tbuckley/cabot-search huggingface dataset:
Development of a standardized, quantitative microarray for gene expression measurement
Authors: Erin L. Crawford, David A. Weaver, James C. Willey
Journal: Cancer Research (2004)

1647  The use of microarrays to measure changes in gene expression pattern has become common practice in many research laboratories. However, with currently available microarray technology, there is poor inter-lab reproducibility. Further, due to gene-to-gene variation in melting temperatures between cDNA and bound sequence, it is difficult to quantify differences in expression among multiple genes in a sample. Here we have combined custom oligo array and Standardized RT (StaRT)-PCR technologies to develop an array that provides standardized, numerical, reproducible gene expression data. In preliminary studies, we spotted arrays with 70-mer oligonucleotides specific for ACTB and CAT StaRT-PCR products. We performed StaRT-PCR using cDNA synthesized from Universal Human Reference RNA (Stratagene) and commercially available (Gene Express, Inc.) standardized mixtures of internal standards (SMIS) containing ACTB and CAT competitive templates (CT). A series of reactions was performed with a 100-fold variation in the ratio of cDNA to SMIS included in the PCR reaction. PCR products were hybridized to the array along with four fluor-labeled probes. Cy5 labeled probes were designed to bind specifically to either ACTB or CAT native template (NT) in the cDNA while Cy3 labeled probes were designed to bind specifically to either ACTB or CAT CT. Bound probe and PCR product were quantified using a ScanArray 4000 (Perkin-Elmer). Array results were compared to data obtained when aliquots of the same PCR products were electrophoresed and quantified with an Agilent 2100 Bioanalyzer (Agilent Technologies)(a previously validated methodology). Average expression values (in units of CAT cDNA molecules/106 ACTB cDNA molecules) for the array and the Bioanalyzer were 1.16 x 103 and 5.06 x 102 respectively. The CV1 was 9% for the array and 33 % for the Bioanalyzer. Both had similar linear dynamic ranges of detection although the Bioanalyzer had a better lower limit of detection. In further experiments, single expression values obtained using the array for cDNAs from an additional 4 bronchogenic carcinoma cell lines and cultured normal human bronchial epithelial cells (NHBEC) from one individual were comparable to results obtained with the Agilent method. A major advantage of this approach is that each measurement is made with internal standards contained in a SMIS that is constant and in sufficient supply (>1012 assays) to be used by all labs for many years. Replicate measurements for these samples are underway as are measurements for additional samples. We are continuing to optimize our hybridization conditions and plan to design and test reagents for additional genes. ELC, DAW and JCW each have a significant financial interest in Gene Express, Inc.
Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in <i>KRAS</i>-Mutant Cancer Cells
Authors: Johanna Erber, Joachim D. Steiner, Jörg Isensee, Leonard A. Lobbes, André Toschka, Filippo Beleggia, Anna Schmitt, Rainer W. J. Kaiser, Florian Siedek, Thorsten Persigehl, Tim Hucho, Hans C. Reinhardt
Journal: Cancer Research (2019)

The advent of molecularly targeted therapeutic agents has opened a new era in cancer therapy. However, many tumors rely on nondruggable cancer-driving lesions. In addition, long-lasting clinical benefits from single-agent therapies rarely occur, as most of the tumors acquire resistance over time. The identification of targeted combination regimens interfering with signaling through oncogenically rewired pathways provides a promising approach to enhance efficacy of single-agent-targeted treatments. Moreover, combination drug therapies might overcome the emergence of drug resistance. Here, we performed a focused flow cytometry-based drug synergy screen and identified a novel synergistic interaction between GLUT1-mediated glucose transport and the cell-cycle checkpoint kinases ATR and CHK1. Combined inhibition of CHK1/GLUT1 or ATR/GLUT1 robustly induced apoptosis, particularly in RAS-mutant cancer cells. Mechanistically, combined inhibition of ATR/CHK1 and GLUT1 arrested sensitive cells in S-phase and led to the accumulation of genotoxic damage, particularly in S-phase. In vivo, simultaneous inhibition of ATR and GLUT1 significantly reduced tumor volume gain in an autochthonous mouse model of KrasG12D -driven soft tissue sarcoma. Taken together, these findings pave the way for combined inhibition of GLUT1 and ATR/CHK1 as a therapeutic approach for KRAS-driven cancers. SIGNIFICANCE: Dual targeting of the DNA damage response and glucose transport synergistically induces apoptosis in KRAS-mutant cancer, suggesting this combination treatment for clinical validation in KRAS-stratified tumor patients.
Metabolism of benzo[a]pyrene in human bronchoalveolar H358 cells by LC-MS
Authors: Trevor Penning, Hao Jiang, Stacy Gelhaus, Dipti Mangal, Ronald Harvey, Ian Blair
Journal: Cancer Research (2007)

1396  Benzo[a]pyrene (BP), is a representative polycyclic aromatic hydrocarbon (PAH), which can be metabolically activated by three enzyme pathways, P450-peroxidase, P4501A1/1B1, and aldo-keto reductases (AKRs). The profile of BP metabolites in human lung epithelial cells using modern methods is not well studied even though lung is a major PAH exposure site due to the inhalation of first and second hand tobacco smoke. In this study, BP-metabolites generated by P450 peroxidase (BP-1,6- and 3,6-dione), by P4501A1/1B1 (3-hydroxyl-BP, BP-7,8- and 9,10-dihydrodiols, and BP-r-7,t-8,t-9,c-10-tetrahydrotetrol), and by AKRs (BP-7,8-dione) in human bronchoalveolar H358 cells were quantified by RP-HPLC with radiometric detection and identified by LC-MS. LC/MS data were acquired using a Thermo Finnigan TSQ Quantum Ultra spectrometer with an atmospheric pressure chemical ionization source operated in the positive-ion mode and on-line chromatography was performed with a Waters Alliance 2690 HPLC system. The eluent on-line was monitored in the selected reaction monitoring mode and full-scan modes and ion-transitions compared to those obtained with authentic synthetic standards. Progress curves showed a lag-phase in the formation of 3-hydroxy-BP > BP-9,10-dihydrodiol > BP-7,8-dihydrodiol > BP-tetrol > BP-1,6-dione and BP-7,8-dione over 24 h. Northern blot analysis showed induction of P4501B1 and AKR1C1 by BP in a time-dependent manner, suggesting that BP stimulates its own metabolism by induction of these key enzymes. By contrast BP-3,6-dione was formed without a lag-phase. Pretreatment with 10 nM TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) eliminated the lag-phase but the levels of the individual metabolites were unaltered suggesting that TCDD induction alters the kinetics of metabolite formation but not metabolite levels. This study provides evidence for the formation of reactive BP metabolites from each of the pathways of PAH-activation in human lung bronchoalveolar cells (Supported by P01-CA092537 and R01-CA39505).
Combination effect of docetaxel plus TS-1 on the human breast cancer xenograft serially transplanted into scid mice
Authors: Akihiko Suto, Tetsuro Kubota, Masakazu Fukushima, Tadashi Ikeda, Toshio Takeshita, Harumi Ohmiya, Masaki Kitajima
Journal: Cancer Research (2004)

5379  Paclitaxel has shown promise in the treatment of ovarian cancer, however, toxicity, in part due to the insoluble nature of paclitaxel, remains a limitation to its use. The present set of studies assessed the effectiveness of nanoparticulate paclitaxel, produced by the techniques of precipitation with compressed antisolvent, in a mouse model of ovarian cancer. Paclitaxel (a gift from NaPro) was dissolved in acetone and sprayed into flowing carbon dioxide at 1200 psi, 32°C through an ultrasonic nozzle at 2 ml/min. Particles were harvested on a stainless steel, titanium dioxide-coated filter. Nanoparticulate paclitaxel was suspended in saline and effects on tumor progression were assessed in a mouse model of epithelial ovarian cancer. Mice were injected ip with ID8 cells and treated with nanoparticulate paclitaxel (18, 36, or 48 mg/kg), paclitaxel (Taxol®, Bristol-Myers Squibb, 12, 18, 36 mg/kg), macroparticle paclitaxel (18, 36, or 48 mg/kg), cremophor or saline ip on days 45,47,49. Mice were observed daily until sacrificed at end-stage, when ascites fluid accumulated and the coat became rough. Nanoparticulate paclitaxel significantly increased survival of tumor-bearing mice compared to control and paclitaxel. Control mice survived 87 days and Taxol® treated mice survived 105 days. Survival of nanoparticulate paclitaxel treated mice was related to dose; the 48 mg/kg dose survived greater than 200 days. Macroparticle paclitaxel mouse survival was between Taxol® and nanoparticulate paclitaxel. Nanoparticulate paclitaxel exhibited reduced toxicity compared to Taxol®; Taxol® LD50 was 36 mg/kg, nanoparticulate paclitaxel treated mice exhibited no apparent toxicity to 48 mg/kg. Mechanisms of increased efficacy of nanoparticulate paclitaxel were explored first by assessment absorption of paclitaxel from the peritoneal cavity. Nanoparticulate paclitaxel or Taxol® was injected into the peritoneal cavity of normal mice and serum concentrations at multiple time points after injection were determined by HPLC. Results from these experiments indicated slower absorption of nanoparticulate paclitaxel from the peritoneal cavity compared Taxol®. These studies demonstrate the ability to produce fine particle paclitaxel. When delivered intraperitoneally nanoparticulate paclitaxel exhibited significant effects on inhibiting the progression of ovarian cancer in a mouse model. The enhanced efficacy of nanoparticulate paclitaxel and the apparent reduced toxicity may be due, at least in part, to altered absorption from the peritoneal cavity.
Labrasol® is an efficacious intestinal permeation enhancer across rat intestine: Ex vivo and in vivo rat studies
Authors: Fiona McCartney, Vincent Jannin, Stéphanie Chevrier, Hakime Boulghobra, Delyan R. Hristov, Nicolas Ritter, Cédric Miolane, Yann Chavant, Frédéric Demarne, David J. Brayden
Journal: Journal of Controlled Release (2019)
Role of the interaction between Tax-1 and histone deacetylase 6 (HDAC6) in HTLV-1 infected cells
Authors: Sebastien Legros, Jean-Francois Dewulf, Mathieu Boxus, Franck Dequiedt, Richard Kettmann, Jean-Claude Twizere
Journal: Cancer Research (2008)

598  Human T cell leukaemia virus type-1 (HTLV-1), the first pathogenic retrovirus discovered in humans 27 years ago is the causative agent of two major diseases: a rapidly fatal leukaemia designated adult T-cell leukaemia (ATL) and a neurological degenerative disease known as tropical spastic paraparesis (TSP) or HTLV-1 associated myelopathy (HAM). Approximately, one in twenty HTLV-1-infected individuals develops malignancy after 40 to 50 years of latency. The viral transcriptional activator and oncoprotein Tax-1 has been the major focus of scientific investigation because of its numerous and crucial roles in the pathogenesis of HTLV-1-induced diseases. In fact, protein-protein interactions with cellular factors are crucial for Tax-1 to perturb the regulation of many cellular pathways.  Histones deacetylases (HDACs) are transcriptional repressors that lead to chromatin compaction and DNA inaccessibility. Dependent on the specificities of their catalytic mechanism, HDACs are divided in two groups: the classical and the silent information regulator 2 (Sir-2)-related protein (sirtuin) groups. Classical HDACs are further divided into class I and class II enzymes based on their homologies with yeast transcriptional regulators. In this study, we examined functional interaction between Tax-1 and classical HDACs. We showed that Tax-1 is able to specifically interact with class I HDAC-1 and -3 and class II HDAC5 and -6. Interaction between Tax-1 and HDACs leads to the inhibition of HTLV-1 promoter activation and may contribute to viral silencing in vivo. In addition, we showed that HDAC6, the first identified HDAC actively maintained in the cytoplasm and that has been shown to coordinate microtubule network, is highly expressed in HTLV-1 infected cells. Since microtubule re-organization is a critical step in cell to cell HTLV-1 infection, we speculate that interaction of Tax1 with HDAC6 may regulate the transfer of viral material between cells.
Clinical Ultimatums: Coercion as Subjection
Authors: C. Maxwell Shannon, John H. Coverdale, Mollie Gordon, Jennifer S. Blumenthal-Barby
Journal: The American Journal of Bioethics (2019)

In their article, “How Payment for Research Participation Can Be Coercive,” authors Millum and Garnett argue that there are two distinct forms of coercion: a more “traditional” view, which they cal...
DLQI‐R scoring improves the discriminatory power of the Dermatology Life Quality Index in patients with psoriasis, pemphigus and morphea
Authors: F. Rencz, L. Gulácsi, M. Péntek, A. Szegedi, É. Remenyik, Z. Bata‐Csörgő, G. Bali, B. Hidvégi, B. Tamási, A.K. Poór, K. Hajdu, P. Holló, Á. Kinyó, M. Sárdy, V. Brodszky
Journal: British Journal of Dermatology (2019)

The Dermatology Life Quality Index (DLQI) rates 'not relevant' responses (NRRs) as the item on the questionnaire having no impact on the patients' lives at all. The DLQI‐Relevant (DLQI‐R) is a recently developed scoring that adjusts the total score of the questionnaire for the number of NRRs indicated by a patient. To compare the discriminatory power of the original and DLQI‐R scoring approaches in terms of absolute and relative informativity. Cross‐sectional data from 637 patients with morphea, pemphigus and psoriasis were used for the analyses. To assess absolute and relative informativity, Shannon's index and Shannon's evenness index were calculated for the 10 items on the questionnaire and for DLQI and DLQI‐R total scores. Mean DLQI and DLQI‐R scores of patients were 6·13 vs. 6·91. In the subset of patients with NRRs (n = 261, 41%), absolute informativity was higher with the DLQI‐R scoring for all eight items with NRR options in all three conditions. The DLQI‐R exhibited a better relative informativity in 8, 8 and 6 items in pemphigus, morphea and psoriasis, respectively. The DLQI‐R led to an improvement in average item‐level informativity in all DLQI score bands up to 20 points. Regarding total scores, the DLQI‐R produced both a higher absolute and relative informativity in all three conditions. In patients with morphea, pemphigus and psoriasis, DLQI‐R scoring improves the discriminatory power of the questionnaire by benefiting from the additional information in NRRs. DLQI‐R scoring may be useful both in clinical practice and research. A scoring chart has been developed to aid physicians with scoring. What's already known about this topic? The original scoring of the Dermatology Life Quality Index (DLQI) rates 'not relevant' responses as the item of the questionnaire having no impact on the patients' lives at all. DLQI‐Relevant (DLQI‐R) is a new scoring developed in 2018 that adjusts the total score of the questionnaire for the number of 'not relevant' responses indicated by patients. The discriminatory power of the DLQI‐R compared with the DLQI has not yet been investigated. What does this study add? In patients with psoriasis, pemphigus and morphea, DLQI‐R scoring improves the discriminatory power of the questionnaire by benefiting from the additional information in 'not relevant' responses. What are the clinical implications of this work? DLQI‐R scoring may help to more accurately quantify patients' health‐related quality of life both in clinical practice and research. A scoring chart has been developed to aid physicians with scoring.
Monitoring subpopulations of CD4+ and CD8+ effector/memory and T regulatory cells in cancer patients: correlations with post-vaccination clinical responses.
Authors: Evelyna Derhovanessian, Karin Hahnel, Lilly Wedel, Graham Pawelec
Journal: Cancer Research (2008)

2837  The immune system plays an important role in eliminating tumors. Accordingly, many immunotherapy protocols have been developed in attempts to boost anti-tumor immune responses in cancer patients. In clinical trials performed to date, however, little correlation has been observed between parameters measured to assess cellular immune responses and clinical outcome. Moreover, when whole-cell vaccines are used, the ambiguity of the immunogenic antigen adds to the complexity of analysis, since it is not clear which components of the immune system contribute more to a favourable immune response. In this study, we have monitored the frequency of monocytes, B-cells, NK-cells, regulatory T-cells and different effector and memory T-cell subsets in cancer patients before and after vaccination with a proprietary allogeneic whole tumor cell line vaccine. Antigen-experienced T-cells can be divided into functionally distinct populations, according to the expression of different cell surface markers, such as CD45RA, CCR7, CD27 and CD28. Using 10-color flow cytometry, we subdivided circulating CD4+ and CD8+ effector memory (EM) (CCR7-,CD45RA-) and TEMRA (CCR7-, CD45RA+) cells according to their surface expression of CD27 and CD28, as well as CD57, a marker up-regulated on very late-differentiated T-cells. Significant alterations were only observed in the T-cell compartment, whereas the frequency of monocytes, B-cells and NK-cells remained unchanged. In both CD4 and CD8 cells, clinical responders but not non-responders showed significant decreases in central memory (CM) (CCR7+ CD45RA-) and a subset of EM (CD27+ CD28+, least differentiated, or EM1) cells (P=0.02 to 0.004). No other differences in any of the above mentioned T-cell subsets were observed. However, the numbers of T regulatory cells, defined as strongly staining for CD4, CD25 and Foxp3, but weakly for CD127, were more highly significantly reduced in responders (P=0.0002) but not non-responders (NS) than any other T cell subsets. These findings indicate better correlation of T regulatory cell subset reductions with clinical responses following vaccination than with changes in any other T cell subsets and emphasis the importance of T regulatory cell status for clinical outcome of immunotherapy.  This work was supported by EC-LSHG-CT-2007-036894 “LifeSpan”, DFG-SFB685-B4 and DFG-PA 361-11/1.
A randomized phase II study of nivolumab monotherapy versus nivolumab combined with ipilimumab in advanced gastrointestinal stromal tumor (GIST).
Authors: Arun S. Singh, Bartosz Chmielowski, J. Randolph Hecht, Lee S. Rosen, Warren Allen Chow, Xiaoyan Wang, Sandra Brackert, Carlos Adame, John Bovill, Elena Schink, Michael Douek, Jomjit Chantharasamee, Karlton Wong, Frederick C. Eilber, John A. Glaspy
Journal: Journal of Clinical Oncology (2019)

11017 Background: Most GISTs are driven by mutations in KIT and PDGFRa and secondary mutations are felt to confer resistance to TKIs. In advanced/metastatic GIST, the benefit of second line TKIs and beyond is progressively less after imatinib failure. As such, novel non-TKI approaches are important to explore. Here we report interim analyses of safety and efficacy in advanced GIST patients treated with immunotherapy. Methods: Patients with advanced/metastatic GIST refractory to at least imatinib were enrolled on a randomized, parallel group, unblinded Phase 2 trial of either nivo (240 mg Q2wks) or nivo (240 mg Q2wks) with ipi (1mg/kg Q6wks) for up to 2 years. The primary endpoint was the objective response rate(ORR) of nivo alone or nivo + ipi by RECIST 1.1 criteria. Imaging was assessed by investigator and 3 independent radiologists. Patients were randomized 1:1 and were restaged every 8 weeks. With a sample size of 20 per group, an exact binomial test with a nominal 0.050 one-sided significance level will have 82% power to detect the difference between the null hypothesis response rate 1.5% and the alternative response rate of 15%. Secondary objectives are to ascertain the PFS, CBR, RR by Choi criteria and safety. Blood and biopsies are also being collected. Results: At cutoff, 29 patients (27 evaluable) with a median of 3 (1-7) lines of prior therapies have started on trial. In the nivo only arm, 7/15 pts had a best response of SD for a CBR of 46.7% with the median PFS being 8.57 wks. In the nivo + ipi arm, 1/12 patients had a PR and 2/12 have SD for a CBR of 25.0% (95% exact C.I. 5.5%-57.2%) with a median PFS of 9.1 wks. 8 patients have been on therapy for more than 6 months and two patients with a KIT Exon 17 mutation had radiographic disease shrinkage. Most AEs were grades 1-2 with fatigue (37%) being the most common. 4 Grade 3/4 AEs occurred in the nivo and ipi arm (hyperglycemia, weakness, diarrhea x 2) and 4 grade 3/4AEs occurred in the nivo arm (DKA, hyperglycemia, rash, fatigue). Pretreatment biopsies have been obtained in all patients and blood has been collected on all patients for correlative analysis. Conclusions: In a heavily pretreated GIST population, responses and disease control with both nivo and nivo + ipi were observed. To date, the drugs have been well tolerated and no new safety signals have been observed in this disease state. Clinical trial information: NCT02880020.
Adenoviral-mediated transfer of Fak-related non-kinase (FRNK) augments drug-induced cytotoxicity in cultured cells derived from squamous cell carcinoma of the head and neck
Authors: Lori J. Kornberg
Journal: Cancer Research (2005)

5023  Focal adhesion kinase (FAK) has received much attention as a transducer of signals generated by integrin- mediated cell adhesion. FAK is overexpressed in several types of human cancer of epithelial origin including those derived from the head and neck region, breast, ovary, colon, prostate, and brain. Although FAK is not an oncogene, studies using cultured cells demonstrate that FAK positively regulates the cell cycle, cell migration, cell invasion, and cell survival. Fak-related non-kinase (FRNK) is an autonomously expressed C-terminal portion of FAK that inhibits FAK activity. I constructed a recombinant adenovirus (Ad-FRNK) that caused an increase in FRNK expression in cultured cells. When cells derived from squamous cell carcinoma of the head and neck region (RPMI 2650 and SCC25) were infected with Ad-FRNK, there was a reduction in FAK autophosphorylation relative to cells infected with a control adenovirus (Ad-Empty) or nothing. The reduction in FAK pY397 phosphorylation was coincident with a large increase in FRNK expression. When RPMI cells were infected with Ad-FRNK, there was a decrease in cell viability relative to Ad-Empty infected cells ranging from 7-18 %, whereas Ad-FRNK generally did not affect the viability of SCC25 cells. As expected, chemotherapeutic agents (etoposide, 5-fluorouracil, cisplatin, paclitaxel) caused a concentration dependent decrease in viability of SCC25 and RPMI 2650 cells. Infection of RPMI 2650 cells and SCC25 cells with Ad-FRNK augmented drug -induced cytoxicity and this effect was most apparent at the higher concentrations of drug. In RPMI 2650 cells, Ad-FRNK and chemotherapeutic agents appeared to cause an additive decrease in cell viability, whereas in SCC25 cells, Ad-FRNK and chemotherapeutic agents appeared to cause a synergistic decrease in cell viability. When apoptosis was measured using a commercially available ELISA that quantitates the formation of histone-/DNA complexes, similar results were obtained. Finally, infection with Ad-FRNK led to substantially decreased migration of cultured SCCHN cells. These results suggest that FAK may be a target for anti-cancer therapies. The Flight Attendant Medical Research Institute supported this work.
Abstract 19204: IL-10 Accentuates Ascending Aortic Aneurysm Formation in a Novel Model Using Beta-Aminopriopionitrile
Authors: Morgan Salmon, Anna Fashandi, Robert B Hawkins, Michael Spinosa, Ashish K Sharma, Gilbert R Upchurch, Gorav Ailawadi
Journal: Circulation (2016)

Introduction: Ascending aortic aneurysms are characterized by elastin fragmentation. The goal of the current study is to increase the penetrance in a model of ascending aortic aneurysm formation us...