CITMIC: Comprehensive Estimation of Cell Infiltration in Tumor Microenvironment based on Individualized Intercellular Crosstalk.

The tumor microenvironment (TME) cells interact with each other and play a pivotal role in tumor progression and treatment response. A comprehensive characterization of cell and intercellular crosstalk in the TME is essential for understanding tumor biology and developing effective therapies. However, current cell infiltration analysis methods only partially describe the TME's cellular landscape and overlook cell-cell crosstalk.

IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA-miRNA interaction network constructed through gene expression data.

Micro ribonucleic acids (miRNAs) play a pivotal role in governing the human transcriptome in various biological phenomena. Hence, the accumulation of miRNA expression dysregulation frequently assumes a noteworthy role in the initiation and progression of complex diseases. However, accurate identification of dysregulated miRNAs still faces challenges at the current stage.

27-Hydroxycholesterol/liver X receptor/apolipoprotein E mediates zearalenone-induced intestinal immunosuppression: A key target potentially linking zearalenone and cancer.

Zearalenone (ZEN) is a mycotoxin that extensively contaminates food and feed, posing a significant threat to public health. However, the mechanisms behind ZEN-induced intestinal immunotoxicity remain unclear. In this study, Sprague-Dawley (SD) rats were exposed to ZEN at a dosage of 5 mg/kg/day b.

DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing.

Background: Traditional approaches to drug development are costly and involve high risks. The drug repurposing approach can be a valuable alternative to traditional approaches and has therefore received considerable attention in recent years.

Findings: Herein, we develop a previously undescribed computational approach, called DrugSim2DR, which uses a network diffusion algorithm to identify candidate anticancer drugs based on a drug functional similarity network.

PathwayTMB: A pathway-based tumor mutational burden analysis method for predicting the clinical outcome of cancer immunotherapy.

Immunotherapy has become one of the most promising therapy methods for cancer, but only a small number of patients are responsive to it, indicating that more effective biomarkers are urgently needed. This study developed a pathway analysis method, named PathwayTMB, to identify genomic mutation pathways that serve as potential biomarkers for predicting the clinical outcome of immunotherapy. PathwayTMB first calculates the patient-specific pathway-based tumor mutational burden (PTMB) to reflect the cumulative extent of mutations for each pathway.

Zearalenone Exposure Disrupts STAT-ISG15 in Rat Colon: A Potential Linkage between Zearalenone and Inflammatory Bowel Disease.

Zearalenone (ZEN), a prevalent mycotoxin contaminating food and known for its intestinal toxicity, has been suggested as a potential risk factor for inflammatory bowel disease (IBD), although the exact relationship between ZEN exposure and IBD remains unclear. In this study, we established a rat model of colon toxicity induced by ZEN exposure to investigate the key targets of ZEN-induced colon toxicity and explore the underlying connection between ZEN exposure and IBD. Histological staining of the rat colon revealed significant pathological changes resulting from ZEN exposure ( < 0.

DTSEA: A network-based drug target set enrichment analysis method for drug repurposing against COVID-19.

The Coronavirus Disease 2019 (COVID-19) pandemic is still wreaking havoc worldwide. Therefore, the urgent need for efficient treatments pushes researchers and clinicians into screening effective drugs. Drug repurposing may be a promising and time-saving strategy to identify potential drugs against this disease.

A pathway-based mutation signature to predict the clinical outcomes and response to CTLA-4 inhibitors in melanoma.

Immune checkpoint inhibitor (ICI) therapy has become a powerful clinical strategy for treating melanoma. The relationship between somatic mutations and the clinical benefits of immunotherapy has been widely recognized. However, the gene-based predictive biomarkers are less stable due to the heterogeneity of cancer at the individual gene level.

[Pathogenesis of glucocorticoid-induced osteoporosis based on label-free mass proteomics].

Objective: To explore pathogenesis of glucocortocoid-induced osteoporosis(GIOP) based on label-free mass proteomics.

Methods: Twevle female Sprague-Dawley(SD) rats were randomly divided into two groups, named as sham group and GIOP group. After one-week adaptive feeding, the rats of GIOP group were administered with dexamethasone via intramuscular injection according to 2.

iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell-cell crosstalk network.

Interactions between Tumor microenvironment (TME) cells shape the unique growth environment, sustaining tumor growth and causing the immune escape of tumor cells. Nonetheless, no studies have reported a systematic analysis of cellular interactions in the identification of cancer-related TME cells. Here, we proposed a novel network-based computational method, named as iATMEcell, to identify the abnormal TME cells associated with the biological outcome of interest based on a cell-cell crosstalk network.

Analysis of Tumor Microenvironment Heterogeneity among Breast Cancer Subtypes to Identify Subtype-Specific Signatures.

Breast cancer is one of the most frequent malignancies in women worldwide. According to 50-gene signature, Prediction Analysis of Microarray 50 (PAM50), breast cancer can be categorized into five molecular subtypes, and these subtypes are highly heterogeneous in different molecular characteristics. However, the landscape of their tumor microenvironment (TME) heterogeneity has not been fully researched.

Identification of comutation in signaling pathways to predict the clinical outcomes of immunotherapy.

Background: Immune checkpoint blockades (ICBs) have emerged as a promising treatment for cancer. Recently, tumour mutational burden (TMB) and neoantigen load (NAL) have been proposed to be potential biomarkers to predict the efficacy of ICB; however, they were limited by difficulties in defining the cut-off values and inconsistent detection platforms. Therefore, it is critical to identify more effective predictive biomarkers for screening patients who will potentially benefit from immunotherapy.

ZeXie decoction alleviates non-alcoholic fatty liver disease in rats: the study of genes, lipids, and gut microbiotas.

Recently, with increasing awareness of health issues, non-alcoholic fatty liver disease (NAFLD) has become an epidemic attracting global attention. As a serious chronic disease, NAFLD is clinically managed with pharmacological interventions that are usually associated with poor long-term efficacy and adverse effects. In this scenario, traditional Chinese medicine (TCM) characterized by "multiple ingredients-multiple targets-multiple pathways" shows promise as a potential option to treat NAFLD.

DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network.

Summary: Drug repurposing is an approach used to discover new indications for existing drugs. Recently, several computational approaches have been developed for drug repurposing in cancer. Nevertheless, no approaches have reported a systematic analysis of pathway crosstalk.

A novel pathway mutation perturbation score predicts the clinical outcomes of immunotherapy.

The link between tumor genetic variations and immunotherapy benefits has been widely recognized. Recent studies suggested that the key biological pathways activated by accumulated genetic mutations may act as an effective biomarker for predicting the efficacy of immune checkpoint inhibitor (ICI) therapy. Here, we developed a novel individual Pathway Mutation Perturbation (iPMP) method that measures the pathway mutation perturbation level by combining evidence of the cumulative effect of mutated genes with the position of mutated genes in the pathways.

Critical Quality Control Methods for a Novel Anticoagulant Candidate LFG-Na by HPSEC-MALLS-RID and Bioactivity Assays.

A low molecular weight fucosylated glycosaminoglycan sodium (LFG-Na) is a novel anticoagulant candidate from the sea cucumber Holothuria fuscopunctata that selectively inhibits intrinsic tenase (iXase). The molecular weight, molecular weight distribution and bioactivities are the critical quality attributes of LFG-Na. The determination of these quality attributes of such an oligosaccharides mixture drug is challenging but critical for the quality control process to ensure its safety and efficacy in clinical use.

Zearalenone-14-Glucoside Is Hydrolyzed to Zearalenone by β-Glucosidase in Extracellular Matrix to Exert Intracellular Toxicity in KGN Cells.

As one of the most important conjugated mycotoxins, zearalenone-14-glucoside (Z14G) has received widespread attention from researchers. Although the metabolism of Z14G in animals has been extensively studied, the intracellular toxicity and metabolic process of Z14G are not fully elucidated. In this study, the cytotoxicity of Z14G to human ovarian granulosa cells (KGN) and the metabolism of Z14G in KGN cells were determined.

Total Flavonoids of Drynariae Rhizoma Improve Glucocorticoid-Induced Osteoporosis of Rats: UHPLC-MS-Based Qualitative Analysis, Network Pharmacology Strategy and Pharmacodynamic Validation.

Background: Glucocorticoid-induced osteoporosis (GIOP) is a common form of secondary osteoporosis caused by the protracted or a large dosage of glucocorticoids (GCs). Total flavonoids of Drynariae rhizoma (TFDR) have been widely used in treating postmenopausal osteoporosis (POP). However, their therapeutic effects and potential mechanism against GIOP have not been fully elucidated.

Deciphering the chemical constituents of Shengjiang Xiexin decoction by ultrahigh-performance liquid chromatography-quadrupole/orbitrap high-resolution mass spectrometry and the impact of 20 characteristic components on multidrug resistance-associated protein 2 in the vesicular transport assay.

Shengjiang Xiexin decoction, a traditional Chinese medical formula, has been utilized to alleviate the delayed-onset diarrhea induced by irino tecan. However, the chemical constituents of this formula and the activities of its constituents remain unclear. In this study, ultrahigh-performance liquid chromatography-quadrupole/orbitrap high-resolution mass spectrometry was employed to comprehensively analyze the chemical constituents of Shengjiang Xiexin decoction.

Integration strategy of network pharmacology in Traditional Chinese Medicine: a narrative review.

Traditional Chinese Medicine (TCM) has been extensively used as a mainstay for treating various pathologies. Combing the pharmacology and systems biology approaches, the network pharmacology (NP) approach was developed to predict the probable mechanism underlying the therapeutic effect of TCM. However, approaches solely based on NP cannot effectively elucidate the curative mechanism in a holistic and reliable manner due to limitations in NP-based methods and complexity of TCM components.

Qualitative Analysis of Drug-Containing Plasma and its Application to Quantitative Analysis and Pharmacokinetic Study of Zexie Decoction Using UPLC-MS/MS.

ZeXie Decoction (ZXD) is one of the traditional Chinese medicine formulas (TCMFs) comprising (Sam.) Juzep. (ZX) and Koidz.

Pan-cancer analysis reveals sex-specific signatures in the tumor microenvironment.

The processes of cancer initiation, progression, and response to therapy are affected by the sex of cancer patients. Immunotherapy responses largely depend on the tumor microenvironment (TME), but how sex may shape some TME features, remains unknown. Here, we analyzed immune infiltration signatures across 19 cancer types from 1771 male and 1137 female patients in The Cancer Genome Atlas to evaluate how sex may affect the tumor mutational burden (TMB), immune scores, stromal scores, tumor purity, immune cells, immune checkpoint genes, and functional pathways in the TME.

Immune Response Is Key to Genetic Mechanisms of SARS-CoV-2 Infection With Psychiatric Disorders Based on Differential Gene Expression Pattern Analysis.

Existing evidence demonstrates that coronavirus disease 2019 (COVID-19) leads to psychiatric illness, despite its main clinical manifestations affecting the respiratory system. People with mental disorders are more susceptible to COVID-19 than individuals without coexisting mental health disorders, with significantly higher rates of severe illness and mortality in this population. The incidence of new psychiatric diagnoses after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is also remarkably high.

Development and Validation of a Three-Gene Prognostic Signature Based on Tumor Microenvironment for Gastric Cancer.

Gastric cancer (GC), which has high morbidity and low survival rate, is one of the most common malignant tumors in the world. The increasing evidences show that the tumor microenvironment (TME) is related to the occurrence and progression of tumors and the prognosis of patients. In this study, we aimed to develop a TME-based prognostic signature for GC.

A Strategy for Screening the Lipid-Lowering Components in Decoction Based on Spectrum-Effect Analysis.

decoction (ARD), comprised of (Sam.) Sam and Koidz. at a ratio of 5 : 2, is a classic traditional Chinese medicine (TCM) formula with successful clinical hypolipidemic effect.