bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B39: Genome structure-based screening identified epigenetically silenced microRNA associated with invasiveness in non-small-cell lung cancer
Authors: Watanabe Kousuke , Goto Akiteru , Fukayama Masashi , Nagase Takahide , Yatomi Yutaka , Ohishi Nobuya , Takai Daiya , Emoto Noriko , Hamano Emi , Amano Yosuke , Ishikawa Rie , Sunohara Mitsuhiro , Kawakami Masanori , Kitano Kentaro , Nakajima Jun 
Published: March 2013

Abstract
microRNA expression is frequently altered in human cancers. Epigenetic silencing, especially DNA methylation, is one of many mechanisms of microRNA suppression in cancer. To search for epigenetically silenced microRNAs in non-small-cell lung cancer (NSCLC), we mapped human microRNAs on autosomal chromosomes and selected in silico 55 microRNAs that met one of the following criteria: (i) microRNAs within CpG islands, (ii) microRNAs within 1 kbp downstream of CpG islands, and (iii) microRNAs within gene introns whose promoters have CpG islands. We treated six NSCLC cell lines with the DNA methylation inhibitor 5-aza-2′-deoxycytidine (5-aza-CdR) and determined the expressions of the 55 microRNAs. Fourteen microRNAs (mir-375, mir-196b, mir-126, mir-34b, mir-127, mir-203, mir-148a, mir-181c, mir-30e, mir-449a, mir-340, mir-486, mir-483, mir-139) were decreased in the cancer cell lines and were induced after 5-aza-CdR treatment. Among the 14 microRNAs, seven (mir-126, mir-34b, mir-203, mir-30e, mir-449a, mir-486, mir-139) were frequently suppressed in primary NSCLCs. After a detailed DNA methylation analysis, we found that mir-34b and mir-126 were silenced by DNA methylation. Mir-34b was silenced by the DNA methylation of its own promoter, while mir-126 was silenced by the DNA methylation of its host gene, EGFL7. A chromatin immunoprecipitation assay revealed H3K9me2 and H3K9me3 in mir-34b and EGFL7, and H3K27me3 in EGFL7. A significant enrichment of H3K27me3 was observed in lung cancer cell lines with decreased mir-126 expression, suggesting the involvement of a polycomb complex in the regulation of EGFL7 and mir-126. The overexpression of mir-34b and mir-126 by plasmid vectors decreased the expression of c-Met and Crk, respectively. The 5-aza-CdR treatment of lung cancer cell line resulted in increased mir-34b expression and decreased c-Met protein. We next analyzed the DNA methylation status of these microRNAs using 99 primary NSCLCs. Mir-34b and mir-126 were methylated in 41% and 7% of all the cases, respectively. The DNA methylation of mir-34b was not associated with c-Met expression determined by immunohistochemistry, but both mir-34b methylation (p = 0.007) and c-Met expression (p = 0.005) were significantly associated with lymphatic invasion in a multivariate analysis. The DNA methylation of mir-34b can be used as a biomarker for an invasive phenotype of lung cancer.
Abstract B4: A “DNA replication stress” gene signature associated with a poor prognosis in early non-small cell lung cancer
Authors: Allera-Moreau Camille , Delisle Marie-Bernadette , Hoffmann Jean-Sebastien , Cazaux Christophe , Rouquette Isabelle , Lepage Benoit , Oumouhou Naima , Gordien Karine , Brouchet Laurent , Mazieres Julien , Pasero Philippe 
Published: March 2013

Abstract
The conventional clinical staging classification is not sufficient to predict the survival of patients who suffer from early lung cancer. Additional prognostic factors are then needed to better forecast their outcome.
Since perturbation of the genome replication i.e. the so-called “replicative stress” is admitted to contribute to neoplasia from its early stages, we hypothesized that genes involved in such process may therefore represent a still under-explored source of such biomarkers.
We specifically assessed in primary tumors and adjacent normal tissues from a series of 93 patients suffering from early- or mid-stage non-small cell lung adenocarcinoma the expression (RT-qPCR) of 77 “DNA replication” genes involved in either initiation/licensing at the 50,000 replication origins dispersed along the genome, elongation of DNA chains onto damaged or undamaged DNA, maintenance of stalled DNA replication forks or intra-S phase DNA damage processing and signaling.
A 4-gene signature separated patients to high-risk and low-risk subgroups with significantly different survival. This prognostic effect was independent on age, sex, treatment, stage classification and expression of proliferation markers.
We propose that a “cancer replisome” signature could be a predictor of the cancer survival and might also help understanding the molecular mechanisms underlying tumor progression in lung cancer patients.
Abstract B41: Consider the source: Normal lung expression classifies cancer histologies, subtypes, and mutations
Authors: Wilkerson Matthew D. , Randell Scott H. , Hayes D. Neil 
Published: March 2013

Abstract
Lung cancer's pathogenesis from normal cell to metastatic disease involves vast and complex genetic alterations. However, a patient's genetic alterations do not completely explain the pathogenic process, for tumors with the same alterations have different features and therapy responses. We hypothesized that differences in ancestral anatomical regions affect pathogenesis and as such would correlate with differences in cancer histology, subtype, and mutations. Anatomical distal and proximal region specimens from normal lungs were collected and assayed by Agilent 44K gene expression microarrays and immunohistochemistry (IHC). 271 surgically extracted lung cancers were assayed by gene expression, IHC, and gene sequencing for EGFR, KRAS, STK11, and TP53. Using the normal lung specimens, a novel classifier was created to assign cancers with an anatomical region using gene expression alone. Cancers classified as distal by gene expression were 84% adenocarcinoma, while 73% of those classified as proximal were squamous cell carcinoma (P&lt;0.001). While this trend of histology and region is consistent with conventional wisdom, our results also suggest that lung cancers retain substantial gene expression from their ancestral anatomical region. Interestingly, the remainder of the cancers that did not follow this trend was explained by our previously described molecular subtypes (1, 2). Of adenocarcinomas classified proximal, 92% were in the Magnoid molecular subtype. Of squamous cell carcinomas classified distal, 60% were in the Secretory molecular subtype. Complementing microarray gene expression, TTF1 IHC protein expression was greater in distal normal specimens compared to proximal. Consistent with distal classification, adenocarcinomas had the greatest TTF1 expression. Of the squamous molecular subtypes, the Secretory subtype exhibited the greatest TTF1 expression, consistent with its distal classification. This Secretory subtype may explain previously reported TTF1-positive squamous cell carcinomas. Finally, gene mutation rates were significantly different between cancers classified as proximal and as distal. EGFR and KRAS mutation rates were greater in distal tumors compared to proximal tumors. In contrast, TP53 mutation rates were greater in proximally classified tumors. These results suggest that ancestral anatomical regions may affect lung cancer pathogenesis by modifying susceptibility to and dependency on different gene mutations. In summary, normal lung anatomical gene expression classifies lung cancers with different histologies, molecular subtypes, and gene mutation rates.
Abstract B44: Development of a serum test for the detection of lung cancer based on oncogenic BARD1 isoform expression
Authors: Irminger-Finger Irmgard , André Pierre-Alain , Pilyugin Maxim , Hegedus Balazs , Laurent Geoffrey J. , Bianco Andrea 
Published: March 2013

Abstract
The BARD1 protein was originally identified as binding partner of the breast cancer gene product, BRCA1. Highly upregulated expression of aberrant isoforms of BARD1, derived from differential splicing, was correlated with poor prognostic factors in breast and ovarian cancer (Wu et al. Int J Can, 2006; Li et al. Can Res, 2007) and decreased patient survival in lung cancer (Zhang et al. Int J Can, 2011).
Previous and ongoing studies have shown that BARD1 isoforms act antagonistically to the functions of BARD1 and BRCA1 as ubiquitin ligase. In particular, BARD1beta is promoting cell proliferation by stabilizing the Aurora kinases (Ryser et al. Can Res 2009; Bosse et al. submitted). Isoforms BARD1-beta and BARD1-pi are specifically upregulated in lung cancer and correlated with poor prognosis (Zhang et al., Int J Can, 2011). Thus, BARD1 isoforms might be drivers of tumorigenesis and potential markers of lung cancer progression, if detectable in the patients' sera.
To this goal, we performed ELISA tests with antibodies against different regions of BARD1 for the detection of BARD1 isoforms in the blood of lung cancer patients. We also generated a peptide library representing 40 epitopes mimicking BARD1 isoforms, for the detection of autoimmune antibodies recognizing epitopes expressed by BARD1 isoforms.
BARD1 protein isoforms could be detected by ELISA in various serum samples, however this detection was always reproducible due to the BARD1 protein instability. We then performed inverse ELISA assays, using peptides for capturing autoimmune antibodies directed against BARD1 isoforms. Using serum samples from 60 non-small cell lung cancer (NSCLC) from time of diagnosis, and 40 control sera from phenotypically healthy volunteers, we could distinguish NSCLC cancer patients and controls. When applying a combination of seven peptides lung cancer was detected with 87 percent sensitivity and 68 percent specificity.
Thus, our data show convincingly that antibodies against BARD1 isoforms are telltales of lung cancer and their detection can be further developed towards a blood test for the early detection of lung cancer. Experiments including larger patients and control group numbers, sera from patients with different types of lung cancer, as well as the comparison of this BARD1 isoform test with the standard test for lung cancer detection (CT scan), are currently ongoing, and should lead to optimized test conditions and a definition of the target patient set.
Abstract B46: Clinicopathologic implications of ALK rearrangement in surgically resected NSCLC: A proposal of molecular algorithm with a small lung biopsy of adenocarcinoma
Authors: Ho Paik Jin , Choi Chang-Min , Kim Hyojin , Jang Se Jin , Sung Sook-Whan , Kim Dong Kwan , Kim Hwa Jung , Yoon Hoil , Lee Choon-Taek , Jheon Sanghoon , Choea Ji-Young , Chung Jin-Haeng 
Published: March 2013

Abstract
Background: To characterize the clinicopathologic features of ALK-rearranged lung cancer, and suggest a molecular test protocol for lung adenocarcinoma in the small biopsy specimen.
Methods: In 735 NSCLC surgical specimens, clinicopathologic features, ALK protein over-expression by immunohistochemistry (IHC), and ALK rearrangement by fluorescence in situ hybridization (FISH) as well as EGFR and KRAS mutation studies were analyzed.
Results: Of the 735 NSCLC cases, 28 (3.8%) were ALK FISH-positive. ALK rearrangement, EGFR and KRAS mutation were mutually exclusive. ALK rearrangement was significantly higher in adenocarcinomas (6.8%, p&lt;0.001), younger age (p&lt;0.0007), women (7.6%, p&lt;0.001), and never-smokers (8.9%, p&lt;0.001) with no gender difference in the adenocarcinoma or never-smoker subgroup. ALK FISH-positivity was not associated with disease recurrence (HR, 0.79; 95% CI, 0.42–1.49) or overall survival (HR, 0.61; 95% CI, 0.24–1.55). However, ALK-rearranged lung cancer tended to show more frequent lymph node metastasis despite its lower T stage. Similar to EGFR-mutated lung cancer, ALK-rearranged lung cancer was enriched in adenocarcinoma, women, and never-smokers. The results of ALK IHC and FISH obtained from tissue microarray (TMA)/biopsy specimens and whole sections after resection were concordant.
Conclusion: ALK rearrangement was not a significant prognostic factor in surgically resectable NSCLC. The clinical profiles of ALK-rearranged lung cancer patients overlapped with those of EGFR-mutated patients. Therefore, we suggest that simultaneous tests for ALK IHC and EGFR mutation (Chung's SNUBH molecular test protocol), which has important implications for the storage and use of small biopsy or cytology samples for genetic analysis.
Abstract B6: Folylpoly-glutamate synthetase and thymidylate synthase are associated with clinical outcome from pemetrexed-based therapy in non-small cell lung cancer (NSCLC)
Authors: Christoph Daniel C. , Loewendick Heike , Peglow Anja , Schuler Martin , Eberhardt Wilfried E. , Hirsch Fred R. , Asuncion Bernadette Reyna , Wynes Murry W. , Gauler Thomas C. , Wohlschlaeger Jeremias , Theegarten Dirk , Welter Stefan , Tran Cindy , Hassan Biftu 
Published: March 2013

Abstract
Background: The antifolate pemetrexed targets multiple enzymes involved in pyrimidine and purine synthesis including thymidylate synthase (TS). After entry into cells, pemetrexed is converted to polyglutamated forms by folylpoly-γ-glutamate synthetase (FPGS), a critical step to achieve full target inhibition. We hypothesized that FPGS and TS protein expression may predict outcome following pemetrexed-treatment of patients with advanced NSCLC, like in malignant pleural mesotheliomas (Christoph et al., J Clin Oncol. 2011: 29 suppl.). This is the largest report on pemetrexed-treatment outcome based on TS and FPGS in Caucasian patients with advanced NSCLC.
Methods: Pretreatment tumor samples from 161 patients (pts) with metastatic NSCLC, treated with pemetrexed combined with platinum (74 pts (46%)) or as single agent (82 pts (51%)) or within other combinations (5 pts (3%)), were retrospectively analyzed. FPGS and TS protein expression levels were evaluated by IHC using the H-Scoring system (0–300), which relies on the product of intensity (range 0 to 3) and the percentage of positive tumor cells (0–100%). Radiographic evaluation of response was performed according to RECIST criteria (version 1.1).
Results: Median pretreatment H-scores were 180 for FPGS (range: 0–280) and 205 (range: 120–290) for TS. Using the log-rank test and the median H-score as cut-off, we found a significant association between low TS protein expression and improved progression-free survival (PFS) (median PFS of 5.5 months vs. 3.4 months; hazard ratio [HR] 0.66, 95% CI, 0.45 to 0.96; P=0.03) or prolonged overall survival (median OS of 33.9 months vs. 15.0 months; hazard ratio [HR] 0.52, 95% CI, 0.31 to 0.86; P=0.01). Moreover, high FPGS protein expression was only associated with better PFS (median PFS of 5.5 months vs. 3.4 months; hazard ratio [HR] 0.58, 95% CI, 0.37 to 0.89; P=0.03). Considering exclusively patients suffering from adenocarcinomas (110 pts (68%)), TS was associated with objective response to pemetrexed-based treatment (mean H-score 192 for responders vs. 210 for non-responders, P=0.03).
Conclusions: We have investigated FPGS and TS protein expressions in tumor specimens from the largest series of pemetrexed-treated Caucasian NSCLC patients. Baseline determination of TS and FPGS expression by IHC using the H-score system is associated with clinical outcome from pemetrexed-based therapy in advanced NSCLC. Further prospective validation studies are warranted.
Abstract A14: Re-expression of microRNA-375 reverses both tamoxifen resistance and accompanying EMT-like properties in breast cancer
Authors: Ward Aoife , Balwierz Aleksandra , Zhang Jitao David , Kueblbeck Moritz , Wiemann Stefan , Hielscher Thomas , Pawitan Yudi , Sahin Ozgur 
Published: March 2013

Abstract
Epithelial-mesenchymal transition (EMT) is an initiating event in tumor cell invasion and metastasis. It has been shown to occur in resistance to a range of cancer therapies, including tamoxifen. MicroRNAs (miRNAs) have been associated with EMT as well as resistance to standard therapies. To investigate the role of miRNAs in the development of resistance to tamoxifen as well as accompanying EMT-like properties, we established a tamoxifen resistant (TamR) model by continually exposing MCF-7 breast cancer cells to tamoxifen. In addition to the molecular changes known to be involved in acquired tamoxifen resistance, TamR cells displayed mesenchymal features and had increased invasiveness. Genome-wide miRNA microarray analysis revealed that miRNA-375 was among the top down-regulated miRNAs in resistant cells. Re-expression of miR-375 was sufficient to sensitize TamR cells to tamoxifen and partly reversed EMT. A combination of mRNA profiling, bioinformatic analysis, and experimental validation identified metadherin/MTDH as a direct target of miR-375. Knockdown of MTDH partially phenocopied the effects of miR-375 on the sensitivity to tamoxifen and the reversal of EMT. We observed an inverse correlation between the expression of miR-375 and its target MTDH in primary breast cancer samples, implying the pathological relevance of targeting. Finally, tamoxifen-treated patients with higher expression of MTDH had a shorter disease-free survival and higher risk of relapse. As most cancer-related deaths occur due to resistance to standard therapies and metastasis, re-expression of miR-375 or targeting MTDH might serve as potential therapeutic approaches for the treatment of tamoxifen resistant breast cancer.
Abstract A16: Molecular mechanisms of EGFR therapy resistance in breast cancer cells
Authors: Castillo-Pichardo Linette , Borrero-Garcia Luis D. , Redis Roxana S. , Calin George A. , Cubano Luis A. , Dharmawardhane Suranganie 
Published: March 2013

Abstract
The purpose of this study is to investigate molecular mechanisms of epidermal growth factor receptor (EGFR) therapy resistance using a syngeneic pair of gefitinib-sensitive and gefitinib-resistant breast cancer cells. Signaling from EGFRs is usually dysregulated in breast, as well as other cancers, where it is commonly associated with an aggressive phenotype and poor outcome. The initial success of targeted therapies for EGFR1 and HER2 has been marred by de novo or acquired resistance. Gefitinib, a small molecule tyrosine kinase inhibitor with high specificity towards EGFR, was proven to be effective for the treatment of non-small cell lung carcinoma (NSCLC). However, clinical trials of gefitinib as a breast cancer therapeutic have failed due to lack of response, probably due to resistance, and adverse toxic effects. We have developed a Gefitinib resistant variant of the gefitinib sensitive human breast cancer cell line SKBR3 (SKBR3 G.R.), with the objective of studying the involvement of micro (mi)-RNAs in therapy resistance. A partial screening of several miRNAs previously shown to be involved in therapy resistance was performed and miRNA (miR-)200a was identified as a downregulated miRNA in the SKBR3 G.R. cells. Members of the miR-200 family play a critical role in the suppression of epithelial-to-mesenchymal transition (EMT) by repressing key mRNAs involved in this process. Additionally, the miR-200 family can regulate tumor cell adhesion, migration, invasion and metastasis; and has been associated with EGFR inhibitor resistance. Herein, we have analyzed the protein expression of EGFR, phospho-EGFR, and miR-200 family targets Zeb1, β-catenin, and the ErbB receptor inhibitor-1 (ERRFI-1 or Mig6) by western blot analysis in SKBR3 and SKBR3 G.R. breast cancer cells. Our results show a significant increase in the expression of EGFR, Zeb1, and β-catenin; whereas, phospho-EGFR and Mig6 expression was significantly downregulated in SKBR3 G.R. cells when compared to parental cells. Therefore, Mig6 expression may not be regulated via miR-200 activity in these cells. Downregulation of Mig6 may explain the increased EGFR levels due to its role in EGFR internalization and subsequent degradation. Since SKBR3 cells are mesenchymal, they do not express E-cadherin, another Zeb1 target. Our results suggest that in cancer cells that have undergone EMT, decreased miR-200a levels, and thus, increased Zeb1 and β-catenin, a potent pro-cancer transcriptional activator in the absence of an E-cadherin axis, is a potential mechanism of Gefitinib resistance in aggressive breast cancer.
This study was supported by NIH/NIGMS SC3GM094824 to SD, the UCC Pilot Project Program, and the UCC Postdoctoral Program sponsored by the PR Science, Technology and Research Trust.
Abstract A18: Reduced NF1 expression in resistance to EGF receptor inhibitory drugs in lung adenocarcinoma
Authors: de Bruin Elza , Cowell Catherine , Howell Michael , Varmus Harold , Politi Katerina , Downward Julian 
Published: March 2013

Abstract
Tyrosine kinase inhibitors, such as erlotinib, exhibit striking efficacy in lung adenocarcinomas with activating mutations in the epidermal growth factor receptor (EGFR). However, patients inevitably develop therapeutic resistance, often due to second site mutations (T790M) in the EGFR. In this study, we aim to identify novel determinants of resistance in order to find new drug targets that may increase the effectiveness of EGFR targeted therapy.
We performed a genome-wide siRNA screen using the PC9 cell line, which harbors an EGFR exon 19 deletion mutation and is exquisitely sensitive to erlotinib. From this screen, we identified genes that upon knockdown had a significantly different effect on cell survival in drug-treated versus untreated conditions. Within the list of candidate genes is the tumor suppressor NF1, encoding the RAS GTPase-activating protein neurofibromin. In addition, low Nf1 expression is associated with the acquisition of resistance in a preclinical mouse model of activated mutant EGFR-driven lung cancer in tumors where the second site mutation in EGFR did not occur.
In vitro experiments show that decreased expression of NF1 results in a failure of erlotinib to fully inhibit RAS-ERK signaling. Treatment of NF1-deficient lung cancer cells with a MEK inhibitor restored their sensitivity to erlotinib both in in vitro and in xenograft experiments. Interestingly, approximately half of the erlotinib resistant tumors in our mouse model regressed upon treatment with erlotinib in combination with a MEK inhibitor, while tumors treated with erlotinib only continued to progress. This suggests that combination of a MEK inhibitor and an EGFR inhibitor may be an effective approach to the treatment of some cases of drug resistant lung cancer.