bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2380: Reduced CD44 and OTP gene expression are strong indicators of poor prognosis in pulmonary carcinoids.
Authors: Swarts Dorian RA , Henfling Mieke , van Neste Leander , van Suylen Robert J. , Dingemans Anne-Marie , Dinjens Winand NM , Haesevoets Annick , Rudelius Martina , Thunnissen Erik , Volante Marco , van Criekinge Wim , van Engeland Manon , Ramaekers Frans CS , Speel Ernst-Jan M. 
Published: August 2014

Abstract
Purpose: Pulmonary carcinoids are well-differentiated neuroendocrine tumors showing usually a favorable prognosis. However, there is a risk for late recurrence and/or distant metastasis. Because histological classification in typical and atypical (AC) carcinoids is difficult and its reliability to predict disease outcome varies, we evaluated three genes as potential prognostic markers, i.e., OTP, CD44 and RET.
Methods: These genes were analyzed in 56 frozen carcinoids by quantitative RT-PCR. RET was further studied by methylation and mutation analysis. Immunohistochemistry for CD44 and OTP protein expression was performed on 292 carcinoids.
Results: Low mRNA expression levels of CD44 (p=1.3e-5) and OTP (p=0.012), and high levels of RET (p=0.0025), were strongly associated with a low 20-year survival of carcinoid patients. High RET expression was not related to promoter hypomethylation or gene mutations. A direct link between gene expression and protein levels was confirmed for CD44 and OTP, but not for RET. Within all carcinoids as well as ACs, absence of CD44 protein was significantly associated with low 20-year survival (p=8.6e-5 and p=0.00015, respectively). The absence of nuclear OTP followed by complete loss of expression was also significantly associated with unfavorable disease outcome in all carcinoids (p=2.9e-5). Multivariate analysis revealed that CD44 and OTP immunostaining combined with histopathology is the optimal indicator for patient outcome.
Conclusions: Our study indicates that CD44 and OTP are strong indicators of poor outcome. We therefore argue for implementation of these markers in routine diagnostics in addition to histopathology to improve subclassification of pulmonary carcinoids into prognostically relevant categories.
Citation Format: Dorian RA Swarts, Mieke Henfling, Leander van Neste, Robert J. van Suylen, Anne-Marie Dingemans, Winand NM Dinjens, Annick Haesevoets, Martina Rudelius, Erik Thunnissen, Marco Volante, Wim van Criekinge, Manon van Engeland, Frans CS Ramaekers, Ernst-Jan M. Speel. Reduced CD44 and OTP gene expression are strong indicators of poor prognosis in pulmonary carcinoids. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2380. doi:10.1158/1538-7445.AM2013-2380
Abstract 2389: Positive or negative clinical implications of PI3K/Akt/mTOR pathway activation for predicting patient response to targeted therapy using multiplexed protein imaging of tumor tissue.
Authors: Derrien-Colemyn Alexandrine , Park Soon , Gillespie John , Lebowitz Michael , Tunon Peter 
Published: August 2014

Abstract
Background: In this ongoing clinical exploratory study, FFPE tissue sections are probed for protein biomarkers along the PI3K/Akt/mTOR pathway. A panel of assays was developed using Layered Immunohistochemistry (L-IHC). L-IHC allows for concurrent measurement of 6-8 proteins (total and/or phosphorylation sites) using a single tissue section. The goal was to discover applications of the technique based on complementary rationales about the implications of pathway activation. Those were: 1) in a scenario where the test indicates drug target activation, analysis for a positive response to an mTOR-targeted tyrosine kinase inhibitor (everolimus and/or temsirolimus) in kidney cancer; or 2) analysis for predicting no response to a HER2-targeted drug (trastuzumab) in breast cancer, assuming a scenario where the test would indicate activation of a functional by-pass pathway.
Methods: FFPE pre-treatment tissue samples from patients (pts) with advanced renal cell carcinoma (aRCC) treated with temsirolimus and/or everolimus, and trastuzumab treated HER2-positive breast cancer pts were studied. In L-IHC tissue-transfer layers, the intensity of specific protein biomarker signals in the cancer regions is visually scored. The expression levels are then summed and correlated with the patient's clinical outcome status.
Results: In the trastuzumab study, four biomarkers were determined to correlate with patient response. A total of 32 responders and 13 non-responders have been analyzed to date. The sum score for a 4-biomarker panel discriminated between responders and non-responders. The test correctly identified 28/32 responders and 10/13 non-responders for a sensitivity of 87%, specificity of 76%, and an accuracy of 81%.
In the mTOR inhibitor study, 35 RCC cases were analyzed, and a composite score based on 6 biomarkers was found to correlate to patient response. 11/14 OR/SD pts (sensitivity 79%) and 18/21 PD pts (specificity 86%).
Conclusions: These results indicate that multiplexed protein analysis of tumor tissue is capable of providing scenario-specific information, which could help guide targeted therapy with either a positive or a negative clinical significance.
Funding source: Supported in part by NCI Grant 5R44CA123994-06 and by 20/20 GeneSystems.
Citation Format: Alexandrine Derrien-Colemyn, Soon Park, John Gillespie, Michael Lebowitz, Peter Tunon. Positive or negative clinical implications of PI3K/Akt/mTOR pathway activation for predicting patient response to targeted therapy using multiplexed protein imaging of tumor tissue. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2389. doi:10.1158/1538-7445.AM2013-2389
Abstract 2396: High EGFR gene copy number predicts poor outcome in triple-negative breast cancer.
Authors: Park Heae Surng , Jang Min Hye , Kim Eun Joo , Kim Hyun Jeong , Lee Hee Jin , Park So Yeon 
Published: August 2014

Abstract
INTRODUCTION: Epidermal growth factor receptor (EGFR) is frequently expressed in triple-negative breast cancer and is emerging as a new therapeutic target. However, the rate of EGFR gene copy number alteration and mutation has been reported to be quite variable and their prognostic significance is poorly defined in triple-negative breast cancer.
METHOD: We examined EGFR protein expression, gene copy number alteration and mutation in 150 cases of tripe-negative breast cancer and correlated their findings with clinical outcome of the patients. EGFR protein expression was evaluated by immunohistochemistry using whole tissue sections and EGFR copy number alteration was assessed by dual-color fluorescence in situ hybridization using tissue microarrays. EGFR mutation analysis was performed by polymerase chain reaction of exon 18 to 21 of EGFR gene and direct sequencing of PCR products.
RESULT: EGFR protein was expressed in 117 of 150 cases (78.0%). High EGFR gene copy number was found in 33.3% of the cases (amplification in 2.0% and high polysomy in 31.3%). Five EGFR mutations were detected in 4 of 150 cases (2.7%) with G719A in exon 18 (n=1), V786M in exon 20 (n=1) and L858R in exon 21 (n=3). One case had two mutations (G719A and L858R). High EGFR copy number, but not EGFR mutation, was correlated with EGFR protein over-expression. In survival analyses, high EGFR copy number gain was found to be a poor prognostic factor for relapse-free survival (p=0.046), especially for metastasis-free survival (p=0.016).
CONCLUSION: EGFR mutation is found to be a rare event in triple-negative breast cancer. However, high EGFR copy number is relatively frequent and is associated with poor clinical outcome in triple-negative breast cancer, suggesting that evaluation of EGFR gene copy number is beneficial for the prediction of outcome in patients with triple-negative breast cancer and selection of the patients for anti-EGFR targeted therapy.
Citation Format: Heae Surng Park, Min Hye Jang, Eun Joo Kim, Hyun Jeong Kim, Hee Jin Lee, So Yeon Park. High EGFR gene copy number predicts poor outcome in triple-negative breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2396. doi:10.1158/1538-7445.AM2013-2396
Abstract 2399: The analytic performance of a TaqMelt PCR assay for the detection of KRAS mutations in formalin-fixed paraffin-embedded tissue (FFPET) samples of Non-Small Cell Lung Cancer (NSCLC).
Authors: Lee Sung C. , Cao Jianli , Adhikary Kiran , Corona Lilia , Lee Nitta , Li Jingchuan , May Theresa , Wu Yiqiao , Brophy Victoria 
Published: August 2014

Abstract
Mutations in the Kras gene that lead to its constitutive activation are quite common in many tumor types including NSCLC. We describe the analytic performance of a TaqMelt PCR assay (cobas® KRAS Mutation Test) that detects 19 mutations in codons 12, 13 and 61 which generates test results within 8 hours. Using a panel of DNA blends from 18 FFPET samples of NSCLC, tested at 4 genomic DNA input levels, the correct mutation call was observed at 5% mutant alleles from the prescribed 50 ng of gDNA/PCR down to 12.5 ng of gDNA/PCR. A separate panel of 194 FFPET samples of NSCLC was tested with the PCR test and compared to Sanger sequencing. There were 15 discordant samples, 9 PCR (+), Sanger (-) and 6 PCR (-), Sanger (+) samples, that were further analyzed using a quantitative 454 sequencing method. All Sanger discordant samples except 1 PCR (+), Sanger (-) sample yielded 454 results that agreed with the PCR result. The PPA, NPA, and overall agreement with sequencing (Sanger resolved by 454) are 100.0%, 98.9% and 99.5%, respectively.
Sanger/454 Sequencing MUT WT Total MUT 99 1 100 cobas® KRAS Mutation Test WT 0 94 94 Total 99 95 194* *Includes 1 result for double mutations by Sanger and excludes 1 invalid result by PCR
The same panel of 194 specimens tested with another lot of the PCR test gave similar performance. When a panel of 8 FFPET samples of NSCLC (including 3 near the limit of analytical sensitivity) was repeatedly tested by 2 operators, using multiple instruments and reagent lots, a correct result was observed for 100% of tests. PCR test results were not affected by repeated freezing and thawing of the DNA sample or test reagents, or by addition of hemoglobin or triglycerides. These studies show that this PCR test is a robust and reproducible assay that 1) detects 19 mutations in codons 12, 13 and 61, 2) requires a small amount of DNA (which can generally be obtained from 1x5 μm section), and 3) is more sensitive and specific than Sanger sequencing.
Citation Format: Sung C. Lee, Jianli Cao, Kiran Adhikary, Lilia Corona, Nitta Lee, Jingchuan Li, Theresa May, Yiqiao Wu, Victoria Brophy. The analytic performance of a TaqMelt PCR assay for the detection of KRAS mutations in formalin-fixed paraffin-embedded tissue (FFPET) samples of Non-Small Cell Lung Cancer (NSCLC). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2399. doi:10.1158/1538-7445.AM2013-2399
Abstract 240: Therapeutic targeting of EMP2 reduces breast cancer stem cells.
Authors: Wadehra Madhuri , Kiyohara Meagan , Ashki Negin 
Published: August 2014

Abstract
There is increasing evidence that tumor-initiating cancer stem cells (CSCs) contribute to tumor metastasis and therapeutic resistance. In breast cancer, metastatic CSCs are defined as CD44+/CD24- and ALDH+, and in this study, we define another marker epithelial membrane protein-2 (EMP2) as a novel target for this population of cells. EMP2 is an oncogene whose expression has been shown to correlate with tumor progression and survival in a number of human cancers including triple negative breast, ovarian, and endometrial tumors. In breast cancer, EMP2 is expressed on the majority of invasive tumors examined, and in particular 70% of triple negative breast tumors showed surface expression of this marker. Clinical data also revealed higher levels of EMP2 in metastatic lesions compared to primary tumors.
In this study, we show new evidence that EMP2 is highly expressed in CSCs. New data suggests that EMP2 upregulates the expression of HIF-1α, CD44, and ALDH and directly contributes to the metastatic potential of the tumor cell. High levels of EMP2 promote mammosphere formation and increased tumor forming potential. In tumors created from these cells, high levels of ALDH+ expression were also observed. In contrast, reduction in EMP2 decreased CD44 expression and ALDH activity both in vitro and in vivo, with the net consequence of poorly vascularized and slow growing tumors.
We have recently developed a novel IgG1 monoclonal antibody to EMP2 and have started testing its therapeutic efficacy. In vitro treatment with EMP2 IgG1 reduced HIF-1α, CD44, and ALDH levels, ultimately leading to caspase mediated apoptosis. Treatment of breast cancer cells with EMP2 IgG1 reduced tumor load in both subcutaneous and metastatic models of breast cancer with a significant improvement in survival. Histological examination of the tumors revealed significant necrosis and elimination of ALDH+ CSCs. These results suggest that targeting EMP2 may reduce CSCs and represent an attractive target for further therapeutic development.
Citation Format: Madhuri Wadehra, Meagan Kiyohara, Negin Ashki. Therapeutic targeting of EMP2 reduces breast cancer stem cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 240. doi:10.1158/1538-7445.AM2013-240
Abstract 2420: The association between severe treatment-related lymphopenia and progression free survival in patients with newly diagnosed squamous cell head and neck cancer.
Authors: Campian Jian L. , Sarai Guneet , Ye Xiaobu , Marur Shanthi , Grossman Stuart A. 
Published: August 2014

Abstract
Background:
Severe treatment-related lymphopenia (TRL) occurs in 50% of glioblastoma and pancreatic cancer patients and is associated with early death from tumor progression. We sought to determine if similar findings were seen in head and neck squamous cell carcinoma (HNSCC).
Patients and Methods:
Eligible patients for this retrospective study had: 1) HNSCC cancer diagnosed in 2007-2009, 2) good performance status, 3) platinum-based chemoradiation, and 4) follow-up at Johns Hopkins. Serial total lymphocyte counts (TLC), overall survival (OS) and progression-free survival (PFS) were analyzed accounting for known prognostic factors.
Results:
Fifty-six adults met eligibility criteria: median age: 57 years, female: 21%, HPV+: 61%, surgery prior to chemoradiation: 16%, stage IVA-IVB: 77%, T stage 3-4: 40% and N stage 2b-3: 56%. Changes in TLC are shown below:
Median TLC:Baseline Median TLC: 2 months post-Rx % with TLC &lt;500: 2 months post-Rx Overall 1660 448 61% HPV- (n = 22) 1770 550 36% HPV+ (n = 34) 1610 320 76%
14/56 patients (25%) had tumor recurrence and 9 (16%) died of their tumor. HPV+ patients had longer PFS (p=0.01) and OS (p=0.006) than HPV- patients. 10/22 HPV- patients had disease progression and 7 died. HPV- patients who developed grade III-IV TRL two months after beginning chemoradiation had a strikingly higher hazard rate for disease progression than those whose TLC remained higher (multivariate analysis HR 6.2, 95%CI: 1.1-35.2; p=0.039). Too few events occurred in the HPV+ cohort for analysis.
Conclusion:
TLCs were normal before chemoradiation. However, two months after chemoradiation ∼60% of patients had severe TLC regardless of HPV status. HPV- patients with severe TRL were much more likely to have disease progression than those without TRL. Prospective studies are needed to confirm these findings which are similar to those reported in other cancers. Preservation of the immune system during chemoradiation may be important to improving PFS and OS.
Citation Format: Jian L. Campian, Guneet Sarai, Xiaobu Ye, Shanthi Marur, Stuart A. Grossman. The association between severe treatment-related lymphopenia and progression free survival in patients with newly diagnosed squamous cell head and neck cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2420. doi:10.1158/1538-7445.AM2013-2420
Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Abstract 2422: Circulating miRNAs as potential biomarkers in prostate cancer pathogenesis.
Authors: Srivastava Anvesha , Ramalinga Malathi , Kumar Deepak , Dimtchev Alexander , Chijioke Juliet , Soldin Offie , Li Xin , Marian Catalin , Suy Simeng , Collins Sean P. , Kumar Deepak 
Published: August 2014

Abstract
Introduction: According to the American Cancer Society, prostate cancer (PCa) is a major health concern for U.S. men and is expected to result in approximately 241,740 new cases and about 28,170 deaths in 2012. African American (AA) men have a 60 percent higher incidence rate and twice the death rate of Caucasian men (CA). Whereas metastasis is the most common cause of death, no specific markers have been assigned to the severity and ethnic biasness of the disease. Deregulation of miRNAs has been observed in various human tumors which emphasize their role in cancer pathogenesis, progression and metastasis. This study was aimed to investigate potential miRNAs involved in PCa. The study also aims to identify potential biomarkers and/or their therapeutic targets which can provide insight into the severity and ethnic biasness of disease.
Methods: Study was divided into three phases: (I) Candidate serum miRNAs were detected by using PCR microarray (learning set of 6 AA and 6 CA PCa patients). (II) Discriminating performance of candidate miRNAs were validated by real-time RT-PCR in serum [AA (20 PCa patients and 16 controls) and CA (16 PCa patients and 16 controls). (III) Functional studies on candidate miRNA(s) were subsequently performed using gain-and loss-of-function approach in cellular assays.
Results: In the discovery phase we obtained 5 miRNAs which were differentially expressed in the AA prostate cancer patients. After careful examination miR-212 and few others were selected for future validation. In the validation set there was an overall high expression of miR-212 in serum of PCa patients as compared to normal individuals (p=0.0110). Subdivision on the basis of ethnicity showed serum expression levels of miR-212 in AA were significantly modulated (p=0.034) as compared to CA PCa patients. Functional validation of miR-212 was done in PC3 and LnCap cell lines.
Conclusion: Our results showed a potential role for miR-212 in the regulation of gene expression which in turn can define the aggressiveness associated in African American PCa patients.
Citation Format: Anvesha Srivastava, Malathi Ramalinga, Deepak Kumar, Alexander Dimtchev, Juliet Chijioke, Offie Soldin, Xin Li, Catalin Marian, Simeng Suy, Sean P. Collins, Deepak Kumar. Circulating miRNAs as potential biomarkers in prostate cancer pathogenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2422. doi:10.1158/1538-7445.AM2013-2422
Abstract 2424: CD40 expression in human solid tumors and NCI60 tumor cell lines.
Authors: Nguyen Dat , Tomaszewski Joseph E. , Hewitt Stephen M. , Doroshow James H. , Yang Sherry X. 
Published: August 2014

Abstract
Cell-surface CD40 is a member of the tumor necrosis factor receptor superfamily (TNFRSF) expressed and functionally well characterized in immune and hematopoietic cells. However, its expression and role in human solid tumors remain to be evaluated. As a molecular target currently with the antibody-based cancer therapy, it is important to characterize expression of CD40 across a range of human solid tumors and cancer cell lines. This could help improve our understanding of biology of CD40 molecule in human cancers especially epithelial tumors, and in turn increase the odds of success of targeting CD40 pathway. Expression of CD40 in the NCI60 human tumor cell lines and common types of human solid tumors were examined by immunohistochemistry in formalin-fixed and paraffin-embedded tumor specimens. CD40, predominantly membranous signal, was constitutively expressed in 15 lines, respectively derived from carcinomas of the breast, colorectum, non-small cell lung, ovary, prostate, and renal cell, of the NCI60 tumor cell line panel, and confirmed by Western blotting and gene expression microarray data available at http://dtp.nci.nih.gov/mtweb/search.jsp. CD40 expression was largely in accordance with the mRNA expression data measured by gene expression profiling. The status of CD40 was verified in MDA-MB-231, T-47D and HCT-116 cells (CD40-positive), and MCF-7 and HT-29 cells (CD40-negative) by Western blot. Moreover, CD40 was detected in tumor cells in 17% (6/34) of breast cancer, 24% (8/34) colorectal cancer, 54% (23/43) non-small cell lung cancer, and 47% (17/36) ovarian cancer. CD40 was also spotted in infiltrating lymphocytes in the tumor stroma. The data indicate that CD40 is expressed in human solid tumors with varying expression frequencies and one quarter of cancer cell lines examined. In addition, we have established a ready-for-use immunohistochemistry assay with an antibody that specifically detects CD40 in formalin-fixed and paraffin-embedded human tumor samples. Its application holds promise to evaluate the prognostic role of CD40 in human cancers.
Citation Format: Dat Nguyen, Joseph E. Tomaszewski, Stephen M. Hewitt, James H. Doroshow, Sherry X. Yang. CD40 expression in human solid tumors and NCI60 tumor cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2424. doi:10.1158/1538-7445.AM2013-2424