@article{health-related quality of life outcomes with two different starting doses of lenvatinib in combination with everolimus for previously treated renal cell carcinoma._2022, url={https://doi.org/10.1093/oncolo/oyac142}, DOI={10.1093/oncolo/oyac142}, abstractNote={Abstract}, journal={The oncologist}, year={2022}, month={Jul} }
 @article{health-related quality-of-life outcomes in patients with advanced renal cell carcinoma treated with lenvatinib plus pembrolizumab or everolimus versus sunitinib (clear): a randomised, phase 3 study._2022, url={https://doi.org/10.1016/S1470-2045(22)00212-1}, DOI={10.1016/s1470-2045(22)00212-1}, abstractNote={Results from the phase 3 CLEAR study showed that lenvatinib plus pembrolizumab improved progression-free survival and overall survival compared with sunitinib in patients with advanced renal cell carcinoma. We aimed to assess the health-related quality-of-life (HRQOL) outcomes from the CLEAR study.This open-label, randomised, phase 3 study was done across 200 hospitals and cancer centres in 20 countries. Patients were required to be 18 years or older, with advanced clear-cell renal cell carcinoma, and a Karnofsky performance status of 70% or higher. Patients who had received previous systemic anticancer therapy for renal cell carcinoma were not eligible. Patients were randomly assigned (1:1:1) to lenvatinib (oral 20 mg per day) plus pembrolizumab (intravenous 200 mg every 21 days), lenvatinib (oral 18 mg per day) plus everolimus (oral 5 mg per day) in 21-day cycles, or sunitinib (oral 50 mg per day, 4 weeks on followed by 2 weeks off). Patients were assigned to treatments with a computer-generated randomisation scheme and were stratified by geographical region and Memorial Sloan Kettering Cancer Center prognostic groups. The primary endpoint, previously reported, was progression-free survival, and HRQOL was a secondary endpoint. Most HRQOL analyses were done in patients who underwent randomisation, received at least one dose of study treatment, and had any HRQOL data. Completion and compliance analyses were done in the full analysis set. Functional Assessment of Cancer Therapy Kidney Symptom Index-Disease-Related Symptoms (FKSI-DRS), European Organisation for the Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (EORTC QLQ-C30), and the EQ-5D-3 Level (EQ-5D-3L) preference questionnaire were administered at baseline and on day 1 of each subsequent 21-day cycle. This study is registered with ClinicalTrials.gov, NCT02811861, and is closed to new participants.Between Oct 13, 2016, and July 24, 2019, 355 patients were randomly assigned to the lenvatinib plus pembrolizumab group, 357 to the lenvatinib plus everolimus group, and 357 to the sunitinib group. Median follow-up for HRQOL analyses was 12·9 months (IQR 5·6-22·3). Because of the promising efficacy and safety results of lenvatinib plus pembrolizumab in the first-line setting, we focus the HRQOL results in this report on that combination versus sunitinib. Mean change from baseline in the lenvatinib plus pembrolizumab group compared with the sunitinib group was -1·75 (SE 0·59) versus -2·19 (0·66) for FKSI-DRS, -5·93 (0·86) versus -6·73 (0·94) for EORTC QLQ-C30 global health status/quality of life (GHS/QOL), and -4·96 (0·85) versus -6·64 (0·94) for the EQ-5D visual analogue scale (VAS). Median time to first deterioration in the lenvatinib plus pembrolizumab group compared with the sunitinib group was 9·14 weeks (95% CI 6·43-12·14) versus 12·14 weeks (9·14-15·29; HR 1·13 [95% CI 0·94-1·35], log-rank p=0·20) for FKSI-DRS, 12·00 weeks (7·29-15·14) versus 9·14 weeks (6·29-12·14; 0·88 [0·74-1·05], log-rank p=0·17) for EORTC QLQ-C30 GHS/QOL, and 9·43 weeks (6·43-12·29) versus 9·14 weeks (6·29-12·00; 0·83 [0·70-0·99], log-rank p=0·041) for the EQ-5D VAS. Median time to definitive deterioration in the lenvatinib plus pembrolizumab group compared with the sunitinib group was 134·14 weeks (95% CI 120·00-not estimable) versus 117·43 weeks (90·14-131·29; HR 0·70 [95% CI 0·53-0·92], log-rank p=0·0081) for FKSI-DRS, 114·29 weeks (102·14-153·29) versus 75·14 weeks (57·29-105·14; 0·60 [0·47-0·77], log-rank p<0·0001) for EORTC QLQ-C30 GHS/QOL, and 124·86 weeks (94·71-134·57) versus 74·86 weeks (54·14-96·00; 0·67 [0·53-0·85], log-rank p=0·0012) for the EQ-5D VAS. No outcomes on any of the instruments significantly favoured sunitinib over lenvatinib plus pembrolizumab. Most HRQOL comparisons of lenvatinib plus everolimus versus sunitinib were similar or favoured sunitinib.These HRQOL results demonstrate that patients given lenvatinib plus pembrolizumab treatment had similar or favourable scores compared with patients given sunitinib, particularly with respect to time to definitive deterioration. These results support the efficacy and safety profile of lenvatinib plus pembrolizumab as first-line therapy for patients with advanced renal cell carcinoma.Eisai (Nutley, NJ, USA) and Merck Sharp & Dohme, a subsidiary of Merck & Co (Kenilworth, NJ, USA).}, journal={The Lancet. Oncology}, year={2022}, month={Apr} }
 @article{lenvatinib versus sorafenib for first-line treatment of unresectable hepatocellular carcinoma: patient-reported outcomes from a randomised, open-label, non-inferiority, phase 3 trial._2021, url={https://doi.org/10.1016/S2468-1253(21)00110-2}, DOI={10.1016/s2468-1253(21)00110-2}, abstractNote={Background Hepatocellular carcinoma is the third-leading cause of cancer-related death worldwide. Preservation of health-related quality of life (HRQOL) during treatment is an important therapeutic goal. The aim of this study was to evaluate the effect of treatment with lenvatinib versus sorafenib on HRQOL. Methods REFLECT was a previously published multicentre, randomised, open-label, non-inferiority phase 3 study comparing the efficacy and safety of lenvatinib versus sorafenib as a first-line systemic treatment for unresectable hepatocellular carcinoma. Eligible patients were aged 18 years or older with unresectable hepatocellular carcinoma and one or more measurable target lesion per modified Response Evaluation Criteria in Solid Tumors criteria, Barcelona Clinic Liver Cancer stage B or C categorisation, Child-Pugh class A, Eastern Cooperative Oncology Group (ECOG) performance status of 1 or lower, and adequate organ function. Patients were randomly assigned (1:1) via an interactive voice–web response system; stratification factors for treatment allocation included region; macroscopic portal vein invasion, extrahepatic spread, or both; ECOG performance status; and bodyweight. Patient-reported outcomes (PROs), collected at baseline, on day 1 of each subsequent cycle, and at the end of treatment, were evaluated in post-hoc analyses of secondary and exploratory endpoints in the analysis population, which was the subpopulation of patients with a PRO assessment at baseline. A linear mixed-effects model evaluated change from baseline in PROs, including European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire Core 30 (QLQ-C30) and hepatocellular carcinoma-specific QLQ-HCC18 scales (both secondary endpoints of the REFLECT trial). Time-to-definitive-deterioration analyses were done based on established thresholds for minimum differences for worsening in PROs. Responder analyses explored associations between HRQOL and clinical response. This study is registered with ClinicalTrials.gov, NCT01761266. Findings Of 954 eligible patients randomly assigned to lenvatinib (n=478) or sorafenib (n=476) between March 14, 2013, and July 30, 2015, 931 patients (n=468 for lenvatinib; n=463 for sorafenib) were included in this analysis. Baseline PRO scores reflected impaired HRQOL and functioning and considerable symptom burden relative to full HRQOL. Differences in overall mean change from baseline estimates in most PRO scales generally favoured the lenvatinib over the sorafenib group, although the differences were not nominally statistically or clinically significant. Patients treated with lenvatinib experienced nominally statistically significant delays in definitive, meaningful deterioration on the QLQ-C30 fatigue (hazard ratio [HR] 0·83, 95% CI 0·69–0·99), pain (0·80, 0·66–0·96), and diarrhoea (0·52, 0·42–0·65) domains versus patients treated with sorafenib. Significant differences in time to definitive deterioration were not observed for other QLQ-C30 domains, and there was no difference in time to definitive deterioration on the global health status/QOL score (0·89, 0·73–1·09). For most PRO scales, differences in overall mean change from baseline estimates favoured responders versus non-responders. Across all scales, HRs for time to definitive deterioration were in favour of responders; median time to definitive deterioration for responders exceeded those for non-responders by a range of 4·8 to 14·6 months. Interpretation HRQOL for patients undergoing treatment for unresectable hepatocellular carcinoma is an important therapeutic consideration. The evidence of HRQOL benefits in clinically relevant domains support the use of lenvatinib compared with sorafenib to delay functional deterioration in advanced hepatocellular carcinoma. Funding Eisai and Merck Sharp & Dohme.}, journal={The lancet. Gastroenterology & hepatology}, year={2021}, month={Jun} }
 @article{patients' satisfaction with long-acting injectable somatostatin analog therapy for neuroendocrine tumors._2021, url={https://europepmc.org/articles/PMC8423948}, DOI={10.1186/s41687-021-00355-5}, abstractNote={Abstract}, journal={Journal of patient-reported outcomes}, year={2021}, month={Sep} }
 @article{utilization and safety of onabotulinumtoxina for the prophylactic treatment of chronic migraine from an observational study in europe._2017, url={https://europepmc.org/articles/PMC5734384}, DOI={10.1177/0333102417724150}, abstractNote={Objective To examine treatment utilization patterns and safety of onabotulinumtoxinA for the prophylactic treatment of chronic migraine in routine clinical practice. }, journal={Cephalalgia : an international journal of headache}, year={2017}, month={Jul} }
 @article{health-related quality of life and disease symptoms in postmenopausal women with hr(+), her2(-) advanced breast cancer treated with everolimus plus exemestane versus exemestane monotherapy._2013, url={https://doi.org/10.1185/03007995.2013.836078}, DOI={10.1185/03007995.2013.836078}, abstractNote={Abstract Objective: Everolimus (EVE)+exemestane (EXE; n = 485) more than doubled median progression-free survival versus placebo (PBO) + EXE (n = 239), with a manageable safety profile and no deterioration in health-related quality-of-life (HRQOL) in patients with hormone-receptor-positive (HR+) advanced breast cancer (ABC) who recurred or progressed on/after nonsteroidal aromatase inhibitor (NSAI) therapy. To further evaluate EVE + EXE impact on disease burden, we conducted additional post-hoc analyses of patient-reported HRQOL. Research design and methods: HRQOL was assessed using EORTC QLQ-C30 and QLQ-BR23 questionnaires at baseline and every 6 weeks thereafter until treatment discontinuation because of disease progression, toxicity, or consent withdrawal. Endpoints included the QLQ-C30 Global Health Status (QL2) scale, the QLQ-BR23 breast symptom (BRBS), and arm symptom (BRAS) scales. Between-group differences in change from baseline were assessed using linear mixed models with selected covariates. Sensitivity analysis using pattern-mixture models determined the effect of study discontinuation on/before week 24. Treatment arms were compared using differences of least squares mean (LSM) changes from baseline and 95% confidence intervals (CIs) at each timepoint and overall. Clinical trial registration: Clinicaltrials.gov: NCT00863655. Main outcome measures: Progression-free survival, survival, response rate, safety, and HRQOL. Results: Linear mixed models (primary model) demonstrated no statistically significant overall difference between EVE + EXE and PBO + EXE for QL2 (LSM difference = −1.91; 95% CI = −4.61, 0.78), BRBS (LSM difference = −0.18; 95% CI = −1.98, 1.62), or BRAS (LSM difference = −0.42; 95% CI = −2.94, 2.10). Based on pattern-mixture models, patients who dropped out early had worse QL2 decline on both treatments. In the expanded pattern-mixture model, EVE + EXE-treated patients who did not drop out early had stable BRBS and BRAS relative to PBO + EXE. Key limitations: HRQOL data were not collected after disease progression. Conclusions: These analyses confirm that EVE + EXE provides clinical benefit without adversely impacting HRQOL in patients with HR+ ABC who recurred/progressed on prior NSAIs versus endocrine therapy alone.}, journal={Current medical research and opinion}, year={2013}, month={Sep} }
 @article{health-related quality of life of patients with advanced breast cancer treated with everolimus plus exemestane versus placebo plus exemestane in the phase 3, randomized, controlled, bolero-2 trial._2013, url={https://doi.org/10.1002/cncr.28010}, DOI={10.1002/cncr.28010}, abstractNote={Abstract}, journal={Cancer}, year={2013}, month={Mar} }
 @article{health-related quality of life in patients with metastatic colorectal cancer treated with panitumumab in first- or second-line treatment._2011, url={https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21989186/?tool=EBI}, DOI={10.1038/bjc.2011.409}, abstractNote={Panitumumab in combination with chemotherapy was evaluated in two pivotal clinical trials in first- and second-line treatment of metastatic colorectal cancer (mCRC), respectively. This analysis compared the health-related quality of life (HRQoL) of patients with or without panitumumab in the two trials.Patients with mCRC were randomised to FOLFOX (first-line trial) or FOLFIRI (second-line trial)±panitumumab. The EuroQoL 5-Dimensions Health State Index (EQ-5D HSI) and Visual Analogue Scale (EQ-5D VAS) were assessed at baseline and monthly follow-up until disease progression. Patients with wild-type KRAS mCRC with baseline and post-baseline HRQoL scores were included. Difference in change from baseline between treatment groups was evaluated using linear mixed and pattern-mixture models.In the first-line trial, 576 patients with wild-type KRAS mCRC (284 panitumumab+FOLFOX4 and 292 FOLFOX4 alone) were included in the HRQoL analyses. In the second-line trial, 530 patients with wild-type KRAS mCRC were included in these analyses (263 panitumumab+FOLFIRI and 267 FOLFIRI alone). There was no significant difference in the change in EQ-5D HSI and VAS scores between treatment groups in either trial.The addition of panitumumab to FOLFOX4 or FOLFIRI in first- or second-line treatment of wild-type KRAS mCRC significantly improved progression-free survival without compromising HRQoL.}, journal={British journal of cancer}, year={2011}, month={Oct} }
 @article{health-related quality of life and colorectal cancer-specific symptoms in patients with chemotherapy-refractory metastatic disease treated with panitumumab._2010, url={https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21190026/?tool=EBI}, DOI={10.1007/s00384-010-1112-5}, abstractNote={Panitumumab monotherapy is approved for chemotherapy-refractory wild-type KRAS metastatic colorectal cancer (mCRC). Patient-reported outcomes—although important in the palliative setting—have not been reported in this patient population. In a phase 3 trial (n = 463), patients with chemotherapy-refractory mCRC were randomized 1:1 to panitumumab plus best supportive care (BSC) or BSC alone. Patient-reported outcomes were assessed using the NCCN/FACT CRC Symptom Index (FCSI) and EQ-5D Index. KRAS tumor status was analyzed in a prospectively defined, retrospective analysis. Average difference in change from baseline between treatment groups was evaluated using linear mixed and pattern-mixture models. KRAS tumor status and post-baseline patient-reported outcomes were available for 363 patients. Linear mixed models indicated significant differences in the FCSI score (difference in least-squares [LS] adjusted means [95% CI]; 5.62 [2.38, 8.86]) and the EQ-5D Index (difference in LS adjusted means [95% CI]; 0.22 [0.12, 0.32]) favoring panitumumab over BSC in patients with wild-type KRAS mCRC. By pattern-mixture analysis, the advantage of panitumumab over BSC was more pronounced in those patients with wild-type KRAS mCRC who did not drop out of the study early. In patients with mutant KRAS mCRC, no differences were observed between groups. Panitumumab-treated patients with wild-type KRAS mCRC maintained better control of CRC symptoms and quality of life compared with BSC alone, extending our understanding of the benefits of panitumumab treatment beyond improvements in progression-free survival.}, journal={International journal of colorectal disease}, year={2010}, month={Dec} }
 @article{help-seeking behavior of women with self-reported distressing sexual problems._2009, url={https://doi.org/10.1089/jwh.2008.1133}, DOI={10.1089/jwh.2008.1133}, abstractNote={OBJECTIVE
The objective was to describe the healthcare and information-seeking behavior of women with self-reported sexual problems and accompanying sexually related personal distress identified from a large, population-based U.S. survey.


METHODS
Women (n = 3,239) aged > or =18 years with self-reported sexual problems of desire, arousal, and/or orgasm accompanied by sexually related personal distress were identified from a cross-sectional mailed survey of 50,002 U.S. households sampled from a national research panel. Healthcare and information-seeking behavior was examined as four ordered categories: sought formal medical advice, sought informal advice, sought information from anonymous sources, and did not seek help or information. Correlates of help seeking for each type of distressing sexual problem were modeled with multivariable proportional odds regression.


RESULTS
Just over a third of women with any distressing sexual problems had sought formal care, most often from a gynecologist or primary care physician; about 80% of the time, the woman, rather than the physician, initiated the conversation. Only 6% of women who sought medical advice scheduled a visit specifically for a sexual problem. Factors related to help seeking were having a current partner and interacting with the healthcare system. Barriers were poor self-perceived health and embarrassment about discussing sexual topics with a physician.


CONCLUSIONS
Our results suggest inadequacies in the U.S. medical care system in addressing sexual problems in women. Gynecologists and primary care physicians, by including discussions about sexual health during routine visits, can increase the likelihood that adequate care can be offered.}, journal={Journal of women's health (2002)}, year={2009}, month={Apr} }
 @article{an assessment of patient preference and adherence to treatment with wellbutrin sr: a web-based survey._2005, url={https://doi.org/10.1016/j.jad.2005.08.018}, DOI={10.1016/j.jad.2005.08.018}, abstractNote={Research has shown that lack of treatment adherence is a serious problem, especially among patients with psychiatric disorders. The current study was conducted to assess adherence and patient preference among individuals taking Wellbutrin SR (bupropion) for depression, as well as their interest in a once-daily formulation of bupropion.A 20-item web-based survey was administered to 527 individuals (276 men and 251 women) recruited through an online panel. All participants were at least 18 years of age, diagnosed with major depressive disorder, and had been taking Wellbutrin SR for at least 6 weeks. Survey items addressed treatment regimen, adherence, satisfaction with Wellbutrin SR, and interest in a once-daily formulation of bupropion.The majority of respondents reported taking Wellbutrin SR twice a day (67%). Only 15% of once-daily users were nonadherent compared to 37% of twice-daily users and 65% of thrice-daily users. The most common reason reported for missing a dose of Wellbutrin SR was simply forgetting to take it (49% of twice-daily users and 65% of thrice-daily users). Results indicated that 77% of twice-daily users and 94% of thrice-daily users were interested in a once-daily formula.A reduction in dosing frequency is favored by Wellbutrin SR users and likely to improve their adherence to treatment. Because greater adherence has been shown to facilitate symptom relief, improvements in quality of life, and reductions in healthcare expenses, the results of this study support the value of the recently released once-daily formulation, Wellbutrin XL.}, journal={Journal of affective disorders}, year={2005}, month={Dec} }
 @article{exploration of low-dose estrogen effects: identification of no observed transcriptional effect level (notel)._2004, url={https://doi.org/10.1080/01926230490483324}, DOI={10.1080/01926230490483324}, abstractNote={Identifying a minimal dose capable of eliciting a biological response is a fundamental issue in a number of scientific fields, including: drug development, signal transduction research, and environmental toxicology. Frequently, proliferation, viability, and other assays based on the cellular response to a treatment are used to assess the threshold dose for minimal activity. Here we propose a novel approach for identifying the effects of low dose treatments and pinpointing the threshold dose. Using microarrays, we examined the transcriptional response of a hormone responsive breast cancer cell line (MCF-7) stimulated with various concentrations of estrogen. Previous studies have focused on transcriptional responses to physiologically relevant concentrations of estrogen. However, relatively few studies have examined the transcriptional effects of concentrations below normal physiologic levels. These doses may not stimulate the expression of any genes or, alternatively, may regulate a different subset of genes that had not been previously characterized as estrogen responsive. We used gene expression profiling, coupled with a detailed analysis of replicates, to measure estrogen effects on many transcriptional targets and found that only physiologically relevant doses of estrogen (1 x 10(-10) M and higher) were capable of inducing a transcriptional response. This study demonstrates the utility of gene expression profiling as a means to identify concentrations that do not elicit a change in gene expression, or simply a No Observed Transcriptional Effect Level (NOTEL). The identification of a NOTEL for a given compound may be beneficial in several different scientific disciplines. For example, in the development of therapeutic drugs, a NOTEL could be used to identify doses of pharmaceutical compounds that are no longer effective at modulating the expression of biomarkers of efficacy.}, journal={Toxicologic pathology}, year={2004}, month={Jul} }
 @article{identification of putative gene based markers of renal toxicity._2004, url={https://europepmc.org/articles/PMC1241901}, DOI={10.1289/ehp.6683}, abstractNote={This study, designed and conducted as part of the International Life Sciences Institute working group on the Application of Genomics and Proteomics, examined the changes in the expression profile of genes associated with the administration of three different nephrotoxicants--cisplatin, gentamicin, and puromycin--to assess the usefulness of microarrays in the understanding of mechanism(s) of nephrotoxicity. Male Sprague-Dawley rats were treated with daily doses of puromycin (5-20 mg/kg/day for 21 days), gentamicin (2-240 mg/kg/day for 7 days), or a single dose of cisplatin (0.1-5 mg/kg). Groups of rats were sacrificed at various times after administration of these compounds for standard clinical chemistry, urine analysis, and histological evaluation of the kidney. RNA was extracted from the kidney for microarray analysis. Principal component analysis and gene expression-based clustering of compound effects confirmed sample separation based on dose, time, and degree of renal toxicity. In addition, analysis of the profile components revealed some novel changes in the expression of genes that appeared to be associated with injury in specific portions of the nephron and reflected the mechanism of action of these various nephrotoxicants. For example, although puromycin is thought to specifically promote injury of the podocytes in the glomerulus, the changes in gene expression after chronic exposure of this compound suggested a pattern similar to the known proximal tubular nephrotoxicants cisplatin and gentamicin; this prediction was confirmed histologically. We conclude that renal gene expression profiling coupled with analysis of classical end points affords promising opportunities to reveal potential new mechanistic markers of renal toxicity.}, journal={Environmental health perspectives}, year={2004}, month={Mar} }
 @article{atm-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and uv irradiation._2003, url={https://doi.org/10.1667/rr3047}, DOI={10.1667/rr3047}, abstractNote={Abstract Heinloth, A. N., Shackelford, R. E., Innes, C. L., Bennett, L., Li, L., Amin, R. P., Sieber, S. O., Flores, K. G., Bushel, P. R. and Paules, R. S. ATM-Dependent and -Independent Gene Expression Changes in Response to Oxidative Stress, Gamma Irradiation, and UV Irradiation. Radiat. Res. 160, 273–290 (2003). Ataxia telangiectasia (AT) is an autosomal recessive disorder characterized by progressive cerebellar degeneration, immunodeficiencies, telangiectasias, sensitivity to ionizing radiation, and high predisposition for malignancies. The ataxia telangiectasia mutated (ATM) gene encodes a protein (ATM) with serine/threonine kinase activity. DNA-double strand breaks are known to increase its kinase activity. While cells from individuals with AT are attenuated in their G1-, S- and G2-phase cell cycle checkpoint functions in response to γ irradiation and oxidative stress, their response to UV irradiation appears to be equivalent to that of wild-type cells. In this study, we investigated changes in gene expression in response to γ irradiation, oxidative stress, and UV irradiation, focusing on the dependence on ATM. Doses for all three treatments were selected that resulted in roughly an equivalent induction of a G1 checkpoint response and inhibition of progression through S phase. To investigate gene expression changes, logarithmically growing wild-type and AT dermal diploid fibroblasts were exposed to either γ radiation (5 Gy), oxidative stress (75 µM t-butyl-hydroperoxide), or UV radiation (7.5 J/m2), and RNA was harvested 6 h after treatment. Gene expression analysis was performed using the NIEHS Human ToxChip 2.0 with approximately 1900 cDNA clones representing known genes and ESTs. All three treatments resulted in distinct patterns of gene expression changes, as shown previously. ATM-dependent and ATM-independent components were detected within these patterns, as were novel indications of involvement of ATM in regulation of transcription factors such as SP1, AP1 and MTF1.}, journal={Radiation research}, year={2003}, month={Sep} }
 @article{changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and wyeth-14,643._2003, url={https://doi.org/10.1093/carcin/bgg011}, DOI={10.1093/carcin/bgg011}, abstractNote={We hypothesized that the mouse liver tumor response to non-genotoxic carcinogens would involve some common early gene and protein expression changes that could ultimately be used to predict chemical hepatocarcinogenesis. In order to identify a panel of genes to test, we analyzed global differences in gene and protein expression in livers from B6C3F1 mice following dietary treatment with two rodent carcinogens, the benzodiazepine anti-anxiety drug oxazepam (2500 p.p.m.) and the hypolipidemic agent Wyeth (Wy)-14,643 (500 p.p.m.) compared with livers from untreated mice. Male mice were exposed for 2 weeks and 1, 3 or 6 months to oxazepam or Wy-14,643 in an age-matched study design. By histopathological evaluation, no liver preneoplastic foci or tumors were detected at 6 months in treated or control groups. By cDNA microarray analysis [NIEHS Mouse Chip (8700 genes); n = 3 individual livers/group, four hybridizations/sample], expression of 36 genes or 220 genes were changed relative to control livers following 6 months of oxazepam or Wy-14,643 treatment, respectively. To obtain a more comprehensive picture of gene/protein expression changes, we also conducted a proteomics study by 2D-gel electrophoresis followed by matrix assisted laser desorption/ionization-mass spectrometry on cytoplasmic, nuclear, and microsomal subcellular fractions of the same liver samples utilized for the cDNA microarray analysis. Real-time PCR, western blot analysis and immunohistochemistry were utilized for validation and to expand the results to other time points. Cyp2b20, growth arrest- and damage-inducible gene beta (Gadd45beta), tumor necrosis factor alpha-induced protein 2 and insulin-like growth factor binding protein 1 (Igfbp5) genes and proteins were upregulated by oxazepam, and Cyp2b20, Cyclin D1, proliferating cell nuclear antigen, Igfbp5, Gadd45beta and cell death-inducing DNA fragmentation factor alpha subunit-like effector A exhibited higher expression after Wy-14,643 treatment. Most of these genes/proteins were also deregulated at 2 weeks. There appeared to be more distinct than common changes in the expression of carcinogenesis-related genes/proteins between the two compounds, suggesting that the major carcinogenic pathways are different for these compounds and may be distinct for different chemical classes.}, journal={Carcinogenesis}, year={2003}, month={Apr} }
 @article{identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation._2003, url={https://doi.org/10.1002/mc.10122}, DOI={10.1002/mc.10122}, abstractNote={Abstract}, journal={Molecular carcinogenesis}, year={2003}, month={Jun} }
 @article{tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells._2003, journal={Molecular cancer research : MCR}, year={2003}, month={Feb} }
 @article{alterations in apoptotic signaling in human idiopathic cardiomyopathic hearts in failure._2002, url={https://doi.org/10.1152/ajpheart.00707.2002}, DOI={10.1152/ajpheart.00707.2002}, abstractNote={ Dilated cardiomyopathy, a disease of unknown etiology and pathogenesis, is associated with heart failure and compensatory hypertrophy. Although cell and animal models suggest a role for altered gene expression in the transition to heart failure, there is a paucity of data derived from the study of human heart tissue. In this study, we used DNA microarray profiling to investigate changes in the expression of genes involved in apoptosis that occur in human idiopathic dilated cardiomyopathic hearts that had progressed to heart failure. We observed altered gene expression consistent with a proapoptotic shift in the TNF-α signaling pathway. Specifically, we found decreased expression of TNF-α- and NF-κB-induced antiapoptotic genes such as growth arrest and DNA damage-inducible ( GADD) 45β, Flice inhibitory protein ( FLIP), and TNF-induced protein 3 ( A20). Consistent with a role for apoptosis in heart failure, we also observed a significant decrease in phosphorylation of BAD at Ser-112. This study identifies several pathways that are altered in human heart failure and provides new targets for therapy. }, journal={American journal of physiology. Heart and circulatory physiology}, year={2002}, month={Sep} }
 @article{computational selection of distinct class- and subclass-specific gene expression signatures._2002, url={https://doi.org/10.1016/s1532-0464(02)00525-7}, DOI={10.1016/s1532-0464(02)00525-7}, abstractNote={In this investigation we used statistical methods to select genes with expression profiles that partition classes and subclasses of biological samples. Gene expression data corresponding to liver samples from rats treated for 24 h with an enzyme inducer (phenobarbital) or a peroxisome proliferator (clofibrate, gemfibrozil or Wyeth 14,643) were subjected to a modified Z-score test to identify gene outliers and a binomial distribution to reduce the probability of detecting genes as differentially expressed by chance. Hierarchical clustering of 238 statistically valid differentially expressed genes partitioned class-specific gene expression signatures into groups that clustered samples exposed to the enzyme inducer or to peroxisome proliferators. Using analysis of variance (ANOVA) and linear discriminant analysis methods we identified single genes as well as coupled gene expression profiles that separated the phenobarbital from the peroxisome proliferator treated samples and discerned the fibrate (gemfibrozil and clofibrate) subclass of peroxisome proliferators. A comparison of genes ranked by ANOVA with genes assessed as significant by mixed linear models analysis [J. Comput. Biol. 8 (2001) 625] or ranked by information gain revealed good congruence with the top 10 genes from each statistical method in the contrast between phenobarbital and peroxisome proliferators expression profiles. We propose building upon a classification regimen comprised of analysis of replicate data, outlier diagnostics and gene selection procedures to utilize cDNA microarray data to categorize subclasses of samples exposed to pharmacologic agents.}, journal={Journal of biomedical informatics}, year={2002}, month={Jun} }
 @article{gene expression analysis reveals chemical-specific profiles._2002, url={https://doi.org/10.1093/toxsci/67.2.219}, DOI={10.1093/toxsci/67.2.219}, abstractNote={The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously promises a significant advance in understanding toxic mechanisms to ultimately aid in protection of public health. Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles of compounds where toxicological and pathological endpoints are well characterized. The validity and utility of a toxicogenomics is dependent on whether gene expression profiles that correspond to different chemicals can be distinguished. The principal hypothesis underlying a toxicogenomic or pharmacogenomic strategy is that chemical-specific patterns of altered gene expression will be revealed using high-density microarray analysis of tissues from exposed organisms. Analyses of these patterns should allow classification of toxicants and provide important mechanistic insights. This report provides a verification of this hypothesis. Patterns of gene expression corresponding to liver tissue derived from chemically exposed rats revealed similarity in gene expression profiles between animals treated with different agents from a common class of compounds, peroxisome proliferators [clofibrate (ethyl-p-chlorophenoxyisobutyrate), Wyeth 14,643 ([4-chloro-6(2,3-xylidino)-2-pyrimidinylthio]acetic acid), and gemfibrozil (5-2[2,5-dimethylphenoxy]2-2-dimethylpentanoic acid)], but a very distinct gene expression profile was produced using a compound from another class, enzyme inducers (phenobarbital).}, journal={Toxicological sciences : an official journal of the Society of Toxicology}, year={2002}, month={Jun} }
 @article{insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells._2002, url={https://europepmc.org/articles/PMC1531694}, DOI={10.1038/sj.neo.7900229}, abstractNote={Activation of the insulin-like growth factor-1 receptor (IGF-1R) by IGF-1 is associated with the risk and progression of many types of cancer, although despite this it remains unclear how activated IGF-1R contributes to cancer progression. In this study, gene expression changes elicited by IGF-1 were profiled in breast epithelial cells. We noted that many genes are functionally linked to cancer progression and angiogenesis. To validate some of the changes observed, the RNA and/or protein was confirmed for c-fos, cytochrome P450 1A1, cytochrome P450 1B1, interleukin-1 beta, fas ligand, vascular endothelial growth factor, and urokinase plasminogen activator. Nuclear proteins were also temporally monitored to address how gene expression changes were regulated. We found that IGF-1 stimulated the nuclear translocation of phosphorylated AKT, hypoxic-inducible factor-1 alpha, and phosphorylated cAMP-responsive element-binding protein, which correlated with temporal changes in gene expression. Next, the promoter regions of IGF-1-regulated genes were searched in silico. The promoters of genes that clustered together had similar regulatory regions. In summary, IGF-1 inscribes a gene expression profile relevant to cancer progression, and this study provides insight into the mechanism(s) whereby some of these changes occur.}, journal={Neoplasia (New York, N.Y.)}, year={2002}, month={May} }
 @article{prediction of compound signature using high density gene expression profiling._2002, url={https://doi.org/10.1093/toxsci/67.2.232}, DOI={10.1093/toxsci/67.2.232}, abstractNote={DNA microarrays, used to measure the gene expression of thousands of genes simultaneously, hold promise for future application in efficient screening of therapeutic drugs. This will be aided by the development and population of a database with gene expression profiles corresponding to biological responses to exposures to known compounds whose toxicological and pathological endpoints are well characterized. Such databases could then be interrogated, using profiles corresponding to biological responses to drugs after developmental or environmental exposures. A positive correlation with an archived profile could lead to some knowledge regarding the potential effects of the tested compound or exposure. We have previously shown that cDNA microarrays can be used to generate chemical-specific gene expression profiles that can be distinguished across and within compound classes, using clustering, simple correlation, or principal component analyses. In this report, we test the hypothesis that knowledge can be gained regarding the nature of blinded samples, using an initial training set comprised of gene expression profiles derived from rat liver exposed to clofibrate, Wyeth 14,643, gemfibrozil, or phenobarbital for 24 h or 2 weeks of exposure. Highly discriminant genes were derived from our database training set using approaches including linear discriminant analysis (LDA) and genetic algorithm/K-nearest neighbors (GA/KNN). Using these genes in the analysis of coded liver RNA samples derived from 24-h, 3-day, or 2-week exposures to phenytoin, diethylhexylpthalate, or hexobarbital led to successful prediction of whether these samples were derived from livers of rats exposed to enzyme inducers or to peroxisome proliferators. This validates our initial hypothesis and lends credibility to the concept that the further development of a gene expression database for chemical effects will greatly enhance the hazard identification processes.}, journal={Toxicological sciences : an official journal of the Society of Toxicology}, year={2002}, month={Jun} }
 @article{wolfinger_gibson_wolfinger_bennett_hamadeh_bushel_afshari_paules_2001, title={Assessing gene significance from cDNA microarray expression data via mixed models}, volume={8}, ISSN={["1066-5277"]}, url={https://doi.org/10.1089/106652701753307520}, DOI={10.1089/106652701753307520}, abstractNote={The determination of a list of differentially expressed genes is a basic objective in many cDNA microarray experiments. We present a statistical approach that allows direct control over the percentage of false positives in such a list and, under certain reasonable assumptions, improves on existing methods with respect to the percentage of false negatives. The method accommodates a wide variety of experimental designs and can simultaneously assess significant differences between multiple types of biological samples. Two interconnected mixed linear models are central to the method and provide a flexible means to properly account for variability both across and within genes. The mixed model also provides a convenient framework for evaluating the statistical power of any particular experimental design and thus enables a researcher to a priori select an appropriate number of replicates. We also suggest some basic graphics for visualizing lists of significant genes. Analyses of published experiments studying human cancer and yeast cells illustrate the results.}, number={6}, journal={JOURNAL OF COMPUTATIONAL BIOLOGY}, author={Wolfinger, RD and Gibson, G and Wolfinger, ED and Bennett, L and Hamadeh, H and Bushel, P and Afshari, C and Paules, RS}, year={2001}, pages={625–637} }
 @article{maps: a microarray project system for gene expression experiment information and data validation._2001, url={https://doi.org/10.1093/bioinformatics/17.6.564}, DOI={10.1093/bioinformatics/17.6.564}, abstractNote={Abstract}, journal={Bioinformatics (Oxford, England)}, year={2001}, month={Jun} }
 @article{predicting human oral bioavailability of a compound: development of a novel quantitative structure-bioavailability relationship._2000, url={https://doi.org/10.1023/a:1007556711109}, DOI={10.1023/a:1007556711109}, abstractNote={{"Label"=>"PURPOSE", "NlmCategory"=>"OBJECTIVE"} The purpose of this investigation was to develop a quantitative structure-bioavailability relationship (QSBR) model for drug discovery and development. {"Label"=>"METHODS", "NlmCategory"=>"METHODS"} A database of drugs with human oral bioavailability was assembled in electronic form with structure in SMILES format. Using that database, a stepwise regression procedure was used to link oral bioavailability in humans and substructural fragments in drugs. The regression model was compared with Lipinski's Rule of Five. {"Label"=>"RESULTS", "NlmCategory"=>"RESULTS"} The human oral bioavailability database contains 591 compounds. A regression model employing 85 descriptors was built to predict the human oral bioavailability of a compound based on its molecular structure. Compared to Lipinski's Rule of Five, the false negative predictions were reduced from 5% to 3% while the false positive predictions decreased from 78% to 53%. A set of substructural descriptors was identified to show which fragments tend to increase/decrease human oral bioavailability. {"Label"=>"CONCLUSIONS", "NlmCategory"=>"CONCLUSIONS"} A novel quantitative structure-bioavailability relationship (QSBR) was developed. Despite a large degree of experimental error, the model was reasonably predictive and stood up to cross-validation. When compared to Lipinski's Rule of Five, the QSBR model was able to reduce false positive predictions.}, journal={Pharmaceutical research}, year={2000}, month={Jun} }