Clinical Tools for Optimizing Therapeutic Decision-Making in Prostate Cancer: A Five-Year Retrospective Analysis.

The effective staging of prostate cancer is essential for optimizing treatment and predicting outcomes. This study assessed the correlation between detailed preoperative diagnostic scores and postoperative outcomes to evaluate the accuracy of cancer restaging and its impact on treatment decisions and prognosis after prostatectomy. This retrospective study analyzed 133 prostate cancer patients who underwent prostatectomies at "Pius Brinzeu" Clinical Emergency Hospital in Timisoara over five years. Preoperative Gleason scores increased significantly across risk categories, from an average of 6.21 in low-risk patients to 7.57 in high-risk patients. This trend continued postoperatively, with scores rising from 7.04 to 8.33, respectively. The average increase in Gleason scores from preoperative to postoperative assessments was most pronounced in high-risk patients, at 0.76. Significant changes in clinical staging included increases in NCCN risk, where high-risk patients showed a 30% increase, and ISUP grade, with a 26.7% increase in the high-risk category. Notably, nodal status changes were also significant in high-risk patients, showing a 23.3% increase. The incidence of MRI-detected adenopathy was notably higher in the high-risk group (50%). Furthermore, there were significant correlations between the preoperative CAPRA score and postoperative ISUP grade (r = 0.261) and the preoperative PIRADS score and postoperative ISUP grade (r = 0.306). Similar observations were made between the preoperative and postoperative Gleason scores (r = 0.286) and the number of positive fragments (r = 0.227) with the postoperative ISUP grading. Furthermore, the preoperative CAPRA score was significantly correlated (r = 0.261) with the postoperative ISUP grading. Preoperative MRI findings, which included assessments of adenopathy and seminal vesicle invasion, were also significantly correlated (r = 0.218) with the postoperative pathological findings. Additionally, a significant correlation was found between the preoperative PIRADS score and postoperative ISUP grade (r = 0.306). In forecasting the aggressiveness and staging of prostate cancer following surgery, preoperative PSA levels showed an AUC of 0.631; the preoperative Gleason score had an AUC adjusted to 0.582, and the number of positive biopsy fragments indicated an AUC of 0.566. These results highlight the necessity of accurate and comprehensive preoperative assessments to better predict disease progression and refine treatment strategies.

Connecting the dots: Computational network analysis for disease insight and drug repurposing.

Network biology is a powerful framework for studying the structure, function, and dynamics of biological systems, offering insights into the balance between health and disease states. The field is seeing rapid progress in all of its aspects: data availability, network synthesis, network analytics, and impactful applications in medicine and drug development. We review the most recent and significant results in network biomedicine, with a focus on the latest data, analytics, software resources, and applications in medicine. We also discuss what in our view are the likely directions of impactful development over the next few years.

The Cavernous Nerve Injury Rat Model: A Pictorial Essay on Post-Radical Prostatectomy Erectile Dysfunction Research.

Understanding and addressing post-radical prostatectomy (RP) erectile dysfunction (ED) is of paramount importance for clinicians. Cavernous nerve (CN) injury rat model studies have provided consistently promising experimental data regarding regaining erectile function (EF) after nerve damage-induced ED. However, these findings have failed to translate efficiently into clinical practice, with post-RP ED therapeutic management remaining cumbersome and enigmatic. This disparity highlights the need for further standardization and optimization of the elaborate surgical preparation protocols and multifaceted reporting parameters involved in reliable CN injury rat model experimentation. Even so, despite its technical complexity, this animal model remains instrumental in exploring the functional implications of RP, i.e., surgical lesions of the neurovascular bundles (NVBs). Herein, besides cavernous nerve (CN) dissection, injury, and electrostimulation, multiple pressure measurements, i.e., mean arterial pressure (MAP) and intra-cavernosal pressure (ICP), must also be achieved. A transverse cervical incision allows for carotid artery cannulation and MAP measurements. Conversely, ICP measurements entail circumcising the penis, exposing the ischiocavernous muscle, and inserting a needle into the corporal body. Finally, using an abdominal incision, the prostate is revealed, and the major pelvic ganglia (MPG) and CNs are dissected bilaterally. Specific surgical techniques are used to induce CN injuries. Herein, we provide a narrative and illustrative overview regarding these complex experimental procedures and their particular requirements, reflecting on current evidence and future research perspectives.

Network controllability solutions for computational drug repurposing using genetic algorithms.

Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over the dynamics of a given network, a problem known as network controllability. We propose in this article a new solution for this problem based on genetic algorithms. We tailor our solution for applications in computational drug repurposing, seeking to maximize its use of FDA-approved drug targets in a given disease-specific protein-protein interaction network. We demonstrate our algorithm on several cancer networks and on several random networks with their edges distributed according to the Erdos-Rényi, the Scale-Free, and the Small World properties. Overall, we show that our new algorithm is more efficient in identifying relevant drug targets in a disease network, advancing the computational solutions needed for new therapeutic and drug repurposing approaches.

A comparative study of genotoxicity endpoints for women exposed to different levels of indoor radon concentrations.

BACKGROUND AND PURPOSE: Radon and its radioactive progenies are the most important source of ionizing radiation of natural origin, being classified as a Group 1 carcinogen. The aim of this study is to investigate the genotoxic effects of a wide range of indoor radon concentrations, as well as the kinetics of the process of repairing DNA-induced lesions by a challenging dose of gamma irradiation. MATERIAL AND METHODS: Female subjects residing in the Baita-Stei radon priority area were selected as the exposed group. The reference group was comprised of women from the same county (Bihor), but located in an area with an average indoor radon concentration typical of the county from which they were taken. Radon concentration values of 300 Bq/m3 and 148 Bq/m3, respectively, were chosen as a threshold in order to capture the impact of radon exposure between the groups. The alkaline comet assay was used in order to measure the DNA damage, as well as the repair kinetics at 2 and 24 h after 2 Gy challenging doses of gamma irradiation using peripheral blood lymphocytes. From the serum of the subjects, the oxidative damage by 8-hydroxydeoxyguanosine as well as the PARP induction was evaluated. The chromosomal aberrations were evaluated using the Cytokinesis Block MicroNucleus Assay. RESULTS: A statistically significant increase was observed in terms of DNA-induced lesions assessed by comet assay for the exposed group compared to the reference group. A positive correlation was obtained between DNA damage and the annual effective dose, respectively with the radon progenies concentrations. A statistically significant difference was also observed for the frequency of the micronuclei between the exposed - reference groups. Significantly faster repair kinetics of DNA-induced lesions was recorded for the first 2 h after gamma irradiation in the reference group compared to the exposed group. Using the threshold of 300 Bq/m3 for radon concentration, faster kinetics of DNA damage repair for people exposed to low radon concentrations, compared to those exposed to higher concentrations for the second phase of DNA repair kinetics was observed. CONCLUSION: An increased radiosensitivity of lymphocytes, as well as slower repair kinetics, may be associated with exposure to higher indoor radon concentrations.

NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks.

MOTIVATION: There is an increasing amount of data coming from genome-wide studies identifying disease-specific survivability-essential proteins and host factors critical to a cell becoming infected. Targeting such proteins has a strong potential for targeted, precision therapies. Typically however, too few of them are drug targetable. An alternative approach is to influence them through drug targetable proteins upstream of them. Structural target network controllability is a suitable solution to this problem. It aims to discover suitable source nodes (e.g. drug targetable proteins) in a directed interaction network that can control (through a suitable set of input functions) a desired set of targets. RESULTS: We introduce NetControl4BioMed, a free open-source web-based application that allows users to generate or upload directed protein-protein interaction networks and to perform target structural network controllability analyses on them. The analyses can be customized to focus the search on drug targetable source nodes, thus providing drug therapeutic suggestions. The application integrates protein data from HGNC, Ensemble, UniProt, NCBI and InnateDB, directed interaction data from InnateDB, Omnipath and SIGNOR, cell-line data from COLT and DepMap, and drug-target data from DrugBank. AVAILABILITYAND IMPLEMENTATION: The application and data are available online at https://netcontrol.combio.org/. The source code is available at https://github.com/Vilksar/NetControl4BioMed under an MIT license.

Oxaliplatin induces different cellular and molecular chemoresistance patterns in colorectal cancer cell lines of identical origins.

BACKGROUND: Cancer cells frequently adopt cellular and molecular alterations and acquire resistance to cytostatic drugs. Chemotherapy with oxaliplatin is among the leading treatments for colorectal cancer with a response rate of 50%, inducing intrastrand cross-links on the DNA. Despite of this drug's efficiency, resistance develops in nearly all metastatic patients. Chemoresistance being of crucial importance for the drug's clinical efficiency this study aimed to contribute to the identification and description of some cellular and molecular alterations induced by prolonged oxaliplatin therapy. Resistance to oxaliplatin was induced in Colo320 (Colo320R) and HT-29 (HT-29R) colorectal adenocarcinoma cell lines by exposing the cells to increasing concentrations of the drug. Alterations in morphology, cytotoxicity, DNA cross-links formation and gene expression profiles were assessed in the parental and resistant variants with microscopy, MTT, alkaline comet and pangenomic microarray assays, respectively. RESULTS: Morphology analysis revealed epithelial-to-mesenchymal transition in the resistant vs parental cells suggesting alterations of the cells' adhesion complexes, through which they acquire increased invasiveness and adherence. Cytotoxicity measurements demonstrated resistance to oxaliplatin in both cell lines; Colo320 being more sensitive than HT-29 to this drug (P < 0.001). The treatment with oxaliplatin caused major DNA cross-links in both parental cell lines; in Colo320R small amounts of DNA cross-links were still detectable, while in HT-29R not. We identified 441 differentially expressed genes in Colo320R and 613 in HT-29R as compared to their parental counterparts (at least 1.5 -fold up- or down- regulation, p < 0.05). More disrupted functions and pathways were detected in HT-29R cell line than in Colo320R, involving genes responsible for apoptosis inhibition, cellular proliferation and epithelial-to-mesenchymal transition. Several upstream regulators were detected as activated in HT-29R cell line, but not in Colo320R. CONCLUSIONS: Our findings revealed a more resistant phenotype in HT-29R as compared to Colo320R and different cellular and molecular chemoresistance patterns induced by prolonged treatment with oxaliplatin in cell lines with identical origins (colorectal adenocarcinomas).