Differential gene expression and protein-protein interaction network profiling of sulfur mustard-exposed rabbit corneas employing RNA-seq data and bioinformatics tools

Dexamethasone mitigates sulfur mustard-induced stem cell deficiency in vivo in rabbit limbal tissue by reducing inflammation and oxidative stress

Sulfur mustard (SM) exposure induces ocular injury primarily to the cornea, limbus, and sclera. Although corneal injuries have been studied in detail, there is a dearth of literature on the effects of SM on limbus, particularly mechanisms underlying its compromised functioning, causing limbal stem cell deficiency (LSCD). LSCD causes impaired corneal repair leading to persistent epithelial defects, mustard gas keratopathy, and prolonged inflammation, resulting in total blindness in case of severe damage. Notably, dexamethasone (Dex) has been reported to treat SM-induced corneal injuries effectively; however, its efficacy for SM-induced limbus injury has not been studied. Hence, delayed/persistent structural damage (H&E and trichrome staining) and loss of LSCs [ΔNp63; immunofluorescence (IF)] in the limbus at day 28 post-SM exposure were assessed. Thereafter, in-depth proteomic analysis (LC-MS/MS) of SM exposed, Dex treated, and control limbal tissues (New Zealand white male rabbits) was performed. SM exposure significantly modulated the expression profile of 66 proteins, of which 62 were significantly reversed with Dex; thus, markedly inhibiting/hindering SM-induced limbal injury. Ingenuity Pathway Analysis predicted the primary involvement of (1) inflammation and immune response-associated pathways via dysregulation of defensin-5, eosinophil peroxidase, corticostatin-6, myeloperoxidase, and cathepsin C; and (2) drug/toxin metabolism and oxidative stress via GSTs, and ALDH1As modulations. IF analysis confirmed that Dex treatment significantly reversed SM-induced increases in human neutrophil peptides, defensin-5, and cathepsin C expression by 68%, 77%, and 90%, respectively. Thus, Dex markedly mitigated SM-induced limbal tissue injuries and prevented LSCD, via SM-induced inflammatory and oxidative stress inhibition, in our studies.

Mustard Gas Induced Corneal Injury Involves Ferroptosis and p38 MAPK Signaling

Purpose

Sulfur mustard gas (SM) exposure to eyes causes multiple corneal injuries including stromal cell loss in vivo. However, mechanisms mediating stromal cell loss/death remains elusive. This study sought to test the novel hypothesis that SM-induced toxicity to human corneal stromal fibroblasts involves ferroptosis mechanism via p38 MAPK signaling.

Methods

New Zealand white rabbit corneas, naïve and SM exposed (200 mg-min/m3 for eight minutes and collected after three days) were used to examine the levels of cell death and reactive oxygen species (ROS) for in vivo studies. Donor human corneas were used to generate primary human corneal stromal fibroblasts (hCSF) for in vitro studies. The hCSFs were exposed to nitrogen mustard (NM; SM analogue) at various timepoints (30 minutes, eight hours, and 24 hours). A p38 MAPK specific inhibitor, SB202190, was also used. Quantitative reverse transcription polymerase chain reaction, Western blotting, reactive oxygen species (ROS), lipid peroxidation, live/dead assay, and RNASeq were used in various investigations.

Results

SM caused a significant increase in cell death and ROS production three days after SM exposure in rabbit corneas. NM exposure to hCSF demonstrated a significant increase in ROS, lipid peroxidation, and ferroptosis biomarkers ACSL4 (inducer) and significant decrease in reducer (SLC7A11 and GPX4) compared to controls in a time-dependent manner. The inhibition of p38 MAPK promoted cell survival and reduced ROS production following mustard gas exposure.

Conclusions

The results of in vivo and in vitro investigations uncovered a novel mechanism that mustard gas toxicity to the cornea involves ferroptosis pathway and p38 MAPK activation.

Transcriptomic landscape of quiescent and proliferating human corneal stromal fibroblasts

This study analyzed the transcriptional changes in primary human corneal stromal fibroblasts (hCSFs) grown under quiescent (serum-free) and proliferating (serum-supplemented) culture conditions to identify genes, pathways, and protein‒protein interaction networks influencing corneal repair and regeneration. Primary hCSFs were isolated from donor human corneas and maintained in serum-free or serum-laden conditions. RNA was extracted from confluent cultures using Qiagen kit and subjected to RNA sequencing (RNAseq) analysis. Differential gene expression (DGE) and pathway enrichment analyses were conducted using DESeq2 and Gene Set Enrichment Analysis (GSEA), respectively. Protein‒protein interaction (PPI) networks were created exploiting the STRING database and analyzed with Cytoscape and the cytoHubba plugin. RNA-seq revealed 5,181 genes that were significantly differentially expressed/changed among the 18,812 annotated genes (p value ˂0.05). A cutoff value of a log2-fold change of ±1.5 or greater was used to identify 674 significantly upregulated and 771 downregulated genes between quiescent and proliferating hCSFs. Pathway enrichment analysis revealed significant changes in genes linked to cell cycle regulation, inflammatory, and oxidative stress response pathways, such as E2F Targets, G2M Checkpoint, and MYC Targets, TNFA signaling via NF-kB, and oxidative phosphorylation. Protein-protein interaction network analysis highlighted critical hub genes. The FGF22, CD34, ASPN, DPT, LUM, FGF10, PDGFRB, ECM2, DCN, VEGFD, OMD, OGN, ANGPT1, CDH5, and PRELP were upregulated, whereas genes linked to cell cycle regulation and mitotic progression, such as BUB1, TTK, KIF23, KIF11, BUB1B, DLGAP5, NUSAP1, CCNA2, CCNB1, BIRC5, CDK1, KIF20A, AURKB, KIF2C, and CDCA8, were downregulated. The RNA sequences and gene count files have been submitted to the Gene Expression Omnibus (accession # GSE260476). Our study provides a comprehensive information on the transcriptional and molecular changes in hCSFs under quiescent and proliferative conditions and highlights key pathways and hub genes.

Transcriptomic and Multi-scale Network Analyses Reveal Key Drivers of Cardiovascular Disease

Cardiovascular diseases (CVDs) and pathologies are often driven by changes in molecular signaling and communication, as well as in cellular and tissue components, particularly those involving the extracellular matrix (ECM), cytoskeleton, and immune response. The fine-wire vascular injury model is commonly used to study neointimal hyperplasia and vessel stiffening, but it is not typically considered a model for CVDs. In this paper, we hypothesize that vascular injury induces changes in gene expression, molecular communication, and biological processes similar to those observed in CVDs at both the transcriptome and protein levels. To investigate this, we analyzed gene expression in microarray datasets from injured and uninjured femoral arteries in mice two weeks post-injury, identifying 1,467 significantly and differentially expressed genes involved in several CVDs such as including vaso-occlusion, arrhythmia, and atherosclerosis. We further constructed a protein-protein interaction network with seven functionally distinct clusters, with notable enrichment in ECM, metabolic processes, actin-based process, and immune response. Significant molecular communications were observed between the clusters, most prominently among those involved in ECM and cytoskeleton organizations, inflammation, and cell cycle. Machine Learning Disease pathway analysis revealed that vascular injury-induced crosstalk between ECM remodeling and immune response clusters contributed to aortic aneurysm, neovascularization of choroid, and kidney failure. Additionally, we found that interactions between ECM and actin cytoskeletal reorganization clusters were linked to cardiac damage, carotid artery occlusion, and cardiac lesions. Overall, through multi-scale bioinformatic analyses, we demonstrated the robustness of the vascular injury model in eliciting transcriptomic and molecular network changes associated with CVDs, highlighting its potential for use in cardiovascular research.

RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing

Purpose

Transdifferentiation of corneal fibroblasts to myofibroblasts in the stroma is a central mechanistic event in corneal wound healing. This study sought to characterize genes and pathways influencing transdifferentiation of human corneal fibroblasts (hCSFs) to human corneal myofibroblasts (hCMFs) using RNA sequencing (RNA-seq) to develop comprehensive mechanistic information and identify newer targets for corneal fibrosis management.

Methods

Primary hCSFs were derived from donor human corneas. hCMFs were generated by treating primary hCSFs with transforming growth factor β1 (TGFβ1; 5 ng/mL) for 72 hours under serum-free conditions. RNA was extracted using the RNeasy Plus Mini Kit and subjected to RNA-seq analysis after quality control testing. Differential gene expression, pathway enrichment, and protein-protein network analyses were performed using DESeq2, GSEA/PANTHER/Reactome, and Cytoscape/cytoHubba, respectively.

Results

RNA-seq analysis of hCMFs and hCSFs identified 3843 differentially expressed genes and transcripts (adjusted P < 0.05). The log(fold change) ≥ ±1.5 filter showed 816 upregulated and 739 downregulated genes between two cell types. Pathway enrichment analysis showed the highest normalized enrichment score for epithelial-to-mesenchymal transition (5.569), followed by mTORC1 signaling (2.949), angiogenesis (2.176), and TGFβ signaling (2.008). Protein-protein interaction network analysis identified the top 20 nodes influencing corneal myofibroblast development. The expression of a novel MXRA5 in corneal stroma and its association with corneal fibrosis was verified by real-time quantitative reverse transcription PCR and immunofluorescence. RNA-seq and gene count files were submitted to the NCBI Gene Expression Omnibus (GSE260476).

Conclusions

This study identified several novel genes involved in myofibroblast development, offering potential targets for developing newer therapeutic strategies for corneal fibrosis.

Tissue-targeted and localized AAV5-DCN and AAV5-PEDF combination gene therapy abrogates corneal fibrosis and concurrent neovascularization in rabbit eyes in vivo

PURPOSE

Corneal fibrosis and neovascularization (CNV) after ocular trauma impairs vision. This study tested therapeutic potential of tissue-targeted adeno-associated virus5 (AAV5) mediated decorin (DCN) and pigment epithelium-derived factor (PEDF) combination genes in vivo.

METHODS

Corneal fibrosis and CNV were induced in New Zealand White rabbits via chemical trauma. Gene therapy in stroma was delivered 30-min after chemical-trauma via topical AAV5-DCN and AAV5-PEDF application using a cloning cylinder. Clinical eye examinations and multimodal imaging in live rabbits were performed periodically and corneal tissues were collected 9-day and 15-day post euthanasia. Histological, cellular, and molecular and apoptosis assays were used for efficacy, tolerability, and mechanistic studies.

RESULTS

The AAV5-DCN and AAV5-PEDF combination gene therapy significantly reduced corneal fibrosis (p < 0.01 or p < 0.001) and CNV (p < 0.001) in therapy-given (chemical-trauma and AAV5-DCN + AAV5-PEDF) rabbit eyes compared to the no-therapy given eyes (chemical-trauma and AAV5-naked vector). Histopathological analyses demonstrated significantly reduced fibrotic α-smooth muscle actin and endothelial lectin expression in therapy-given corneas compared to no-therapy corneas on day-9 (p < 0.001) and day-15 (p < 0.001). Further, therapy-given corneas showed significantly increased Fas-ligand mRNA levels (p < 0.001) and apoptotic cell death in neovessels (p < 0.001) compared to no-therapy corneas. AAV5 delivered 2.69 × 107 copies of DCN and 2.31 × 107 copies of PEDF genes per μg of DNA. AAV5 vector and delivered DCN and PEDF genes found tolerable to the rabbit eyes and caused no significant toxicity to the cornea.

CONCLUSION

The combination AAV5-DCN and AAV5-PEDF topical gene therapy effectively reduces corneal fibrosis and CNV with high tolerability in vivo in rabbits. Additional studies are warranted.