Arafat Rahman Oany

Orphan nuclear receptor 4A1 (NR4A1) and NR4A2 exhibit pro-oncogenic activities in most solid tumors, and this study investigates the role of both receptors and the dual NR4A1/2 1,2-bis(3’-indolyl)-1-(3,5-disubstitutedphenyl)methane (DIM-3,5) ligands as inducers of ferroptosis in colon cancer cells. DIM-3,5 ligands induced reactive oxygen species (ROS) enhancement, as indicated by BODIPY fluorescence, a marker of lipoperoxidation, and increased formation of malondialdehyde (MDA), a lipoperoxide degradation product, in colon cancer cells; this was accompanied by modulated expression of key ferroptotic genes, including the transferrin receptor (TFR/CD71, induced), glutathione peroxidase 4 (GPX4, decreased), and SLC7A11 (decreased). Molecular analysis of GPX4 regulation by NR4A using knockdown, promoter analysis, and chromatin immunoprecipitation showed that GPX4 is regulated by NR4A2/Sp4, where NR4A2 acts as a ligand-dependent cofactor of the DNA-bound Sp4 transcription factor. The 3,5-dichloro analog (DIM-3,5-CI ₂ ) (2.5 mg/kg/day) also inhibits colon tumor growth in a syngeneic mouse xenograft model bearing CT26 mouse colon cancer cells, and analysis of tumor-infiltrating lymphocytes shows that DIM-3,5-CI ₂ increased CD8 ⁺ T cells, decreased g-MDSC, increased M1/M2 macrophage ratios, and an increased percentage of B cells to enhance immune surveillance. Thus, the dual NR4A1/2 DIM-3,5 ligands induce ferroptosis in tumors/cancer cells, and this was accompanied by modification of the immune system.

Background/Objectives: The orphan nuclear receptors 4A1 (NR4A1) and NR4A2 are overexpressed in multiple solid tumors, and both receptors exhibit tumor promoter-like activities. A recent study reported that luteolin, a flavonoid that binds NR4A1, decreased the expression of the pro-oncogenic receptor tyrosine kinase MerTK in colon cancer cells. Methods/Results: In this study, we observed that MerTK protein was expressed in human SW480 and HCT116 and mouse CT26 colon cancer cell lines, and was significantly downregulated after treatment with 1,1-bis(3′-indolyl)-1-(3,5-disubstitutedphenyl)methane (DIM-3,5) compounds, which are dual NR4A1/NR4A2 ligands. Moreover, knockdown of NR4A1 and NR4A2 also decreased MerTK protein expression and DIM-3,5 ligands, and receptor knockdown also decreased MerTK RNA levels expression. MerTK expression was also downregulated by knockdown of Sp1, Sp3, or Sp4 and by treatment with mithramycin. Subsequent studies using chromatin immunoprecipitation and transfection of a MERTK (promoter)–luciferase construct containing transcriptionally active GC-rich promoter elements indicated that MerTK expression in colon cancer cells was regulated by NR4A/Sp complexes, including NR4A1, NR4A2, Sp1, Sp3, and Sp4 transcription factors. Conclusions: The participation of NR4A1 and NR4A2 in the regulation of MerTK indicates that DIM-3,5 ligands represent a novel class of agents that can be used to inhibit MerTK expression in cancer cells by acting as dual NR4A1 and NR4A2 inverse agonists.

Background/Objective: Coffee is the most highly consumed beverage worldwide, and coffee drinkers exhibit decreased mortality and protection from aging-related diseases. This study investigates the role of orphan nuclear receptor 4A1 (NR4A1) in mediating the effects of brewed coffee and the major polyphenolic and polyhydroxy compounds in brewed coffee and also in determining their binding to NR4A1. Methods: The interactions of brewed coffee and several of the major individual compounds in brewed coffee with the ligand-binding domain of NR4A1 were determined using a fluorescent binding assay. For specific compounds, binding was also carried out by surface plasmon resonance, and molecular docking studies were also performed. NR4A1-responsive Rh30 cancer cells were used as models to determine NR4A1-dependent transactivation, cell growth inhibition and inhibition of specific gene products, and in some studies, knockdown of NR4A1 by RNA interference was also determined. Inhibition of lipopolysaccharide-induced IkBα by key polyphenolics was also investigated in RAW264.7 macrophages. Results: Brewed coffee and several polyphenolics, including caffeic acid, ferulic acid, chlorogenic acid, p-coumaric acid, several cinnamic acid derivatives, kahweol, and cafestrol, bound NR4A1 in binding assays, and most Kd values were <10 µM. Brewed coffee and the major polyphenolics inhibited growth of NR4A1-responsive Rh30 cells, and this was attenuated in NR4A1-deficient Rh30 cells. These same compounds also exhibited NR4A1-dependent effects on transactivation and gene product responses in Rh30 and RAW264.7 macrophages and exhibited inverse NR4A1 agonist activity. In contrast, the NR4A1-dependent activity of caffeine and quinic acid was highly variable, suggesting that they are selective NR4A1 ligands. Conclusions: The results of this study demonstrate that brewed coffee and its major polyphenolics and polyhydroxy constituents are NR4A1 ligands and that NR4A1 may play an important role in the health-protective effects of coffee. These results, coupled with recent studies, indicate that NR4A1 and its ligands may play an important role in diet and health.

Ferroptosis is an iron-dependent cell death pathway that involves multiple genes, including the transferrin receptor (TFRC/CD71), glutathione peroxidase 4 (GPX4) and cystine-glutamate antiporter (SLC7A11). This study is based on the hypothesis that orphan nuclear receptor 4A1 (NR4A1) and NR4A2 maintain low levels of ferroptosis in triple negative breast cancer (TNBC) cells and bis-indole derived (CDIM) compounds act as NR4A1/2 ligands that induce ferroptosis by enhancing CD71 expression. 1,1-Bis(3′-indolyl)-1-(3,5-disubstitutedphenyl)methane (DIM-3,5) analogs were investigated for their cytotoxicity and effects on NR4A1 and NR4A2 regulated genes and induction of ferroptosis. Several assays also determined enhanced lipoperoxidation, reactive oxygen species and malondialdehyde formation in TNBC cells. Knockdown of NR4A1, NR4A2, Sp1 and Sp4 was carried out by RNA interference. Molecular mechanisms of NR4A1/2-mediated regulation of CD71 expression were determined using CD71-luciferase promoter constructs, overexpression of Sp1 and chromatin immunoprecipitation (ChIP) assays. Initial studies show that DIM-3,5 analogs act as an inverse NR4A1/NR4A2 agonists that downregulate the pro-oncogenic responses/gene products regulated by both receptors in TNBC cells. DIM-3,5 analogs also induced ROS, malondialdehyde and lipoperoxide formation in TNBC cells, and this was accompanied by decreased expression of GPX4 and SLC7A11 and induction of CD71. Induction of CD71, an important biomarker of ferroptosis was observed after treatment of TNBC cells with DIM-3,5 analogs, knockdown of NR4A1, NR4A2, Sp1 or Sp4 demonstrating that induction of CD71 was coregulated by both receptors. Moreover, both promoter and ChIP analysis indicated that NR4A1 and NR4A2 acted as ligand-dependent cofactors of Sp1/4-mediated expression of CD71 in TNBC cells. Thus, CD71, a key biomarker of ferroptosis is an NR4A1/2/Sp regulated gene that can be directly targeted by DIM-3,5 inverse NR4A1/2 agonists to induce ferroptosis in TNBC cells.

Ferroptosis is an iron-dependent cell death pathway that involves multiple genes including the transferrin receptor (TFRC/CD71), glutathione peroxidase 4 (GPX4) and SLC7A11. This study is based on the hypothesis that orphan nuclear receptor 4A1 (NR4A1) and NR4A2 maintain low levels of ferroptosis in triple negative breast cancer (TNBC) cells and that bis-indole derived (CDIM) compounds act as NR4A1/2 ligands that induce ferroptosis by enhancing CD71 expression. 1,1-Bis(3’-indolyl)-1-(3,5-disubstitutedphenyl)methane (DIM-3,5) analogs were investigated for their cytotoxicity and effects on NR4A1 and NR4A2 regulated genes and induction of ferroptosis by cytotoxicity, western blot and RT-PCR. Several assays also determined enhanced lipoperoxidation, reactive oxygen species and malondialdehyde formation in TNBC cells. Knockdown of NR4A1, NR4A2, Sp1 and Sp4 was carried out by RNA interference. Molecular mechanisms of NR4A1/2-mediated regulation of CD71 expression were determined using CD71-luciferase promoter constructs, overexpression of Sp1 and chromatin immunoprecipitation (ChIP) assays. Initial studies show that DIM-3,5 act as an inverse NR4A1/NR4A2 agonist that downregulated the pro-oncogenic responses/gene products regulated by both receptors in TNBC cells. DIM-3,5 analogs also induced ROS, malondialdehyde and lipoperoxide formation in TNBC cells and this was accompanied by indicators of ferroptosis that include decreased expression of GPX4 and SLC7A11 and induction of CD71. Induction of CD71, an important biomarker of ferroptosis was observed after treatment of TNBC cells with DIM-3,5 analogs, knockdown of NR4A1, NR4A2, Sp1 or Sp4 demonstrating that induction of CD71 was coregulated by both receptors. Moreover, both promoter and ChIP analysis indicated that NR4A1 and NR4A2 acted as ligand-dependent cofactors of Sp1/4-mediated expression of CD71 in TNBC cells. CD71, a key biomarker of ferroptosis is an NR4A1/2/Sp regulated gene that can be directly targeted by DIM-3,5 inverse NR4A1/2 agonists to induce ferroptosis in TNBC cells.

Polyfluoroalkyl substances (PFAS) are widely used industrial compounds that have been identified as contaminants in almost every component of the global ecosystem, and in human studies, higher levels of PFAS have been correlated with increased incidence of multiple diseases. Based on the results of human and laboratory animal studies, we hypothesize that the orphan nuclear receptor 4A1 (NR4A1) may be a critical target for some PFAS such as the legacy linear polyfluorooctanesulfonate (PFOS) and other sulfonates. We show that PFOS and related compounds bound the ligand binding domain (LBD) of NR4A1 and induced the growth of several cancer cell lines and enhanced tumor growth in an athymic nude mouse model. Using NR4A1-responsive rhabdomyosarcoma Rh30 cells as a model, PFOS induced NR4A1-dependent cell proliferation and Rh30 cell migration and invasion. Moreover, in Rh30 cells, PFOS also induces several NR4A1-regulated genes including the PAX3-FOXO1 oncogene and downstream gene products, and in a chromatin immunoprecipitation assay, PFOS does not decrease NR4A1 binding to the promoter. These results demonstrate that PFOS is an NR4A1 ligand and enhances tumorigenesis through the activation of this receptor.

The human nuclear receptor (NR) superfamily consists of 48 genes that are ligand-activated transcription factors that play a key role in maintaining cellular homeostasis and in pathophysiology. NRs are important drug targets for both cancer and non-cancer endpoints as ligands for these receptors can act as agonists, antagonists or inverse agonists to modulate gene expression. With two exceptions, the classical mechanism of action of NRs involves their interactions as monomers, dimers or heterodimers with their cognate response elements (cis-elements) in target gene promoters. Several studies showed that a number of NR-regulated genes did not directly bind their corresponding cis-elements and promoter analysis identified that NR-responsive gene promoters contained GC-rich sequences that bind specificity protein 1 (Sp1), Sp3 and Sp4 transcription factors (TFs). This review is focused on identifying an important sub-set of Sp-regulated genes that are indirectly coregulated through interactions with NRs. Subsequent studies showed that many NRs directly bind Sp1 (or Sp3 and Sp4), the NR/Sp complexes bind GC-rich sites to regulate gene expression and the NR acts as a ligand-modulated nuclear cofactor. In addition, several reports show that NR-responsive genes contain cis-elements that bind both Sp TFs and NRs, and mutation of either cis-element results in loss of NR-responsive (inducible and/or basal). Regulation of these genes involves interactions between DNA-bound Sp TFs with proximal or distal DNA-bound NRs, and, in some cases, other nuclear cofactors are required for gene expression. Thus, many NR-responsive genes are regulated by NR/Sp complexes, and these genes can be targeted by ligands that target NRs and also by drugs that induce degradation of Sp1, Sp3 and Sp4.

Cystic fibrosis (CF), a fatal autosomal recessive disorder, is triggered by a genetic alteration of the CF transmembrane conductance regulator (CFTR) gene. On a global scale, around one in 3000 live births are affected with CF annually. While diagnosis and therapy are available for CF patients with non-specific and rare mutations, the current research is dedicated to exploring customized biomarkers, genes, signaling networks, and therapy for improving the management of CF. Although still in the early stages of development and validation, mRNA and gene-based treatment strategies are aimed to target patients who are resistant to CFTR gene restoration therapies. In this study, we utilized the systems biology approaches integrated with gene expression analysis to identify novel biomarkers and pathways for CF treatment. At first, out of 54,676 differentially expressed genes, we identified 104 upregulated and 107 downregulated genes. The upregulated genes were largely concentrated on Glutamatergic synapses, and the downregulated genes were enriched in ubiquitin-mediated proteolysis. Utilizing the enrichment analysis, we explored deeper into the pathways linked to these genes, with emphasis on relevant pathways involving bronchial epithelial cells. Following the enrichment analysis, we identified six essential genes: WWP2, RNASEL, CUL1, CDC42, HDAC4, and UBA2. Furthermore, the discovered genes were evaluated using expression profile analysis. Finally, our data indicate that the WWP2 gene has a critical role in CF management. The current findings provide a coherent theoretical foundation for future experiments to further explore the WWP2 gene as a unique and prognostic target for developing an effective CF therapeutic approach.

Cystic Fibrosis (CF) is the most common lethal autosomal recessive disorder characterized by the defective function of the CF transmembrane conductance regulator (CFTR) gene. Worldwide, the incidence ratio of CF is approximately 1:3000 in live births per annum. Recently, the number of adult patients has been reported to outnumber the number of pediatric sufferers. Though the diagnosis and treatment are available for CF patients’ corrective treatment for non-specific mutations, patients with rare mutations, advances in personalized biomarkers, and whether other genes and signaling pathways are related to CF are being investigated and they are also in the early stage of development and validation. In the present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from transcriptomic profiling. Initially, we identified 104 up-regulated and 107 down-regulated genes from a total of 54676 differentially expressed genes. The up-regulatory genes mainly concentrate on Glutamatergic synapses, and the down-regulatory genes are on Ubiquitin mediated proteolysis. The involved pathways associated with these genes were also assessed through pathway enrichment, and we mainly focused on different pathways related to bronchial epithelial cells. After the subsequent enrichment of these genes, we have identified 6 hub genes, WWP2; RNASEL; CUL1; CDC42; HDAC4, and UBA2, which play a crucial role in CF and are verified by expression profile analysis. Our study found that the WWP2 gene in CF, as reported here for the first time.

Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC retains its fatality rate of about half of the infected population globally. The major screening biomarkers and therapeutic target identification have now become a global concern. In the present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4643 differentially expressed genes. The up-regulatory genes mainly concentrate on immune-inflammatory responses, and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment, and we mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC and are verified by expression profile analysis. From our study, we have found that genes LILRB2 and CYBB play crucial roles in CC, as reported here for the first time. Furthermore, the survivability of the hub genes was also assessed, and among them, finally, CXCR4 has been identified as one of the most potential differentially expressed genes that might play a vital role in the survival of CC patients. Thus, CXCR4 could be used as a prognostic and/or diagnostic biomarker and a drug target for CC.