bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 737: Signficant DLX4 expression in inflammatory breast cancer tumors from African American patients
Authors: Jeong Jaehong , Naab Tammey , Ongkeko Martin , Makambi Kepher , Khan Farhan A. , Blancato Jan 
Published: July 2017

Abstract
Purpose: To examine protein expression characteristics of Distal-less homeobox4 (DLX4) in inflammatory breast cancer (IBC) cases from an African-American population to determine if a) DLX4 over-expression occurs in IBC vs. normal mammary tissue and b) over-expression is associated with clinico-pathologic features such as ER, PR, HER2.
Experimental Design: Twenty nine blocks of formalin-fixed paraffin-embedded (FFPE) tissues from well-characterized human IBC cases were used for immuno-histochemical staining (IHC). Tumor tissues were from African American subjects seen at Howard University Hospital. Normal breast tissues from 30 mammoplasties were controls. IHC results were assigned intensity and percentage scores based upon intensity of positive staining and % of stained cells. Percentage scores were assigned as 0, 1 (0%-25%), 2 (26%-50%), 3 (51%-75%) or 4 (76%-100%) and intensity scores were assigned 0, 1+, 2+ or 3+. For the analysis of the IHC, a percentage score of 3 or 4 was considered high and an intensity score of 2+ or 3+ was categorized as high. Chi-square and Fisher’s exact tests were used for analysis.
Results: The staining pattern for the categorized cohort in which 82.8% (24 out of 29) of IBC cases showed high percentages of positive cells staining for DLX4 protein, while 40.0% (12 out of 30) normal breast tissues demonstrated DLX4 expression (P=0.001). In terms of staining intensity, 75.9% (22 out of 29) of IBC cases showed a high level of intensity, compared to 20.0% (6 out of 30) of normal breast tissues (P&lt;0.001). In terms of the association between breast cancer characteristics and IHC staining, intensity of DLX4 was higher in HER2- (87.0%, 20 out of 23) than HER2+ (33.3%, 2 out of 6; P=0.018). Other associations were not statistically significant in this pilot study.
Conclusions: DLX4 expression is significantly higher in this pilot study of IBC cases from AA patients than in normal breast tissue cases. In addition, HER2- is associated with high intensity of DLX4 expression in IBC.
Associations DLX4 protein expression (IHC) In IBC and normal breast tissuesLowHighP-valuePercent positivityn (%)n (%)Controls (n=30)18 (60.0)12 (40.0)0.001IBCs (n=29)5 (17.2)24 (82.8)Staining intensityn (%)n (%)Controls (n=30)24 (80.0)6 (20.0)&lt;0.001IBCs (n=29)7 (24.1)22 (75.9)
Citation Format: Jaehong Jeong, Tammey Naab, Martin Ongkeko, Kepher Makambi, Farhan A. Khan, Jan Blancato. Signficant DLX4 expression in inflammatory breast cancer tumors from African American patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 737. doi:10.1158/1538-7445.AM2017-737
Abstract 746: TaqMan Rare Mutation Assays targeting the TERT promoter region
Authors: Laig Marion , Varma Kamini , Venkatesh Vidya 
Published: July 2017

Abstract
The enzyme Telomerase maintains telomeres at the ends of chromosomes. The Telomerase Reverse Transcriptase (TERT) gene codes for the enzyme’s catalytic domain and is not expressed in normal somatic cells. As a consequence, normal cells acquire senescence by shortening of their telomeres during cell division and eventually undergo apoptosis. In contrast to normal somatic cells, expression of TERT is reinstated in cancer cells causing escape from senescence and apoptosis by maintaining the telomeres. It has recently been shown that mutations in the TERT promoter region play a key role in regulating and reinstating TERT expression. 90% of cancers carry a mutation in the TERT promoter region. Mutations like C228T and C250T create new binding site for the E26 transformation-specific (ETS) transcription factor that regulates TERT expression. Experimental evidence showed that the ETS factor GA-binding protein, alpha subunit (GABPA) binds to the de novo ETS motif and activates TERT transcription in cancer cells.
We undertook a project designing TaqMan Rare Mutation assays addressing mutations in the TERT promoter. These assays are TaqMan SNP Genotyping assays that are optimized for use in digital PCR with the Applied Biosystems QuantStudio 3D. In digital PCR, partitioning the sample into many individual reaction wells facilitates detection and quantification of rare mutant alleles. TaqMan SNP Genotyping Assays ensure reliable discrimination of mutant and wild-type allele. This will enable easy and sensitive detection of TERT promoter mutations in cancer research samples. These assays are suitable for detection in liquid biopsy applications with cell free DNA (cfDNA).
Assay design proved to be challenging due to high GC content and repetitive elements in this region of the TERT gene and required varying both the assay design and experimental cycling conditions. Template for wet-lab testing was synthetic plasmid carrying the mutation spiked into wild-type genomic DNA and wild-type genomic DNA control.
The result was a TaqMan Rare Mutation assay detecting the C228T mutation in the TERT promoter region. We showed that designing TaqMan Rare Mutation Assays for digital PCR is feasible for the challenging TERT promoter region. Work addressing additional mutations in this region is ongoing.
For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Marion Laig, Kamini Varma, Vidya Venkatesh. TaqMan Rare Mutation Assays targeting the TERT promoter region [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 746. doi:10.1158/1538-7445.AM2017-746
Abstract 747: An improved fixative for histomorphology, recovery of nuclic acids and proteins
Authors: Hewitt Stephen M. , Chung Joon-Yong , Perry Candice , Ylaya Kris , Smith William M-A , Star Robert A. 
Published: July 2017

Abstract
Neutral Buffered Formalin (NBF) has been the primary diagnostic fixative for histopathology for nearly a century. The limitations of NBF are well known, especially with reference to the analysis of RNA and proteins. Alternative fixatives have been proposed, but not been widely adopted. Recently, the US Environmental Protection Agency (EPA) classified formaldehyde as a carcinogen, further tilting the balance away from the continued use of NBF. We recently described a fixative based on 70% ethanol and phosphate buffered saline, called BE70. Using BE70 as the base fixative, we have developed a modular fixative in which different chemicals can be supplemented for “fit for purpose” applications. The addition of guanidinium salts to BE70 , termed BE70G results in a fixative in which both proteins and nucleic acids are improved in quantity and quality after extraction from the paraffin block. The guanidinium replaces non-freezable water, and prevents hydrolysis and oxidation of the biomolecules. Histomorphology is not disrupted at lower concentrations, with only alterations of hematoxylin intensity at higher concentrations. Studies are underway to evaluate the stability of RNA and protein in the tissue block as well as on cut sections. This fixative, BE70G has the potential to address a number of challenges facing the development of precision biomarkers, while preserving histomorphology, and improving the safety of pathology staff. Other formulations are currently being evaluated that may support applications for cytology and electron microscopy. The goal is a well characterized fixative, in which modifications to the chemistry are defined and can be applied to obtain the optimal pathology specimen for both histomorphologic and molecular analysis.
Citation Format: Stephen M. Hewitt, Joon-Yong Chung, Candice Perry, Kris Ylaya, William M-A Smith, Robert A. Star. An improved fixative for histomorphology, recovery of nuclic acids and proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 747. doi:10.1158/1538-7445.AM2017-747
Abstract 76: Synthetic lethal targeting of BRCA mutant tumors with antibody linked pyrrolobenzodiazepine dimers
Authors: Zhong Haihong , Tammali Ravinder , Chen Cui , Fazenbaker Christine , Maureen Kennedy , Monks Noel , Harper Jay , Herbst Ronald , Tice Dave 
Published: July 2017

Abstract
Pyrrolbenzodiazepine dimers (PBDs) are amongst the most potent DNA alkylating agents, with activity against a broad spectrum of tumors. PBDs form cross-links within the minor groove of DNA causing double strand breaks (DSB). DNA repair genes such as BRCA1 and BRCA2 play important roles in homologous recombination repair (HRR) of DSB. Cells defective in BRCA1 or BRCA2 are known to be sensitive to DNA interstrand crosslinks. Accordingly, it is possible that PBD-based ADCs will have enhanced killing of cells (synthetic lethality) in which HR processes are defective by inactivation of BRCA1 or BRCA2 genes in breast, ovarian and other cancers. To determine anti-tumor activity of PBD dimers, we have used MEDI0641, PBD-dimer conjugated to anti-5T4 antibody, against BRCA wild type and mutant xenograft tumor models. MEDI0641 was &gt;3-fold more potent in BRCA1 or BRCA2 mutant models than in wild-type xenografts. Similar observations were seen in 25 patient-derived xenograft (PDX) models (19 breast and 6 ovarian) bearing mutations in BRCA1 or BRCA2 (blinded to 5T4 expression) treated with MEDI0641. Out of a total of 25 PDX models, 17 models had tumor regression with a single administration of MEDI0641 at 0.3 mg/kg (response rate = 68%), and 14 models showed response to 0.1 mg/kg of MEDI0641 (response rate = 56%). In BRCA wild-type PDX models, a higher dose of 1 mg/kg was required to achieve full anti-tumor efficacy. Retrospective analysis of 5T4 expression in PDX tumors demonstrated no correlation between efficacy and target expression in BRCA mutant PDX models. To further delineate the role of BRCA1/2 mutations in determining sensitivity to PBD, we used siRNA knock-down of both BRCA1 and BRCA2 in the DNA repair wild type HeLa cells. Knockdown of BRCA genes sensitized Hela cells to PBD payload and MEDI0641 in vitro. Anti-tumor activity of MEDI0641 was further examined in isogenic BRCA2 knockout xenograft models. Genetic deletion of BRCA2 markedly increased anti-tumor activity of MEDI0641. In conclusion, PBD based ADCs may have improved therapeutic window in cancer patients with somatic BRCA mutations.
Citation Format: Haihong Zhong, Ravinder Tammali, Cui Chen, Christine Fazenbaker, Kennedy Maureen, Noel Monks, Jay Harper, Ronald Herbst, Dave Tice. Synthetic lethal targeting of BRCA mutant tumors with antibody linked pyrrolobenzodiazepine dimers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 76. doi:10.1158/1538-7445.AM2017-76
Abstract 760: Detection of EGFR T790M mutation by ddPCR in untreated NSCLC patients: Correlation with clinical outcome
Authors: Ganzinelli Monica , Rulli Eliana , Tamborini Elena , Busico Adele , Russo Giuseppe Lo , Corrao Giulia , Vitali Milena , Garassino Marina Chiara , Broggini Massimo , Marabese Mirko 
Published: July 2017

Abstract
Background: Activating EGFR mutations are associated with response to first generation tyrosine kinase inhibitors (TKI) that significantly increased PFS and OS in NSCLC patients. However, almost invariably, patients relapse while in treatment with TKI, mostly for the presence of EGFR T790M mutation. New second and third generation EGFR inhibitors active against T790M are now under development with very promising results. To date it is not known if the presence of T790M (and its amount) at diagnosis influences clinical outcome of patients with activating EGFR mutation.
Methods: We analysed 50 cases with NSCLC. 48 patients harbour TKI sensitizing mutation in either exon 19 (N=24) or 21 (N=19). 2 EGFR wt patients (blinded to the investigator) were analysed in parallel. These patients were screened by ddPCR for the presence of T790M mutation using Biorad QX200 Droplet Digital PCR System. We used rough DNA extract from FFPE sections after deparaffinization and proteinase K digestion, as available in pathology unit for daily diagnosis.
Results: 12 samples failed to amplify, maybe due to the poor quality of DNA. 13 samples produced results, but were excluded for the analysis because of too low number of calls retrieved. T790M mutation was detected in a significant proportion of remaining cases. Among the latter, 4 patients were sampled after TKI treatment and here the percentage of T790M were higher compared to those patients not treated [0.65% - 28% vs 0.019% - 1.65%, respectively]. One out four of these patients was not detected by routinely method of sequencing (Sanger or RT-PCR). T790M positive samples harboured mutations affecting exon 19 or 21 in equal manner.
Conclusions: ddPCR has proven to be a sensitive method to detect T790M mutation, although the quality of DNA could affect the results. The system has been challenged for specificity an sensitivity and the results proved to be clinically relevant. The correlation between the T790M positivity and clinical outcome will be available and we plan to define a ddPCR threshold value which can help in selecting those patients who are likely to have early recurrence under first generation TKI and that could therefore be directly shifted to second or third generation inhibitors.
Citation Format: Monica Ganzinelli, Eliana Rulli, Elena Tamborini, Adele Busico, Giuseppe Lo Russo, Giulia Corrao, Milena Vitali, Marina Chiara Garassino, Massimo Broggini, Mirko Marabese. Detection of EGFR T790M mutation by ddPCR in untreated NSCLC patients: Correlation with clinical outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 760. doi:10.1158/1538-7445.AM2017-760
Abstract 762: A concordance study of the ArcherDX RevealTM ctDNA 28 NGS panel and Biocept’s Target SelectorTM mutation assay using ctDNA collected in Biocept CEE-sureTM blood collection tubes
Authors: Poole Jason C. , Kudlow Brian , Stefanelli Jill , Mishkin Skyler , Pham Anh , Chen Jeff , Singh Veena M. , Stahl Josh , Arnold Lyle J. 
Published: July 2017

Abstract
Biocept’s Target Selector technology is a targeted hotspot mutation panel designed to enrich for mutant targets in a large excess of WT DNA. The test is specific to small regions of interest, is highly sensitive, validated down to 7 mutant copies in a background of 14,000 WT at &gt;98% sensitivity. The ArcherDX Reveal ctDNA test is a 28 gene NGS panel that targets key oncogene activating mutations, drug resistance mutations, in addition to full coverage of TP53. The Reveal ctDNA assay utilizes Anchored Multiplex PCR to enrich, tag, and efficiently capture short ctDNA fragments. Both technologies are designed specifically for use with plasma associated ctDNA. We undertook to evaluate the feasibility of using the ArcherDX Reveal ctDNA 28 NGS panel with the DNA extracted from plasma collected with Biocept’s patented blood collection tube which has been validated at room temperature for 4 days for circulating tumor cells and 8 days for ctDNA. The ability to build complex, targeted libraries, free of chemically induced mutations is of major importance for the detection of the vanishingly rare mutations that can be present in the plasma of cancer patients. We found that high quality NGS libraries were produced from plasma collected and stored in the Biocept blood tube, indicating that little damage occurred to the DNA during preservation. In addition, the two methods were found to be highly concordant and complementary when using both mutation positive and negative patient samples. The Target-Selector assay was the more sensitive, however, the ArcherDX panel revealed several additional mutations not targeted by the Biocept Target Selector assay.
Citation Format: Jason C. Poole, Brian Kudlow, Jill Stefanelli, Skyler Mishkin, Anh Pham, Jeff Chen, Veena M. Singh, Josh Stahl, Lyle J. Arnold. A concordance study of the ArcherDX RevealTM ctDNA 28 NGS panel and Biocept’s Target SelectorTM mutation assay using ctDNA collected in Biocept CEE-sureTM blood collection tubes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 762. doi:10.1158/1538-7445.AM2017-762
Abstract 769: Matched-pair comparisons of chemotherapy plus bevacizumab versus chemotherapy alone as third-line treatment or beyond for advanced non-small cell lung cancer
Authors: Hu Binbin , Lu You , Zhou Xiaojuan , Li Qian , Xiang Mengmeng 
Published: July 2017

Abstract
Background: The addition of bevacizumab to chemotherapy has proven efficacy as first-line treatment for advanced NSCLC. Whether this combination still be efficient as salvage treatment for NSCLC patients who have not received bevacizumab previously remains unclear. This retrospective matched-pair study was designed to compare the efficacy and safety of chemotherapy plus bevacizumab with chemotherapy alone as third-line treatment or beyond for NSCLC patients.
Methods: Patients with stage IV NSCLC who had received single-agent chemotherapy plus bevacizumab after failure of at least two prior regimens were enrolled in this study. Each of them was matched with two patients who had received chemotherapy alone (1:2) by age (within ±5 years), sex, smoking history, histology, EGFR mutation status and number of prior regimens. Tumor response rate, survival and toxicity analyses were performed.
Results: Between January 2011 and June 2016, a total of 40 patients who had received chemotherapy plus bevacizumab (chemotherapy-bevacizumab group) were matched with 80 patients who had received chemotherapy alone (chemotherapy-alone group) as third-line treatment or beyond. Objective response rate (ORR) and Disease control rate (DCR) were improved for chemotherapy-bevacizumab compared with chemotherapy alone (ORR, 22.5% v 6.2%, respectively, p= .014; DCR, 62.5% v 40.0%, respectively, p= .032). Progression-free survival was prolonged for chemotherapy-bevacizumab compared with chemotherapy alone (median, 3.9 v 2.5 months, respectively; HR, 0.64; 95%CI, 0.43 to 0.97; p = .032). Incidence of severe (≥ grade 3) adverse events was low and similar across groups.
Conclusion: The combination of chemotherapy and bevacizumab can be an efficient alternative salvage treatment for NSCLC patients who have not received bevacizumab previously. But taking this combination as first-line treatment for advanced NSCLC still should be a priority.&lt;!–EndFragment–&gt;
Note: This abstract was not presented at the meeting.
Citation Format: Binbin Hu, You Lu, Xiaojuan Zhou, Qian Li, Mengmeng Xiang. Matched-pair comparisons of chemotherapy plus bevacizumab versus chemotherapy alone as third-line treatment or beyond for advanced non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 769. doi:10.1158/1538-7445.AM2017-769
Abstract 788: Less is more: macrophage depletion via CSF1/CSF1R pathway improves anti-VEGF therapy after adaptive resistance
Authors: Lyons Yasmin A. , Pradeep Sunila , Hansen Jean M. , Wagner Michael J. , Dood Robert L. , Wu Sherry Y. , Previs Rebecca A. , Hu Wei , Coleman Robert L. , Sood Anil K. 
Published: July 2017

Abstract
Objectives: Anti-angiogenesis therapy shows clinical benefit in patients with high-grade serous ovarian cancer (HGSC), but adaptive resistance typically occurs. Thus, approaches to overcome such resistance are needed. Here, we systematically assessed immune cell populations enriched during adaptive resistance and identify novel therapeutic avenues.
Methods: A series of in vitro and in vivo (immune competent and nude mice) experiments were carried out. Animals were treated with anti-VEGF antibody continuously until resistance emerged, at which point full immune profiling was performed. Based on these results, efficacy of AC708 (CSF1R inhibitor to target tumor-associated macrophages) was tested in the adaptive-resistance models. F4/80 antibody was used as a macrophage marker.
Results: On the basis of full immune profiling, we detected significantly increased macrophage infiltration in tumors with anti-VEGF antibody resistance compared to tumors from sensitive mice (p&lt;0.0001). Given the dominant role of CSF1R in macrophage function and overexpression of CSF1R in HGSC, we added AC708 following emergence of adaptive resistance to anti-VEGF antibody. Mice treated with AC708 after anti-VEGF antibody resistance demonstrated complete response upon completion of the experiment, while those that did not receive AC708 still had abundant tumor. To mimic treatment with the AURELIA regimen, we next treated mice with anti-VEGF antibody and paclitaxel until resistance emerged, and then AC708 was added. The addition of AC708 restored response to anti-angiogenesis therapy, resulting in 82% lower tumor burden compared to treatment with anti-VEGF antibody and paclitaxel alone (p &lt; 0.0001), and a substantial decrease in macrophages (p&lt;0.0004).
Conclusions: The addition of CSf1R inhibitor to anti-VEGF therapy and taxane chemotherapy results in robust anti-tumor effects. To confirm these findings, a clinical trial at our institution is nearing activation. The REDIRECT (RandomizEd Induction DIscontinuation TRial of EmaCTuzumab) trial will randomize patients to continue weekly paclitaxel and biweekly bevacizumab with or without a CSF1R inhibitor (emactuzumab) following an induction phase.
Citation Format: Yasmin A. Lyons, Sunila Pradeep, Jean M. Hansen, Michael J. Wagner, Robert L. Dood, Sherry Y. Wu, Rebecca A. Previs, Wei Hu, Robert L. Coleman, Anil K. Sood. Less is more: macrophage depletion via CSF1/CSF1R pathway improves anti-VEGF therapy after adaptive resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 788. doi:10.1158/1538-7445.AM2017-788