An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15

Death associated protein kinase 1 predicts the prognosis and the immunotherapy response of various cancers

BACKGROUND

Death Associated Protein Kinase 1 (DAPK1) is a calcium/calmodulin-dependent serine/threonine kinase, which has been reported to be a tumor suppressor with unbalanced expression in various tissues. However, its function in tumor immunotherapy is still unclear.

METHODS

The online GEPIA2 database was used to support TCGA results. We explored the DAPK1 pan-cancer genomic alteration analysis using the cBioPortal web tool. The Human Protein Atlas (HPA) was employed to mine DAPK1 protein information. We verified the expression of DAPK1 in lung adenocarcinoma samples using RT-qPCR. Subsequently, the relationship between the expression of DAPK1 and the clinical stage was analyzed. We used TIMER2.0 as the primary platform for studying DAPK1-related immune cell infiltration. Associations between DAPK1 and immunotherapy biomarkers were analyzed using Spearman correlation analysis. TMB and MSI expression was also examined. Finally, we used Kaplan-Meier Plots to evaluate the relationship between DAPK1 expression and the efficacy of immunotherapy.

RESULTS

DAPK1 is aberrantly expressed in most cancer types and has prognostic power in various cancers. Gene mutation was the most common DAPK1 alteration across pan-cancers. The DAPK1 protein was mainly localized to tumor cell centrosomes. DAPK1 was also significantly associated with immune-activated hallmarks, immune cell infiltration, and the expression of immunomodulators. Notably, DAPK1 can also significantly predict responses to anti-PD1 and anti-CTLA-4 therapy in cancer patients.

CONCLUSIONS

Our findings suggest that DAPK1 may not only be an effective prognostic factor in cancer patients but may also function as a promising predictive immunotherapy biomarker for cancer patients treated with immune checkpoint inhibitors.

Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods

We used a structure-based drug discovery approach to identify novel inhibitors of human dihydroorotate dehydrogenase (DHODH), which is a therapeutic target for treating cancer and autoimmune and inflammatory diseases. In the case of acute myeloid leukemia, no previously discovered DHODH inhibitors have yet succeeded in this clinical application. Thus, there remains a strong need for new inhibitors that could be used as alternatives to the current standard-of-care. Our goal was to identify novel inhibitors of DHODH. We implemented prefiltering steps to omit PAINS and Lipinski violators at the earliest stages of this project. This enriched compounds in the data set that had a higher potential of favorable oral druggability. Guided by Glide SP docking scores, we found 20 structurally unique compounds from the ChemBridge EXPRESS-pick library that inhibited DHODH with IC50, DHODH values between 91 nM and 2.7 μM. Ten of these compounds reduced MOLM-13 cell viability with IC50, MOLM-13 values between 2.3 and 50.6 μM. Compound 16 (IC50, DHODH = 91 nM) inhibited DHODH more potently than the known DHODH inhibitor, teriflunomide (IC50, DHODH = 130 nM), during biochemical characterizations and presented a promising scaffold for future hit-to-lead optimization efforts. Compound 17 (IC50, MOLM-13 = 2.3 μM) was most successful at reducing survival in MOLM-13 cell lines compared with our other hits. The discovered compounds represent excellent starting points for the development and optimization of novel DHODH inhibitors.

Emerging roles of a chemoattractant receptor GPR15 and ligands in pathophysiology

Chemokine receptors play a central role in the maintenance of immune homeostasis and development of inflammation by directing leukocyte migration to tissues. GPR15 is a G protein-coupled receptor (GPCR) that was initially known as a co-receptor for human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV), with structural similarity to other members of the chemoattractant receptor family. Since the discovery of its novel function as a colon-homing receptor of T cells in mice a decade ago, GPR15 has been rapidly gaining attention for its involvement in a variety of inflammatory and immune disorders. The recent identification of its natural ligand C10orf99, a chemokine-like polypeptide strongly expressed in gastrointestinal tissues, has established that GPR15-C10orf99 is a novel signaling axis that controls intestinal homeostasis and inflammation through the migration of immune cells. In addition, it has been demonstrated that C10orf99-independent functions of GPR15 and GPR15-independent activities of C10orf99 also play significant roles in the pathophysiology. Therefore, GPR15 and its ligands are potential therapeutic targets. To provide a basis for the future development of GPR15- or GPR15 ligand-targeted therapeutics, we have summarized the latest advances in the role of GPR15 and its ligands in human diseases as well as the molecular mechanisms that regulate GPR15 expression and functions.

Multi-omics integration analysis of GPCRs in pan-cancer to uncover inter-omics relationships and potential driver genes

G protein-coupled receptors (GPCRs) are the largest drug target family. Unfortunately, applications of GPCRs in cancer therapy are scarce due to very limited knowledge regarding their correlations with cancers. Multi-omics data enables systematic investigations of GPCRs, yet their effective integration remains a challenge due to the complexity of the data. Here, we adopt two types of integration strategies, multi-staged and meta-dimensional approaches, to fully characterize somatic mutations, somatic copy number alterations (SCNAs), DNA methylations, and mRNA expressions of GPCRs in 33 cancers. Results from the multi-staged integration reveal that GPCR mutations cannot well predict expression dysregulation. The correlations between expressions and SCNAs are primarily positive, while correlations of the methylations with expressions and SCNAs are bimodal with negative correlations predominating. Based on these correlations, 32 and 144 potential cancer-related GPCRs driven by aberrant SCNA and methylation are identified, respectively. In addition, the meta-dimensional integration analysis is carried out by using deep learning models, which predict more than one hundred GPCRs as potential oncogenes. When comparing results between the two integration strategies, 165 cancer-related GPCRs are common in both, suggesting that they should be prioritized in future studies. However, 172 GPCRs emerge in only one, indicating that the two integration strategies should be considered concurrently to complement the information missed by the other such that obtain a more comprehensive understanding. Finally, correlation analysis further reveals that GPCRs, in particular for the class A and adhesion receptors, are generally immune-related. In a whole, the work is for the first time to reveal the associations between different omics layers and highlight the necessity of combing the two strategies in identifying cancer-related GPCRs.

Therapeutic and prognostic potential of GPCRs in prostate cancer from multi-omics landscape

Prostate cancer (PRAD) is a common and fatal malignancy. It is difficult to manage clinically due to drug resistance and poor prognosis, thus creating an urgent need for novel therapeutic targets and prognostic biomarkers. Although G protein-coupled receptors (GPCRs) have been most attractive for drug development, there have been lack of an exhaustive assessment on GPCRs in PRAD like their molecular features, prognostic and therapeutic values. To close this gap, we herein systematically investigate multi-omics profiling for GPCRs in the primary PRAD by analyzing somatic mutations, somatic copy-number alterations (SCNAs), DNA methylation and mRNA expression. GPCRs exhibit low expression levels and mutation frequencies while SCNAs are more prevalent. 46 and 255 disease-related GPCRs are identified by the mRNA expression and DNA methylation analysis, respectively, complementing information lack in the genome analysis. In addition, the genomic alterations do not exhibit an observable correlation with the GPCR expression, reflecting the complex regulatory processes from DNA to RNA. Conversely, a tight association is observed between the DNA methylation and mRNA expression. The virtual screening and molecular dynamics simulation further identify four potential drugs in repositioning to PRAD. The combination of 3 clinical characteristics and 26 GPCR molecular features revealed by the transcriptome and genome exhibit good performance in predicting progression-free survival in patients with the primary PRAD, providing candidates as new biomarkers. These observations from the multi-omics analysis on GPCRs provide new insights into the underlying mechanism of primary PRAD and potential of GPCRs in developing therapeutic strategies on PRAD.

Detecting the critical states during disease development based on temporal network flow entropy

Complex diseases progression can be generally divided into three states, which are normal state, predisease/critical state and disease state. The sudden deterioration of diseases can be viewed as a bifurcation or a critical transition. Therefore, hunting for the tipping point or critical state is of great importance to prevent the disease deterioration. However, it is still a challenging task to detect the critical states of complex diseases with high-dimensional data, especially based on an individual. In this study, we develop a new method based on network fluctuation of molecules, temporal network flow entropy (TNFE) or temporal differential network flow entropy, to detect the critical states of complex diseases on the basis of each individual. By applying this method to a simulated dataset and six real diseases, including respiratory viral infections and tumors with four time-course and two stage-course high-dimensional omics datasets, the critical states before deterioration were detected and their dynamic network biomarkers were identified successfully. The results on the simulated dataset indicate that the TNFE method is robust under different noise strengths, and is also superior to the existing methods on detecting the critical states. Moreover, the analysis on the real datasets demonstrated the effectiveness of TNFE for providing early-warning signals on various diseases. In addition, we also predicted disease deterioration risk and identified drug targets for cancers based on stage-wise data.

The Role of GPR15 Function in Blood and Vasculature

Since the first prominent description of the orphan G protein-coupled receptor 15 (GPR15) on lymphocytes as a co-receptor for the human immunodeficiency virus (HIV) type 1 and 2 and the first report about the GPR15-triggered cytoprotective effect on vascular endothelial cells by recombinant human thrombomodulin, several decades passed before the GPR15 has been recently deorphanized. Because of new findings on GPR15, this review will summarize the consequences of GPR15 signaling considering the variety of GPR15-expressing cell types and of GPR15 ligands, with a focus on blood and vasculature.

Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer

Recent publications have presented research showing that WD repeat domain 4 (WDR4) plays a significant role in various kinds of malignant tumours. However, the expression profile of WDR4 is still unspecified, as is its significance in the analysis of human pan-cancer. We conducted an in-depth analysis of three aspects of WDR4 expression patterns from 33 types of cancer and determined the value of WDR4 for prognostic prediction and carcinoma drug resistance prediction. WDR4 was expressed in different cancer cell lines at inconsistent levels. Aberrant expression of WDR4 has been observed in various malignant cancers and is significantly implicated in overall survival outcomes. The expression level of WDR4 is also strongly associated with tumour immunity, such as immune scores and tumour-infiltrating immune cells. The level of WDR4 is related to microsatellite instability and tumour mutation burden in several types of malignancy, and validation studies implied that WDR4-associated terms and pathways are involved in malignancy. We explored the expression level of WDR4 across 33 types of cancer and showed that WDR4 plays a significant role during cancer development. More crucially, WDR4 is associated with immune infiltration, which suggests that WDR4 could be an immunotherapy target in cancers. In summary, our research showed that WDR4 plays a vital role in tumorigenesis and has the potential for to be targeted with treatments.

Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients

Background

Although accumulating evidence suggested that a molecular signature panel may be more effective for the prognosis prediction than routine clinical characteristics, current studies mainly focused on colorectal or colon cancers. No reports specifically focused on the signature panel for rectal cancers (RC). Our present study was aimed at developing a novel prognostic signature panel for RC.

Methods

Sequencing (or microarray) data and clinicopathological details of patients with RC were retrieved from The Cancer Genome Atlas (TCGA-READ) or the Gene Expression Omnibus (GSE123390, GSE56699) database. A weighted gene coexpression network was used to identify RC-related modules. The least absolute shrinkage and selection operator analysis was performed to screen the prognostic signature panel. The prognostic performance of the risk score was evaluated by survival curve analyses. Functions of prognostic genes were predicted based on the interaction proteins and the correlation with tumor-infiltrating immune cells. The Human Protein Atlas (HPA) tool was utilized to validate the protein expression levels.

Results

A total of 247 differentially expressed genes (DEGs) were commonly identified using TCGA and GSE123390 datasets. Brown and yellow modules (including 77 DEGs) were identified to be preserved for RC. Five DEGs (ASB2, GPR15, PRPH, RNASE7, and TCL1A) in these two modules constituted the optimal prognosis signature panel. Kaplan-Meier curve analysis showed that patients in the high-risk group had a poorer prognosis than those in the low-risk group. Receiver operating characteristic (ROC) curve analysis demonstrated that this risk score had high predictive accuracy for unfavorable prognosis, with the area under the ROC curve of 0.915 and 0.827 for TCGA and GSE56699 datasets, respectively. This five-mRNA classifier was an independent prognostic factor. Its predictive accuracy was also higher than all clinical factor models. A prognostic nomogram was developed by integrating the risk score and clinical factors, which showed the highest prognostic power. ASB2, PRPH, and GPR15/TCL1A were predicted to function by interacting with CASQ2/PDK4/EPHA67, PTN, and CXCL12, respectively. TCL1A and GPR15 influenced the infiltration levels of B cells and dendritic cells, while the expression of PRPH was positively associated with the abundance of macrophages. HPA analysis supported the downregulation of PRPH, RNASE7, CASQ2, EPHA6, and PDK4 in RC compared with normal controls.

Conclusion

Our immune-related signature panel may be a promising prognostic indicator for RC.

Targeting of FK506 binding protein 5 by miR-203 affects the progression of breast cancer via regulating the fatty acid degradation pathway and potential drug-repurposing

Increasing number of studies have suggested that microRNA (miR)-203 is a potential prognostic marker for breast cancer. However, the specific molecular mechanism underlying the effects of miR-203 remains unknown. The present study aimed to explore the molecular target and underlying mechanisms of action of miR-203 in breast cancer via bioinformatics analysis and cellular assays, such as wound healing assay and western blotting. In the present study, 17 candidate target genes of miR-203 were identified in the downregulated differentially expressed genes from Affymetrix microarray and TargetScan 7.2 database. Subsequently, FK506 binding protein 5 (FKBP5) was considered as the miR-203 target by 3 different hub gene analysis methods (EcCentricity, Betweenness and Stress). FKBP5 protein expression was significantly downregulated in SUM159 cells transfected with miR-203 mimics compared with SUM159 cells transfected with miR-203 negative control (NC) in western blot analysis. High expression of FKBP5 was associated with poor prognosis in breast cancer based on the results obtained from the Kaplan-Meier Plotter database. In addition, the wound healing assay indicated that the inhibition of migration due to miR-203 overexpression in SUM159 cells was reversed by FKBP5 overexpression. These results suggested that miR-203 may directly target FKBP5. In addition, Gene Set Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that miR-203 might play a role in breast cancer via the 'fatty acid degradation' KEGG pathway. Notably, the levels of fatty acids were significantly reduced in SUM159 cells transfected with miR-203 mimics compared with SUM159 cells transfected with miR-203 NC when assessed by the fatty acid content assay. Finally, virtual screening analysis revealed that ZINC000003944422 may be a potential inhibitor of FKBP5. In summary, the present study demonstrated that miR-203 may directly target FKBP5 in breast cancer via fatty acid degradation and potential drugs, hence providing a novel treatment approach for breast cancer.

Post-transcriptional suppression of G protein-coupled receptor 15 (GPR15) by microRNA-1225 inhibits proliferation, migration, and invasion of human colorectal cancer cells

The G protein-coupled receptors (GPRs) have been shown to regulate several cancer related processes. The aberrant expression of GPRs has been linked to the development of several cancers. The present study was designed to examine the expression and decipher the role of GPR15 in the development of human colorectal cancer. The results revealed GPR15 to be significantly (P < 0.05) upregulated in colorectal cancer cells. The silencing of GPR15 inhibited the growth of the colorectal cancer cells via induction of apoptosis. Induction of apoptosis in colorectal cancer cells was associated increase in Bax and decrease in Bcl-2 expression. The silencing of GPR-15 also caused a significant (P < 0.05) decline in the migration and invasion of the colorectal cancer cells. Bioinformatic analysis and luciferase assay revealed that the expression of GPR15 to be post-transcriptionally regulated by microRNA-1225 (miR-1225). The expression of miR-1225 was found to significantly (P < 0.05) downregulated in colorectal cancer cells and its overexpression caused suppression of GPR15 and inhibited the proliferation of the colorectal cancer cells. Nonetheless, overexpression of GPR15 could avoid the growth inhibitory effects of miR-1225. The results suggest that the GPR15/miR-1225 axis play an important role in the development of colon rectal cancer and exhibit therapeutic implications for its treatment.

Inflammatory biomarker relationships with helper T cell GPR15 expression and cannabis and tobacco smoking

OBJECTIVE

Smoking is associated with numerous inflammatory and autoimmune conditions. The goal of this study was to examine whether increased expression of G-protein-coupled receptor 15 (GPR15) on helper T cells in smokers could predispose to these conditions through its relationship with inflammatory biomarkers.

METHODS

We used flow cytometric measurement of GPR15⁺CD3⁺CD4⁺ helper T cells and serum assays for C-reactive protein (CRP) and 17 cytokines drawn from peripheral blood samples from a cohort of n = 62 primarily African American young adults (aged 27-35 years). These variables were examined cross-sectionally in conjunction with serum biomarkers of tobacco (cotinine) and cannabis (tetrahydrocannabinol) use and lifestyle factors potentially impacting immune function in correlational analyses and linear regression models.

RESULTS

Tobacco and cannabis smoking were strongly associated with increased GPR15 expression on helper T cells (p < 0.001), which was in turn was strongly associated with the ratio of pro-inflammatory to anti-inflammatory cytokines (p < 0.001). Mediation analyses indicated increased GPR15 expression accounted for roughly half of the relationship between smoking variables and pro-inflammatory to anti-inflammatory cytokine balance. CRP was not associated with cannabis or tobacco use or GPR15+ expression, but was associated with body mass index (p < 0.001). These relationships persisted after controlling for lifestyle and medical factors impacting immune function.

CONCLUSIONS

Increased expression of GPR15 by helper T cells in smokers may mediate some of the relationship between smoking and a pro-inflammatory cytokine milieu. Better understanding of this relationship may help uncover how smoking increases the risk of inflammatory diseases.

Identification of Small-Molecule Regulators of Testicular Receptor 4 via a Drug Repurposing Screening

The testicular receptor 4 (TR4) is a nuclear receptor implicated in multiple pathological processes, including cancer development, chemotherapy, and radiotherapy resistance. However, no effective TR4 small-molecule regulator is available to date. Here, we assessed a physical-interaction-based surface plasmon resonance imaging assay for discovery of TR4 regulators. We screened 1018 FDA-approved drugs and obtained 126 drugs with K _D values below 10^-6 M. The dual-luciferase-based biological assay verified four activatory compounds and two inhibitory compounds against TR4. Among them, nilotinib exhibited the most potent inhibitor, with an EC₅₀ of 1.05 μM, while genistein represented the most potent activator, with an EC₅₀ of 2.42 μM. Both drugs were predicted to bind in the ligand binding pocket of TR4. The circular dichroism spectroscopic assay revealed differed conformation changes upon nilotinib or genistein binding. These results established our combined physical and biological approaches as a highly effective way to identify and develop new TR4 regulators.