Inhibition of Indoleamine 2,3-Dioxygenase Exerts Antidepressant-like Effects through Distinct Pathways in Prelimbic and Infralimbic Cortices in Rats under Intracerebroventricular Injection with Streptozotocin.

The application of intracerebroventricular injection of streptozotocin (ICV-STZ) is considered a useful animal model to mimic the onset and progression of sporadic Alzheimer's disease (sAD). In rodents, on day 7 of the experiment, the animals exhibit depression-like behaviors. Indoleamine 2,3-dioxygenase (IDO), a rate-limiting enzyme catalyzing the conversion of tryptophan (Trp) to kynurenine (Kyn), is closely related to depression and AD. The present study aimed to investigate the pathophysiological mechanisms of preliminary depression-like behaviors in ICV-STZ rats in two distinct cerebral regions of the medial prefrontal cortex, the prelimbic cortex (PrL) and infralimbic cortex (IL), both presumably involved in AD progression in this model, with a focus on IDO-related Kyn pathways. The results showed an increased Kyn/Trp ratio in both the PrL and IL of ICV-STZ rats, but, intriguingly, abnormalities in downstream metabolic pathways were different, being associated with distinct biological effects. In the PrL, the neuroprotective branch of the Kyn pathway was attenuated, as evidenced by a decrease in the kynurenic acid (KA) level and Kyn aminotransferase II (KAT II) expression, accompanied by astrocyte alterations, such as the decrease in glial fibrillary acidic protein (GFAP)-positive cells and increase in morphological damage. In the IL, the neurotoxicogenic branch of the Kyn pathway was enhanced, as evidenced by an increase in the 3-hydroxy-kynurenine (3-HK) level and kynurenine 3-monooxygenase (KMO) expression paralleled by the overactivation of microglia, reflected by an increase in ionized calcium-binding adaptor molecule 1 (Iba1)-positive cells and cytokines with morphological alterations. Synaptic plasticity was attenuated in both subregions. Additionally, microinjection of the selective IDO inhibitor 1-Methyl-DL-tryptophan (1-MT) in the PrL or IL alleviated depression-like behaviors by reversing these different abnormalities in the PrL and IL. These results suggest that the antidepressant-like effects linked to Trp metabolism changes induced by 1-MT in the PrL and IL occur through different pathways, specifically by enhancing the neuroprotective branch in the PrL and attenuating the neurotoxicogenic branch in the IL, involving distinct glial cells.

A fusion framework of deep learning and machine learning for predicting sgRNA cleavage efficiency.

CRISPR/Cas9 system is a powerful tool for genome editing. Numerous studies have shown that sgRNAs can strongly affect the efficiency of editing. However, it is still not clear what rules should be followed for designing sgRNA with high cleavage efficiency. At present, several machine learning or deep learning methods have been developed to predict the cleavage efficiency of sgRNAs, however, the prediction accuracy of these tools is still not satisfactory. Here we propose a fusion framework of deep learning and machine learning, which first deals with the primary sequence and secondary structure features of the sgRNAs using both convolutional neural network (CNN) and recurrent neural network (RNN), and then uses the features extracted by the deep neural network to train a conventional machine learning model with LGBM. As a result, the new approach overwhelmed previous methods. The Spearman's correlation coefficient between predicted and measured sgRNA cleavage efficiency of our model (0.917) is improved by over 5% compared with the most advanced method (0.865), and the mean square error reduces from 7.89 × 10-3 to 4.75 × 10-3. Finally, we developed an online tool, CRISep (http://www.cuilab.cn/CRISep), to evaluate the availability of sgRNAs based on our models.

IntiCom-DB: A Manually Curated Database of Inter-Tissue Communication Molecules and Their Communication Routes.

Inter-tissue communication (ITC) is critical for maintaining the physiological functions of multiple tissues and is closely related to the onset and development of various complex diseases. Nevertheless, there is no well-organized data resource for known ITC molecules with explicit ITC routes from source tissues to target tissues. To address this issue, in this work, we manually reviewed nearly 190,000 publications and identified 1408 experimentally supported ITC entries in which the ITC molecules, their communication routes, and their functional annotations were included. To facilitate our work, these curated ITC entries were incorporated into a user-friendly database named IntiCom-DB. This database also enables visualization of the expression abundances of ITC proteins and their interaction partners. Finally, bioinformatics analyses on these data revealed common biological characteristics of the ITC molecules. For example, tissue specificity scores of ITC molecules at the protein level are often higher than those at the mRNA level in the target tissues. Moreover, the ITC molecules and their interaction partners are more abundant in both the source tissues and the target tissues. IntiCom-DB is freely available as an online database. As the first comprehensive database of ITC molecules with explicit ITC routes to the best of our knowledge, we hope that IntiCom-DB will benefit future ITC-related studies.

Integrative Transcriptomic Analysis Identify Potential m6A Pathway-Related Drugs That Inhibit Cancer Cell Proliferation.

Recent studies have found that m6A modification of mRNA may play important roles in the progression of various types of cancers. However, current knowledge about drugs that can interfere with m6A methylation and inhibit cancer cell proliferation is still far from comprehensive. To this end, we performed integrative analysis on transcriptome data with perturbation of m6A writers or erasers and identified consensus m6A-related differentially expressed genes (DEGs). Comparative analysis of these m6A-related DEGs with Connectivity Map signatures highlight potential m6A-targeted drugs. Among them, we experimentally verified the inhibitory effects of AZ628 on the proliferation of human breast cancer cell lines and R428 on the proliferation of human melanoma cell lines. Both drugs can significantly reduce the cellular level of m6A modification. These results suggest an m6A-related new target pathway by AZ628 and R428 and provide new candidate m6A-related drugs that inhibit cancer cell proliferation.