Biostimulants help plants to cope with abiotic stresses and using those obtained by recycling waste bioproducts is an eco-friendly technology with great potential. Quinoa (Chenopodium quinoa Willd.) is a highly nutritious grain originally cultivated in the Andes but now spreading worldwide. Before consumption, quinoa seeds undergo a dehulling process that produces large amounts of a waste product rich in saponins and other bioactive compounds. In this study, the by-product of quinoa seed dehulling (quinoa hull powder, QHP) was analysed for its plant biostimulant activity. The objective was to analyze whether QHP could improve growth and induce biochemical and transcriptional changes under control or saline (25, 50, and 100 mM NaCl) conditions in the model plant Arabidopsis thaliana. QHP was supplied either by pre-soaking seeds prior to sowing (seed priming) or added to the seedling growth medium. Complete and partial recovery of germinability to control levels was observed in seeds primed with 0.05 mg mL-1 QHP in the presence of 50 and 100 mM NaCl, respectively. Seedlings transferred to QHP-supplemented saline medium showed improved shoot and root biomass and primary root length as well as reduced oxidative stress (MDA, and H2O2 production). RT-qPCR analysis of stress-responsive genes revealed that some were induced by QHP alone while salt-induced expression of others was modulated by QHP. The phytochemical composition of QHP suggests that, in addition to saponins, protective compounds, such as proline, spermidine, carotenoids, and polyphenols, could be potentially responsible for its activity.

Aromatic ring-hydroxylating dioxygenases (ARHDs) play a crucial role in the aerobic biodegradation of both natural and anthropogenic aromatic compounds. Although their ability to process contaminants is not entirely understood, it is thought to have evolved from the transformation of structurally similar secondary plant metabolites (SPMs). Hence, to investigate this connection, we tested a variety of SPMs from the monoterpene and flavonoid classes as carbon sources and transcriptional effectors of several phylogenetically distant ARHD genes involved in the degradation of aromatic pollutants. Specifically, we focused on bphA1, nahA1 and phtA1 in Rhodococcus opacus C1, whose genomic analysis is also presented hereinafter, and bphA1a, nahA1-bphA1b and etbA1ab in Rhodococcus sp. WAY2. Whilst induction was only observed with (R)-carvone for bphA1a and nahA1-bphA1b of strain WAY2, and with p-cymene for nahA1 and nahA1-bphA1b of strains C1 and WAY2, respectively, an extensive inhibition by flavonoids was observed for most of the genes in both strains. To the best of our knowledge, our study is the first to report the effect of flavonoids and monoterpenes on the transcription of nahA1, etbA1 and phtA1 genes. In addition, we show that, in contrast to pseudomonads, many flavonoids inhibit the transcription of the ARHD genes in rhodococci. Thus, our work provides a new perspective on flavonoids as the transcriptional effectors of ARHDs, highlighting the significant variability of these enzymes and the divergent responses that they elicit. Moreover, our results contribute to understanding the complex interactions between microorganisms and SPMs and provide insights into the molecular basis of a number of them.

Adjuvants are crucial in vaccines and cancer therapies, enhancing therapeutic efficacy through diverse mechanisms. In vaccines, adjuvants are traditionally valued for amplifying immune responses, ensuring robust and long-lasting protection against pathogens. In cancer treatments, adjuvants can boost the effectiveness of chemotherapy or immunotherapy by targeting tumor antigens, rendering cancer cells more vulnerable to treatment. Recent research has uncovered new molecular-level effects of the adjuvants, mainly through epigenetic mechanisms. Epigenetics encompasses heritable modifications in gene expression that do not alter the DNA sequence, impacting processes such as DNA methylation, histone modification, and non-coding RNA expression. These epigenetic changes play a pivotal role in regulating gene activity, influencing immune pathways, and modulating the strength and duration of immune responses. Whether in vaccines or cancer treatments, understanding how adjuvants interact with epigenetic regulators offers significant potential for developing more precise, cell-targeted therapies across various medical fields. This review delves into the evolving role of adjuvants and their interactions with epigenetic mechanisms. It also examines the potential of harnessing epigenetic changes to enhance adjuvant efficacy and explores the novel use of epigenetic inhibitors as adjuvants in therapeutic settings.

Embigin (EMB) is a transmembrane glycoprotein highly expressed in glioblastoma multiforme (GBM), yet its role in GBM progression remains unclear. In this study, we investigate the function of intracellular EMB in promoting GBM progression and evaluate the effect of Ganxintriol A, a traditional Chinese herbal extract, in GBM treatment.

The chronic illness known as oral submucous fibrosis (OSF) results in tissue fibrosis, precancerous lesions, and scarring. It usually manifests itself in the buccal mucosa. It frequently occurs in the buccal mucosa. Von Hippel-Lindau (VHL) is an essential component of E3 ubiquitin ligase complex. The loss of VHL led to reduced fibrotic responses, accompanied by ameliorated fiber deposition. However, the precise impact of VHL on OSF is yet unclear. OSF tissues and normal mucosal tissues were applied to analyze the distinct expression of VHL and histone deacetylase 6 (HDAC6). Oral fibroblasts were treated to arecoline to simulate OSF in vitro, and molecular biological experiments were conducted to identify the role of VHL in buccal mucosa fibroblasts (BMFs). VHL was downregulated and HDAC6 was upregulated in OSF tissues and BMFs. Overexpression of VHL inhibited fibrosis in arecoline-treated BMFs. VHL inhibits the level of HDAC6 by inducing the ubiquitination of HDAC6. Knockdown of HDAC6 reduces the fibrogenic ability of BMFs. Furthermore, overexpression of HDAC6 contributes to the activation of NF-κB signaling in BMFs. HDAC6 selective inhibitor ACY-1215 inhibited the NF-κB signaling pathway. VHL attenuated arecoline-induced OSF by inhibiting the ubiquitination of HDAC6 and blocking NF-κB pathway. As a result, our study offers new perspectives into the discovery of novel tactics that can be employed against OSF.

The formation of biofilm by foodborne pathogens increases the risk of foodborne diseases, resulting in major health risks. Research on strategies for eliminating biofilm formation by foodborne pathogens is urgently needed. Therefore, the objective of this study was to construct a new technique for controlling foodborne bacteria and inhibiting the biosynthesis of biofilm via using natural products. The essential orange oil (EOO) and cell-free filtrate of Lactobacillus pentosus RS2 were used as antibacterial and antibiofilm agents against B. cereus RS1, the strongest biofilm-forming strain. The mixture of cell-free filtrate (CFF) and EOO (CFF/EOO) was the best antibiofilm agent under all tested conditions. The minimal inhibitory concentration (MIC) test revealed that 400 μl ml-1 CFF and 16 μl ml-1 EOO completely inhibited the growth of B. cereus. The treatment of three commercial surfaces with CFF/EOO resulted in a high reduction in biofilm synthesis, with adhesion percentages of 33.3, 36.3, and 40.8% on stainless steel, aluminum foil, and aluminum, respectively. The aluminum surface had the greatest adhesion with B. cereus RS1 among the three tested surfaces. These results were confirmed by expression analysis of three essential coding genes, sinR, calY, and spo0A, participating in biofilm formation in B. cereus. The biofilm-negative regulator gene sinR was overexpressed, whereas the biofilm-positive regulator genes calY and spo0A were down-expressed in B. cereus RS1 after treatment with antibiofilm agents, compared with those in the untreated sample. This study revealed that CFF/EOO was more effective at activating sinR (2.099 ± 0.167-fold increase) and suppressing calY and spo0A (0.314 ± 0.058 and0.238 ± 0.04-fold decrease, respectively) compared to control. This result confirmed the biochemical estimation of biofilm formation in B. cereus after treatment with all the experimental agents. The EOO and CFF of L. pentosus RS2 can be used as strong antibacterial and antibiofilm agents against foodborne bacteria. These products reduced the biofilm formation on trade surfaces affecting the expression of three essential biofilm regulatory genes. This study considered novel research concerning the potential antibiofilm activity of EOO combined with CFF of L. pentosus and the molecular analysis of genes regulating biofilm production under stress of CFF/EOO.

Environmental factors play an important role in anthocyanin biosynthesis, and potassium, an essential nutrient for blueberry growth, can act as an enzyme activator. However, few reports exist on the transcriptional and anthocyanin metabolic changes in blueberries regulated by potassium. The results indicated that potassium treatment significantly increased the contents of malvidin, petunidin, and delphinidin in blueberry fruits and accelerated early color development, particularly favoring the accumulation of darker pigments such as malvidin, petunidin, and delphinidin when applied at the young fruit stage. Transcriptome analysis identified 102 glucose metabolism-related genes and 12 differential potassium transport genes potentially involved in potassium-mediated anthocyanin synthesis and accumulation, with AKT1 and KUP potassium transporters being upregulated under potassium fertilization. In the anthocyanin biosynthesis pathway, 13 genes, including UFGT, F3H, CHI, HCT, C12RT1, DFR, and F3'5'H, were closely linked to flavonoid and anthocyanin metabolite synthesis regulated by potassium. Furthermore, potassium treatment markedly enhanced the activities of key enzymes, F3H, F3'5'H, and UFGT, in the anthocyanin synthesis pathway of blueberry fruits. Overall, these findings elucidate the influence of potassium application timing on anthocyanin synthesis and provide valuable insights into the molecular mechanisms governing anthocyanin biosynthesis in blueberries.

Carbon dots, are now considered safe, environment-friendly materials. Spermidine carbon dots (Spd-CDs) have been used as new agrochemicals for abiotic stress, but in-depth studies of salt stress remain scarce. Here, foliar application of Spd-CDs improved salt stress tolerance in tomatoes, and the beneficial effects were concentration-dependent. Tomato seedlings supplied with Spd-CDs (3.0 mg/L) had a greater height, a higher maximum quantum yield of PSII, and a higher net photosynthetic rate than controls after being exposed to 120 mM NaCl for 7 d. Molecular evidence showed that Spd-CDs promoted H2O2 molecule production by inducing the expression of respiratory burst oxidase homolog 1 (rboh1) and polyamine oxidase 5 (pao5), thus causing H2O2 molecule production and conferring resistance to salt stress. The role of RBOH1- and PAO5-dependent H2O2 molecule generation was evaluated by manipulating endogenous H2O2 levels and in rboh1 and pao5 mutants. Spd-CDs-meditated H2O2 regulation of salt tolerance could be articulated by reducing iron deficiency, maintaining ion homeostasis, and reducing root-to-shoot Na+ loading. Overall, the ROS signal molecule produced by RBOH1 and PAO5 protein was involved in the control of salt tolerance by Spd-CDs. These findings demonstrate that Spd-CDs are an effective and durable strategy to improve plant performance under salt stress, and to increase food security and quality.

Although bacterial cells typically contain a single chromosome, some species are naturally polyploid and carry multiple copies of their chromosome. Polyploid chromosomes can be identical or heterogeneous, the latter giving rise to bacterial heterozygosity. Although the benefits of heterozygosity are well studied in eukaryotes, its consequences in bacteria are less understood. Here, we examine this question in the context of antibiotic resistance to understand how bacterial genomic heterozygosity affects bacterial survival. Using a cell-wall-deficient model system in the actinomycete Kitasatospora viridifaciens, we found that heterozygous cells that contain different chromosomes expressing different antibiotic resistance markers persist across a broad range of antibiotic concentrations. Recombinant cells containing the same resistance genes on a single chromosome also survive these conditions, but these cells pay a significant fitness cost due to the constitutive expression of these genes. By contrast, heterozygous cells can mitigate these costs by flexibly adjusting the ratio of their different chromosomes, thereby allowing rapid responses in temporally and spatially variable environments. Our results provide evidence that bacterial heterozygosity can increase adaptive plasticity in bacterial cells in a similar manner to the evolutionary benefits provided by multicopy plasmids in bacteria.

The current study evaluated the effects of dietary supplementation of Triphala (TR) on yellow perch (Perca flavescens) growth performance, immune response, related gene expression, and intestinal histological structure. The experimental design included four groups: one control group (0% TR/ kg diet) and three TR-supplemented groups with 2, 4, and 6%/kg diet for four weeks and each group was allocated in triplicates with 30 fish each. Sampling included three fish from each replicate for evaluating immune response and gene expression. Findings showed that Triphala markedly improved growth performance, Immunoglobulin M (IgM) levels, lysozyme activity, and Nitric Oxide (NO) activity with the most significant (p < 0.05) results for 6% TR/kg diet group. The TR groups also showed significantly decreased glucose and cortisol concentrations with the lowest values for the 6% TR/kg diet group. Moreover, TR-incorporated groups revealed significantly upregulated expression (p < 0.05) of growth [Insulin-Like Growth Factor-1 (IGF-1)] and immune [Alpha 2 Macroglobulin (A2M), Serum Amyloid A (SAA) and Complement Component C3 (CCC3)] genes in incorporated groups, specially the 6% TR group. Moreover, the intestinal morphometric histological analysis revealed that villus length was increased in a dose-dependent manner, coping with other enhanced parameters. Current results endorse the positive effects of Triphala incorporation on yellow perch farming as a safe alternative option to enhance growth performance, immune response, related gene expression, and intestinal histology.

Osimertinib, a third-generation EGFR-tyrosine kinase inhibitor, is the first-line therapy for lung cancer harboring EGFR mutations. The mechanisms underlying osimertinib resistance are diverse, with approximately half remaining unknown. Epigenetic dysregulation is implicated in drug resistance; however, the mechanisms remain unclear. Therefore, we investigated epigenetic involvement in osimertinib resistance and its therapeutic potential. We established osimertinib-resistant cells and used an assay for transposase-accessible chromatin using sequencing to evaluate chromatin accessibility, finding significant changes post-resistance. Combining the assay for transposase-accessible chromatin and RNA sequencing data, we identified FGF1 as a resistance-related gene regulated by histone modifications. FGF1 induced osimertinib resistance, and its suppression attenuated resistance. Bromodomain and extra-terminal domain inhibitors combined with osimertinib overcame osimertinib resistance by reducing FGF1 expression. Increased FGF1 expression was observed in osimertinib-resistant clinical samples. This combination therapy was effective in cell lines and mouse xenograft models. These results suggest targeting histone modifications using bromodomain and extra-terminal domain inhibitors as a novel approach to overcoming osimertinib resistance.

Inflammatory bowel disease (IBD) encompasses chronic inflammation of the colon and rectum, posing significant health challenges. Previous studies have shown potential therapeutic effects of natural compounds on IBD. Chrysin, a naturally occurring flavonoid, has been suggested to modulate inflammatory pathways and gut microbiota, but its comprehensive impact on ulcerative colitis remains inadequately explored.

Doxorubicin (DOX)-associated cardiotoxicity is characterized by long-term manifestations, whose mechanisms remain incompletely understood, and is exacerbated by various risk factors, with age being a prominent contributor. The objective of this study was to assess the enduring cardiac molecular impacts of DOX in old CD-1 male mice, focusing on ubiquitinated proteins. At 19 months of age, DOX group received a cumulative dose of 9.0 mg/kg of DOX, while control animals got saline solution. Animals were sacrificed 2 months after the administration. DOX induced heart structural changes and increased proteolytic activity. Additionally, increased protein ubiquitination was observed in DOX group, despite the decreased content of the E3 ubiquitin-protein ligase Atrogin-1. A search of poly-ubiquitinated proteins, enriched by tandem ubiquitin-binding entities (TUBEs), showed increased poly-ubiquitination of proteins associated with sarcomere organization and mitochondrial metabolism processes by DOX. Increased mitochondrial density inferred by higher citrate synthase activity was found in DOX group. Moreover, decreased biogenesis and auto(mito)phagy occurred in DOX animals, proven by decreased peroxisome proliferator-activated receptor γ coactivator 1 α, Beclin1 and microtubule-associated protein light chain 3 content. These findings indicate a reduction in mitochondrial biogenesis and accumulation of dysfunctional mitochondria in the aged heart, along with elevated levels of poly-ubiquitinated proteins after DOX treatment. Thus, the disruption of mitochondrial remodeling and impaired protein ubiquitination emerge as enduring consequences of DOX-induced cardiotoxicity, persisting for even 2 months after DOX exposure. This underscores the long-lasting impact of DOX, with significant effects continuing beyond the period of administration, which advocates for longer clinical surveillance.

Endocrine resistance remains a significant therapeutic challenge in estrogen receptor-positive (ER+) breast cancer, the most common subtype, contributing to increased morbidity and mortality. The interaction between ER and HER family receptors, particularly HER2 and epidermal growth factor receptor (EGFR), drives resistance to standard therapies such as tamoxifen and trastuzumab by activating key signaling pathways, including PI3K/AKT and RAS/MAPK. Dysregulated miRNAs, which are non-coding gene expression regulators, have been linked to therapy response.

Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step toward engineering improved drought resilience. However, the molecular responses to drought are complex as they depend on multiple factors, including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is especially challenging. In this study, we investigated tissue-specific responses to mild drought (MD) in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, and demonstrated the benefits of transcriptome fixation for studying mild stress responses at a single-cell level. We present a curated and validated single-cell atlas, comprising 50 797 high-quality cells from almost all known cell types present in the leaf. All cell type annotations were validated with a new library of reporter lines. The curated data are available to the broad community in an intuitive tool and a browsable single-cell atlas (http://www.single-cell.be/plant/leaf-drought). We show that the mesophyll contains two spatially separated cell populations with distinct responses to drought: one enriched in canonical abscisic acid-related drought-responsive genes, and another one enriched in genes involved in iron starvation responses. Our study thus reveals a dual adaptive mechanism of the leaf mesophyll in response to MD and provides a valuable resource for future research on stress responses.

Isorhamnetin (ISO), a dietary flavonoid, has been shown to possess antioxidant, anti-cancer, and anti-inflammatory properties. Cancer-associated fibroblasts (CAFs), found in the tumor microenvironment of several types of cancer including pancreatic ductal adenocarcinoma (PDAC) impact the tumor growth and development of chemoresistance. Thus, modulating CAFs is an attractive mean to increase the efficacy of therapies targeting cancer cells. In this study, the anti-proliferative effect of ISO and the underlying transcriptomic profile of ISO-treated PDAC-derived CAFs were investigated. ISO treatment showed a time- and concentration-dependent decrease in cell viability with a slight increase in apoptotic cells. Microarray and cell cycle analyses revealed ISO induced downregulation of pathways in cell cycle and DNA replication; and G2/M checkpoint. Cell cycle analysis showed cells in the G2/M phase were increased. In response to the treatment, hallmark for p53 pathway genes, known to regulate cell cycle checkpoints, were highly upregulated. Moreover, ISO-treated cells had an increased area of the mitochondrial network, but lower mitochondrial membrane potential accompanied by a decrease of ATP production, measured by oxygen consumption rate. Inflammatory gene expression of IL1A1, IL6, CXCL1, and LIF were significantly inhibited in ISO-treated CAFs. Taken together, our results demonstrated that the cytostatic effect of ISO on human CAFs was mediated by inducing cell cycle arrest at G2/M phase associated with activation of p21, impaired mitochondrial homeostasis, and inhibition of inflammatory mediators gene expression, warranting further investigation for its use in combinatorial therapy that target both the cancer and the tumor microenvironment as a whole.

RNA guanine (G)-quadruplexes (rG4) are unique noncanonical structures composed of stacked guanine quadruplexes that play diverse roles in regulating gene expression, from transcription to protein synthesis. This study proposes a new splice-switching therapy using G-quadruplex-inducing antisense oligonucleotides (G-ASOs) to reinstate dystrophin expression in Duchenne muscular dystrophy (DMD) models. G-ASOs consist of two functionally independent domains that enable the formation of RNA/DNA hetero-G-quadruplex (hG4) structures. The antisense domain binds to complementary sequences within the target RNA, while the G-rich domain, which contains a sequence of continuous guanines (G-tract), interacts with the G-rich region of target RNA to form an hG4 structure. This precise binding forms an hG4 structure that effectively interrupts alternative splicing. In contrast to the traditional methods that block sterically, this technique employs steric hindrance by forming hG4 structures. Significantly, our findings show that hG4 structures can still form effectively even when the G-rich region of the target RNA and the antisense sequence are as much as 70 nucleotides apart. To address the challenges associated with G-quadruplex formation via G-ASO self-assembly, we developed bulge-containing G-ASOs. This enhancement improves both the efficiency of hG4 formation and the induction of exon-skipping therapy. In summary, this study highlights the potential of G-ASOs in gene therapy, specifically DMD, and marks significant progress in the development of novel therapeutic strategies. These findings highlight the effectiveness of G-ASOs in exon-skipping therapy and demonstrate the advancements in RNA structural manipulation.

We performed an integrated analysis of genome-wide DNA methylation and expression datasets in normal cells and healthy animals exposed to polyphenols with estrogenic activity (i.e. phytoestrogens). We identified that phytoestrogens target genes linked to disrupted cellular homeostasis, e.g. genes limiting DNA break repair (RNF169) or promoting ribosomal biogenesis (rDNA). Existing evidence suggests that DNA methylation may be governed by sirtuin 1 (SIRT1) deacetylase via interactions with DNA methylating enzymes, specifically DNMT3B. Since SIRT1 was reported to be regulated by phytoestrogens, we test whether phytoestrogens suppress genes related to disrupted homeostasis via SIRT1/DNMT3B-mediated transcriptional silencing. Human MCF10A mammary epithelial cells were treated with phytoestrogens, pterostilbene (PTS) or genistein (GEN), followed by analysis of cell growth, DNA methylation, gene expression, and SIRT1/DNMT3B binding. SIRT1 occupancy at the selected phytoestrogen-target genes, RNF169 and rDNA, was accompanied by consistent promoter hypermethylation and gene downregulation in response to GEN, but not PTS. GEN-mediated hypermethylation and SIRT1 binding were linked to a robust DNMT3B enrichment at RNF169 and rDNA promoters. This was not observed in cells exposed to PTS, suggesting a distinct mechanism of action. Although both SIRT1 and DNMT3B bind to RNF169 and rDNA promoters upon GEN, the two proteins do not co-occupy the regions. Depletion of SIRT1 abolishes GEN-mediated decrease in rDNA expression, suggesting SIRT1-dependent epigenetic suppression of rDNA by GEN. These findings enhance our understanding of the role of SIRT1-DNMT3B interplay in epigenetic mechanisms mediating the impact of phytoestrogens on cell biology and cellular homeostasis.

Studies have shown that essential oils not only increase cell viability but also affect lipid metabolism in mammals. However, the extent to which these effects are realized in goose liver has not yet been fully elucidated. The object of research is to investigate the effects of four essential oil mixtures (juniper oil, mint oil, thyme oil, rosemary oil) on lipid metabolic gene expressions in goose. We measured mRNA levels of metabolic genes (ACSBG2, ELOVL1, ELOVL2, CYP2Cl9, CYP2K1), antioxidative gene (SOD1) and very low-density lipoprotein triglyceride (VLDL) synthesis genes (APOB, FOXO1, MTTP), in goose (Anser anser) liver. Search groups were formed as C (control; no additives), EK1 (0.4 mL/L essential oil mixture supplemented) and EK2 (0.8 mL/L essential oil mixture supplemented). The relative expression levels of genes in the liver were measured using RT-qPCR. β-Actin was used as reference gene control for normalization of qPCR data. As a result, essential oil supplementation downregulated metabolic genes compared to the control group. APOB gene among VLDL genes was significantly downregulated. Antioxidative effect gene was downregulated in parallel with the others. This indicates that essential oil intake with drinking water downregulates the genes involved in lipid metabolism in goose liver. Our data show that essential oils have a significant effect on the regulation of genes and pathways involved in hepatic lipid metabolism.

Background: Rat models are widely used to study cataracts due to their cost-effectiveness and prominent physiological and genetic similarities to humans The objective of this study was to identify genes involved in cataractogenesis due to galactose exposure in rats. Methods: We analyzed four datasets from the Gene Expression Omnibus, including both ex vivo and in vivo models of cataracts in different rat strains. Feature selection tools were used to identify genes potentially relevant in cataract-related gene expression. A decision tree algorithm was implemented, and its predictions were interpreted using SHAP and LIME. To validate gene expression levels, PCR was conducted on six rat lenses cultured in M199 medium and galactose to induce cataract and six lenses cultured in M199 alone. Results: Using feature selection tools, four key genes-PLAGL2, CMTM7, PCYT1B, and NR1D2-were identified. Only PCYT1B was significantly differentially expressed between the cataract and control groups across analyzed datasets. The model showed strong predictive performance, particularly in ex vivo datasets. SHAP and LIME analyses revealed that CMTM7 had the largest impact on model predictions. PCR results did not show significant differences in gene expression between the cataract and control groups. Conclusion: The decision tree model trained on an in vivo dataset could predict ex vivo and in vivo cataracts despite no significant gene expression differences found between the cataract and control groups. Given a small number of samples, larger studies are needed to validate our findings.