bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1888: Protein kinase C beta II suppresses colorectal cancer by regulating IGF1 mediated cell survival
Authors: Dowling Catriona M. , Phelan James , Callender Julia A. , Cathcart Mary Clare , Mehigan Brian , McCormick Paul , Dalton Tara , Coffey John C. , Newton Alexandra C. , O’Sullivan Jacintha , Kiely Patrick A.
Published: July 2016

Despite extensive efforts, cancer therapies directed at the Protein Kinase C (PKC) family of serine/threonine kinases have failed in clinical trials. These therapies have been directed at inhibiting PKC and have, in some cases, worsened disease outcome. Here we examine colon cancer patients and show not only that PKC Beta II is a tumour suppressor, but patients with low levels of this isozyme have significantly decreased disease free survival. Specifically, analysis of gene expression levels of all PKC genes in matched normal and cancer tissue samples from colon cancer patients revealed a striking down-regulation of the gene coding PKC Beta in the cancer tissue (n = 21). Tissue microarray analysis revealed a dramatic down-regulation of PKC Beta II protein levels in both the epithelial and stromal diseased tissue (n = 166). Of clinical significance, low levels of the protein in the normal tissue of patients is associated with a low (10%) 10 year survival compared with a much higher (60%) survival in patients with relatively high levels of the protein. Consistent with PKC Beta II levels protecting against colon cancer, overexpression of PKC Beta II in colon cancer cell lines reveals that PKC Beta II reverses transformation in cell based assays. Further to this, activation of PKC Beta II in an IGF-1 dependent manor showed a downregulation of AKT, indicating a role for PKCs in regulating IGF-1 mediated cell survival. Thus, PKC Beta II is a tumour suppressor in colon cancer and low levels serve as a predictor for poor survival outcome.

Citation Format: Catriona M. Dowling, James Phelan, Julia A. Callender, Mary Clare Cathcart, Brian Mehigan, Paul McCormick, Tara Dalton, John C. Coffey, Alexandra C. Newton, Jacintha O’Sullivan, Patrick A. Kiely. Protein kinase C beta II suppresses colorectal cancer by regulating IGF1 mediated cell survival. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1888.
Abstract 190: Mechanism of CDKN3 overexpression in cancer
Authors: Fan Chao , Chen Lu , Huang Qingling , Shen Tao , Welsh Eric A. , Teer Jamie K. , Cress W Douglas , Wu Jie
Published: July 2016

The cyclin-dependent kinase inhibitor 3 (CDKN3) is a dual specificity protein tyrosine phosphatase (PTP) known to dephosphorylate CDK1/2 on the activating Thr-161/Thr-160. Paradoxically, CDKN3 mRNA is often overexpressed in human cancer. It was reported that CDKN3 overexpression may be associated with splicing variants or mutations that produce dominant-negative CDKN3. We found that CDKN3 is overexpressed in non-small cell lung cancer (NSCLC) and that CDKN3 overexpression is prognostic of poor overall survival in three cohorts of lung adenocarcinoma. We next analyzed CDKN3 transcripts in a panel of 24 cell lines and lung adenocarcinoma tissues and also examined CDKN3 mutations in the Cancer Genome Atlas (TCGA) and the Moffitt Cancer Center's Total Cancer Care® (TCC) projects. Two CDKN3 transcripts were detected in all samples. These CDKN3 transcripts represent the full length CDKN3 mRNA and a normal transcript lacking exon 2, which encodes an out of frame 23-amino acid peptide with little homology to CDKN3. CDKN3 mutations were very rare and no disruptive mutation was found. Significantly, in synchronized cell cultures, CDKN3 mRNA and protein were elevated during the mitosis phase of cell cycle. Furthermore, CDKN3 expression had the highest correlation with mitotic-associated genes in lung adenocarcinoma tissues. Knocking down of CDKN3 prolonged the mitotic phase of cell cycle. Thus, CDKN3 overexpression in lung adenocarcinoma is not attributed to alternative splicing or mutation but is due to increased mitotic activity. Our data also suggest that CDKN3 is important for mitotic exit.

Citation Format: Chao Fan, Lu Chen, Qingling Huang, Tao Shen, Eric A. Welsh, Jamie K. Teer, W Douglas Cress, Jie Wu. Mechanism of CDKN3 overexpression in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 190.
Abstract 1901: Leptin modulation of PCSC, HDAC, and microRNA in pancreatic adenocarcinoma
Authors: Tchio Cynthia M. , Harbuzariu Adriana , Harmon Tia , Beech Derrick , Gonzalez-Perez Ruben
Published: July 2016

Background: Obesity is an important risk factor of Pancreatic Adenocarcinoma (PA) and it is characterized by the accumulation of excessive body fat and a Body Mass Index (BMI) value greater than 30. Obesity is also characterized by high levels of leptin, which has been consistently associated with the development of many different cancer including PA. Leptin can induce the proliferation of Pancreatic Cancer Stem Cells (PCSC), which are responsible for chemoresistance, invasiveness and reoccurrence of PA. PCSC express specific cell markers and can form tumorspheres in vitro. Obesity can alter the DNA acetylation and microRNA activity which are also linked to PA progression. We hypothesized that high level of leptin could modulate Histone Deacetylase (HDAC) and microRNA activity in PA cells, which induce PCSC changes and tumor progression.

Methods: The PA cell lines were cultured in mammocult media that contained heparin and hydrocortisone, which will allow the proliferation of tumorspheres enriched with PCSCs. The cells were cultured with leptin, chemotherapeutic drug, and leptin signaling inhibitor IONP-LPrA2. Tumorspheres formation (number and size) was determined after 1 week of treatment. Additionally, the levels of PCSC markers, HDAC1, HDAC2, HDAC3, and HDAC8 in tumorspheres were determined using flow cytometry, western blot, and RT-PCR. In addition, the effects of treatments on miR21 and miR200a/c levels were determined using RT-PCR.

Results: Leptin induced PA tumorspheres formation and size, which was accompanied by higher level of PCSC markers (CD24, CD44, ESA, and ALDH1). Moreover, leptin affected the level of HDACs, miR21 and miR200a/c in PA tumorspheres. IONP-LPrA2 abrogated leptin effects and decreased PCSC which were spared by chemotherapeutics.

Conclusion: Obesity signals via leptin could be involved in the increase PA aggressiveness and chemoresistance, which may be linked to the increase of PCSC. Leptin could induce PA progression and chemoresistance via modulation of HDAC and miRNA.

Acknowledgement: This work was supported by the DOD W81XWH-13-1-0382; NIH/SBIR1R41CA183399-01A1; Pilot Project Award from MSM/Tuskegee University/UAB Cancer Center Partnership grant 5U54CA118638; PC SPORE Grant from UAB to RRGP; Calvin Johnson Jr. Foundation Pancreatic Cancer Research Scholarship to CITM, and facility and support services at Morehouse School of Medicine (1G12RR026250-03; NIH RR03034 and 1C06 RR18386).

Citation Format: Cynthia M. Tchio, Adriana Harbuzariu, Tia Harmon, Derrick Beech, Ruben Gonzalez-Perez. Leptin modulation of PCSC, HDAC, and microRNA in pancreatic adenocarcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1901.
Abstract 1904: MiR641 regulates EMT, ovarian cancer stem cell and angiogenesis by targeting p63/miR200 axis
Authors: Li Yajuan , Richards Edward , Coppola Mark , Xu Cheng-Xiong , Cheng Jin Q.
Published: July 2016

MiR641 is an uncharacterized miRNA which locates intron 1 of AKT2, a gene residing in the chromosome 19q13.2 amplicon and frequently amplified/overexpressed in refractory ovarian cancer. Here, we demonstrated that frequent upregulation of miR641 was observed in human ovarian cancer tissues and in ovarian cancer cell lines. Knockdown of miR641 inhibited cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT) as well as angiogenesis and ovarian cancer stem cell growth. Enforced expression of miR641 had opposite effect. In addition, ectopic expression of miR641 promoted VEGF protein expression and secretion but had no effect on VEGF mRNA level. Mechanistically, we found that miR641 directly targeted the 3’UTR of p63 and reduced p63 expression, which leads to a decrease of miR200a/b. As a result, ZEB1 and VEGF, two validated targets of miR200, were upregulated by miR641 overexpression. Furthermore, expression of miR641 induced anchorage-independent growth. Taken together, these findings suggest that miR641 is an onco-miRNA and plays a pivotal role in ovarian oncogenesis.

Citation Format: Yajuan Li, Edward Richards, Mark Coppola, Cheng-Xiong Xu, Jin Q. Cheng. MiR641 regulates EMT, ovarian cancer stem cell and angiogenesis by targeting p63/miR200 axis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1904.
Abstract 1911: ΔNp63α promotes TGFβ-induced metastasis by silencing a microRNA network restraining wound healing
Authors: Rodriguez Calleja Lidia , Jacques camille , Lamoureux Francois , Baud’huin Marc , Quillard Thibault , Verrecchia Franck , Heymann Dominique , Ellisen Leif , Ory Benjamin
Published: July 2016

Primary cancer cell dissemination is the key event in metastasis, yet context-specific determinants remain largely undefined. Multiple reports have suggested an anti-metastatic role for the p53 family member p63 linked to its minor epithelial isoform, TAp63. However, the role and contribution of the major p63 isoform, ΔNp63α, remain largely undefined. Here we report a distinct and TAp63-independent mechanism in which ΔNp63α-expressing cells, in a TGFβ-rich microenvironment, are positively selected for metastatic dissemination. We define the molecular mechanism of this effect, through ΔNp63α-mediated repression of miR-527 and miR-665 and the subsequent upregulation of two TGFβ pathway major effectors, SMAD4 and TβRII. Furthermore, we provide evidence that this mechanism reflects a fundamental role for ΔNp63α in the normal wound healing response. We show that ΔNp63α and miR-527/665 control the TGFβ-dependent signaling that switches off anti-migratory miR-198 by downregulating the regulatory factor KSRP. Collectively, these findings reveal a novel microRNA network orchestrated selectively by ΔNp63α that is involved in the physiological regulation of wound healing but is hijacked by tumors to promote metastatic dissemination.

Citation Format: Lidia Rodriguez Calleja, camille Jacques, Francois Lamoureux, Marc Baud’huin, Thibault Quillard, Franck Verrecchia, Dominique Heymann, Leif Ellisen, Benjamin Ory. ΔNp63α promotes TGFβ-induced metastasis by silencing a microRNA network restraining wound healing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1911.
Abstract 1912: Combinatorial targeting of PI3K and MAPK signaling pathways using microRNAs to inhibit tumor growth and metastasis in breast cancer
Authors: Mutlu Merve , Saatci Ozge , Eyupoglu Erol , Raza Umar , Sahin Ozgur
Published: July 2016

PI3K/Akt and MAPK signaling pathways, regulating cancer cell proliferation, apoptosis and metastasis, are among the top most deregulated pathways in cancer. Current kinase inhibitors used in clinics have limited success since one of these pathways gets activated when the other is suppressed. Alternatively, simultaneous silencing of both pathways results in high toxicity. Here, we aimed to establish a microRNA-based, non-toxic approach to inhibit these pathways simultaneously in breast cancer. By analyzing our previously published Reverse Phase Protein Array (RPPA) data showing differential expression of 26 proteins upon overexpression of 733 different miRNAs, we selected top miRNAs significantly deregulating PI3K and MAPK pathways as well as cell cycle. We narrowed down the list by selecting miRNAs whose predicted targets were among the PI3K and MAPK pathway elements. We came up with a tumor suppressor miRNA affecting both in vitro viability and migration/invasion of breast cancer cells. We identified the set of differentially expressed genes in breast cancer patients under low and high expression of the miRNA. A significant association was observed between the expression of the miRNA or its identified gene signature and clinico-pathological properties of breast cancer patients. Combinatorial knockdown of targets of the miRNA that are in PI3K and MAPK pathways as a cocktail phenocopied the tumor suppressive effects of the miRNA in breast cancer cell lines. Notably, low expression of the target cocktail predicts a better outcome in breast cancer patients. Overall, we identified a tumor suppressor miRNA to be used an alternative to current kinase inhibitor-based therapies for major subtypes of breast cancer by suppressing both PI3K and MAPK pathways and as a result inhibiting proliferation and migration/invasion in breast cancer.

Citation Format: Merve Mutlu, Ozge Saatci, Erol Eyupoglu, Umar Raza, Ozgur Sahin. Combinatorial targeting of PI3K and MAPK signaling pathways using microRNAs to inhibit tumor growth and metastasis in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1912.
Abstract 1919: Nitric oxide stimulates expression of miRNA-155 through the BRCA1-dependent pathway
Authors: Hawley Justin , Yakovlev Vasily A.
Published: July 2016

Previously we demonstrated that nitric oxide (NO), generated in macrophages or released from the NO-donors, inhibits expression of the breast cancer type 1 susceptibility protein (BRCA1) in the different cell lines (Yakovlev, Cancer Res., 2013). BRCA1 protein contributes to cell viability in multiple ways, including homologous recombination repair (HRR) of DNA double-stand breaks (DSBs), cell-cycle checkpoint control, mitotic spindle assembly, and regulation of chromosome segregation. In addition BRCA1 protein (in association with histone deacetylase 2) epigenetically suppresses oncogenic microRNA-155 (miR-155) expression (Chang, Nature Med., 2011). miR-155 is an established multifunctional oncomiR, which regulates many pro-oncogenic pathways. miR-155 gene was found to be over expressed in several solid tumors, such as thyroid carcinoma, breast cancer, colon cancer, cervical cancer, pancreatic ductal adenocarcinoma, and lung cancer, where it is considered to be a marker of poor prognosis.

We hypothesized that overproduction of NO can stimulate expression of miR-155 through the BRCA1-dependent pathway. A-549 (lung cancer) and MCF-10A (normal breast epithelial) cell lines were incubated with different concentrations of NO-donor DETA NONOate (0 - 300μM). After 24 or 48 hours of incubation cells were analyzed for the BRCA1 and miR-155 expression. Both cell lines demonstrated significant dose- and time-dependent downregulation of BRCA1 expression along with significant stimulation of miR-155 expression. Cell lines infected with adenovirus vector expressing the wild type BRCA1 abolished stimulation of miR-155 in response to NO-donor treatment, compared with the cell lines infected with an empty adenovirus vector.

To analyze the effect of NO-dependent stimulation of miR-155 expression, we measured the protein levels of miR-155 targets: DNA mismatch repair (MMR) proteins - MSH2, MSH6, MLH1; SH-2 containing inositol 5’-polyphosphatase 1 (SHIP1); and suppressor of cytokine signaling 1 (SOCS1). Western blot demonstrated time- and dose-dependent amount decrease for all targeted proteins with the one exception: expression level of SHIP1 protein in A-549 cell line was undetectable even in the non-treated control.

In future studies we will investigate the role of NO-BRCA1-miR-155 pathway on the MMR capacity and stimulation of microsatellite instability.

Citation Format: Justin Hawley, Vasily A. Yakovlev. Nitric oxide stimulates expression of miRNA-155 through the BRCA1-dependent pathway. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1919.
Abstract 1920: miR-211 directly targets pyruvate dehydrogenase kinase 4 to inhibit cellular growth and glucose metabolism in triple negative breast cancer
Authors: Guda Maheedhara R. , Asuthkar Swapna , Das Soumen , Seal Sudipta , Tsung Andrew J. , Velpula Kiran K.
Published: July 2016

Deregulated metabolism and aerobic glycolysis are common to many kinds of tumors including, breast cancers driven by a plethora of transcription factors. One such is hypoxia-inducible factor-1α (HIF-1α) known to drive the expression of glycolytic target genes. Here, we identify

PDK4 (pyruvate dehydrogenase kinase 4) as a key regulator of HIF-1α signaling. In triple-negative human breast cancer (TNBC) cell lines, we investigated the contribution of PDK4 and HIF-1α to experimental tumor growth, core glucose metabolism and ionizing radiation effects. When these TNBC cells were exposed to 4, 6 and 8Gy treatment, we observed a linear increase in the expression levels of PDK4 and HIF-1α genes. In this study we also report that miR-211, a microRNA predicted to target PDK4 is suppressed in TNBC patient specimens as evidenced by in situ hybridization analysis. The expression levels of PDK4, HIF-1α and RICTOR were reduced with miR-211 over expression while the levels of PDH and FH were observed to be increased. Further, we observed that miR-211 conjugated to cerium oxide nanoparticles (nanoceria) showed increased cytotoxicity. Similar effects were observed when these TNBCs were treated with 5mM DCA, a potent metabolic inhibitor of PDK. Combinatory suppression of PDK4 and HIF-1α exerted synergistic inhibition of lactate released suggesting of reversal of aerobic glycolysis. Alternatively, TCGA datasets were predictive of patient survival, with a PDK4/miR-211 signature robustly predicting poor patient prognosis. Overall, our findings suggest that combined targeting of PDK4 signaling cascade with miR-211 and DCA in combination specifically regulate core glucose metabolism in TNBC.

Citation Format: Maheedhara R. Guda, Swapna Asuthkar, Soumen Das, Sudipta Seal, Andrew J. Tsung, Kiran K. Velpula. miR-211 directly targets pyruvate dehydrogenase kinase 4 to inhibit cellular growth and glucose metabolism in triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1920.
Abstract 1926: Hippo pathway effectors YAP/TAZ integrate tissue mechanics and Wnt signaling to regulate microRNA biogenesis
Authors: Han Siyang , Nelson Celeste M.
Published: July 2016

Although mechanical cues including extracellular matrix (ECM) stiffness are known to regulate cell and tissue behavior, it remains unclear how these mechanical cues integrate with biochemical signals to control these processes. The Hippo pathway and its transcriptional coactivators YAP and TAZ, which have emerged as major regulators of organ size, proliferation and cancer development, are thought to be involved in this integration. In addition to being regulated by the canonical Hippo pathway, YAP/TAZ have been found to mediate responses to both biochemical and mechanical signals including ECM stiffness and Wnt signaling. Moreover, recent studies have shown that microRNAs (miRNAs) are sensitive to mechanical cues and YAP/TAZ may regulate miRNA biogenesis through mechanotransduction. Although misregulation of YAP/TAZ and miRNA expression are frequently observed in multiple cancers, which appears to be associated with the altered mechanics of the tumor microenvironment, the signaling mechanisms controlling these processes remain poorly understood and controversial. Here we examine how YAP/TAZ integrate biochemical and mechanical signals to regulate miRNA biogenesis. We found that Wnt3A and stiff ECM synergistically lead to nuclear accumulation and activation of YAP/TAZ. Surprisingly, ECM stiffness induces miRNA-18a expression while Wnt3A signaling has an opposite effect on miRNA-18a expression depending on the stiffness of the cellular microenvironment. Thus, YAP/TAZ activity may define a mechanism by which cells respond to ECM stiffness and Wnt signaling to control miRNA biogenesis.

Citation Format: Siyang Han, Celeste M. Nelson. Hippo pathway effectors YAP/TAZ integrate tissue mechanics and Wnt signaling to regulate microRNA biogenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1926.
Abstract 1937: Dysregulation of lincRNAs is a major driver of aberrant epigenomes during tumorigenesis
Authors: Merry Callie R. , Forrest Megan E. , Markowitz Sanford , Khalil Ahmad M.
Published: July 2016

It has now been unequivocally demonstrated that the process of tumorigenesis is driven by both genetic and epigenetic alterations, but the mechanisms of epigenetic dysregulations remain to be elucidated. Work in our laboratory has demonstrated that numerous long intergenic non-coding RNAs (lincRNAs) become dysregulated in human cancers, and a significant subset of these lincRNAs are associated with histone-modifying enzymes and DNA methyltransferases in healthy, non-tumor cells. Based on these observations, we tested an exceptionally novel hypothesis that dysregulation of chromatin-associated lincRNAs is a major mechanism driving cancer-associated aberrant epigenomes. To test this novel concept, we have performed experiments to modulate the expression of specific chromatin-associated lincRNAs in cancer cells, and assessed their impact on the epigenome. Consistent with our hypothesis, modulating the expression of lincRNAs in cancer cells resulted in massive reprogramming of their epigenomes. These epigenomic changes impacted the growth of cancer cells and global gene expression. Mapping the genomic occupancy sites of lincRNAs, and intersection of those sites with altered genomic regions in tumors, further supported direct roles of lincRNAs in modulating chromatin structure. These findings demonstrate key roles of chromatin-associated lincRNAs in suppressing tumorigenesis in normal human tissues by regulating the epigenome.

Citation Format: Callie R. Merry, Megan E. Forrest, Sanford Markowitz, Ahmad M. Khalil. Dysregulation of lincRNAs is a major driver of aberrant epigenomes during tumorigenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1937.
Abstract 1941: Plasma levels of miRNA-155 as a powerful diagnostic marker for dedifferentiated liposarcoma
Authors: Boro Aleksandar , Bauer David , Born Walter , Fuchs Bruno
Published: July 2016

PURPOSE: Atypic lipomatous tumors (ALT) and dedifferentiated liposarcomas (DDLS) are closely related liposarcoma subtypes, often difficult to distinguish but they exhibit an entirely different clinical outcome. Recently discovered regulatory functions of miRNAs in liposarcoma progression prompted us to investigate miRNAs as potential diagnostic biomarkers in liposarcoma with a main focus on circulating miRNAs for fast and reliable differential diagnosis.

PATIENTS AND METHODS: Tumor and blood samples of 35 patients with lipomatous lesions collected between June 2011 and September 2014 were analyzed by qRT-PCR. They included 10 lipomas, 7 ALT, 5 DDLS and 13 myxoid liposarcomas (MLS). Ten samples of normal fat tissue and blood from 20 healthy volunteers were used as controls.

RESULTS: A meta-analysis of public data on miRNA expression in liposarcoma revealed 9 miRNAs with potential diagnostic power. Out of these, miRNA-155 was found significantly elevated in the circulation of DDLS patients as compared to the plasma levels detected in all other liposarcoma subtypes and in healthy subjects. miRNA-155 levels in the plasma samples correlated significantly (r = 0.41,p = 0.02) with those in corresponding tumor extracts. This correlation was even more pronounced in an analysis of plasma and tumor extracts of malignant liposarcoma subtypes alone (r = 0.51,p = 0.02). Receiver operating characteristic analysis indicated that plasma miRNA-155 levels have a high diagnostic accuracy for distinguishing DDLS from healthy subjects (AUC = 0.91,p = 0.005) and from lipomas (AUC = 0.86,p = 0.02), MLS (AUC = 0.92,p = 0.006) and most importantly ALT (AUC = 0.91,p = 0.01) patients.

CONCLUSION: In conclusion, this study identified miRNA-155 as a first blood biomarker for the differential diagnosis of DDLS.

Citation Format: Aleksandar Boro, David Bauer, Walter Born, Bruno Fuchs. Plasma levels of miRNA-155 as a powerful diagnostic marker for dedifferentiated liposarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1941.
Abstract 1965: CRISPR/cas9, an innovative genomic tool to knock down microRNA
Authors: Chang Hong , Yi Bin , Ma Ruixia , Zhao Hongyou , Xi Yaguang
Published: July 2016

MicroRNAs are a set of small and non-coding RNA molecules showing the “master” role in regulation of coding-gene expression at the post-transcriptional/translational levels. Several methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, their robustness, specificity, and stability cannot be highly satisfied with the increased demand on microRNA functional research. CRISPR/cas9 system is emerging as a novel genome editing tool that has been exclusively studied in coding-genes knockdown, but its indication in microRNA research has not been explored yet. In this project, we clone CRISPR/cas9 constructs with designated single guide RNAs targeting biogenesis processing sites of the selected microRNAs, miR-200b and miR-17. Our results demonstrate that CRISPR/cas9 can robustly reduce the expression of these microRNAs up to 96%. More significantly, our data support high specificity and low off-target effect of CRISPR/cas9 in editing microRNA genes. Given this feature, it possesses an advantage to knockdown microRNAs in same family or with highly conserved sequences superior to antisense inhibitors and sponges. In addition, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models. In conclusion, we develop a novel method by adapting CRISPR/cas9 system to downregulate microRNA expression, which shows improved robustness, specificity, and stability than the previously established methodologies.

Citation Format: Hong Chang, Bin Yi, Ruixia Ma, Hongyou Zhao, Yaguang Xi. CRISPR/cas9, an innovative genomic tool to knock down microRNA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1965.
Abstract 1968: Systematic validation of microRNA based prognostic biomarkers for stage II, III and IV colorectal cancer
Authors: Ma Dongling , Xue Yaqi , Fesler Andrew , Zhai Haiyan , Yang Jie , Ieamniramit Apisri , Li Wenzhe , Ju Jingfang
Published: July 2016

microRNA (miRNA) based biomarkers have great potential due to their critical regulatory functions, superior stability, and relative small number compared to mRNAs. We have previously discovered a number of miRNAs that play key roles in colon cancer stem cell resistance and demonstrated their clinical potential as prognostic biomarkers. In this study, we have validated the prognostic potential of a panel of miRNAs in 204 stage II, III, and IV colorectal cancer specimens by qRT-PCR analysis. Many of the miRNAs have been functionally validated to be important in contributing to chemoresistance to 5-FU based chemotherapy. We also determined that miR-16 is the most consistent miRNA for expression normalization. We have validated several miRNAs that are significantly associated with disease free survival (DFS) and overall survival (OS) of stage II, III and IV colorectal cancer patients. This study, together with some of the previous studies, establishes a solid foundation for miRNA based precision management of colorectal cancer.

Citation Format: Dongling Ma, Yaqi Xue, Andrew Fesler, Haiyan Zhai, Jie Yang, Apisri Ieamniramit, Wenzhe Li, Jingfang Ju. Systematic validation of microRNA based prognostic biomarkers for stage II, III and IV colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1968.
Abstract 197: Phospholipids regulate the localization and oncogenic potential of protein tyrosine kinase 6 in prostate cancer
Authors: Wozniak Darren J. , Hitchinson Ben , Bie Wenjun , Gaponenko Vadim , Tyner Angela L.
Published: July 2016

Background: Protein tyrosine kinase 6 (PTK6, also called BRK) is an intracellular SRC-related tyrosine kinase that does not possess canonical localization signals. Lack of targeting yields flexibility in its intracellular localization and access to substrates. PTK6 is observed in the nuclei of prostate epithelial cells where it promotes differentiation and inhibits growth. PTK6 is activated at the plasma membrane in PTEN-deficient mouse prostate tumors where the concentration of PIP3 is high due to PTEN loss of function. Membrane-associated PTK6 induces cell transformation, the epithelial-mesenchymal transition, and tumor cell metastasis. In human prostate cancer, active PTK6 associates with the plasma membrane and its increased expression correlates with metastasis and poor survival. Our studies aimed to characterize how the mislocalization and activation of PTK6 in prostate cancer is regulated.

Results: Based on our observation that loss of PTEN induces accumulation of PTK6 at the membrane, we hypothesized that PTK6 binds to the plasma membrane secondary messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3). Amino acid sequence alignment predicts H52, Y53, and K54 of PTK6 as a potential PIP3 binding site, which resembles the lipid-binding HYK domain of tyrosine kinases BTK and Abl. Using NMR saturation transfer difference (STD) experiment, we observed that the SH2 domain of PTK6 contains a binding site for inositol trisphosphate (IP3) a soluble PIP3 mimic. As predicted, statistical analysis identified Y53 of the PTK6 HYK motif within the SH2 domain as a residue with substantial chemical shift perturbations (CSPs) induced by independent titrations with PIP3 analogs IP3, IP4, and 1,2-dihexanoyl PIP3 in 15N HSQC, as compared to controls. Using autophosphorylated and unphosphorylated PTK6, NMR STD experiments show that only active (pY342) PTK6 binds to IP3. Treatment of prostate cancer cells with the PI3K inhibitor wortmannin reduces active PTK6 at the plasma membrane.

Conclusions: Our data demonstrate that active PTK6 is recruited to the plasma membrane through direct interactions with PIP3. Membrane association places PTK6 in close proximity to its oncogenic substrates AKT, FAK and BCAR1, thereby promoting tumor progression. These findings may facilitate identification of novel PTK6 inhibitors that block its association with the membrane, while not affecting its tumor suppressive role in the nucleus.

This work is funded by NIH grant 1R01CA188427 to ALT and VG.

Citation Format: Darren J. Wozniak, Ben Hitchinson, Wenjun Bie, Vadim Gaponenko, Angela L. Tyner. Phospholipids regulate the localization and oncogenic potential of protein tyrosine kinase 6 in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 197.
Abstract 1982: BRD4-FOXO axis maintains differentiated mammary epithelial phenotype by regulating p63 and GRHL3 expression
Authors: Nagarajan Sankari , Bedi Upasana , Budida Anusha , Xie Wanhua , Hamdan Feda Hisham Moh’d , Mishra Vivek Kumar , Najafova Zeynab , Alawi Malik , Indenbirken Daniela , Knapp Stephan , Chiang Cheng-Ming , Grundhoff Adam , Scheel Christina H. , Kari Vijayalakshmi , Wegwitz Florian , Johnsen Steven A.
Published: July 2016

Bromodomain-containing protein 4 (BRD4) is an important epigenetic reader which promotes gene transcription to modulate cell-specific functions and is under intensive investigation for its potential as an anti-tumor therapeutic target. However, the role of BRD4 in non-transformed cells remains unclear. Using RNA sequencing and chromatin immunoprecipitation-sequencing analyses in normal basal-like breast epithelial cells, we demonstrate that BRD4 is required for the expression of epithelial-specific genes and suppression of stem cell-like properties by binding to the distal regions of epithelial-related genes. Moreover, BRD4 occupancy correlates with enhancer activity and enhancer RNA (eRNA) transcription of these genes. Interestingly, we show that BRD4 perturbation regulates the expression of p63 and Grainy Head-like transcription factor-3, GRHL3, whose depletion partially mimics BRD4 inhibition and impairs a differentiated phenotype. By binding to the distal regions of p63 and GRHL3, BRD4 promotes RNA polymerase-II occupancy and thus affects eRNA transcription. Motif analyses on cell-specific BRD4 binding sites predict the involvement of FOXO transcription factors. Consistently, inhibition of EGFR-AKT signalling activates FOXO1 function and promotes the expression of p63 and GRHL3. Activation of Src kinase signaling decreases RNA polymerase-II occupancy on BRD4 target genes and enhancers. Altogether, these findings provide evidence that BRD4 promotes a differentiated epithelial phenotype in non-transformed mammary cells at least in part through the activation of p63 and GRHL3 expression by associating with FOXO factors.

Citation Format: Sankari Nagarajan, Upasana Bedi, Anusha Budida, Wanhua Xie, Feda Hisham Moh’d Hamdan, Vivek Kumar Mishra, Zeynab Najafova, Malik Alawi, Daniela Indenbirken, Stephan Knapp, Cheng-Ming Chiang, Adam Grundhoff, Christina H. Scheel, Vijayalakshmi Kari, Florian Wegwitz, Steven A. Johnsen. BRD4-FOXO axis maintains differentiated mammary epithelial phenotype by regulating p63 and GRHL3 expression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1982.
Abstract 1985: Oncogenic activation of RNA binding proteins and c-Myc signaling in hepatocellular carcinoma
Authors: Hien Dang T. , Takai Atsushi , Forgues Marshonna , Wang Xin Wei
Published: July 2016

Global transcriptomic alterations of both coding and non-coding RNA species are a ubiquitous feature associated with human cancers including hepatocellular carcinoma (HCC). Dysregulation of RNA-binding proteins (RBPs), the key regulators of RNA processing, is one mechanism in which cancer cells select to promote tumorigenesis. We analyzed genomic alterations amongst a family of more than 800 mRNA RBPs (mRBPs) in 1,225 clinical specimens from HCC patients and found that RBPs are significantly activated through gene amplification in a subset of tumors with poor prognosis, suggesting their potential oncogenic roles in HCC progression. Amongst the top candidates, RD binding protein (RDBP) was further characterized for its oncogenic role and effects on the HCC transcriptome. While the activation of RDBP induced an oncogenic phenotype, the abrogation of RDBP in HCC cells significantly decreased cancer associated phenotypes such as cell proliferation, migration/invasion and tumorigenicity in vivo. Further analyses revealed that RDBP-dependent genes were tumor-related with a significant enrichment for c-Myc targets, suggesting interplay between RDBP and c-Myc signaling. Similar data were also found in HCC clinical specimens where c-Myc amplification was uncommon. Consistently, the RDBP-dependent c-Myc target gene signature was able to predict HCC patient survival in two independent cohorts of more than 400 patients. Our results demonstrate that oncogenic activation of RDBP is a novel mechanism that contributes to global transcriptome imbalance, which is selective for the activation of c-Myc oncogenic signaling in HCC. Concurrent with the current model that indicates that c-Myc can promote tumorigenesis through transcription dysregulation, our current work suggests that therapies focused on targeting RDBP may be valuable for clinical treatment of many different tumors with activated c-Myc signaling, including HCC.

Citation Format: Dang T. Hien, Atsushi Takai, Marshonna Forgues, Xin Wei Wang. Oncogenic activation of RNA binding proteins and c-Myc signaling in hepatocellular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1985.
Abstract 2: Metabolomics analysis reveals distinct profiles of non-muscle invasive and muscle-invasive bladder cancer
Authors: Sahu Divya , Lotan Yair , Wittmann Bryan , Neri Bruce , Hansel Donna
Published: July 2016

Background: Bladder cancer affects >70,000 patients annually in the United States. Despite its high incidence, therapeutic options are limited in early or late stage. We wanted to identify key metabolic pathways that were altered in bladder cancer development and progression.

Experimental Design: We performed global metabolomics profiling of benign urothelium, high-grade non-muscle invasive bladder cancer and advanced, muscle-invasive bladder cancer using GC-MS and LC-MS platforms. This analysis was coupled with publicly available data on transcriptomics of key enzymes, to determine pathways that may be suitable for future therapeutics development.

Results: Categorical pathways globally dysregulated in cancer relative to benign urothelium included glucose, TCA cycle, lipid, amino acid and nucleotide pathways. Bladder cancers demonstrated Warburg metabolism, with elevated glucose utilization to

drive glycolysis and sorbitol pathway intermediates. Elevated late TCA cycle intermediates, coupled with higher levels of amino acids and dipeptides, suggest the possibility of anaplerotic activity in bladder cancer as a mechanism to sustain energy production. Medium and long chain fatty acids were produced at the expense of dicarboxylic fatty acids. Muscle-invasive bladder cancers showed enhanced use of COX and LOX metabolomics pathways and a possible role for inflammation in regulating NAD+ synthesis in muscle-invasive bladder cancer. Transcriptomic profiling validated that the majority of metabolomics pathway alterations corresponded to gene expression changes of enzymes responsible for metabolite production.

Conclusions: This study identifies multiple parallel metabolomics changes unique to non-muscle invasive and muscle-invasive bladder cancer that can be used to justify testing novel therapeutics targeting metabolic pathways in bladder cancer.

Citation Format: Divya Sahu, Yair Lotan, Bryan Wittmann, Bruce Neri, Donna Hansel. Metabolomics analysis reveals distinct profiles of non-muscle invasive and muscle-invasive bladder cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2.
Abstract 2001: Elucidate the functions of TBX3 in AR positive prostate cancer
Authors: zhu. sinan
Published: July 2016

TBX3 is a transcriptional repressor belonging to the T-box gene family. It is involved in lineage specification in mammary gland, limb and heart during embryonic development. Mutations in TBX3 can cause ulnar-mammary syndrome, affecting limb, apocrine gland, tooth, hair and genital development. TBX3 is amplified/mutated in a variety of cancers, including melanoma, bladder, breast and prostate cancer. Recent findings suggest there is a strict correlation between estrogen receptor and TBX3 expression in mammary gland and TBX3 is mutated in 9% of invasive lobular breast cancer. However, little is known about the functions of TBX3 in hormone-dependent tumors. Here we screened several AR+ and AR- prostate cancer cell line and we found that the expression of TBX3 and AR is positively correlated. Moreover, in benign human prostate tissue, TBX3 localization is overlapped with that of AR. Knocking down TBX3 by siRNA resulted in decreased cell proliferation and cell cycle arrest in AR+ cell line Lncap and Vcap, but there was no effect on AR- cell line PC3 and DU14 upon TBX3 knock-down. TBX3 ChIP-seq in both Lncap and Vcap revealed co-binding of TBX3, ETS transcriptional factors and FOXA1 on AR targeted genes. Gene Set Enrichment Analysis (GSEA) of RNA-seq data from Lncap cells infected with lentivirus expressing siSCR or siTBX3 indicated that TBX3 suppresses AR and ETV1 signaling. In conclusion, our data suggests that TBX3 is essential for AR+ prostate cancer cell growth and may play a role in regulating androgen signaling.

Citation Format: sinan zhu. Elucidate the functions of TBX3 in AR positive prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2001.
Abstract 2004: Nucleation of transcriptional super-enhancers at tumor oncogenes by small insertions
Authors: Abraham Brian J. , Hnisz Denes , Weintraub Abraham S. , Kwiatkowski Nicholas , Li Charles H. , Rahman Sunniyat , Li Zhaodong , Lee Tong Ihn , Look A Thomas , Mansour Marc , Young Richard A.
Published: July 2016

Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics[1,2,3,4]. Super-enhancers are acquired by cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs)[5]. In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 oncogene. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in cancers. This approach uses data from genome-wide ChIP-Seq studies that map locations of enhancer-binding proteins to identify short DNA sequences missing from reference genomes. We have found and catalogued many additional genomic insertions in 80 additional cancers. An additional insertion has been functionally characterized and determined to be a bona fide enhancer-nucleating insertion that exists in patient genomes. I will describe new insights into the regulation of cancer that occur due to nucleation of novel regulatory elements.

[1] Hnisz, Abraham, Lee, et al., Cell 2013

[2] Loven, Hoke, Lin, et al., Cell 2013

[3] Kwiatkowski, et al., Nature, 2014

[4] Wang, et al., Cell, 2015

[5] Mansour et al., Science 2014

Citation Format: Brian J. Abraham, Denes Hnisz, Abraham S. Weintraub, Nicholas Kwiatkowski, Charles H. Li, Sunniyat Rahman, Zhaodong Li, Tong Ihn Lee, A Thomas Look, Marc Mansour, Richard A. Young. Nucleation of transcriptional super-enhancers at tumor oncogenes by small insertions. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2004.
Abstract 2013: The PAX3-FOXO1 oncogene drives aneuploidy and overrides aneuploidy-associated proliferative defects in alveolar rhabdomyosarcoma
Authors: Hollenbach Andrew D. , Loupe Jacob M. , Miller Patrick J. , Bonner Benjamin P. , Maggi Elaine C. , Vijayaraghavan Jyothi , Zabaleta Jovanny , Taylor Christopher M. , Miller Fern , Crabtree Judy S.
Published: July 2016

Alveolar Rhabdomyosarcoma (ARMS) is primarily defined by the t(2;13)(q35;q14) translocation, which generates the PAX3-FOXO1 oncogene. Despite the fact that ARMS are frequently aneuploid, like a majority of other solid tumors, it is unknown whether PAX3-FOXO1 contributes to the development and/or persistence of aneuploidy. In this study we show that PAX3-FOXO1 serves as the driver mutation to promote aneuploidy by globally altering gene regulatory networks essential for maintaining proper chromosome number and structure. Further, we demonstrate that PAX3-FOXO1 overrides aneuploid-dependent growth arrest by altering the expression of growth factor related regulatory networks. Finally, we present evidence that phosphorylation of PAX3-FOXO1 contributes to these gene regulatory network changes. This is the one of the first studies describing how an oncogene and post-translational modifications of the corresponding oncoprotein drive the acquisition of aneuploidy and override proliferation defects in malignant transformation. The mechanism for PAX3-FOXO1 described in this work has implications for other solid tumors where large-scale genomics studies may elucidate how global alterations contribute to tumor phenotypes allowing the development of much needed multi-faceted tumor-specific therapeutic regimens.

Citation Format: Andrew D. Hollenbach, Jacob M. Loupe, Patrick J. Miller, Benjamin P. Bonner, Elaine C. Maggi, Jyothi Vijayaraghavan, Jovanny Zabaleta, Christopher M. Taylor, Fern Miller, Judy S. Crabtree. The PAX3-FOXO1 oncogene drives aneuploidy and overrides aneuploidy-associated proliferative defects in alveolar rhabdomyosarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2013.