MSIMEP: Predicting microsatellite instability from microarray DNA methylation tumor profiles

Deficiency in DNA MMR activity results in tumors with a hypermutator phenotype, termed microsatellite instability (MSI). Beyond its utility in Lynch syndrome screening algorithms, today MSI has gained importance as predictive biomarker for various anti-PD-1 therapies across many different tumor types. Over the past years, many computational methods have emerged to infer MSI using either DNA- or RNA-based approaches. Considering this together with the fact that MSI-high tumors frequently exhibit a hypermethylated phenotype, herein we developed and validated MSIMEP, a computational tool for predicting MSI status from microarray DNA methylation tumor profiles of colorectal cancer samples. We demonstrated that MSIMEP optimized and reduced models have high performance in predicting MSI in different colorectal cancer cohorts. Moreover, we tested its consistency in other tumor types with high prevalence of MSI such as gastric and endometrial cancers. Finally, we demonstrated better performance of both MSIMEP models vis-à-vis a MLH1 promoter methylation-based one in colorectal cancer.

3D Printed Tacrolimus Rectal Formulations Ameliorate Colitis in an Experimental Animal Model of Inflammatory Bowel Disease

The aim of this study was to fabricate novel self-supporting tacrolimus suppositories using semisolid extrusion 3-dimensional printing (3DP) and to investigate their efficacy in an experimental model of inflammatory bowel disease. Blends of Gelucire 44/14 and coconut oil were employed as lipid excipients to obtain suppository formulations with self-emulsifying properties, which were then tested in a TNBS (2,4,6-trinitrobenzenesulfonic acid) induced rat colitis model. Disease activity was monitored using PET/CT medical imaging; maximum standardized uptake values (SUVmax), a measure of tissue radiotracer accumulation rate, together with body weight changes and histological assessments, were used as inflammatory indices to monitor treatment efficacy. Following tacrolimus treatment, a significant reduction in SUVmax was observed on days 7 and 10 in the rat colon sections compared to non-treated animals. Histological analysis using Nancy index confirmed disease remission. Moreover, statistical analysis showed a positive correlation (R2 = 71.48%) between SUVmax values and weight changes over time. Overall, this study demonstrates the effectiveness of 3D printed tacrolimus suppositories to ameliorate colitis and highlights the utility of non-invasive PET/CT imaging to evaluate new therapies in the preclinical area.

Evaluation of the therapeutic activity of melatonin and resveratrol in Inflammatory Bowel Disease: A longitudinal PET/CT study in an animal model

Inflammatory Bowel Disease (IBD) is a group of chronic disorders of the gastrointestinal tract, which two main types are Crohn's disease and ulcerative colitis. Although conventional therapeutic strategies have demonstrated to be effective in the IBD treatment, it is necessary to incorporate novel therapeutic agents that target other mechanisms involved in the pathogenesis of the disease, such as oxidative stress. For this reason, the efficacy in vivo of two antioxidant compounds, melatonin and resveratrol, has been investigated in an animal model of TNBS (2, 4, 6-trinitrobenzenesulfonic acid) induced colitis. PET/CT (Positron emission tomography/Computer Tomography) scans were performed to assess disease activity and evaluate treatment response. SUV_max (Standardized Uptake Value) values, body weight changes and histological evaluation were used as inflammatory indices to measure the efficacy of both treatments. SUV_max values increased rapidly after induction of colitis, but after the beginning of the treatment (day 3) a statistically significant decrease was observed on days 7 and 10 in treated animals compared to the non-treated group. This remission of the disease was also confirmed by histological analysis of the colon tissue using the Nancy histological index (p value < 0.05 for differences between non-treated and both groups of treated animals). Moreover, statistical analysis showed a correlation (R² = 65.52%) between SUV_max values and weight changes throughout the treatment. Overall, this study demonstrates the potential of resveratrol, and melatonin in lower extent, as therapeutic agents in the IBD treatment.

Non-computer-assisted liquid-based cytology for diagnosis of oral squamous cell carcinoma

The development of oral squamous cell carcinoma (OSCC) occasionally follows the neoplastic progression of other premalignant lesions. Although biopsy is the definitive diagnostic method, liquid-based cytology is an adequate method for screening suspicious lesions. We compared liquid-based cytology to histology for diagnosis of OSCC in patients with oral lesions that raised clinical suspicion of malignancy. Our sample consisted of 48 patients. Cytological samples were obtained by scraping the lesion superficially using Cytobrush®. We conducted cytological and histopathological evaluation of all preparations. We estimated sensitivity and specificity levels as well as positive and negative predictive values. The degree of inter-observer agreement for both methods was assessed using the kappa index. Twenty-eight (58.3%) of the cases finally were diagnosed with OSCC and 20 (41.7%) were determined to be premalignant lesions. We observed eight false negatives and no false positives; OSCC prevalence was 56.5%. The values for diagnostic indices were: sensitivity, 69% (CI 95%, prevalence 51.87); specificity, 100%; positive predictive value, 100%; negative predictive value, 71% (CI 95% 54.82). A kappa index of 0.622 (CI 95% 0.93, 0.39) was observed.

Comparison of three sampling instruments, Cytobrush, Curette and OralCDx, for liquid-based cytology of the oral mucosa

Exfoliative cytology of the oral cavity is a simple and noninvasive technique that permits the study of epithelial cells. Liquid-based cytology is an auxiliary diagnostic tool for improving the specificity and sensitivity of conventional cytology. The objective of our study was to compare the quality of normal oral mucosa cytology samples obtained using three different instruments, Cytobrush®, dermatological curette and Oral CDx® for liquid-based cytology. One hundred four cytological samples of oral cavity were analyzed. Samples were obtained from healthy volunteer subjects using all three instruments. The clinical and demographic variables were age, sex and smoking habits. We analyzed cellularity, quality of the preparation and types of cells in the samples. All preparations showed appropriate preparation quality. In all smears analyzed, cells were distributed uniformly and showed no mucus, bleeding, inflammatory exudate or artifacts. We found no correlation between the average number of cells and the type of instrument. The samples generally consisted of two types of cells: superficial and intermediate. No differences were found among the cytological preparations of these three instruments. We did not observe basal cells in any of the samples analyzed.