Antisense oligonucleotide development for the selective modulation of CYP3A5 in renal disease

Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures

BACKGROUND

Xenobiotic exposures can extensively influence the expression and alternative splicing of drug-metabolizing enzymes, including cytochromes P450 (CYPs), though their transcriptome-wide impact on splicing remains underexplored. This study used a well-characterized splicing event in the Cyp2b2 gene to validate a sandwich-cultured primary rat hepatocyte model for studying global splicing in vitro. Using endpoint PCR, RNA sequencing, and bioinformatics tools (rSeqDiff, rMATs, IGV), we analyzed differential gene expression and splicing in CYP and nuclear receptor genes, as well as the entire transcriptome, to understand how xenobiotic exposures shape alternative splicing and activate xenosensors.

METHODS

Primary rat hepatocytes in sandwich culture were exposed to two methylenedioxybenzene (MDB) congeners and carbamazepine, with gene expression and splicing assessed. A 3D-clustergram integrating KEGG pathway analysis with differential gene expression provided distinct splicing landscapes for each xenobiotic, showing that splicing diversity does not always align with gene expression changes.

RESULTS

Endpoint PCR revealed a Cyp2b2v to wild-type Cyp2b2 splicing ratio near 1:1 (100%) under most conditions, while RNA-seq showed a stable baseline closer to 40%. C6-MDB reduced this ratio to ~ 50% by PCR and ~ 39% by RNA-seq, showing slight method-dependent variations yet consistent trends. In contrast, exon 6 skipping in Cyp1a1 occurred only with MDB exposure, implicating AHR activation. Xenobiotic treatments also induced alternative splicing in defensome and stress-responsive genes, including the phase II enzyme Gstm3, Albumin, Orm1, and Fxyd1, highlighting their roles in xenobiotic response modulation. Significant splicing changes in factors such as SRSF1, SRSF7, and METTL3 suggest a coordinated feedback loop involving epitranscriptomic modulation and cross-talk within SR protein networks, refining splice site selection, transcript stability, and cellular fate.

CONCLUSIONS

This study demonstrates how xenobiotic structural features influence gene expression and splicing, revealing splicing patterns that expand our understanding of transcriptome diversity and function. By identifying regulatory mechanisms, including AHR activation, epitranscriptomic modulation, and crosstalk within SR protein networks, that shape adaptive responses to xenobiotic stress, this work offers insights into the splicing and transcriptional networks that maintain cellular homeostasis. These findings provide predictive biomarkers for toxic exposures and highlight the potential of splicing profiles as diagnostic tools for assessing the health impacts of chemical exposure.

Associations Between CYP3A5 (c.6986A>G) Gene Polymorphism and Kidney Impairment in Hypertensive Adults Without Cystatin C Elevation

OBJECTIVE

This study aimed to explore the potential role of CYP3A5 (c. 6986A>G) gene polymorphism in predicting kidney function impairment in patients with hypertension who did not have elevated serum cystatin C.

METHODS

We recruited a group of patients with hypertension who did not have elevated cystatin C and analyzed the CYP3A5 (c. 6986A>G) gene polymorphism. Chi-square tests were used to compare the clinical characteristics and genotypic distribution between the two groups. Logistic regression analysis was used to explore the association between CYP3A5 (c.6986A>G) gene polymorphism and renal function impairment in hypertension with non-elevated cystatin.

RESULTS

In patients with hypertension who participated in the study, there was a significant association between CYP3A5 (c. 6986A>G) gene polymorphism and kidney function impairment (p < 0.05). Patients with the CYP3A5 (c. 6986A>G) mutation display a greater risk of kidney function impairment.

CONCLUSION

CYP3A5 (c. 6986A>G) gene AA homozygote polymorphism significantly increases risk of kidney function impairment in patients with hypertension with normal cystatin C. However, further studies are needed to validate this association and to further understand the mechanism of CYP3A5 (c. 6986A>G) gene polymorphism in kidney function impairment in patients with hypertension.

Normoglycemia and physiological cortisone level maintain glucose homeostasis in a pancreas-liver microphysiological system

Current research on metabolic disorders and diabetes relies on animal models because multi-organ diseases cannot be well studied with standard in vitro assays. Here, we have connected cell models of key metabolic organs, the pancreas and liver, on a microfluidic chip to enable diabetes research in a human-based in vitro system. Aided by mechanistic mathematical modeling, we demonstrate that hyperglycemia and high cortisone concentration induce glucose dysregulation in the pancreas-liver microphysiological system (MPS), mimicking a diabetic phenotype seen in patients with glucocorticoid-induced diabetes. In this diseased condition, the pancreas-liver MPS displays beta-cell dysfunction, steatosis, elevated ketone-body secretion, increased glycogen storage, and upregulated gluconeogenic gene expression. Conversely, a physiological culture condition maintains glucose tolerance and beta-cell function. This method was reproducible in two laboratories and was effective in multiple pancreatic islet donors. The model also provides a platform to identify new therapeutic proteins, as demonstrated with a combined transcriptome and proteome analysis.

Development of a kidney microphysiological system hardware platform for microgravity studies

Determining the physiological effects of microgravity on the human kidney is limited to relatively insensitive tests of biofluids (blood and urine) that do not return abnormal results until more than 50% of kidney function is lost. We have developed an "organ on chip" microphysiological model of the human kidney proximal tubule (PT-MPS) that can recapitulate many kidney functions and disease states and could play a critical role in determining mechanisms of early kidney dysfunction in microgravity. However, the ground-based PT-MPS system is incompatible with spaceflight as it requires a large pneumatic system coupled to a cell incubator for perfusion and intensive hand-on manipulation. Herein, we report the hardware engineering and performance of the Kidney Chip Perfusion Platform (KCPP), a small, advanced, semi-autonomous hardware platform to support kidney microphysiological model experiments in microgravity. The KCPP is composed of five components, the kidney MPS, the MPS housing and valve block, media cassettes, fixative cassettes, and the programable precision syringe pump. The system has been deployed twice to the ISSNL (aboard CRS-17 and CRS-22). From each set of ISSNL experiments and ground-based controls, we were able to recover PT-MPS effluent for biomarker analysis and RNA suitable for transcriptomics analysis demonstrating the usability and functionality of the KCPP.

RNA therapeutics for kidney injury

RNA therapy involves utilizing RNA-based molecules to control biological pathways, aiming to cure specific diseases. As our understanding of RNA functions and their roles has expanded, the application of RNA therapies has broadened to target various therapeutic points. This approach holds promise for treating a range of diseases, including kidney diseases. Therapeutic RNA can be employed to target specific genes or pathways implicated in the development of kidney conditions, such as inflammation, fibrosis, and oxidative stress. This review highlights the therapeutic potential of RNA-based therapies across different types of kidney diseases, encompassing infection, inflammation, nephrotoxicity, and ischemia/reperfusion injury. Furthermore, studies have pinpointed the specific kidney cells involved in RNA therapy. To address challenges hindering the potential impact of RNA-based drugs on their targets, nanotechnology is integrated, and RNA-loaded vehicles with ligands are explored for more efficient outcomes.

Development of a Kidney Microphysiological System Hardware Platform for Microgravity Studies

Study of the physiological effects of microgravity on humans is limited to non-invasive testing of astronauts. Microphysiological models of human organs recapitulate many functions and disease states. Here we describe the development of an advanced, semi-autonomous hardware platform to support kidney microphysiological model experiments in microgravity.

The potential of RNA-based therapy for kidney diseases

Inherited kidney diseases (IKDs) are a large group of disorders affecting different nephron segments, many of which progress towards kidney failure due to the absence of curative therapies. With the current advances in genetic testing, the understanding of the molecular basis and pathophysiology of these disorders is increasing and reveals new potential therapeutic targets. RNA has revolutionized the world of molecular therapy and RNA-based therapeutics have started to emerge in the kidney field. To apply these therapies for inherited kidney disorders, several aspects require attention. First, the mRNA must be combined with a delivery vehicle that protects the oligonucleotides from degradation in the blood stream. Several types of delivery vehicles have been investigated, including lipid-based, peptide-based, and polymer-based ones. Currently, lipid nanoparticles are the most frequently used formulation for systemic siRNA and mRNA delivery. Second, while the glomerulus and tubules can be reached by charge- and/or size-selectivity, delivery vehicles can also be equipped with antibodies, antibody fragments, targeting peptides, carbohydrates or small molecules to actively target receptors on the proximal tubule epithelial cells, podocytes, mesangial cells or the glomerular endothelium. Furthermore, local injection strategies can circumvent the sequestration of RNA formulations in the liver and physical triggers can also enhance kidney-specific uptake. In this review, we provide an overview of current and potential future RNA-based therapies and targeting strategies that are in development for kidney diseases, with particular interest in inherited kidney disorders.

Space Medicines for Space Health

Scientists from around the world are studying the effects of microgravity and cosmic radiation via the "off-Earth" International Space Station (ISS) laboratory platform. The ISS has helped scientists make discoveries that go beyond the basic understanding of Earth. Over 300 medical experiments have been performed to date, with the goal of extending the knowledge gained for the benefit of humanity. This paper gives an overview of these numerous space medical findings, critically identifies challenges and gaps, and puts the achievements into perspective toward long-term space traveling and also adding benefits to our home planet. The medical contents are trifold structured, starting with the well-being of space travelers (astronaut health studies), followed by medical formulation research under space conditions, and then concluding with a blueprint for space pharmaceutical manufacturing. The review covers essential elements of our Earth-based pharmaceutical research such as drug discovery, drug and formulation stability, drug-organ interaction, drug disintegration/bioavailability/pharmacokinetics, pathogen virulence, genome mutation, and body's resistance. The information compiles clinical, medicinal, biological, and chemical research as well as fundamentals and practical applications.