3D/2D comparison study of cyclosporine A transcriptomic
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: S-DIXA-091 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description: Not available
| S-DIXA-092 | biostudies-other
Project description:As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans.Fifty IMRT plans were selected from the authors' clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated ("evaluated dose distributions") and Monte Carlo-recalculated ("reference dose distributions") dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma.The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D).The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must be noted that clinical 2D versus 3D datasets may have additional differences--for example, if 2D measurements are made with a different dosimeter than 3D measurements. Factors such as inherent dosimeter differences may be an important additional consideration to the extra dimension of available data that was evaluated in this study.
| S-EPMC3977814 | biostudies-other
Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique.
* To evaluate the visual overload in surgeons using 3D laparoscopic technique.
| 2220465 | ecrin-mdr-crc
Project description:Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids composed of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in colon cancer cells that can be further studied to target pivotal lipid production pathways.
| S-EPMC9526240 | biostudies-literature
Project description:Primary human hepatocytes (PHHs) are commonly used for in vitro studies of drug-induced liver injury. However, when cultured as 2D monolayers, PHH lose crucial hepatic functions within hours. This dedifferentiation can be ameliorated when PHHs are cultured in sandwich configuration (2Dsw), particularly when cultures are regularly re-overlaid with extracellular matrix, or as 3D spheroids. In this study, the 6 participating laboratories evaluated the robustness of these 2 model systems made from cryopreserved PHH from the same donors considering both inter-donor and inter-laboratory variability and compared their suitability for use in repeated-dose toxicity studies using 5 different hepatotoxins with different toxicity mechanisms. We found that expression levels of proteins involved in drug absorption, distribution, metabolism, and excretion, as well as catalytic activities of 5 different CYPs, were significantly higher in 3D spheroid cultures, potentially affecting the exposure of the cells to drugs and their metabolites. Furthermore, global proteomic analyses revealed that PHH in 3D spheroid configuration were temporally stable whereas proteomes from the same donors in 2Dsw cultures showed substantial alterations in protein expression patterns over the 14 days in culture. Overall, spheroid cultures were more sensitive to the hepatotoxic compounds investigated, particularly upon long-term exposures, across testing sites with little inter-laboratory or inter-donor variability. The data presented here suggest that repeated-dosing regimens improve the predictivity of in vitro toxicity assays, and that PHH spheroids provide a sensitive and robust system for long-term mechanistic studies of drug-induced hepatotoxicity, whereas the 2Dsw system has a more dedifferentiated phenotype and lower sensitivity to detect hepatotoxicity.
| S-EPMC5888952 | biostudies-literature
Project description:Real-time three-dimensional (RT-3D) echocardiography has entered the clinical practice but true incremental value over standard two-dimensional echocardiography (2D) remains uncertain when applied to stress echo. The aim of the present study is to establish the additional value of RT-3D stress echo over standard 2D stress echocardiography. We evaluated 23 consecutive patients (age = 65 +/- 10 years, 16 men) referred for dipyridamole stress echocardiography with Sonos 7500 (Philips Medical Systems, Palo, Alto, CA) equipped with a phased - array 1.6-2.5 MHz probe with second harmonic capability for 2D imaging and a 2-4 MHz matrix-phased array transducer producing 60 x 70 volumetric pyramidal data containing the entire left ventricle for RT-3D imaging. In all patients, images were digitally stored in 2D and 3D for baseline and peak stress with a delay between acquisitions of less than 60 seconds. Wall motion analysis was interpreted on-line for 2D and off-line for RT-3D by joint reading of two expert stress ecocardiographist. Segmental image quality was scored from 1 = excellent to 5 = uninterpretable. Interpretable images were obtained in all patients. Acquisition time for 2D images was 67 +/- 21 sec vs 40 +/- 22 sec for RT-3D (p = 0.5). Wall motion analysis time was 2.8 +/- 0.5 min for 2D and 13 +/- 7 min for 3D (p = 0.0001). Segmental image quality score was 1.4 +/- 0.5 for 2D and 2.6 +/- 0.7 for 3D (p = 0.0001). Positive test results was found in 5/23 patients. 2D and RT-3D were in agreement in 3 out of these 5 positive exams. Overall stress result (positive vs negative) concordance was 91% (Kappa = 0.80) between 2D and RT-3D. During dipyridamole stress echocardiography RT-3D imaging is highly feasible and shows a high concordance rate with standard 2D stress echo. 2D images take longer time to acquire and RT-3D is more time-consuming to analyze. At present, there is no clear clinical advantage justifying routine RT-3D stress echocardiography use.
| S-EPMC2474587 | biostudies-literature
Project description:BackgroundThe clinical education of interns on hepatocellular carcinoma (HCC) is both crucial and difficult in China, even if the education reform has advanced constantly over the years. The value of specific 3D printing model (3DPM) in clinical education of HCC is uncertain, and relevant literatures are very few. This study aimed to explore the effects of a patient-specific 3D printing liver model on the clinical education of HCC.MethodsThree laparoscopic hepatectomies were collected. For each case, a 3D virtual reconstruction (3DVR) and 3DPM were created using multi-detector computed tomography (MDCT) data, respectively. A total of 62 interns were randomly assigned to each group (3DPM, 3DVR, and MDCT groups) through a table of random numbers for random grouping. Following lecture-based HCC education, interns in each group selected a corresponding model of HCC. All interns were tested on the hepatic tumor locations, the vessels adjacent to them, surgical planning, and test time using the centesimal system score within 90 min. A questionnaire investigation on the degree of satisfaction, interest, and helpfulness for improving the comprehension ability of liver anatomy and 3D spatial structures was also recorded. The 3DPM group were compared with both 3DVR and MDCT group by theoretical examination scores and questionnaire survey satisfaction to evaluate the effects of 3DPM on the interns' clinical education in HCC.ResultsAll the interns completed the test and questionnaire. The 3DPM group gained significantly higher scores on the following test contents: indicating the correct tumor location (3DPM vs. 3DVR, MDCT: 36.7±4.8 vs. 33.2±5.8, 26.8±10.0, P=0.03, P<0.01, respectively), accurately identifying the relationship between the tumor and vessels (3DPM vs. 3DVR, MDCT: 37.1±4.6 vs. 31.6±3.7, 30.0±5.8, P<0.01, P<0.01, respectively), and designing appropriate surgical plans (3DPM vs. 3DVR, MDCT: 8±2.7 vs. 4.9±2.7, 5.9±3.8, P<0.01, P=0.04, respectively). The 3DPM group showed a higher degree of satisfaction (86.2%), interest (92.1%), and helpfulness (80.5%) for improving the comprehension ability of liver anatomy and 3D spatial structures.ConclusionsThe clinical teaching by utilizing 3DPM can significantly improve the professional theoretical level, strengthen clinical thinking and comprehensive ability, and improve the teaching effects of HCC for medical interns.
| S-EPMC10007920 | biostudies-literature
Project description:IntroductionHigh-resolution magnetic resonance imaging (MRI) of the cervical spinal cord is important to provide accurate diagnosis and pathological assessment of injuries. MEDIC (Multiple Echo Data Image Combination) sequences have been used in clinical MRI; however, a comparison of the performance of 2D and 3D MEDIC for cervical spinal cord imaging has not been reported. The aim of this study is to compare axial 2D and 3D MEDIC for the visualisation of the grey matter (GM) and white matter (WM) of the human cervical spinal cord.MethodsEight healthy participants were scanned using Siemens Prismafit 3T MRI. T2*-weighted gradient spoiled 2D and 3D MEDIC sequences were acquired at 0.4 × 0.4 × 3.0 and 0.3 × 0.3 × 3.0 mm resolutions, with the acquisition times of 6 and 7 min, respectively. Quantitative analyses of the images were made based on the image signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and non-uniformity (NU). Two independent radiologists (CS and FN), each provided Likert scoring assessments of anatomical visibility of the GM and WM structures and image clarity for all samples.ResultsQuantitative evaluation showed that 3D MEDIC provided higher SNR, higher CNR and lower NU than 2D MEDIC. However, 2D MEDIC provided better anatomical visibility for the GM, WM and CSF, and higher image clarity (lower artefacts) compared to 3D MEDIC.Conclusions2D MEDIC provides better information for depicting the internal structures of the cervical spinal cord compared to 3D MEDIC.
| S-EPMC7890925 | biostudies-literature
Project description:Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.
| S-EPMC5334570 | biostudies-literature
Project description:Cervical cancer remains a significant health challenge for women worldwide, with a disproportionate impact on developing regions like sub-Saharan Africa. Taking advantage of recent advancements in developing suitable preclinical models to study cell proliferation, differentiation, and gene expression, we used RNA sequencing to compare the transcriptomic profiles of SiHa cervical cancer cells grown in 3D versus 2D culture systems. Pathway analysis of 3D cultures revealed upregulation of immune activation, angiogenesis, and tissue remodeling pathways. The high expression of cytokines, chemokines, matrix metalloproteinases, and immediate early genes, suggests that 3D cultures replicate the tumor microenvironment better than 2D monolayer cultures. HPV gene expression analysis further demonstrated higher expression levels of HPV16 E1, E2, E6, and E7 genes in 3D versus 2D cultures. Further, by using a set of linear models, we identified 79 significantly differentially expressed genes in 3D culture compared to 2D culture conditions, independent of HPV16 viral gene effects. We subsequently validated five of these genes at the protein level in both the SiHa cell line and a newly developed, patient-derived cervical cancer cell line. In addition, correlation analysis identified 26 human genes positively correlated with viral genes across 2D and 3D culture conditions. The top five 3D versus 2D differentially expressed and HPV-correlated genes were validated via qRT-PCR in our patient derived cell line. Altogether, these findings suggest that 3D cultures provide superior model systems to explore mechanisms of immune evasion, cancer progression and antiviral therapeutics.
| S-EPMC11347336 | biostudies-literature