Drug Metabolism Pathways Research Articles

Comparative genomics based exploration of xenobiotic degradation patterns in Glutamicibacter, Arthrobacter, and Pseudarthrobacter isolated from diverse ecological habitats

Xenobiotics pose a substantial threat to environmental integrity by disrupting normal ecosystems. The genus Arthrobacter, known for its metabolic versatility can degrade several xenobiotic compounds. Arthrobacter strains have also undergone frequent taxonomic revisions and reclassifications to strains including Pseudarthrobacter and Glutamicibacter. Here, we present the complete genome sequence of Glutamicibacter protophormiae strain NG4, isolated from a coastal area surrounded by chemical plants. Further, through comparative genomics involving 55 strains from Glutamicibacter, Arthrobacter, and Pseudarthrobacter, we elucidated taxonomic relationships and xenobiotic degradation potential. Our genomics-based findings revealed a generally even distribution of xenobiotic-degrading genes and pathways among the studied strains. Glutamicibacter species emerged as potential candidate for steroid degradation. A significant number of host-specific and environmental isolates predominantly possessed pathways for 4-hydroxybenzoate (4-HB) degradation and only the environmental isolates possessed benzoate degradation pathway. Certain Arthrobacter and Pseudarthrobacter species isolated from the environmental settings were identified as potential degraders of toluene, xylene, and phenanthrene. Notably, most strains contained pathways for azathioprine, capecitabine, and 5-fluorouridine pharmaceutical drug metabolism. Overall, our findings shed light on microbial metabolic diversity among 55 strains isolated from diverse sources and hint the importance of strict environmental monitoring. Further, for the application of the putative xenobiotic degrading strains, experimental validation is required in the future.

De novo transcriptome assembly and differential gene expression analysis in different developmental stages of Agriotes sputator (click beetle)

Wireworms, the larva of click beetle (Agriotes species), are one of the most destructive pests of horticultural crops in North America, responsible for considerable economic losses in Canada. Agriotes sputator (A. sputator) species is a predominant wireworm pest attacking potato fields in Eastern Canada. However, no information about its genome-wide gene expression profile, specifically for the genes involved with development is available to date. Therefore, we generated the transcriptome profile of A. sputator during five developmental stages, including the three larval stages and adult male and female click beetle. Out of 714.7 million raw reads, de novo assembly generated 564,561 transcripts. The data were subjected to differential expression analysis using DESeq2, gene ontology, annotation, and pathway analyses. A total of 34,709 differentially expressed genes (DEGs) were significant (log2 fold change > 2, padj < 0.05) across the developmental stages. Functional analysis of DEGs identified development signaling, metabolism, transport, cellular mechanisms, and drug metabolism (cytochrome p450) pathways. This study provides comprehensive sequence resources and potential gene differences at different developmental stages of A. sputator. These findings will represent a major step towards developing sustainable methods to control this widely distributed pest in agricultural fields.

Differences in the DNA methylome of T cells in adults with asthma of varying severity

BackgroundDNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity are less well-defined.ObjectiveTo examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation.MethodsPeripheral blood T cells from 35 adults with asthma in Beijing, China, were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores.ResultsSignificant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway.ConclusionThese findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to differences in clinical indices of asthma.

Caveolin-1 modulates cisplatin sensitivity in oral squamous cell carcinoma through ferroptosis.

Cisplatin-based chemotherapy is widely used for the treatment of oral squamous cell carcinoma (OSCC), but drug resistance and decreased sensitivity often occur during the treatment, greatly weakening its therapeutic effect. Caveolin-1 (CAV1), a protein related to ferroptosis, is involved in regulating the resistance and sensitivity of various tumor chemotherapies. This study aims to investigate whether CAV1 can regulate the sensitivity of OSCC to cisplatin through ferroptosis. Through bioinformatics analysis, we analyzed the expression of CAV1 in OSCC and its impact on prognosis analyzed the relationship between CAV1 and tumor immune infiltration, and verified the expression of CAV1 in OSCC through immunohistochemistry experiments. We silenced the expression of CAV1 in OSCC cells through lentiviral transfection and evaluated the cell migration and invasion abilities through wound healing and Transwell assays, respectively. CCK8 assay was used to assess the sensitivity of cells to cisplatin, and ferroptosis-related biochemical marker changes were measured. Western blot was performed to detect the expression of ferroptosis-related proteins. The results revealed a high expression of CAV1 in OSCC, and its high expression predicted poor prognosis in OSCC. CAV1 is associated with drug metabolism pathways in OSCC, and its expression affects the infiltration levels of various immune cells in tumors. Further experiments indicated that CAV1 can inhibit ferroptosis and cisplatin sensitivity in cancer cells, promoting their migration and invasion. CAV1 promotes the progression of OSCC and can affect the sensitivity of cisplatin by regulating cellular ferroptosis.

Network Pharmacology Study of Compound Ligustrazine in Gastric Cancer Therapy

To explore the potential role and mechanism of compound tetramethylpyrazine in gastric cancer therapy by using network pharmacology analysis combined with gene function annotation and clinical data analysis. SwissTargetPrediction database was used to screen the potential drug action sites of compound tetramethylpyrazine, and the OMIM and Genecard databases were used in combination to obtain gastric cancer-related targets. Intersection analysis was performed to identify potential therapeutic targets. Subsequently, the method of ClusterProfiler was used to perform functional annotation of the downstream targets of intersection. In addition, The Cancer Genome Atlas (TCGA) database was used to obtain the original data of gastric cancer patients, and the immune infiltration analysis, miRNA analysis, transcriptional regulation analysis of key genes, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), nomogram model construction, and genome-wide association studies (GWAS) were performed. Through network pharmacological screening, we found 14 potential therapeutic targets through which tetramethylpyrazine acted on gastric cancer. Functional annotation showed that these targets were mainly involved in the pathways for hormone metabolism, drug metabolism, and signal transduction. Based on log rank test, the expression of the key genes, ELANE and MPO, showed significant difference in the comparison of gastric cancer survival curves (P<0.05), and were closely associated with immune cell infiltration. In addition, GSEA and GSVA results suggested that ELANE and MPO might influence the development of gastric cancer through multiple signaling pathways. In this study, by using multiple analysis methods in an integrated way, we found that ligustrazine may have therapeutic effects on gastric cancer by regulating the potential targets of ELANE and MPO, as well as the relevant signaling pathways.

Deciphering mechanisms of UV filter (benzophenone-3)- and high temperature-induced adverse effects in the coral Acropora tenuis, using ecotoxicogenomics

Coral reefs are at risk of bleaching due to various environmental and anthropogenic stressors such as global warming and chemical pollutants. However, there is little understanding of stressor-specific mechanisms that cause coral bleaching. Therefore, conducting accurate ecotoxicological risk assessments and deciphering modes of action of potentially deleterious ultraviolet (UV) filters (sunscreen compounds) are crucial issues. In this study, we evaluated the toxicity and bleaching effect of benzophenone-3 (BP-3), which is widely used in sunscreen products, on the reef-building coral Acropora tenuis. Furthermore, to understand differences in UV filter- and temperature-induced adverse effects, a comparative ecotoxicogenomic approach using RNA-seq was integrated into a toxicity test to clarify differences in gene expression changes induced by BP-3 and heat stress (31 °C). The lethal concentration 50 % (LC50) was calculated as 3.9 mg/L, indicating that the aquatic environmental risk on corals posed by BP-3 was low based on the risk assessment in this study. Differentially expressed genes related to oxidative stress and extracellular matrix organization were involved in coral responses to both BP-3 and heat stress, but their patterns differed. Whereas immune and heat-shock responses were activated in response to heat stress, activation of a drug metabolism pathway and several signal transduction pathways were identified in BP-3 treatment groups. Our study enhances understanding of stress responses in corals induced by UV filters and thermal stress. Using potential gene markers identified in this study for eco-epidemiological surveys of stressed corals, we urgently need to develop effective countermeasures.

Effects of cortisone in zebrafish (Danio rerio): Insights into gut microbiota interactions and molecular mechanisms underlying DNA damage and apoptosis

Cortisone can enter aquatic ecosystems and pose a risk to organisms therein. However, few studies have explored the effects of cortisone on the gut microbiota of aquatic organisms. Here, we exposed zebrafish (Danio rerio) to cortisone at environmentally relevant concentrations (5.0, 50.0, or 500.0 ng L−1) for 60 days to explore its toxicological effects and their association with gut microbiota changes. The terminal deoxynucleotidyl transferase-mediated dUTP–biotin nick-end labeling assay revealed that exposure to 50 ng L−1 cortisone significantly increased the intestinal cell apoptosis rate, 8-hydroxydeoxyguanosine contents, and caspase-3 and caspase-8 activities. Moreover, the transcriptome analysis results demonstrated a notable downregulation in the expression of most differentially expressed genes associated with apoptosis pathways, as well as changes in DNA replication, oxidative stress, and drug metabolism pathways; these results indicated the occurrence of cortisone-induced stress response in zebrafish. Molecular docking analysis revealed that cortisone can bind to caspase-3 through hydrogen bonds and hydrophobic interactions but that no such interactions occur between cortisone and caspase-8. Thus, cortisone may induce oxidative DNA damage and apoptosis by activating caspase-3. Finally, the 16S rRNA sequencing results demonstrated that cortisone significantly affected microbial community structures and functions in the intestinal ecosystem. These changes may indicate gut microbiota response to cortisone-induced intestinal damage and inflammation. In conclusion, the current results clarify the mechanisms underlying intestinal response to cortisone exposure and provide a basis for evaluating the health risks of cortisone in animals.

Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response.

Drugs represent our first, and sometimes last, line of defense for many diseases, yet despite decades of research we still do not fully understand why a given drug works in one patient and fails in the next. The human gut microbiome is one of the missing puzzle pieces, due to its ability to parallel and extend host pathways for drug metabolism, along with more complex host-microbiome interactions. Herein, we focus on the well-established links between the gut microbiome and drugs for heart disease and cancer, plus emerging data on neurological disease. We highlight the interdisciplinary methods that are available and how they can be used to address major remaining knowledge gaps, including the consequences of microbial drug metabolism for treatment outcomes. Continued progress in this area promises fundamental biological insights into humans and their associated microbial communities and strategies for leveraging the microbiome to improve the practice of medicine.

Take-out food enhances the risk of MPs ingestion and obesity, altering the gut microbiome in young adults

Young people are consuming large amounts of microplastics (MPs) due to the booming development of the take-out industry. To investigate the association between MPs exposure and obesity, 121 volunteers were divided into high MPs exposure (HME) and low MPs exposure (LME) according to the frequency of take-out food consumption. Fecal samples were collected for MPs detection using Raman spectra analysis, and identification of the gut microbiota was based on 16 S rDNA/ITS, while metabolite analysis was performed by LC-MS/MS. High levels of MPs and body mass index (BMI) were observed in the HME group (P < 0.05). Both the multiple linear regression (MLR) model and the binary logistic regression (BLR) (OR: 1.264, 95 % CI: 1.108–1.441, P < 0.001) analysis showed a positive correlation between MPs content and BMI. Microbial community analysis revealed that Veillonella, Alistipes and Dothideomycotes (pathogenic fungi) increased in HME participants, whereas Faecalibacterium and Coprococcus decreased. Meanwhile, analysis of stool metabolites showed that vancomycin resistance, selenocompound metabolism and drug metabolism pathways were enhanced in HME participants. These findings indicate that frequent consumption of take-out food may elevate the intake of microplastics, consequently modifying the gut microbiota and metabolites of young adults, and could represent a potential risk factor for obesity.

P7C3 ameliorates barium chloride-induced skeletal muscle injury activating transcriptomic and epigenetic modulation of myogenic regulatory factors.

Skeletal muscle injury affects the quality of life in many pathologies, including volumetric muscle loss, contusion injury, and aging. We hypothesized that the nicotinamide phosphoribosyltransferase (Nampt) activator P7C3 improves muscle repair following injury. In the present study, we tested the effect of P7C3 (1-anilino-3-(3,6-dibromocarbazol-9-yl) propan-2-ol) on chemically induced muscle injury. Muscle injury was induced by injecting 50 µL 1.2% barium chloride (BaCl2) into the tibialis anterior (TA) muscle in C57Bl/6J wild-type male mice. Mice were then treated with either 10 mg/kg body weight of P7C3 or Vehicle intraperitoneally for 7 days and assessed for histological, biochemical, and molecular changes. In the present study, we show that the acute BaCl2-induced TA muscle injury was robust and the P7C3-treated mice displayed a significant increase in the total number of myonuclei and blood vessels, and decreased serum CK activity compared with vehicle-treated mice. The specificity of P7C3 was evaluated using Nampt+/- mice, which did not display any significant difference in muscle repair capacity among treated groups. RNA-sequencing analysis of the injured TA muscles displayed 368 and 212 genes to be exclusively expressed in P7C3 and Veh-treated mice, respectively. There was an increase in the expression of genes involved in cellular processes, inflammatory response, angiogenesis, and muscle development in P7C3 versus Veh-treated mice. Conversely, there is a decrease in muscle structure and function, myeloid cell differentiation, glutathione, and oxidation-reduction, drug metabolism, and circadian rhythm signaling pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction (qPCR) and reverse transcription-qPCR analyses identified increased Pax7, Myf5, MyoD, and Myogenin expression in P7C3-treated mice. Increased histone lysine (H3K) methylation and acetylation were observed in P7C3-treated mice, with significant upregulation in inflammatory markers. Moreover, P7C3 treatment significantly increased the myotube fusion index in the BaCl2-injured human skeletal muscle in vitro. P7C3 also inhibited the lipopolysaccharide-induced inflammatory response and mitochondrial membrane potential of RAW 264.7 macrophage cells. Overall, we demonstrate that P7C3 activates muscle stem cells and enhances muscle injury repair with increased angiogenesis.

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota.

N-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms. After treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways. Compared to the control group, the values of Cmax, AUC0-8, AUC0-∞, t1/2 in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmax values decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism. Antibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposure in vivo by inhibiting pathways related to NBP metabolism.

Differences in the DNA Methylome of T cells in Adults With Asthma of Varying Severity.

DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity or asthma endotypes are less well-defined. To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation. Peripheral blood T cells from 35 adults with asthma in Beijing, China were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores. Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway. These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to the phenotype and severity of their overall disease.

Identification of New Substrates and Inhibitors of Human CYP2A7.

CYP2A7 is one of the most understudied human cytochrome P450 enzymes and its contributions to either drug metabolism or endogenous biosynthesis pathways are not understood, as its only known enzymatic activities are the conversions of two proluciferin probe substrates. In addition, the CYP2A7 gene contains four single-nucleotide polymorphisms (SNPs) that cause missense mutations and have minor allele frequencies (MAFs) above 0.5. This means that the resulting amino acid changes occur in the majority of humans. In a previous study, we employed the reference standard sequence (called CYP2A7*1 in P450 nomenclature). For the present study, we created another CYP2A7 sequence that contains all four amino acid changes (Cys311, Glu169, Gly479, and Arg274) and labeled it CYP2A7-WT. Thus, it was the aim of this study to identify new substrates and inhibitors of CYP2A7 and to compare the properties of CYP2A7-WT with CYP2A7*1. We found several new proluciferin probe substrates for both enzyme variants (we also performed in silico studies to understand the activity difference between CYP2A7-WT and CYP2A7*1 on specific substrates), and we show that while they do not act on the standard CYP2A6 substrates nicotine, coumarin, or 7-ethoxycoumarin, both can hydroxylate diclofenac (as can CYP2A6). Moreover, we found ketoconazole, 1-benzylimidazole, and letrozole to be CYP2A7 inhibitors.

Investigating Immunotoxicity in Black Carp (Mylopharyngodon piceus) Fingerlings Exposed to Niclosamide.

Niclosamide (NIC) is a potent salicylanilide molluscicide/helminthicide commonly utilized for parasite and mollusc control in aquatic environments. Due to its persistent presence in water bodies, there is growing concern regarding its impact on aquatic organisms, yet this remains inadequately elucidated. Consequently, this study aims to assess the hepatotoxic effects and detoxification capacity of black carp (Mylopharyngodon piceus) in a semi-static system, employing various parameters for analysis. NIC was applied to juvenile black carp at three different concentrations (0, 10 and 50 μg/L) for 28 days in an environmentally realistic manner. Exposure to 50 μg/L NIC resulted in an increase in hepatic lysozyme (LYZ), alkaline phosphatase (ALP), and complement 4 (C4) levels while simultaneously causing a decrease in peroxidase (POD) activity. Additionally, NIC exposure exhibited a dose-dependent effect on elevating serum levels of LYZ, ALP, complement 3 (C3), C4, and immunoglobulin T (IgT). Notably, the mRNA levels of immune-related genes tnfα, il8, and il6, as well as nramp and leap2, were upregulated in fish exposed to NIC. RNA-Seq analysis identified 219 differentially expressed genes (DEGs) in M. piceus after NIC exposure, with 94 upregulated and 125 downregulated genes. KEGG and GO analyses showed enrichment in drug metabolism pathways and activities related to oxidoreductase, lip oprotein particles, and cholesterol transport at 50 μg/L NIC. Additionally, numerous genes associated with lipid metabolism, oxidative stress, and innate immunity were upregulated in NIC-exposed M. piceus. Taken together, these findings indicate that NIC has the potential to cause hepatotoxicity and immunotoxicity in M. piceus. This research offers important insights for further understanding the impact of molluscicide/helminthicide aquatic toxicity in ecosystems.

Abstract 1598: Individualized longitudinal assessment reveals therapy-induced tumor and microenvironment dynamics in preclinical pancreatic cancer models

Abstract Background &amp; Aim: Progression and therapeutic resistance in pancreatic cancer depends on the ability of cancer cells to adopt specific cell states. These phenotypes largely depend on environmental tissue niches. Here, we investigated therapy-induced tumor dynamics in vivo at single-cell spatial and temporal resolution in different subtypes of PDAC using several genetically engineered mouse models, which reflect distinct human PDAC ecosystems. Methods &amp; Results: We established orthotopic tumor models of pancreatic cancer with distinct tumor microenvironment (TME) formation (reactive vs deserted stroma), which were monitored for tumor growth to define tumor response patterns under MAPK inhibition. Serial ultrasound-guided biopsy sampling was performed to collect tissues from the same tumors at pre-treatment, responsive and recurrence periods.Transcriptomic analysis of biopsies using the Mfuzz algorithm delineated highly dynamic gene and pathway activities during treatment. Reactive, but not deserted, TME showed an upregulation of immune-related pathways (antigen presentation, T cell receptor, NK cytotoxicity) immediately after MAPK inhibition in regressed tumors that dropped dramatically during recurrence of tumors, in which upregulation of TGF-b signaling was observed. In the deserted stroma model, on the other hand, an enrichment in drug metabolic pathways during recurrence was observed.CAF cluster deconvolution analysis revealed an increase in a LRRC15+ CAF cluster, which was TGF-b-driven and immunosuppressive, during recurrence period only in the reactive model. The dynamic changes of immune cells and CAFs were validated at protein level by multiplex immunofluorescent imaging. Cmputational spatial analysis revealed a tumor-encapsulating and CD8+ cytotoxic T cell-repelling pattern exhibited by LRRC15+FAP+ CAFs, implying a potential role of this CAF subset in T cell suppression during recurrence in reactive subtype. Using spectral cell sorting with CellView image technology, specific CAF subsets, tumor cells as well as immune cell subsets based on 30+ markers and cell morphology were isolated, characterized and assessed by ex vivo functional assays to confirm the immunosuppressive and tumor protective mechanism mediated by CAFs. Conclusion: Longitudinal in vivo assessment of distinct PDAC subtypes provides deep mechanistic insights to accurately unlock specific response patterns of tumors with heterogeneous TME dynamics upon therapeutic perturbation, leveraging identification of key nodes for intervention. Citation Format: Jens T. Siveke, Rui Fang, Phyllis Fung-Yi Cheung, Jiajin Yang, Juanfei Peng, Kristina Althoff, Konstantinos Savvatakis. Individualized longitudinal assessment reveals therapy-induced tumor and microenvironment dynamics in preclinical pancreatic cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1598.

An esterase-activatable nanoprodrug mitigates severe spinal cord injury via alleviating ferroptosis and reprogramming inflammatory microenvironment

Spinal cord injury (SCI) is a devastating condition with limited efficacious treatment options. Recent research has revealed the potential of functional nanomedicines to inhibit ferroptosis and reduce inflammatory response, offering a promising therapeutic approach for SCI. Urolithin A (UA) exhibits outstanding antioxidant and anti-inflammatory properties in different neurodegenerative disorders. Intriguingly, whether UA can antagonize ferroptosis remains unknown, and its specific impact on SCI and underlying mechanisms have not been extensively explored. Given the pathological response of esterase overexpression in the SCI microenvironment, taken advantages of nanotechnology in precise targeted delivery, flexible structure design and effective enhancement of drug metabolism pathways, in this study, a novel silica-based integrated nanocarrier is constructed by incorporating carbamate-bridged UA into silica nanoparticles. The resulting PEGylated UA silicon hybrid NPs (PUASi NPs) are sensitive and could be specifically recognized and cleaved by esterase. The findings from both in vitro and in vivo experiments demonstrate that the continuous release of UA from PUASi NPs exhibits notable anti-ferroptotic and anti-inflammatory effects, thus contributing to the improvement of functional recovery in mice suffering from SCI. Collectively, this esterase-activatable nanoprodrug strategy offers an alternative therapeutic regimen for clinical intervention in SCI, with promising prospects for translation into clinical practice.

SPINK1 Overexpression Correlates with Hepatocellular Carcinoma Treatment Resistance Revealed by Single Cell RNA-Sequencing and Spatial Transcriptomics.

Low efficacy of treatments and chemoresistance are challenges in addressing refractory hepatocellular carcinoma (HCC). SPINK1, an oncogenic protein, is frequently overexpressed in many HCC cases. However, the impact of SPINK1 on HCC treatment resistance remains poorly understood. Here, we elucidate the functions of SPINK1 on HCC therapy resistance. Analysis of SPINK1 protein level reveals a correlation between elevated SPINK1 expression and unfavorable prognosis. Furthermore, intercellular variations in SPINK1 expression levels are observed. Subsequent examination of single cell RNA-sequencing data from two HCC cohorts further suggest that SPINK1-high cells exhibit heightened activity in drug metabolic pathways compared to SPINK1-low HCC cells. High SPINK1 expression is associated with reduced sensitivities to both chemotherapy drugs and targeted therapies. Moreover, spatial transcriptomics data indicate that elevated SPINK1 expression correlates with non-responsive phenotype during treatment with targeted therapy and immune checkpoint inhibitors. This is attributed to increased levels of drug metabolic regulators, especially CES2 and CYP3A5, in SPINK1-high cells. Experimental evidence further demonstrates that SPINK1 overexpression induces the expression of CES2 and CYP3A5, consequently promoting chemoresistance to sorafenib and oxaliplatin. In summary, our study unveils the predictive role of SPINK1 on HCC treatment resistance, identifying it as a potential therapeutic target for refractory HCC.

Comparative transcriptomic and phenotypic analysis of induced pluripotent stem cell hepatocyte-like cells and primary human hepatocytes.

Primary human hepatocytes (PHHs) are used extensively for in vitro liver cultures to study hepatic functions. However, limited availability and invasive retrieval prevent their widespread use. Induced pluripotent stem cells exhibit significant potential since they can be obtained non-invasively and differentiated into hepatic lineages, such as hepatocyte-like cells (iHLCs). However, there are concerns about their fetal phenotypic characteristics and their hepatic functions compared to PHHs in culture. Therefore, we performed an RNA-sequencing (RNA-seq) analysis to understand pathways that are either up- or downregulated in each cell type. Analysis of the RNA-seq data showed an upregulation in the bile secretion pathway where genes such as AQP9 and UGT1A1 were higher expressed in PHHs compared to iHLCs by 455- and 15-fold, respectively. Upon immunostaining, bile canaliculi were shown to be present in PHHs. The TCA cycle in PHHs was upregulated compared to iHLCs. Cellular analysis showed a 2-2.5-fold increase in normalized urea production in PHHs compared to iHLCs. In addition, drug metabolism pathways, including cytochrome P450(CYP450) and UDP-glucuronosyltransferase enzymes, were upregulated in PHHs compared to iHLCs. Of note, CYP2E1 gene expression was significantly higher (21,810-fold) in PHHs. Acetaminophen and ethanol were administered to PHH and iHLC cultures to investigate differences in biotransformation. CYP450 activity of baseline and toxicant-treated samples was significantly higher in PHHs compared to iHLCs. Our analysis revealed that iHLCs have substantial differences from PHHs in critical hepatic functions. These results have highlighted the differences in gene expression and hepatic functions between PHHs and iHLCs to motivate future investigation.

Acceleration of infectious disease drug discovery and development using a humanized model of drug metabolism

A key step in drug discovery, common to many disease areas, is preclinical demonstration of efficacy in a mouse model of disease. However, this demonstration and its translation to the clinic can be impeded by mouse-specific pathways of drug metabolism. Here, we show that a mouse line extensively humanized for the cytochrome P450 gene superfamily ("8HUM") can circumvent these problems. The pharmacokinetics, metabolite profiles, and magnitude of drug-drug interactions of a test set of approved medicines were in much closer alignment with clinical observations than in wild-type mice. Infection with Mycobacterium tuberculosis, Leishmania donovani, and Trypanosoma cruzi was well tolerated in 8HUM, permitting efficacy assessment. During such assessments, mouse-specific metabolic liabilities were bypassed while the impact of clinically relevant active metabolites and DDI on efficacy were well captured. Removal of species differences in metabolism by replacement of wild-type mice with 8HUM therefore reduces compound attrition while improving clinical translation, accelerating drug discovery.

Kinase Inhibitors FDA Approved 2018-2023: Drug Targets, Metabolic Pathways, and Drug-Induced Toxicities.

Small molecule kinase inhibitors are one of the fastest growing classes of drugs, which are approved by the US Food and Drug Administration (FDA) for cancer and noncancer indications. As of September 2023, there were over 70 FDA-approved small molecule kinase inhibitors on the market, 42 of which were approved in the past five years (2018-2023). This minireview discusses recent advances in our understanding of the pharmacology, metabolism, and toxicity profiles of recently approved kinase inhibitors with a central focus on tyrosine kinase inhibitors (TKIs). In this minireview we discuss the most common therapeutic indications and molecular target(s) of kinase inhibitors FDA approved 2018-2023. We also describe unique aspects of the metabolism, bioactivation, and drug-drug interaction (DDI) potential of kinase inhibitors; discuss drug toxicity concerns related to kinase inhibitors, such as drug-induced liver injury; and highlight clinical outcomes and challenges relevant to TKI therapy. Case examples are provided for common TKI targets, metabolism pathways, DDI potential, and risks for serious adverse drug reactions. The minireview concludes with a discussion of perspectives on future research to optimize TKI therapy to maximize efficacy and minimize drug toxicity. SIGNIFICANCE STATEMENT: This minireview highlights important aspects of the clinical pharmacology and toxicology of small molecule kinase inhibitors FDA approved 2018-2023. We describe key advances in the therapeutic indications and molecular targets of TKIs. The major metabolism pathways and toxicity profiles of recently approved TKIs are discussed. Clinically relevant case examples are provided that demonstrate the risk for hepatotoxic drug interactions involving TKIs and coadministered drugs.