rate.

[Materials and Methods] Tissue specimens were obtains from 83 patients with OSCC after surgery or biopsy. Immunohistochemistry was used to assess SOX2 and Oct4 protein using at least 10% staining-positive cells as the definition of positive staining. [Results] Immunohistochemical analysis of 83 cases showed that 31 cases (37%) expressed SOX2. There was no significant association between SOX2 expression and tumor size, invasion mode or histological differentiation. However, there was significant association between SOX2 expression and distant metastasis or disease-free survival rate at stage 1 and 2 patients. Otherwise, fifty three cases (64%) of 83 OSCC patients expressed Oct4. There was significant association between Oct4 expression and histological differentiation. There was no significant association between Oct4 expression and tumor size, invasion mode, metastasis, or disease-free survival rate.

[Conclusions] These findings suggested that the expression of SOX2 may be good marker indicating survival in patients with stage 1 and 2 OSCC.

Citation Format: Tetsuya Tamatani, Natsumi Takamaru, Go Ohe, Takayuki Nakagawa, Naito Kurio, Keiko Kudou, Yoshiko Yamamura, Takamitsu Mano, Youji Miyamoto. The clinicopathologic roles of SOX2 and Oct4 expressions in stage 1 and 2 oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3061.
Abstract 3157: p53 inactivation and STAT2 cooperate to enhance migration and metastasis of colon tumor cells
Authors: Gamero Ana M. , Kotredes Kevin , Abezis Aliza , Gohimukkula Sruthi R. , Afanassiev Alexandra , Cremers Tess , Swain John J.
Published: August 2018

STAT2 is a pivotal signaling component in the antiviral and antiproliferative effects of type I and type III interferon (IFN), but its role in cancer remains understudied. To date, only IFNs are known to activate STAT2. Work by us and others has demonstrated that STAT2 deficiency impairs the antitumor effects of type I IFN, supporting its role in suppressing tumor growth. With the availability of Stat2-/- mice, we interrogated the tumor-suppressive role of STAT2 by employing the AOM/DSS model of colitis-associated cancer and the spontaneous ApcMin/+ model of colorectal cancer (CRC). In both cancer models, loss of STAT2 reduced the number of adenomas, showing that under specific conditions STAT2 can be tumorigenic. Next, immunohistochemical staining of human normal colon and CRC tumors revealed elevated STAT2 protein in both adenomas and adenocarcinomas, suggesting that STAT2 is implicated in human CRC. Conversion of adenomas to adenocarcinomas is linked to loss of p53 function, which occurs in >50% of colorectal cancers. Therefore, we evaluated whether STAT2 altered the aggressive phenotype of p53-deficient colon carcinoma cells. We silenced STAT2 in isogenic p53 null and p53 wild-type tumor cells. STAT2 knockdown in p53 null colon carcinoma cells reduced migration of 3D tumor spheroids and tumor colony formation while no effect was seen in p53 wild-type tumor cells. We also observed that STAT2 knockdown in p53 null tumor cells increased protein levels of the marker of epithelial-mesenchymal transition, E-cadherin. Conversely, overexpression of STAT2 in p53 null cells reduced E-cadherin protein. In vivo, STAT2 knockdown delayed subcutaneous tumor growth of p53 null tumor cells. Furthermore, using an experimental liver metastasis tumor model, STAT2 knockdown abrogated the formation of tumor nodules in the liver. RNA-seq profiling of subcutaneous p53 null tumors revealed a subset of genes that were differentially expressed in a STAT2-dependent manner. Clinically, analysis of the TCGA database showed a STAT2 transcriptional signature in colorectal tumors that we are presently correlating with p53 alterations. Overall, we conclude that STAT2 enhances tumor growth and can contribute to disease progression by promoting migration and invasion when normal p53 function is lost.

Citation Format: Ana M. Gamero, Kevin Kotredes, Aliza Abezis, Sruthi R. Gohimukkula, Alexandra Afanassiev, Tess Cremers, John J. Swain. p53 inactivation and STAT2 cooperate to enhance migration and metastasis of colon tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3157.
Abstract 328: Targeting Mcl-1 enhances DNA replication stress sensitivity for cancer therapy
Authors: Chen Guo , Magis Andrew , Xu Ke , Park Dongkyoo , Yu David , Owonikoko Taofeek , Sica Gabriel , Satola Sarah , Ramalingam Suresh , Curran Walter , Doetsch Paul , Deng Xingming
Published: August 2018

DNA double-strand breaks (DSBs) are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways. Here we report that Mcl-1 acts as a functional switch in pathway choice between HR and NHEJ. Mcl-1 was cell cycle-regulated, with expression peaking in S/G2 phase when HR occurred. Endogenous Mcl-1 depletion reduced HR and enhanced NHEJ. Mcl-1 overexpression resulted in a net increase in HR over NHEJ. Mcl-1 directly interacted with Ku via its BH1 and BH3 domains, which are required for Mcl-1 to inhibit Ku-mediated NHEJ and promote Mre11 complex-mediated DNA resection and HR-dependent DSB repair. Using the Mcl-1 BH1 domain (aa256-265) as docking site, we identified a novel small molecule, MI-223, that directly bound to BH1 and blocked Mcl-1-stimulated HR DNA repair leading to a significant sensitization of cancer cells to hydroxyurea- or olaparib-induced DNA replication stress. Combined treatment with MI-223 and hydroxyurea or olaparib exhibited a strong synergy against lung cancer in vivo. This mechanism-driven combination of agents provides a highly attractive therapeutic strategy to improve lung cancer outcome.

Citation Format: Guo Chen, Andrew Magis, Ke Xu, Dongkyoo Park, David Yu, Taofeek Owonikoko, Gabriel Sica, Sarah Satola, Suresh Ramalingam, Walter Curran, Paul Doetsch, Xingming Deng. Targeting Mcl-1 enhances DNA replication stress sensitivity for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 328.
Abstract 3437: Genomic alterations, mutation burden, and microsatellite instability status of Chinese intrahepatic cholangiocarcinoma
Authors: Cao Jingyu , Jiang Bo , Liu Zimin , Shu Weibin , Li Lei , Yang Han , Li Hua , Xiao Zhiyu , Yan Maolin , Lin Jie , Liu Siqin , Zhang Peng , Javle Milind , Yao Ming , Wang Kai , Zhao Haitao
Published: August 2018

Background: Intrahepatic cholangiocarcinoma (ICC) is often diagnosed at an advanced stage with limited therapeutic options and poor prognosis. Targeted and immune-therapy have yielded promising therapeutic effects in various solid tumor patients (pts). Thus the understanding of ICC genomic profiling, especially which of Chinese pts, seems to be necessary for the treatment strategy for ICC.

Methods: Comprehensive genomic profiling of molecular alterations and predictive biomarkers to personalized treatment genes were performed on Formalin Fixed Paraffin Embedded (FFPE) samples and matched blood samples of 69 Chinese ICC pts. Genomic alterations (GAs) including substitutions, short and long insertion/deletions (indels), copy number variations and gene rearrangements were assessed. Tumor mutation burden (TMB) of total somatic substitutions and indels per megabase after filtering known driver mutations was calculated. Microsatellite instability (MSI) status was determined by identifying and scoring multiple mono-nucleotide repeats loci.

Results: Median age of the 69 ICC pts was 58 years (range: 38-88), and male vs female was approximately 3:1. Average of 3.7 GAs /sample and 0.9 actionable GAs/sample were detected. The most widespread genomic alterations among the pts were revealed as TP53 (44.9%), ARIDIA (23.2%), KRAS (18.8%), BAP1 (14.5%), IDH1/2 (14.5%), PIK3CA (11.6%), FGFR2/3 (10.1%), MLC1 (8.7%), CDKN2A/B (8.7%), BRAF (7.2%), TERT (7.2%), PBRM1 (7.2%). The actionable mutations of the PI3K/mTOR pathway were found in 18.8% of the pts. In total, pts with one or more actionable GAs were 62.3%. Pts presented MSI-high were 7.2% of the total. Proportion was 10.1% for the pts with TMB value higher than 20 mut/Mb, and 32.8% for those higher than 10 mut/Mb. The TMB range of the 69 pts was 1.1 to 58.4 mut/Mb, and median was 7.4 mut/Mb.

Conclusions: In our study, 62.3% of Chinese ICC pts were detected to have actionable GAs which could potentially guide and influence their personalized treatments. The identification of more frequent high TMB level than the published western populations indicated that Chinese ICC pts may more likely derive therapeutic benefits from immune checkpoint inhibitors.

Citation Format: Jingyu Cao, Bo Jiang, Zimin Liu, Weibin Shu, Lei Li, Han Yang, Hua Li, Zhiyu Xiao, Maolin Yan, Jie Lin, Siqin Liu, Peng Zhang, Milind Javle, Ming Yao, Kai Wang, Haitao Zhao. Genomic alterations, mutation burden, and microsatellite instability status of Chinese intrahepatic cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3437.