Electronic Journal of Biotechnology

Circulating exosomal miRNA signatures as potential biomarkers and therapeutic targets in biliary colic

2025-11-18T14:38:12+00:00

Background: Biliary colic (BC), characterized by intermittent pain due to gallstone-related bile duct obstruction, remains poorly understood at the molecular level. Circulating exosomal microRNAs (miRNAs) have emerged as potential biomarkers for various diseases. This study aimed to identify exosomal miRNA profiles in BC patients and explore their therapeutic implications.

Results: Analysis of plasma exosomal miRNAs from 10 BC patients during acute attacks and 10 healthy controls (HCs) revealed distinct expression patterns separating BC from HC groups. Integration of differential expression analysis, WGCNA, and LASSO regression identified 7 key miRNAs (hsa-miR-142-3p, hsa-miR-32-5p, hsa-miR-374a-3p, hsa-miR-155-5p, hsa-miR-425-3p, hsa-miR-584-5p, hsa-miR-185-5p) strongly associated with BC. Support vector machine models using these miRNAs achieved excellent diagnostic performance (AUC = 1.0, where AUC represents Area Under the Curve). miRNA-targeting drugs including Remlarsen and Cobomarsen showed potential for therapeutic intervention.

Conclusions: This study identified specific exosomal miRNA signatures that distinguish BC patients from HC and revealed potential miRNA-targeting therapeutics. These findings advance our understanding of BC pathophysiology and provide direction for developing novel diagnostics and treatments.

Tianma granules: Bridging traditional medicine and modern science to combat colorectal cancer via ferroptosis

2025-11-18T14:54:39+00:00

Background: This study aims to investigate the ferroptosis-inducing effects of Tianma Granules (TMGs) in colorectal cancer and elucidate its molecular mechanisms. Ferroptosis, an iron-dependent form of regulated cell death, represents a novel therapeutic target for cancer. We combined network pharmacology with experimental validation to explore TMG’s anti-cancer potential through ferroptosis modulation.

Results: Network pharmacology identified 382 ferroptosis-related genes overlapping with 12,944 CRC-associated targets (p < 0.05), with SLC7A11, GPX4, SAT1, PTGS2, and GLS2 prioritized as core targets. In vitro, TMG dose-dependently suppressed CRC cell proliferation (p < 0.05), elevated reactive oxygen species (p < 0.05) and ferrous ion levels (p < 0.01), effects reversed by ferroptosis inhibitor, Ferrostatin-1. c-Casp3 levels were unchanged (p > 0.05), excluding apoptosis. Transmission electron microscopy revealed mitochondrial cristae fragmentation and vacuolation, hallmark features of ferroptosis. Molecular analyses demonstrated TMG-mediated downregulation of SLC7A11 and GPX4, alongside upregulation of SAT1, PTGS2, and GLS2 (p < 0.05). In xenograft models, high-dose TMG (23.2 g/kg) reduced tumor volume, attenuated cachexia, and elevated intratumoral ROS and Fe²⁺ levels (p < 0.01), corroborating ferroptosis induction in vivo.

Conclusions: TMG suppresses CRC progression by inducing ferroptosis via dual inhibition of SLC7A11/GPX4 and activation of SAT1/PTGS2/GLS2. This study bridges traditional medicine and ferroptosis biology, positioning TMG as a novel therapeutic candidate for CRC.

Chufeng Yisun Decoction treats dry eye syndrome by inhibiting the PI3K/Akt pathway

2025-11-18T15:13:15+00:00

Background: Dry eye disease seriously affects people’s work and life. Chufeng Yisun Decoction is a traditional Chinese medicine decoction used in treating dry eye disease. This study aims to explore the core active ingredients, targets, and mechanisms of CFYSD in dry eye disease, providing new insights for the dry eye disease treatment.

Results: A total of 196 target genes were screened from Chufeng Yisun Decoction, and 170 genes were related to dry eye disease. Gene Ontology and KEGG enrichment analyses showed that Chufeng Yisun Decoction influenced dry eye disease through “Lipid and atherosclerosis”, “Fluid shear stress and atherosclerosis”, and “PI3K-Akt”. The core targets of Chufeng Yisun Decoction in treating dry eye disease were Akt1 and IL-1β. The core active ingredients were kaempferol, wogonin, and quercetin. Molecular docking results showed that the binding energies of kaempferol and Akt1, wogonin and Akt1, quercetin and Akt1, and quercetin and IL-1β were −6.1, −6.1, −6.1, and −7.9 kcal/mol, respectively. Chufeng Yisun Decoction significantly alleviated cell damage and reduced PI3K/Akt pathway-related protein expression. PI3K activation partially reversed the therapeutic effect of Chufeng Yisun Decoction on dry eye disease.

Conclusions: Chufeng Yisun Decoction treats dry eye disease by inactivating the PI3K/Akt pathway through multi-ingredients and multi-targets.

Transcriptomic and metabolomic profiling reveals key mechanisms of alkaline stress tolerance in rice

2025-11-18T15:29:29+00:00

Background: Alkaline stress severely restricts rice growth and yield by disrupting ion balance, nutrient uptake, and oxidative metabolism. Clarifying the molecular mechanisms of tolerance is vital for breeding resilient varieties. This study explores transcriptional and metabolic adaptations in an alkali-tolerant (Qijing 10, LD) and sensitive (Tengxi 138, WL) rice variety under alkaline stress.

Results: Transcriptomic analysis revealed 1297 differentially expressed genes (DEGs) in the sensitive variety under alkaline stress (TWL), primarily enriched in pathways related to antioxidant enzyme synthesis (e.g., peroxidase genes), transmembrane ion transport, and membrane lipid stabilization pathways. In contrast, the tolerant variety (TLD) exhibited only 38 DEGs, suggesting transcriptional homeostasis achieved via suppression of stress-related gene overactivation. Metabolomic profiling demonstrated stable levels of key lipids (phosphatidic acid, galactolipids) and osmolytes (proline, betaine) in the tolerant variety under stress, whereas the sensitive variety accumulated lipid peroxidation products (malondialdehyde, MDA) and displayed dysregulated carbohydrate metabolic dysregulation. Integrated multi-omics analysis indicated that the tolerant variety coordinated lipid metabolism gene modulation with antioxidant metabolite accumulation, establishing dual barriers for ROS scavenging and membrane protection. Conversely, transcriptional dysregulation in the sensitive variety led to metabolic collapse.

Conclusions: Alkaline tolerance in rice hinges on the synergistic modulation of stress-responsive genes and metabolic networks to preserve redox equilibrium and membrane function. The tolerant variety’s capacity to stabilize transcriptional activity and metabolic flux underlies its resilience. These results elucidate key molecular and metabolic determinants of alkaline tolerance, offering strategic targets for breeding rice cultivars adapted to alkaline environments.

Whole-genome analysis and biosynthetic gene cluster profiling of Stenotrophomonas sp. ASucR1 isolated from Sof Umer Cave, Ethiopia

2025-11-18T16:14:37+00:00

Background: Sof Umer Cave is a unique habitat that hosts industrially significant microbes. In this study, Stenotrophomonas sp. ASucR1 was isolated from the cave rock and screened for antimicrobial activity. High-molecular-weight genomic DNA was extracted and subjected to whole-genome sequencing using the Illumina NovaSeq platform. Comprehensive genomic and biosynthetic gene cluster (BGC) profiling was conducted.

Results: In vitro tests revealed that Stenotrophomonas sp. ASucR1 exhibited a broad spectrum of antagonistic activity. Functional genome annotation identified diverse biosynthetic gene clusters (BGCs) and metabolic pathways, including genes involved in the synthesis of secondary metabolites. A total of 19 BGCs were identified, several of which showed no matches in the minimum information about a biosynthetic gene cluster (MiBIG) database, indicating the presence of previously uncharacterized bioactive compounds. Single-nucleotide polymorphism (SNP) analysis showed that 91.5% of variants were identified within coding regions, with 85.84% being synonymous. Classification of SNPs and insertion-deletion mutations through clusters of orthologous groups (COG) analysis highlighted their association with key biological functions.

Conclusions: This study highlights the metabolic versatility and biosynthetic potential of Stenotrophomonas sp. ASucR1, a promising candidate for antimicrobial development and biotechnological applications. The identification of various biosynthetic gene clusters paves the way for exploring bioactive compounds with pharmaceutical significance.

ALYREF promotes malignant behaviors and inhibits ferroptosis in colon cancer cells by stabilizing PCSK9 mRNA

2025-11-18T17:15:03+00:00

Background: Colon cancer is a prevalent malignancy causing significant global morbidity and mortality. The RNA methyltransferase Aly/REF export factor (ALYREF), which binds 5-methylcytosine (m5C)-modified messenger RNA, represents a potential diagnostic and therapeutic target in cancer. However, its specific role and mechanism in colon cancer progression remain unexplored.

Results: ALYREF expression was significantly elevated in colon cancer tissues and cell lines compared to normal controls. Depletion of ALYREF suppressed colon cancer cell proliferation, migration, and invasion, while simultaneously promoting apoptosis and ferroptosis. Analysis revealed proprotein convertase subtilisin/kexin type 9 (PCSK9) is highly expressed in colon cancer and positively regulated by ALYREF. Mechanistically, ALYREF directly bound to and stabilized PCSK9 messenger RNA in a manner dependent on m5C modification. Crucially, the anti-tumor effects resulting from ALYREF knockdown were reversed by overexpressing PCSK9. Consistent with cellular findings, silencing ALYREF significantly inhibited tumor growth in vivo using xenograft models.

Conclusions: This study demonstrates that ALYREF drives colon cancer malignancy by stabilizing PCSK9 messenger RNA via m5C methylation, thereby enhancing PCSK9 expression. These findings establish the ALYREF/PCSK9 axis as a critical mechanism in colon cancer progression, highlighting its potential as a novel therapeutic target for intervention.

Qualitative phytochemical analysis, thin-layer chromatographic profiling, and antimicrobial potential of banana cultivars

2025-11-18T18:36:20+00:00

Background: Banana plants possess numerous medicinal properties due to the presence of various phytochemicals. This study aimed to assess the phytochemical profile of the crude extracts of leaf, pseudostem, and corm parts of selected banana cultivars via standard techniques and thin-layer chromatography (TLC) and to evaluate their antimicrobial activities against several food-borne and clinically important human pathogens, including two Gram-positive bacteria, six Gram-negative bacteria, and four yeasts.

Results: The results demonstrated that the Cachaco (41%), Tereza (38%), Fougamou (30%), Pelipita (28%), Giant Cavendish (26%), and Kluai Teparot (26%) cultivars presented significant antimicrobial activity against pathogens compared with Dole (24%), Namwah Khom (20%), and Mbwazirume (16%) cultivars. Moreover, the leaves (40%) of cultivars extracted in water (61%) and acetone (55%) yielded the most active antimicrobial extracts compared with the pseudostem (33%) and corm (26%) extracts prepared in ethanol (38%) or hexane (28%). Overall, the antimicrobial activities with the lowest 50% inhibitory concentration (IC₅₀) values, especially those with values less than 200 µg/mL for bacteria and 100 µg/mL for yeasts, were reported in the leaves of Cachaco and Giant Cavendish, followed by different parts of Tereza, Pelipita, and other banana cultivars. Phytochemical analysis and TLC profiling confirmed the presence of various groups of phytochemicals in the extracts of the selected banana cultivars.

Conclusions: This study revealed that the Cachaco, Giant Cavendish, Pelipita, and Tereza cultivars possess significant antimicrobial activity, warranting further bioassay-guided antimicrobial studies for the isolation and identification of bioactive compounds, which could be useful as novel drug candidates with the highest potency.

Mapping the genomic position of xylanase genes on Bacillus safensis FB03 and optimizing the xylanase fermentation medium by Box-Behnken Design from an unconventional carbon source

2025-11-18T18:48:31+00:00

Background: The ability of Bacillus safensis to synthesize xylanase and other industrially important enzymes utilizing lignocellulosic biomass makes it advantageous for a variety of biotechnology applications. Thus, the current investigation aimed to optimize conditions and medium components for maximizing xylanase production by a newly isolated Bacillus safensis strain using banana rachis (peel of banana tree) as a novel source of carbon.

Results: Upon employing Box-Behnken Design (BBD) statistical approach, the highest enzyme activity was obtained 25.24 U/ml at 2 g/L banana rachis, 1 g/L yeast extract, 1 g/L K₂HPO₄, 5 g/L NaNO₃, 35°C and 72 h of incubation time. The purified enzyme showed 10 times higher enzyme activity (143.6 U/ml) with 2.3 mg/ml protein concentration. The enzyme was found to maintain stability up to 60°C in a wide range of pH (6 to 10). Analysis of whole genome sequencing data revealed the presence of xylanase production and xylan metabolic genes (xynA, xynB, xylP, xylT) on Bacillus safensis FB03. Also, from genome annotation, different carbohydrate metabolic genes such as glycoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), auxiliary activities (AAs), and carbohydrate binding modules (CBMs) were identified.

Conclusions: In accordance with our research, banana rachis can be considered as a major medium component to develop an economical fermentation process for the production of xylanase by Bacillus safensis FB03. Additionally, identification of the genomic location of xyl genes provides valuable insight towards genetic engineering for the development of a more potent industrial strain.

METTL16 promotes osteosarcoma progression by inducing m6A methylation of the UBE3A and Notch signaling pathway

2025-11-18T19:08:31+00:00

Background: N6-methyladenosine (m⁶A) methylation plays a key role in osteosarcoma (OS) progression. This study aimed to elucidate the function and mechanism of methyltransferase 16 (METTL16), an m⁶A methyltransferase, in OS progression.

Results: Bioinformatics analysis with quantitative reverse-transcription polymerase chain reaction (qRT-PCR) revealed high METTL16 expression in OS. After performing cell functional experiments, METTL16 silencing was shown to decrease the proliferation, migration, and invasion of OS cells. Using qRT-PCR, methylated RNA immunoprecipitation quantitative polymerase chain reaction (MeRIP-qPCR), Western blotting, luciferase, RNA-binding protein immunoprecipitation (RIP), and RNA stability assays, METTL16 induced the m⁶A methylation of ubiquitin protein ligase E3A (UBE3A) to promote UBE3A expression and mRNA stability in OS cells in a fragile X messenger ribonucleoprotein 1 (FMR1)-dependent manner. Moreover, in vitro and in vivo results showed that UBE3A activated the Notch signaling pathway, thereby promoting OS cell malignancy. METTL16 knockdown partly reversed the oncogenic role of UBE3A in OS cells.

Conclusions: METTL16 acts as a tumor promotor in OS progression by modulating UBE3A expression via m⁶A methylation to activate the Notch signaling pathway. The findings highlight the therapeutic potential of disrupting the METTL16–UBE3A–Notch pathway axis in OS.

Kaixin San in treating vascular dementia via regulating the Bcl-2/Beclin-1/LC3A/B signaling pathway via animal experiments and network pharmacology analysis

2025-11-18T19:38:57+00:00

Background: Kaixin San (KXS), a traditional Chinese herbal formula, is used to treat vascular dementia (VaD), but its active ingredients and mechanisms remain unclear. This study combined animal experiments with network pharmacology to explore how KXS modulates the Bcl-2/Beclin-1/LC3A/B pathway in VaD treatment.

Results: LC‒MS/MS identified 164 active ingredients in the KXS ethanol extract. In 2-vessel occlusion model rats, KXS significantly improved learning and memory (p < 0.05 or p < 0.01) and reduced hippocampal CA1 neuronal damage. Western blotting showed KXS upregulated Bcl-2/Bcl-XL and downregulated Beclin-1, LC3A/B, and Bax (p < 0.05). Immunofluorescence confirmed increased Bcl-2 and decreased Beclin-1 expression. Network pharmacology predicted 73 targets and 174 pathways, with TNF, AKT1, IL-1β, PTGS2, and ESR1 as key targets. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis linked these targets to cancer, atherosclerosis, and AGE-RAGE signaling pathways.

Conclusions: KXS alleviates VaD by modulating autophagy and apoptosis via Bcl-2/Beclin-1/LC3A/B, with multi-target, multi-pathway effects. These findings support further investigation of KXS as a potential therapy for VaD.