Simulating complex patient populations with hierarchical learning effects to support methods development for post-market surveillance

Funding Information: This work was funded by a grant from the National Heart, Lung, and Blood Institute (NHLBI; grant number 1R01HL149948). The funding agency was not involved in the design of the study, collection and analysis of data, interpretation of results, or writing of the manuscript. Publisher Copyright: © 2023, The Author(s).Peer reviewedPublisher PD

Transcriptome and DNA methylation changes modulated by sulforaphane induce cell cycle arrest, apoptosis, DNA damage, and suppression of proliferation in human liver cancer cells

Abnormal epigenetic alterations are one of the keystones of cancer development. Epigenetic targeting drugs have become a promising and effective cancer therapy strategy. However, due to the high toxicity and unclear mechanisms of action of these drugs, natural compounds that cause epigenetic modulation have also been studied. Sulforaphane (SFN) is a promising bioactive compound for epigenetic targeting therapy. In this study, we investigate the effects of SFN on gene expression and DNA methylation in human hepatocellular carcinoma cells (HepG2). Using high throughput technologies in combination with cell-based assays, we find SFN is a potent anticancer agent, as it induces DNA damage, mitotic spindle abnormalities followed by apoptosis and proliferation inhibition in HepG2 cells. Our results show the upregulation of DNA damage response and cell cycle checkpoint genes. Also, we find the downregulation of cellular pathways frequently overexpressed in human cancer. As expected, SFN exerts epigenetic modulation effects by inhibiting histone deacetylases (HDACs). SFN might affect the activity of oncogenic transcription factors through methylation of its binding sites motifs. Our findings offer insights into SFN chemopreventive molecular effects in HepG2 cells and highlight SFN as a valuable natural approach to cancer therapy for future investigatio

Effects of sulforaphane on the oxidative response, apoptosis, and the transcriptional profile of human stomach mucosa cells in vitro

Oxidative stress is a critical factor in the pathogenesis of several gastrointestinal diseases. Sulforaphane (SFN), a bioactive compound found in cruciferous vegetables, activates the redox-sensitive nuclear erythroid 2-related factor 2 (NRF2). In addition to its protective role, SFN exerts cytotoxic effects on cancer cells. However, there is a lack of information concerning the toxicity of SFN in normal cells. We investigated the effects of SFN on cell viability, antioxidant defenses, and gene expression in human stomach mucosa cells (MNP01). SFN reduced ROS formation and protected the cells against induced oxidative stress but high concentrations increased apoptosis. An intermediate SFN concentration (8 μM) was chosen for RNA sequencing studies. We observed upregulation of genes of the NRF2 (antioxidant) pathway, the DNA damage response, and apoptosis signaling; whereas SFN downregulated cell cycle and DNA repair pathway genes. SFN may be cytoprotective at low concentrations and cytotoxic at high concentrations

Simulating complex patient populations with hierarchical learning effects to support methods development for post-market surveillance.

BACKGROUND: Validating new algorithms, such as methods to disentangle intrinsic treatment risk from risk associated with experiential learning of novel treatments, often requires knowing the ground truth for data characteristics under investigation. Since the ground truth is inaccessible in real world data, simulation studies using synthetic datasets that mimic complex clinical environments are essential. We describe and evaluate a generalizable framework for injecting hierarchical learning effects within a robust data generation process that incorporates the magnitude of intrinsic risk and accounts for known critical elements in clinical data relationships. METHODS: We present a multi-step data generating process with customizable options and flexible modules to support a variety of simulation requirements. Synthetic patients with nonlinear and correlated features are assigned to provider and institution case series. The probability of treatment and outcome assignment are associated with patient features based on user definitions. Risk due to experiential learning by providers and/or institutions when novel treatments are introduced is injected at various speeds and magnitudes. To further reflect real-world complexity, users can request missing values and omitted variables. We illustrate an implementation of our method in a case study using MIMIC-III data for reference patient feature distributions. RESULTS: Realized data characteristics in the simulated data reflected specified values. Apparent deviations in treatment effects and feature distributions, though not statistically significant, were most common in small datasets (n < 3000) and attributable to random noise and variability in estimating realized values in small samples. When learning effects were specified, synthetic datasets exhibited changes in the probability of an adverse outcomes as cases accrued for the treatment group impacted by learning and stable probabilities as cases accrued for the treatment group not affected by learning. CONCLUSIONS: Our framework extends clinical data simulation techniques beyond generation of patient features to incorporate hierarchical learning effects. This enables the complex simulation studies required to develop and rigorously test algorithms developed to disentangle treatment safety signals from the effects of experiential learning. By supporting such efforts, this work can help identify training opportunities, avoid unwarranted restriction of access to medical advances, and hasten treatment improvements

Jaboticaba peel: Antioxidant compounds, antiproliferative and antimutagenic activities

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)This paper reports on the anthocyanin and antioxidant contents, an the 'in vitro' antiproliferative and 'in vivo' mutagenic/antimutagenic activities of freeze-dried jaboticaba peel (JP). According to the proximate composition, JP showed a high dietary fiber content. The identification and quantification of the JP anthocyanins was carried out by HPLC-PDA and LC-MS/MS, which revealed the presence of two compounds: delphinidin 3-glucoside and cyanidin 3-glucoside (634.75 and 1963.57 mg 100 g(-1) d. w., respectively). JP showed a strong antioxidant potential: 25,514.24+/-3037 mu M TE g(-1), 45.38+/-0.50 mu g mL(-1) and 9458+/-97 mu M TEAC g(-1), for ORAC, DPPH and ABTS, respectively. The polar JP extract demonstrated antiproliferative effects against leukemia (K-562), and the non-polar extract was the most active against prostate cancer cell (PC-3), according to the antiproliferative assay. The micronucleus test in mice demonstrated that the polar JP extract induced no DNA damage and hence it showed no cytotoxic properties on mice bone marrow cells and caused no mutagenic effects. (C) 2012 Elsevier Ltd. All rights reserved.491596603Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FINEPConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Effect of intensive exercise on plasmatic neutrophil elastase level in eventing and endurance horses

Reasons for performing the study – Intensive exercise induces a systemic inflammatory response characterized by an increase of blood neutrophil count and myeloperoxidase (MPO) release. Neutrophil elastase (NE) could also contribute to tissues lesions by their proteinase activities. Objective – To compare plasmatic NE concentrations before and after different forms of intensive exercise. Materials and Methods – EDTA blood samples were taken from 51 eventing horses (EvH) and 32 endurance horses (EndH) were sampled before the race (T0). Blood sampling was performed 2 h (T1) after completing either phase D of a one or two star eventing competition (n=51) or a 120 or 160 km endurance race (n=32). Plasmatic NE and MPO were measured by a specific equine ELISA. Neutrophil counts and creatine kinase (CK) levels were also measured. A Wilcoxon test for paired samples was used to compare mean values of neutrophils, CK, MPO and NE at T0 and T1 in EvH and in EndH. Correlations were calculated between all the 4 parameters in EvH and EndH. Results – At T0, mean NE levels were 14.43 ± 3.63 ng/ml for EvH and 11.7 ± 2.11 ng/ml for EndH. The competition induced a significant increase of NE levels in (58.57 ± 24.06 ng/mL) EvH and (95.74 ± 22.70 ng/mL) EndH (p < 0,05). NE was significantly (p < 0,0001) correlated to MPO in EvH (r = 0.293) and EndH (0.594) and to CK (r = 0.297) in EndH (p<0.0001). Neutrophils, CK and MPO were significantly increased between T0 and T1 in both types of horses. Conclusions – Significant increase of NE was observed after intense exercise with a significant correlation between NE and MPO. The huge variability in MPO and ELT, indicates, that not all horses show the same intensity of systemic inflammatory response