Integrative models of histopathological images and multi-omics data predict prognosis in endometrial carcinoma.

Objective: This study aimed to predict the molecular features of endometrial carcinoma (EC) and the overall survival (OS) of EC patients using histopathological imaging. Methods: The patients from The Cancer Genome Atlas (TCGA) were separated into the training set (n = 215) and test set (n = 214) in proportion of 1:1. By analyzing quantitative histological image features and setting up random forest model verified by cross-validation, we constructed prognostic models for OS. The model performance is evaluated with the time-dependent receiver operating characteristics (AUC) over the test set. Results: Prognostic models based on histopathological imaging features (HIF) predicted OS in the test set (5-year AUC = 0.803). The performance of combining histopathology and omics transcends that of genomics, transcriptomics, or proteomics alone. Additionally, multi-dimensional omics data, including HIF, genomics, transcriptomics, and proteomics, attained the largest AUCs of 0.866, 0.869, and 0.856 at years 1, 3, and 5, respectively, showcasing the highest discrepancy in survival (HR = 18.347, 95% CI [11.09-25.65], p < 0.001). Conclusions: The results of this experiment indicated that the complementary features of HIF could improve the prognostic performance of EC patients. Moreover, the integration of HIF and multi-dimensional omics data might ameliorate survival prediction and risk stratification in clinical practice.

Criteria for judging the immune markers of COVID-19 disease vaccines.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sweeping the world, effective and affordable vaccines are in urgent need. A reliable system for the assessment of SARS-CoV-2 vaccines would boost the development of vaccines and reduce the research cost. We constructed a logistic regression model and analyzed the relationship between antibody (Ab) level and efficacy of different vaccine types. The relationship between assessment dates and Ab levels was depicted by plotting the mean of Ab levels evolved over time and a fitted cubic polynomial model. Anti-spike immunoglobulin G (IgG) could best estimate the vaccine efficacy (VE) (adjusted R 2  = 0.731) and neutralizing Ab to live SARS-CoV-2 also explained a fine relationship (adjusted R 2 = 0.577). Neutralizing Abs to live SARS-CoV-2 in inactivated virus vaccines reached a peak during days 40-60, and their receptor-binding domain (RBD)-IgG peaked during days 40-50. For messenger RNA (mRNA) and viral vector vaccines, their neutralizing Ab to live SARS-CoV-2 peaked later than day 40, and for RBD-IgG during days 30-50. For mRNA and viral vector vaccines, their peak time of Abs was later than that in inactivated virus vaccines. RBD-IgG peaked earlier than Ab to live SARS-CoV-2. Anti-spike IgG and Ab to live SARS-CoV-2 may be good immune markers for VE assessment.

High throughput circRNA sequencing analysis reveals novel insights into the mechanism of nitidine chloride against hepatocellular carcinoma.

Nitidine chloride (NC) has been demonstrated to have an anticancer effect in hepatocellular carcinoma (HCC). However, the mechanism of action of NC against HCC remains largely unclear. In this study, three pairs of NC-treated and NC-untreated HCC xenograft tumour tissues were collected for circRNA sequencing analysis. In total, 297 circRNAs were differently expressed between the two groups, with 188 upregulated and 109 downregulated, among which hsa_circ_0088364 and hsa_circ_0090049 were validated by real-time quantitative polymerase chain reaction. The in vitro experiments showed that the two circRNAs inhibited the malignant biological behaviour of HCC, suggesting that they may play important roles in the development of HCC. To elucidate whether the two circRNAs function as "miRNA sponges" in HCC, we identified circRNA-miRNA and miRNA-mRNA interactions by using the CircInteractome and miRwalk, respectively. Subsequently, 857 miRNA-associated differently expressed genes in HCC were selected for weighted gene co-expression network analysis. Module Eigengene turquoise with 423 genes was found to be significantly related to the survival time, pathology grade and TNM stage of HCC patients. Gene functional enrichment analysis showed that the 423 genes mainly functioned in DNA replication- and cell cycle-related biological processes and signalling cascades. Eighteen hubgenes (SMARCD1, CBX1, HCFC1, RBM12B, RCC2, NUP205, ECT2, PRIM2, RBM28, COPS7B, PRRC2A, GPR107, ANKRD52, TUBA1B, ATXN7L3, FUS, MCM8 and RACGAP1) associated with clinical outcomes of HCC patients were then identified. These findings showed that the crosstalk between hsa_circ_0088364 and hsa_circ_0090049 and their competing mRNAs may play important roles in HCC, providing interesting clues into the potential of circRNAs as therapeutic targets of NC in HCC.

The effect of L-carnosine on the circadian resetting of clock genes in the heart of rats.

It is reported that the circadian timing system may be included in the mechanism by which L-carnosine (Car) affects multiple physiological alterations including blood glucose, cardiovascular functions etc. However, it is not clear whether Car would affect the circadian rhythm of clock genes in the heart and what is the possible mechanism underlying. To clarify these issues, we compared the effects of Car on the expression of circadian genes in the heart of normal and vagotomized rats under control and jet lag conditions. The normal and vagotomized (va) male Wistar rats were divided into three groups respectively. The control and va-Control groups (fed with regular chow) were sampled before the reversal of LD cycle and feeding schedule (day 0). The normal and va-Normal resetting groups (fed with regular chow) as well as the Car and va-Car resetting groups (fed with Car-containing diet) were sampled on day 3 and day 5 after the experimental jet lag. Car-feeding obviously enhanced the resetting rates of clock genes (Bmal1, Dec1, Cry1) in the heart of normal rats after the experimental jet lag. The unilateral surgical vagotomy didn't alter the diurnal expression patterns and resetting rates of the examined clock genes in normal diet feeding rats. In contrast, it abolished the Car-induced rapid resetting of the clock genes in the heart. Therefore, Car feeding plays a positive role in the circadian resynchronization of the heart clock, which is underlied by the autonomic nervous system.

Effects of light on the circadian rhythm of diabetic rats under restricted feeding.

The aim of this study was to investigate whether the entrainment of light cue is affected or not in diabetic animals. We found that the individual light/dark (LD) reversal showed a tissue- and gene-specific effect on the circadian phases of peripheral clock genes, which was generally similar between the control and diabetic rats. In the liver and heart, the peak phases of examined clock genes (Bmal1, Rev-erbα, Per1, and Per2) were slightly shifted by 0∼4 h in the liver and heart of control and diabetic rats. However, we found that the peak phases of these clock genes were greatly shifted by 8∼12 h after the LD reversal for 7 days in the pineal gland of both control and diabetic rats. However, the activity rhythm was greatly different between two groups. After the individual LD reversal, the activity rhythm was completely shifted in the control rats but retained in the diabetic rats. These observations suggested that the behavioral rhythm of diabetic rats may be uncoupled from the master clock after the individual LD reversal. Moreover, we also found that the serum glucose levels of diabetic rats kept equally high throughout the whole day without any shift of peak phase after the individual reversal of LD cycle. While the serum glucose levels of control rats were tightly controlled during the normal and LD reversal conditions. Thus, the impaired insulin secretion induced uncontrollable serum glucose level may result in uncoupled activity rhythm in the diabetic rats after the individual LD reversal.