tbuckley/cabot-search huggingface dataset:
Characterization of novel inhibitors of histone deacetylases
Authors: Elena D. Eliseeva, Kwon-Joong Yong, Alexander B. Dimtchev, Sung A. Lee, Anatoly Dritschilo, Mira Jung
Journal: Cancer Research (2005)

611  Reversible modification of histones and other cellular proteins by acetylation is widely accepted to be one of the key mechanisms regulating gene expression and protein activity. Recent studies suggest that histone deacetylases (HDACs) play important roles in the regulation of cell proliferation and differentiation. HDAC inhibitors have been demonstrated to inhibit cancer cell growth in vitro and in vivo, and several of them are currently being studied as potential anticancer agents in clinical trials. We studied 10 newly synthesized HDAC inhibitors (structurally different analogues of hydroxamic acid (1), mercaptoacetamide (2), and biphenylalanine (7)) using several cancer cell lines (SQ-20B, PC-3, MCF-7, HeLa, and Jurkat). To characterize these inhibitors, we analyzed their effects on cell proliferation, cell cycle, and pertinent protein expression. The values of HDAC inhibitors IC50 were determined for these cancer cells and normal human cells after 24 and 48 hours of treatment. Cytotoxicity assays revealed Jurkat cells most sensitive at nM ranges to all the inhibitors tested, while little toxicity was observed in normal cells. Induction of p21Cip1 expression was observed within 2-12 h of treatment depending on the cell line. FACS analysis demonstrated that cells were predominantly accumulated in either G1 or G2 phase of the cell cycle, albeit concentration-dependent. Currently, using PC-3 and MCF-7 cell lines in which the expression of HDACs was suppressed by RNA interference (RNAi), we are investigating target-specificities of these HDAC inhibitors on HDAC family members. These studies could provide valuable instruments for further elucidation of specific HDAC functions in normal and tumor cells, and potentially result in development of more efficient therapeutics for cancer treatment.
Blocking mTOR by rapamycin reduces HIF-1α function in human gastric cancer cells in vitro and inhibits angiogenesis and tumor growth in vivo
Authors: Sven A. Lang, Dagmar Klein, Gudrun Koehl, Christine Wagner, Corina Desousa, Hans J. Schlitt, Pompiliu Piso, Lee M. Ellis, Edward K. Geissler, Oliver Stoeltzing
Journal: Cancer Research (2005)

1136  Hypoxia inducible factor-1α (HIF-1α) is a known promoter of invasive and metastatic tumor growth of solid malignancies, including gastric cancer. Since the mammalian target of rapamycin (mTOR) may modulate HIF-1α activity via interference with the PI3K/Akt signaling pathway, we hypothesized that inhibition of mTOR with rapamycin (RAPA) may inhibit cancer cell invasiveness in vitro, and impair angiogenesis and tumor growth of human gastric cancer cells in vivo. The effect of RAPA on HIF-1α expression in gastric cancer cells (TMK-1) was investigated by Western blot analyses of nuclear protein extracts under hypoxic and non-hypoxic conditions. HIF-1α target gene expression was assessed by real-time RT PCR under same conditions. We next determined whether RAPA may exhibit a direct cytotoxic effect on TMK-1 cells by MTT assays under serum-reduced conditions. As HIF-1α may modulate cell motility, cell migration and invasion were investigated in in vitro assays under the presence or absence of RAPA using modified Boyden chambers. Modulation of angiogenesis in vivo by RAPA treatment (1.5 mg/kg/day) was first evaluated in the dorsal-skin-fold chamber (DSFC) model. Effects of mTOR inhibition on tumor growth were subsequently investigated in a subcutaneous tumor model (SQ), where mice received either RAPA (1.5 mg/kg/day) or vehicle (control) by intraperitoneal injection. The results showed that RAPA dramatically reduced HIF-1α protein expression in cells in response to hypoxia, compared to controls. Interestingly, in RT-PCR analysis mTOR inhibition lead to a 40-50% reduction in constitutive VEGF-B and PDGF-B expression, and reduced induction by hypoxia. In vitro, mTOR inhibition significantly reduced cell migration and invasion of gastric cancer cells under normoxic conditions (P
G1P3 (ISG 6-16), an interferon (IFN) stimulated survival factor antagonizes TRAIL/Apo2L induced apoptosis in myeloma cells
Authors: Venugopalan Cheriyath, Mohamad Hussein, Keith Glaser, Christine Healan-Greenberg, Jeffrey Waring, Ernest Borden
Journal: Cancer Research (2007)

5152  TRAIL/Apo2L was one of the most potent pro-apoptotic genes induced (>100 fold) in myeloma cells following IFN-α2b. Yet  200 fold) and IFN-α1b, IFN-α2b and IFN-β markedly increased G1P3 expression in all myeloma cell lines tested. G1P3 encodes a 13 kD protein that has a putative mitochondrial localization sequence and belongs to the FAM protein family. Myeloma cells expressing G1P3 were resistant to TRAIL/Apo2L induced mitochondrial perturbation, cytochrome c release and apoptosis. TRAIL (50 ng/ml) for 24 hr markedly increased apoptosis (from 4% to 77.5%) of vector transduced cells and higher concentrations of TRAIL (100 ng/ml) resulted in a further increase to 93.6%. Compared to control cells only 4.3% of G1P3 cells underwent apoptosis with 50 ng/ml of TRAIL and 16.3% with 100 ng/ml of TRAIL. However, overexpression of G1P3 did not result in bortezomib (a proteasome inhibitor) resistance, suggesting specificity of G1P3 for the intrinsic apoptosis pathway. Further, 52% knockdown of IFN-α2b induced G1P3 mRNA with an siRNA resulted in a 10 fold increase in apoptosis (4.1% with control siRNA vs. 40.3% with G1P3 siRNA) of RPMI 8266 cells suggesting a pro-survival role for G1P3 upon IFNs stimulation. Data thus identified the direct role of a mitochondrial localized prosurvival ISG in antagonizing the effect of TRAIL/Apo2L, a pro-apoptotic ISG in myeloma. Ability to overcome G1P3 mediated anti-apoptotic signals could open new avenues for increasing the efficacy of therapies for myeloma or other malignancies.
Biochemical mechanism of acetaminophen (APAP) toxicity in human melanocytic melanoma cell lines: a tyrosinase produrg activation approach
Authors: Nikhil Vad, Garret Yount, Dan Moore, Tiffany Nguyen, Jon Weidanz, Majid Moridani
Journal: Cancer Research (2008)

1289  Purpose: In this work, we investigated the biochemical mechanism of acetaminophen (APAP) induced toxicity in human melanocytic melanoma cell lines. Because tyrosinase is found abundantly in melanoma it was hypothesized that tyrosinase can be utilized as a molecular target for selective bioactivation of APAP, as a prodrug, to cytotoxic quinone reactive intermediate species, hence resulting in selective toxicity in melanoma cells. Experimental procedures: UV-VIS spectra was used to investigate the enzymatic oxidation of APAP by tyrosinase enzyme. GSH depletion was used to measure the extent of APAP metabolism by tyrosinase and rat liver microsomes. The toxicity of APAP was investigated in four melanocytic melanoma cell lines (which express functional tyrosinase), and in four non-melanoma cell lines and one amelanocytic melanoma cell line (which do not express functional tyrosinase) using MTT assay. The biochemical mechanism of APAP was investigated in human SK-MEL-28 melanocytic melanoma cell line using a number of modulators. Results: Our findings indicate that APAP was metabolized 87% by tyrosinase and 33% by liver microsomes as measured by GSH depletion at 2 h. Ascorbic acid and NADH, quinone reducing agents, were significantly depleted during the enzymatic oxidation of APAP by tyrosinase. The IC50 (48 h) of APAP towards SK-MEL-28, MeWo and SK-MEL-5, B16-F0 melanoma cells was 100 µM which is within APAP therapeutic concentration when given at a regular dose as an antipyretic and analgesic drug. However, at 100 µM APAP showed no significant toxicity towards human BJ, Saos-2, SW-620, and PC3 non-melanoma cell lines and human C32 amelanocytic melanoma cell line, thus demonstrating that APAP was selectively toxic towards melanocytic melanoma cells. Dicoumarol, a diaphorase inhibitor, and 1-bromoheptane, a GSH depleting agent, enhanced APAP toxicity towards SK-MEL-28 cells. Ascorbic acid, a reducing agent, and GSH were effective in preventing APAP cell toxicity. Trifluoperazine and cyclosporin A, inhibitors of permeability transition pore in mitochondria, significantly prevented APAP induced cell toxicity. APAP caused time and dose-dependent decline in intracellular GSH concentration, which preceded cell toxicity. APAP also led to ROS formation in melanoma cells which was exacerbated by dicoumarol and 1-bromoheptane whereas cyslosporin A and trifluoperazine prevented it. Conclusion: Our investigation suggests that APAP, as a prodrug, was activated by melanoma tyrosinase to cytotoxic quinone intermediate species in melanoma cells, and that intracellular GSH depletion, ROS formation and induced mitochondrial toxicity contributed towards APAP’s selective toxicity in melanocytic melanoma cell lines.
Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections
Authors: John I. Robinson, William H. Weir, Jan R. Crowley, Tiffany Hink, Kimberly A. Reske, Jennie H. Kwon, Carey-Ann D. Burnham, Erik R. Dubberke, Peter J. Mucha, Jeffrey P. Henderson
Journal: Journal of Clinical Investigation (2019)

Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
Nomogram to Predict the Benefit of Intensive Treatment for Locoregionally Advanced Head and Neck Cancer
Authors: Loren K. Mell, Hanjie Shen, Phuc Felix Nguyen-Tân, David I. Rosenthal, Kaveh Zakeri, Lucas K. Vitzthum, Steven J. Frank, Peter B. Schiff, Andy M. Trotti, James A. Bonner, Christopher U. Jones, Sue S. Yom, Wade L. Thorstad, Stuart J. Wong, George Shenouda, John A. Ridge, Qiang E. Zhang, Quynh-Thu Le
Journal: Clinical Cancer Research (2019)

Abstract Purpose: Previous studies indicate that the benefit of therapy depends on patients' risk for cancer recurrence relative to noncancer mortality (ω ratio). We sought to test the hypothesis that patients with head and neck cancer (HNC) with a higher ω ratio selectively benefit from intensive therapy. Experimental Design: We analyzed 2,688 patients with stage III–IVB HNC undergoing primary radiotherapy (RT) with or without systemic therapy on three phase III trials (RTOG 9003, RTOG 0129, and RTOG 0522). We used generalized competing event regression to stratify patients according to ω ratio and compared the effectiveness of intensive therapy as a function of predicted ω ratio (i.e., ω score). Intensive therapy was defined as treatment on an experimental arm with altered fractionation and/or multiagent concurrent systemic therapy. A nomogram was developed to predict patients' ω score on the basis of tumor, demographic, and health factors. Analysis was by intention to treat. Results: Decreasing age, improved performance status, higher body mass index, node-positive status, P16-negative status, and oral cavity primary predicted a higher ω ratio. Patients with ω score ≥0.80 were more likely to benefit from intensive treatment [5-year overall survival (OS), 70.0% vs. 56.6%; HR of 0.73, 95% confidence interval (CI): 0.57–0.94; P = 0.016] than those with ω score &amp;lt;0.80 (5-year OS, 46.7% vs. 45.3%; HR of 1.02, 95% CI: 0.92-1.14; P = 0.69; P = 0.019 for interaction). In contrast, the effectiveness of intensive therapy did not depend on risk of progression. Conclusions: Patients with HNC with a higher ω score selectively benefit from intensive treatment. A nomogram was developed to help select patients for intensive therapy.
Nucleotide excision repair of DNA adducts derived from the binding of the equine estrogen metabolite 4-OHEN to dC and dA adducts in vitro.
Authors: Dandan Chen, Alexander Kolbanovskiy, Anant Shastry, Shuang Ding, Suse Broyde, Judy L. Bolton, Bennette Van Houten, Nicholas E. Geacintov
Journal: Cancer Research (2006)

5255  The catechol 4-hydroxyequilenin (4-OHEN) is a metabolite of the equine estrogen equilenin, a component of a widely prescribed formulation that is used as a hormone replacement treatment for post-menopausal women. Our focus is on studying the physical and biochemical properties of DNA adducts that are formed when 4-OHEN is auto-oxidized to o-quinones that bind to dC and dA in DNA to form unusual cyclic adducts. The stereochemically defined 4-OHEN-dC and 4-OHEN-dA lesions were site-specifically incorporated into oligonucleotide duplexes and their susceptibilities to removal by nucleotide excision repair (NER) proteins were investigated. Computer modeling studies indicate that the dC adducts adopt unusual conformations and cause significant perturbations of the normal B-DNA structure since duplexes containing such adducts are strongly destabilized. The effects of temperature on NER were investigated using the prokaryotic UvrABC proteins from the thermophilic organism B. caldotenax to assess the mechanisms of recognition and incision associated with these bulky adducts. Although both the 4-OHEN-dC and -dA adducts form chemically analogous cyclic adducts that distort the double helices, the 4-OHEN-dC adducts are incised more efficiently than the dA adducts at both 37 °C and 55 °C. The repair efficiencies can also depend on adduct stereochemistry and sequence context. Research supported by NIH grants CA 73638 (J.L. Bolton, P.I.) and CA112412.
The role of Chk1 and Mre11/Nbs1/Rad50 in S phase arrest induced by DNA damage
Authors: Kristen Garner, Aime Levesque, Alan Eastman
Journal: Cancer Research (2008)

4233  Many anticancer agents cause DNA damage which activates cellular checkpoints to arrest cell cycle progression. The arrest provides time for DNA repair so that the cells can survive. The Mre11/Rad50/Nbs1 (MRN) complex is a regulator of the S phase checkpoint, and defective MRN enhances chemo- and radio-sensitivity. The colon cancer cell line HCT116 was identified as defective in S phase arrest following incubation with the topoisomerase I inhibitor SN38, and was found to express very low levels of MRN proteins. Transfection with Mre11 also elevated Rad50 and Nbs1 because it stabilizes the complex, and rescued the defect in S phase arrest. To determine the frequency of defects in the MRN complex, we have screened the 59 available cell lines of the NCI60 panel for expression of Mre11, Rad50 and Nbs1. We also screened the panel for defects in S phase arrest in response to DNA damage induced by SN38. We hypothesized, based on our data from HCT116 cells, that low levels of MRN proteins would correlate with lack of S phase arrest. Consistent with this hypothesis, the ovarian cancer cell line IGROV1 lacked MRN and failed to arrest in S phase when damaged. In contrast, we found cell lines such as HCC2998 which also failed to arrest in S, but exhibited high levels of MRN. We investigated the impact of MRN in more detail by suppressing its expression in MDA-MB-231 cells. Despite suppression of MRN, these cells still remained arrested in S phase when damaged. We also suppressed the checkpoint protein Chk1 in MDA-MB-231 cells and found that these cells now failed to arrest in S. This latter result suggested that activation of Chk1 is necessary for S phase arrest. However, further analysis of two of the three cells lines that failed to arrest in S phase (HCT116 and IGROV1) showed that they both activated Chk1 when damaged. Hence, Chk1 appears necessary but not sufficient for S phase arrest in SN38-damaged cells, but the ability to arrest in S can not be explained by the status of the MRN complex. These results demonstrate that cancer cell lines exhibit many different defects in cell cycle checkpoint regulation. These defects may provide a unique sensitivity of a particular tumor subtype to chemotherapeutic agents and the results may help to design rational therapies targeted at cells with these defects.
Levels of analysis and problems of evidential support in the study of asymmetric conflict
Authors: Dragos Simandan
Journal: Behavioral and Brain Sciences (2019)

The contribution by De Dreu and Gross oversimplifies the complexity of the topic. I provide counterarguments that undermine the two sweeping contentions on which the article's argument depends, and I argue that asymmetric conflict is best understood at the finer-grained level of studying the sequences of strikes and counterstrikes that the rival actors have in store for one another.
The Folate Pathway Inhibitor Pemetrexed Pleiotropically Enhances Effects of Cancer Immunotherapy
Authors: David A. Schaer, Sandaruwan Geeganage, Nelusha Amaladas, Zhao Hai Lu, Erik R. Rasmussen, Andreas Sonyi, Darin Chin, Andrew Capen, Yanxia Li, Catalina M. Meyer, Bonita D. Jones, Xiaodong Huang, Shuang Luo, Carmine Carpenito, Kenneth D. Roth, Alexander Nikolayev, Bo Tan, Manisha Brahmachary, Krishna Chodavarapu, Frank C. Dorsey, Jason R. Manro, Thompson N. Doman, Gregory P. Donoho, David Surguladze, Gerald E. Hall, Michael Kalos, Ruslan D. Novosiadly
Journal: Clinical Cancer Research (2019)

Abstract Purpose: Combination strategies leveraging chemotherapeutic agents and immunotherapy have held the promise as a method to improve benefit for patients with cancer. However, most chemotherapies have detrimental effects on immune homeostasis and differ in their ability to induce immunogenic cell death (ICD). The approval of pemetrexed and carboplatin with anti-PD-1 (pembrolizumab) for treatment of non–small cell lung cancer represents the first approved chemotherapy and immunotherapy combination. Although the clinical data suggest a positive interaction between pemetrexed-based chemotherapy and immunotherapy, the underlying mechanism remains unknown. Experimental Design: Mouse tumor models (MC38, Colon26) and high-content biomarker studies (flow cytometry, Quantigene Plex, and nCounter gene expression analysis) were deployed to obtain insights into the mechanistic rationale behind the efficacy observed with pemetrexed/anti-PD-L1 combination. ICD in tumor cell lines was assessed by calreticulin and HMGB-1 immunoassays, and metabolic function of primary T cells was evaluated by Seahorse analysis. Results: Pemetrexed treatment alone increased T-cell activation in mouse tumors in vivo, robustly induced ICD in mouse tumor cells and exerted T-cell–intrinsic effects exemplified by augmented mitochondrial function and enhanced T-cell activation in vitro. Increased antitumor efficacy and pronounced inflamed/immune activation were observed when pemetrexed was combined with anti-PD-L1. Conclusions: Pemetrexed augments systemic intratumor immune responses through tumor intrinsic mechanisms including immunogenic cell death, T-cell–intrinsic mechanisms enhancing mitochondrial biogenesis leading to increased T-cell infiltration/activation along with modulation of innate immune pathways, which are significantly enhanced in combination with PD-1 pathway blockade. See related commentary by Buque et al., p. 6890
Correlation of hypermethylation of hMLH1, HPP1, p14ARF, p16INk4A and APC in primary adenocarcinomas of the small bowel
Authors: Björn Ldm Brücher, Heinz Höfler, Jörg R. Siewert, Mario Sarbia
Journal: Cancer Research (2005)

854  Background: Small bowel adenocarcinomas are very rare tumour entities. Epigenetic alterations, like hypermethylation in mismatch repair genes and tumour suppressor genes, seem to be important for the carcinogenesis in tumours of the gastrointestinal tract, but have not been investigated so far in primary adenocarcinoma of the small bowel. Aims: We evaluated the prevalence of the hypermethylation of hMLH1, HPP1, p14ARF, p16INk4A and APC in primary adenocarcinomas of the small bowel and in primary adenocarcinoma of the stomach. Methods: Paraffin-embedded tumour samples from 27 patients with primary adenocarcinoma of the small bowel and 50 patients with primary adenocarcinoma of the stomach, who underwent surgical resection between January 1987 and december 2003 were investigated. The hypermethylation of hMLH1, HPP1, p14ARF, p16INk4A and APC were surveyed by means of mehtylation-specific real-time PCR. Results: In patients with primary adenocarcinoma a significant higher rate of hypermethylation of HPP1 (78% versus 54%, p=0.039), p16INk4A (30% versus 10%, p=0.023) and a significant lower rate of hypermethylation of APC (59% versus 84%, p=0.016) was observable compared to patients with primary adenocarcinomas of the stomach. No significant differences in hypermethylation of hMLH1, HPP1, p14ARF, p16INk4A and APC were found regarding tumour-sub-location (duodenal or jejunal) and most clinicopathological parameters, like age, sex, grading, WHO-classification, Lauren classification or TNM-categories. Patients with postoperatively locally advanced tumour categories (pT3/4) showed a higher rate of hypermethylation of HPP1 (90%) compared to early tumour categories (p=0.042). Conclusions: Our findings suggest, that hypermethylation of hMLH1, HPP1, p14ARF, p16INk4A and APC are frequent in primary adenocarcinomas of the small bowel. The differences of the hypermethylation spectrum of small bowel and stomach cancer give significant account of the epigenetic differences of both tumour entities.