bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of complex oncogene signatures in human cancer specimens and cell lines
Authors: Ethier Stephen P. , Atikkuke Govindaraja , Haddad Ramsi 
Published: May 2015

Abstract
Activated oncogenes are the genetic drivers of human cancer progression. Oncogenes become activated by structural DNA alterations including gene amplification accompanied by gene over expression, point mutations, and gene translocations/rearrangements. Data from recent clinical trials using targeted agents strongly suggest that clinical efficacy of these drugs is optimal when the target is an activated oncogene. However, it is also clear that even among patients that respond to drugs that target activated oncogenes, the level and duration of response is highly variable. One possible reason for heterogeneity in response to oncogene-targeted agents is the genomic context of a particular activated oncogene is not the same in all patients. Thus, the genomic context of an oncogene-target can have a dramatic influence on drug efficacy. Therefore, the ability to detect and diagnose complex oncogene signatures in human cancer specimens is vital for better predictions of the efficacy of targeted agents, and to design personalized therapeutic strategies. In our Oncogenomics laboratory, we have been working to identify candidate amplified and point mutated oncogenes in human breast, ovarian and lung cancer specimens and cell lines. To obtain individual oncogene signatures, we have used high resolution array comparative genomic hybridization coupled with a novel gene expression algorithm that allows for the identification of genes that are over expressed within amplicons in individual specimens, and Sequenom analysis for identification of point mutated oncogenes. These approaches have allowed us to elucidate complex oncogene signatures for over 50 cancer cell lines and specimens. Analysis of these data sets suggests that oncogene combinations across specimens is nearly random. Thus, knowing the status of one oncogene such as HER-2 does not predict what other oncogenes may be activated in the specimen or cell line. Indeed, we have observed HER-2 amplifications in the context of amplifications of oncogenes in the 11q12 or 8p11 amplicons, among others, and in the presence of absence of PIK3CA mutations. Furthermore, analysis of the effects of small molecule inhibitors of HER-2 at the level of cell survival/proliferation and gene expression demonstrated a dramatic effect of oncogene context on response to a targeted agent. In particular, PIK3CA mutations in the presence of HER-2 amplification and over expression was associated with a greatly attenuated response of the cells to the HER-2 targeted agent. Collectively, these results point to a need for a molecular diagnostic platform that can accurately identify the causal driving oncogenes in an individual cancer biopsy specimen in order to optimize clinical trial design, and develop personalized therapeutic strategies.
Comparison of signal transduction drug response markers in immortalized cell lines and primary patient specimens
Authors: Ceceris Kyra D. , Ervin Paul R. , Cassino Theresa R. 
Published: May 2015

Abstract
Background: The epidermal growth factor pathway is an important driver of cancer growth. Erlotinib is a small molecule protein-kinase inhibitor targeting the epidermal growth factor receptor (EGFR) that may benefit a select subtype of cancer patients. However, identification of the characteristics of patients who may benefit from the use of erlotinib is not easy. Previous publication explored the activation of signal transduction proteins in the EGFR pathway as a method of determining erlotinib response and demonstrated that lung cancer cell lines characterized by increased pEGFR/pAKT ratios are more resistant to erlotinib. The aim of this study was to compare the activation of signal transduction markers in the EGFR pathway between immortalized cell lines and primary cultures of patient-derived tumor cells. Predictive potential of pEGFR/pAKT ratios in both immortalized cell lines and primary cultures of lung cancer cells was also compared.
Methods: Western blotting and In-Cell western analysis were used to determine the activation state of the EGFR signaling pathway. Signaling pathway components were compared in the presence and absence of erlotinib treatment in immortalized lung cancer cell lines and primary cultures of lung cancer specimens. Chemosensitivity of cell lines and specimens to erlotinib was determined using an in vitro drug response marker. Cells were treated with a 10 dose concentration range of erlotinib for 72 hours and the remaining post-treatment live cells were enumerated by nuclear staining.
Results: The pEGFR/pAKT ratio was increased in erlotinib-responsive immortalized cell lines when compared to non-responsive cell lines (p&lt;0.05). This difference in pEGFR/pAKT ratio was significant after treatment with erlotinib as well. The difference in pEGFR/pAKT ratios in response to erlotinib treatment between erlotinib-responsive and non-responsive primary cultures of lung cancer cells was not, however, statistically significant.
Conclusion: These studies confirmed that pEGFR/pAKT ratios may be indicative of erlotinib response in immortalized lung cancer cell lines. However, when evaluating the signal transduction markers in patient-derived primary cultures, no correlation with in vitro erlotinib response was found. These results highlight the value of using in vitro drug response markers, which utilize primary patient tissue, in the development of predictive biomarkers.
Helicobacter pylori strain genotyping based on the amplification and sequencing of cagA gene
Authors: Garcia Daniella , Delgado Maria del Pilar , Quiroga Andres , Bravo Maria Mercedes , Jaramillo Carlos A. 
Published: May 2015

Abstract
Relevance: H. pylori presence has been described as a high risk factor of suffering gastric cancer, which is the fourth most common cancer in Colombia. Some studies [1, 2]; point out that when a genotypic characterization of different strains of this microorganism is carried out, more than one genotype can be found in the same patient can be found.
Purpose: To characterize different H.pylori cagA genotypes that occur in the same patient sample (biopsy) applying molecular and bioinformatic techniques.
Methods: cagA positive strains (n=35) from Instituto Nacional de Cancerología (Bogotá-Colombia), bank s samples were included as study material. Tissue DNA was extracted and used to amplify the 3’ region of the cagA gene by PCR [3]. The NTC11637 H. pylori strain was included as a positive control. PCR products were visualized in 2% agarose gels and the amplified fragments were purified using a commercial kit. As a final stage, a precipitation based on ethanol and EDTA was done and reaction products were sequenced. The obtained sequences were edited and submitted to a bioinformatic analysis using AASA, a program designed to characterize the EPIYA phosphorylation motifs localized in the C-terminal of the CagA protein by Rothstain, Yañez and Vivas (Los Andes University Thesis, 2008).
Results: The molecular and bioinformatic approach described allowed strain characterization. The applied strategy leads to verify the presence of the A, B and C EPIYA motifs in different combinations. ABC group was the most frequent motif found (48%). These results match those of previous reports in Colombia, nevertheless it is important to remark that amplicons with different molecular sizes can have the same EPIYA motif and that amplicons with similar sizes can have different EPIYA motifs.
Conclusions: The current strategy demonstrated to be useful in the identification and posterior characterization of more than one genotype of the different H. pylori strains present in the same biopsy sample. This molecular and bioinformatics approach combined with other techniques seems to be a good alternative to establish if an infection by H. pylori is the result of a coinfection or a microevolution process.
References: 1. Aras, R.A., et al., Natural variation in populations of persistently colonizing bacteria affect human host cell phenotype. The Journal of infectious diseases, 2003. 188(4): p. 486-496. 2. Panayotopoulou, E., et al., Strategy to characterize the number and type of repeating EPIYA phosphorylation motifs in the carboxyl terminus of CagA protein in Helicobacter pylori clinical isolates?†. Journal of Clinical Microbiology, 2007. 45(2): p. 488-495. 3. Yamaoka, Y., et al., Relationship between the cagA 3'repeat region of Helicobacter pylori, gastric histology, and susceptibility to low pH. Gastroenterology, 1999. 117(2): p. 342-349.
Regulation of Crm1 expression in cancer cells
Authors: Watt Pauline J. van der , Leaner Virna D. 
Published: May 2015

Abstract
Crm1 (or exportin 1) is a member of the karyopherin β protein family that mediates the nuclear export of cargo proteins and certain RNAs from the nucleus into the cytoplasm. We previously identified increased expression of Crm1 mRNA and protein in cervical tumours compared to normal epithelium, and increased Crm1 expression in transformed fibroblasts compared to normal fibroblasts. Moreover, Crm1 overexpression in cancer/transformed cells was found to be necessary for cell survival, implicating Crm1 as an attractive target for cancer therapy. We hypothesized that the increased expression of Crm1 in cancer/transformed cells derives from altered Crm1 promoter activity, yet no studies to date have investigated what regulates the Crm1 promoter. This study therefore set out to clone and characterize the Crm1 promoter. The cloned Crm1 promoter (-1405 to +99) was significantly more active in cancer and transformed cells compared to normal, correlating well with endogenous Crm1 protein levels. In order to define promoter regions responsible for the differential activity, deletion constructs were generated, and the −175 to +99 region was identified as important. Mutation of two CCAAT boxes and a GC box in this region significantly diminished Crm1 promoter activity in transformed and cancer cells, while having only a minor effect on Crm1 promoter activity in normal cells. In addition, ChIP assays revealed in vivo binding of NFY/CBP and Sp1 transcription factors to the CCAAT boxes and GC box of the Crm1 promoter in cancer and transformed cells, while binding was undetectable in normal cells. Interestingly, NFY and Sp1 expression levels were considerably elevated in transformed and cancer cells compared to normal. Taken together, we show that NFY- and Sp1-mediated activation of the Crm1 promoter contributes to Crm1 overexpression in cancer and transformed cells.
The role of p21-activated kinase 3 (PAK3) in activating protein 1 (AP-1) induced oncogenesis
Authors: Holderness Nina , Donninger Howard , Birrer Michael J. , Leaner Virna 
Published: May 2015

Abstract
Activating protein 1 (AP-1) is a fundamental transcription factor that plays a role in cell proliferation, differentiation and apoptosis. Little is known about the role of the diverse downstream targets of the active AP-1 complex, a dimer comprising of the Jun, Fos or ATF bZIP-domain proteins. Deregulation of AP-1 has been linked to many cancers, with its over-expression leading to the transformation of normal cells. Previous studies utilizing a doxycycline-inducible cJun/AP-1 construct identified PAK3, a serine/threonine kinase signal transduction molecule, as a potential AP-1-target involved in the AP-1 characteristic transformation. PAK3 has been implicated in a variety of pathological disorders and over-expression of other PAK-family members has been linked to certain cancers. This project aims to investigate the role of PAK3 in cJun/AP-1 induced oncogenesis. Quantitative RT-PCR and Western Blot Analysis showed elevated PAK3 expression at both the mRNA and protein level in cJun-overexpressing cells. PAK3 expression levels were also elevated in transformed human and cancer cell lines compared to normal cells. Analysis of the PAK3 promoter using promoter luciferase assays identified a putative AP-1 binding site, at position +52 to +60, which may be responsible for the increased PAK3 promoter activity in response to cJun/AP-1 over-expression. siRNA inhibition of the PAK3 protein showed the regression of the morphological phenotype and migratory potential associated with cJun-transformed cells. However PAK3 inhibition showed no significant effect on the proliferative response of cJun-transformed cells. This study suggests a potential regulation of cJun/AP-1 on PAK3 as well as a role for PAK3 in AP-1 induced transformation; specifically that associated with cell morphology and migration.
Dysregulation of the expression of miR204 mediates migration and invasion of endometrial cancer by regulating FOXC1
Authors: Wong Y. F. , Cheung T.H. , Lau T.S. , Chan L.K.Y. , Yim S.F. , Wang V.W. , Smith D.I. 
Published: May 2015

Abstract
microRNAs (miRNAs) regulate gene expression and some have been shown to function as either oncogenes or tumor suppressors (oncomirs). Changes in miRNA expression have been observed in many human cancers but their role in endometrioid endometrial cancer (EEC) remains poorly understood. We studied the expression of 365 human miRNAs using Taqman low density arrays in 98 EECs as well as 60 normal endometria. Potentially interesting miRNAs were then validated by qRT-PCR.
Expression of highly deregulated miRNAs on malignant cell properties was also examined in vitro using pre-/anti-miRNA transfection. Predicted mRNA targets for the miRNA of interest were also verified. We identified 16 significantly deregulated miRNAs in EEC and 7 of these are reported for the first time. Of these, miR-7, miR-194 and miR-449b knockdown and miR-204 induction repressed migration, invasion and extracellular matrix-adhesion in HEC1A endometrial cancer cells. For the cancer progression dysregulation of the expression of miR204 mediates migration and invasion of endometrial cancer by regulating FOXC1-related miR-204, FOXC1 was determined as its target gene possessing two miR-204-binding sites at the 3’-untranslated region. FOXC1 expression was inversely related to miR-204 expression in EEC. Functional analysis also revealed the involvement of FOXC1 in migration of HEC1A cells.
We have identified dysfunctional miRNAs in endometrial cancer and elucidated the crucial role of miR-204-FOXC1 interaction in endometrial cancer progression. This work provides insight into miRNA-based diagnostic and therapeutic approaches for endometrial cancers.
Molecular basis of aberrant expression of alkaline phosphatase in renal brush border membrane from renal cell carcinoma patients
Authors: Sharma Ujjawal , Singh Sarwan Kumar , Prasad Rajendra 
Published: May 2015

Abstract
The incidence of renal cell carcinoma (RCC) has been increasing worldwide. It continues to present a diagnostic and therapeutic challenge. It accounts for approximately 3% of adult malignancies and 90-95% of neoplasm arising from kidney. RCC originates from proximal tubular epithelium of adult kidney. Alkaline phosphatase is abundantly expressed on the BBM and serves as an excellent marker for its integrity. Earlier reports have demonstrated that the activities of brush border membrane (BBM) enzymes are altered in cancer cells. The present study was conducted to find out the molecular basis of altered expression/activity of ALP in BBM from RCC in comparison to normal renal BBM. Total 30 histopathologically confirmed cases of RCC were included in the present study. The specific activity of ALP was drastically reduced in homogenate as well as in BBM from RCC as compared to BBM from adjacent normal kidney parenchyma. SDS-PAGE study showed that the BBM proteins of higher molecular weights were poorly expressed in BBM from RCC as compare to BBM from adjacent normal kidney parenchyma. Incubation of gel with BCIP/NBT dye showed that the expression of ALP in BBM from RCC was reduced as compared to adjacent normal kidney BBM. Western blot analysis using anti ALP antibody also confirmed the reduced expression of ALP in RCC BBM. Further, to check whether this reduced expression of ALP occurs at mRNA level, a semi quantitative RT-PCR was done, which showed markedly reduced expression of ALP mRNA in RCC as compared to adjacent normal kidney.
Trastuzamab antibody drug conjugates demonstrate robust in vitro antitumor activity in HER2 amplified breast cancer cell lines
Authors: Mohan Sankar , O'Brien Carol , Savage Heidi , Phillips Gail , Stern Howard , Lackner Mark , Pandita Ajay 
Published: May 2015

Abstract
Breast cancer is a heterogeneous disease with molecular subtypes characterized by distinct histopathology and gene expression signatures. HER2 oncogene amplification and over-expression is a defining feature of the HER2-amplified subtype of breast cancer. Currently, assays for detecting gene amplification and protein over-expression are used as diagnostic assays for the selection of patients for HER2-targeted therapies. In the present study, we compared the sensitivity of several HER2-targeted therapies across a panel of 31 breast cancer cell lines and correlated the sensitivity of the cell lines with HER2 positivity, as determined by IHC, qPCR and FISH. The agents utilized for the cell line screening were trastuzamab (Herceptin), two trastuzamab antibody-drug conjugates (ADCs) that employ an anti-mitotic agent, and a small molecule inhibitor of HER2 kinase activity. HER2 testing revealed 32% of the cell lines to be positive for HER2 by qPCR and FISH, and 90% of these demonstrated gene amplification in the form of clusters, as detected by FISH, or more than 10 copies as detected by qPCR. Several of the cell lines exhibited polysomy for chromosome 17 with accompanying extra copies of HER2 but did not meet the criteria for HER2 amplification. The HER2 IHC assay revealed 10 cell lines to be positive (2+, 3+) by IHC, with 8 exhibiting high-level expression (3+). The agents tested were more efficacious in the HER2-amplified cell lines, with wideranging activity observed in response to the ADCs. Cell lines exhibiting polysomy for HER2 and 1+ expression by IHC were less responsive to any of the agents tested. Consistent with previous reports, many of the cell lines resistant to trastuzamab or the small molecule HER2 inhibitor exhibited deregulation of the PI-3 kinase pathway illustrated by mutations in the PIK3CA gene or loss of PTEN protein expression. Interestingly, the majority of these resistant cell lines were sensitive to ADCs. In summary, our study demonstrates a high sensitivity to ADCs in breast cancer cell lines harboring high-level amplification of the HER2 gene and suggests these agents may overcome in vitro resistance conferred by activation of the PI-3 kinase pathway.
A simple method based on fluorescence probes for cancer diagnosis
Authors: Chang Ta-Chau , Kang Chi-Chih 
Published: May 2015

Abstract
A simple, rapid, and noninvasive method at low cost based on fluorescence of 3,6-Bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC) staining was applied for point-of-care screening of cancer cells [1]. Further application to clinic malignant neck lumps showed that the diagnostic accuracy of this simple method alone is ~80 % [2]. In addition, the combination of the BMVC test and the fine-needle aspiration (FNA) cytology can reduce the non-diagnostic cases and improve the diagnostic accuracy. Since a small amount of the sample collected for clinic test is used for BMVC test, it can be widely used in Hospital and Medical Center either for a first-line screening tool or an adjuvant method to other methods for cancer diagnosis.
The success of the BMVC test for cancer diagnosis is mainly due to two distinct properties of BMVC: significant increase of the fluorescence quantum yield upon interaction with DNA and dramatic difference in the intracellular localization between the nucleus of cancer cells and the lysosome of normal cells. Here we have modified the molecular properties of BMVC derivatives to elucidate the possible correlation between molecular structure and cellular localization. Moreover, a better fluorescence probe than BMVC is screened for the detection of a single cancer cell by optimizing fluorescence contrast between cancer cells and normal cells by using a simple device. Our results not only provide invaluable information for targeting specific cellular organelles, but also establish new molecular principles for cancer diagnosis and treatment design. Further experiments show that BMVC can kill the CL1-0 cancer cells, but less damage the MRC-5 normal cells after irradiation at ~480 nm for several seconds.
1. Kang, C.C. et al. Analyst 132, 745-9 (2007).
2. Liao, L.J. et al. Analyst 134, 708-11 (2009).
Developing novel peptide inhibitors to chromosomal cohesion using mRNA display for nanodrug delivery in breast cancer therapy
Authors: McCullum Elizabeth O. , Pati Debananda 
Published: May 2015

Abstract
Several specific molecular networks mediate the cellular proliferation of tumorigenic cells. One signaling pathway of interest is the transition from metaphase to anaphase which is dependent on cleavage of the cohesin protein complex by separase, an endopeptidase. A normal transition allows the protein complex to form, sister chromatid cleavage and the onset of anaphase. However, failure to properly assemble or maintain the integrity of this complex results in the premature separation of chromatids (PCS), mitotic arrest and apoptosis in cultured cells. This research effort will focus on the identification of cohesin Rad21, a proapoptotic protein that is over-expressed in breast cancer cells, mimcs for the induction of apoptosis in the cohesin-disrupted tumors. Using mRNA display, Rad21 mimetopes will be selected to bind a SMC-1 target in the formation of standard cohesin complex assembly. The pool of isolated peptides will be further characterized for their specificity, induction of PCS, mitotic arrest and apoptosis both in vitro and in vivo. Finally, peptides will be conjugated to a RAFT-peptide scaffold drug delivery system to exclusively target rapidly proliferating breast tumor cells. The potential advantages provide an area of promising therapeutics for antitumor effects when coupled with chemotherapy at the point of early detection.