Mutant Genes Research Articles

Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential.

Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.

Unraveling antibiotic resistance in Achromobacter mucicolens IA strain: genomic insights, structural analysis, and prospects for targeted therapeutics

ABSTRACT The mortality rate of infectious diseases caused by Achromobacter mucicolens is increasing. The enhanced antibiotic resistance among bacterial species through genetic transfer and mutations in the efflux mediating genes has made the treatment quite challenging. A. mucicolens is an aerobic, gram-negative, and non-fermenting opportunistic pathogen found in immunocompromised patients. A. mucicolens shows resistance against beta-lactams and other antibiotics through intrinsic resistance mechanisms, including multi-drug efflux pumps and beta-lactamases. In this study, the clinical isolate whole genome sequencing of A. mucicolens data was analyzed to identify the genes and mutations responsible for antimicrobial resistance. The identified genes and their mutants were then subjected to structural analysis to better understand the impact of mutations on the protein structure, and domain analysis was performed to investigate the role of domains in antibiotic resistance. A total of 4 genes, acrR, macB, msbA, and tolC , were identified with significant mutations, whereas macB was shortlisted for further analysis based on the conserved regions, sequence alignment, and the maximum number of mutations. All the mutants of the macB gene contain the two common domains, the ABC transporter-like ATP-binding domain and the AAA + ATPase domain. These domains are crucial in efflux mediating drug transport and can be targeted to design novel drugs for treating infections caused by A. mucicolens . IMPORTANCE Achromobacter species represent a significant threat as opportunistic pathogens, particularly in healthcare settings. Their resilience to antibiotics, demonstrated by strains like A. mucicolens , poses a serious challenge in treating infections, especially in immunocompromised patients. This study emphasizes the critical need for heightened vigilance among healthcare professionals regarding Achromobacter infections. By analyzing the whole genome sequencing data of A. mucicolens , the study sheds light on the genetic basis of antimicrobial resistance, aiding in more targeted treatment strategies. Furthermore, structural and domain analyses offer insights into how mutations impact protein structure and function, crucial for developing effective interventions. Ultimately, implementing rigorous sanitation measures and antibiotic stewardship protocols is needed to mitigate the spread of Achromobacter and safeguard vulnerable patient populations.

Emerging Role of Gene Therapy in Cancer

Cancer is one of the leading causes of death in the world, and researchers have been persistently studying the treatment of cancer. Although traditional treatment methods such as surgery, chemotherapy and radiotherapy are effective, they are often accompanied by serious side effects, drug resistance or limited effects on certain types of cancer. Therefore, it is urgent to develop more accurate and effective treatment plans. Cancer gene therapy is an innovative method to treat or prevent cancer by introducing or editing genetic material. Gene therapy brings new hope to the treatment of cancer, repairing mutant genes, activating the immune system or directly inducing cancer cell death. This review introduces some hot strategies of cancer gene therapy, including suicide gene therapy, tumor suppressor gene activation, immunotherapy, inhibition of oncogene activation, antiangiogenic gene therapy. The principles, application examples and advantages and disadvantages of these therapies in clinical research are also discussed. In addition, the challenges faced by gene therapy in improving safety and reducing side effects, and points out the direction of future research are also described, aiming to promote the transformation of these innovative therapies into conventional clinical applications.

A CC-Type Glutaredoxins GRX480 Functions in Cadmium Tolerance by Maintaining Redox Homeostasis in Arabidopsis

Cadmium (Cd) toxicity causes oxidative stress damage in plant cells. Glutaredoxins (GRXs), a type of small oxidoreductase, play a crucial role in modulating thiol redox states. However, whether GRXs act in Cd stress remains to be identified. Here, we reveal that Arabidopsis GRX480, a member of the CC-type family, enhances plant Cd stress tolerance. The GRX480 mutants exhibit enhanced sensitivity to Cd stress, manifested by shortened root, reduced biomass, lower chlorophyll and proline levels, and decreased photosynthetic efficiency compared with the wild type. The Cd concentration in GRX480 mutants is higher than the wild type, resulting from the inhibition of Cd efflux and transport genes transcription. Lower levels of GSH were detected in Cd-treated GRX480 mutants than in the wild type, indicating that GRX480 regulates plant Cd tolerance by influencing the balance between GSH and GSSG. Furthermore, the hyperaccumulation of reactive oxygen species (ROS) is associated with decreased expression of H2O2 scavenging genes in Cd-treated GRX480 mutants. Additionally, more toxic reactive carbonyl species (RCS), produced during oxidative stress, accumulate in Cd-treated GRX480 mutants than in wild type. Overall, our study establishes a critical role of GRX480 in response to Cd stress, highlighting its multifaceted contributions to detoxification and the maintenance of redox homeostasis.

Identification and characterization of LuxR solo homolog PplR in pathogenic Pseudomonas plecoglossicida NB2011

Pseudomonas plecoglossicida is a causative agent of visceral granulomas in large yellow croaker (Larimichthys crocea). Quorum sensing (QS) is widely involved in imparting virulence to pathogenic bacteria; however, it has not been studied in P. plecoglossicida. In this study, we annotated a LuxR family transcriptional regulator in P. plecoglossicida NB2011 and designated as PplR. We aligned the protein sequence by BlastP and Clustal X2, monitored the N-acyl-homoserine lactone (AHL) signal production through cross-feeding bioassay and HC-MS/MS; investigated exogenous AHL signal binding by recombinant expression and thin layer chromatography; constructed a deletion mutant of the target gene by method of double homologous recombination; sequenced the transcript RNA and analyzed the data; additionally, characterized phenotypes of wild type and mutant strain. The LuxR homolog PplR was found to share high similarity with PpoR—the LuxR solo of Pseudomonas putida—without a cognate LuxI. The wild-type strain did not produce any AHL signals and the recombinant LuxR protein was found to bind C6-L-homoserine lactone (C6-HSL), C8-HSL, 3-oxo-C10-HSL, and 3-oxo-C12-HSL. RNA-seq analysis indicated 84 differentially expressed genes—5 upregulated and 79 downregulated—mainly enriched in gene ontology terms, such as flagella-dependent motility, integral component of membrane, DNA binding and transcription, and metal ion binding, suggesting that PplR is a master transcription regulator. The mutant strain showed attenuated biofilm-forming ability and stress resistance, and the data support a role for PplR in the regulation of these traits in P. plecoglossicida NB2011 independent of the presence of AHL signals. This is the first study to provide QS-related information on P. plecoglossicida.

OsSTP1 mediates sucrose allocation to regulate rice responses to different nitrogen supply levels

Improving the nitrogen use efficiency is an effective way to increase the yield of rice, and maintaining carbon-nitrogen balance is essential for the normal growth and development of rice. To investigate the impact of the sucrose transporter protein OsSTP1 on nitrogen absorption in rice, in this study, we constructed transgenic lines overexpressing the sucrose transporter gene OsSTP1 (OsSTP1-OE1, OsSTP1-OE2) and mutant transgenic lines (osstp1-1, osstp1-2) from the wild type TB309. Further, we conducted a hydroponic experiment with four nitrogen supply levels of free nitrogen (FN, 0 mg/L), low nitrogen (LN, 10 mg/L), normal nitrogen (NN, 40 mg/L), and high nitrogen (HN, 80 mg/L) to study the responses of each line to different nitrogen supply levels during the seedling stage. The results showed that compared with the wild type and mutant lines in the LN group, the OsSTP1-overexpressing lines exhibited significantly increased biomass, root length, and plant height, decreased soluble sugar content in the leaves, and increased soluble sugar content in the roots. The results indicate that the soluble sugars produced by leaf photosynthesis are transported to the roots through the phloem to promote root growth and nitrogen uptake, thus increasing the aboveground biomass. This study has identified that OsSTP1 can affect the long-distance transport of carbohydrates from source to sink to promote root growth, ultimately influencing rice's absorption and accumulation of nitrogen, improving nitrogen use efficiency and providing reference for reducing nitrogen fertilizer application.

Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying human MIR96 mutations.

Progressive hearing loss is a common problem in the human population with no effective therapeutics currently available. However, it has a strong genetic contribution, and investigating the genes and regulatory interactions underlying hearing loss offers the possibility of identifying therapeutic candidates. Mutations in regulatory genes are particularly useful for this, and an example is the microRNA miR-96, a post-transcriptional regulator which controls hair cell maturation. Mice and humans carrying mutations in miR-96 all exhibit hearing impairment, in homozygosis if not in heterozygosis, but different mutations result in different physiological, structural and transcriptional phenotypes. Here we present our characterisation of two lines of mice carrying different human mutations knocked-in to Mir96. We have carried out auditory brainstem response tests to examine their hearing with age and after noise exposure and have used confocal and scanning electron microscopy to examine the ultrastructure of the organ of Corti and hair cell synapses. Bulk RNA-seq was carried out on the organs of Corti of postnatal mice, followed by bioinformatic analyses to identify candidate targets. While mice homozygous for either mutation are profoundly deaf from 2weeks old, the heterozygous phenotypes differ markedly, with only one mutation resulting in hearing impairment in heterozygosis. Investigations of the structural phenotype showed that one mutation appears to lead to synaptic defects, while the other has a much more severe effect on the hair cell stereociliary bundles. Transcriptome analyses revealed a wide range of misregulated genes in both mutants which were notably dissimilar. We used the transcriptome analyses to investigate candidate therapeutics, and tested one, finding that it delayed the progression of hearing loss in heterozygous mice. Our work adds further support for the importance of the gain of novel targets in microRNA mutants and offers a proof of concept for the identification of pharmacological interventions to maintain hearing.

Resistance risk assessment of Rhizoctonia solani to four fungicides.

Hexaconazole, thifluzamide, difenoconazole and azoxystrobin are widely used fungicides for the control of Rhizoctonia solani in China. However, few studies have assessed the sensitivity and resistance risk of R. solani to these four fungicides. The sensitivities of 126 R. solani isolates to hexaconazole, thifluzamide, difenoconazole and azoxystrobin were determined, with average half maximal effective concentration (EC50) values of 0.0386, 0.0659, 0.663 and 1.508 μg mL-1, respectively. Field resistance monitoring of the four fungicides showed that the three isolates had moderate resistance to difenoconazole. Resistant mutants to the four fungicides were obtained by fungicide adaptation, and resistance could be stably inherited by most mutants. Compared with those of the parent isolates, the biological characteristics of hexaconazole-resistant mutants exhibited enhanced or similar compound fitness index (CFI), whereas most of the other mutants displayed reduced or comparable CFI. There was evidence of positive cross-resistance between hexaconazole and difenoconazole. In the presence of fungicides, the expression of the CYP51 genes in hexaconazole- and difenoconazole-resistant mutants significantly increased, the expression of SDH genes in thifluzamide-resistant mutants significantly decreased, and the expression of the Cyt b gene in azoxystrobin-resistant mutants did not significantly change. Based on these data, we speculated that R. solani had a low-to-medium resistance risk to four fungicides. The change of target gene expression may be one of the reasons for fungicide resistance in R. solani. This study provides a theoretical basis for monitoring resistance emergence and developing resistance management strategies to control R. solani. © 2024 Society of Chemical Industry.

Characterization of the gibberellic oxidase gene SdGA20ox1 in Sophora davidii (Franch.) skeels and interaction protein screening.

Gibberellin 20-oxidases (GA20oxs) are multifunctional enzymes involved in regulating gibberellin (GA) biosynthesis and controlling plant growth. We identified and characterized the GA20ox1 gene in a plant height mutant of Sophora davidii, referred to as SdGA20ox1. This gene was expressed in root, stem, and leaf tissues of the adult S. davidii plant height mutant, with the highest expression observed in the stem. The expression of SdGA20ox1 was regulated by various exogenous hormones. Overexpression of SdGA20ox1 in Arabidopsis resulted in significant elongation of hypocotyl and root length in seedlings, earlier flowering, smaller leaves, reduced leaf chlorophyll content, lighter leaf color, a significant increase in adult plant height, and other phenotypes. Additionally, transgenic plants exhibited a substantial increase in biologically active endogenous GAs (GA1, GA3, and GA4) content, indicating that overexpression of SdGA20ox1 accelerates plant growth and development. Using a yeast two-hybrid (Y2H) screen, we identified two SdGA20ox1-interacting proteins: the ethylene receptor EIN4 (11430582) and the rbcS (11416005) protein. These interactions suggest a potential regulatory mechanism for S. davidii growth. Our findings provide new insights into the role of SdGA20ox1 and its interacting proteins in regulating the growth and development of S. davidii.

Role of gene polymorphism in the development of disorders of the lipid profile in individuals exposed to chemicals

Introduction. The prevalence of arterial hypertension and dyslipidemia in the Russian population exceeds 50%. By a number of working industrial factors have been proved to play the negative role in their development. The results of earlier studies indicate to the epigenetic role of toxic substances in relation to various genes. The aim of the study was to establish associations of polymorphic variants of cardiovascular risk genes with disorders of lipid metabolism in workers performing liquidation works in the accumulated environmental risks zone. Materials and methods. Ninety two and 82 employees from Federal Environmental Operator (FEO) and EMERCOM, respectively were studied. Parameters of lipid metabolism and polymorphic variants of APOE Cys130Arg (rs429358) and PPARG Pro12Ala (rs1801282) genes were investigated. Results. In FEO workers, each variant allele of the APOE Cys130Arg gene is associated with impaired LDL-C concentration in an additive manner (OR = 2.69; 95% CI = 1.03–7.08, p=0.04). Carrying either the T/C or C/C variant allele of this polymorphic variant or the C/G or G/G polymorphic variant Pro12Ala of the PPARG gene increases the odds of developing abnormalities in total cholesterol levels by more than 3.5-times. The risk influence of the mutant genotype G/G and allele G on the increase of Apo B concentration was also established. In EMERCOM workers, the presence of both alleles of this polymorphic variant increased the probability of a decrease in HDL-H levels by 5 times. Limitations. Male persons are employees of the FEO and the Ministry of Emergency Situations. Age accounts of 30–50 years. Conclusions. An increased risk of deviations of total cholesterol concentration, proatherogenic cholesterol, and lipoprotein fractions associated with the PPARG Pro12Ala and APOE Cys130Arg genes polymorphisms was found in FEO workers, whereas only the reduced high-density lipoprotein cholesterol risk in carriers of the PPARG Pro12Ala gene mutant allele was found in EMERCOM workers.

PMCNA_RS00975 activates NF-κB and ERK1/2 through TLR2 and contributes to the virulence of Pasteurella multocida.

Pasteurella multocida is a pathogenic bacterium known to cause hemorrhagic septicemia and pneumonia in poultry. Reports have indicated that certain proteins, either directly involved in or regulating iron metabolism, are important virulence factors of P. multocida. Therefore, understanding virulent factors and analyzing the role of pro-inflammatory cytokines can help us elucidate the underlying pathogenesis. In this study, the PMCNA_RS00975 protein, a putative encapsuling protein encoded by a gene from a specific prophage island of the pathogenic strain C48-1 of P. multocida, was investigated. To further explore the impact of the PMCNA_RS00975 protein on pathogenicity, a PMCNA_RS00975 gene mutant of P. multocida strain C48-1 was constructed using positive selection technology. Subcellular localization was performed to determine the location of the PMCNA_RS00975 protein within P. multocida. The recombinant protein PMCNA_RS00975 of P. multocida was soluble expressed, purified, and its role in pro-inflammatory cytokines was investigated. The mutant exhibited significantly reduced pathogenicity in the mice model. Furthermore, subcellular localization indicated that the PMCNA_RS00975 protein was located at the outer membrane and expressed during infection of P. multocida. Additionally, our experiments revealed that recombinant PMCNA_RS00975 protein promotes the secretion of the IL-6 pro-inflammatory cytokines triggered by the TLR2 receptor via NF-κB and ERK1/2 signaling pathways in the macrophages. This study identified a novel virulence factor in the C48-1 strain, providing a basis for understanding the pathogenesis and directions for the development of attenuated vaccines against P. multocida.

An efficient CRISPR-Cas12a-mediated MicroRNA knockout strategy in plants.

In recent years, the CRISPR-Cas9 nuclease has been used to knock out MicroRNA (miRNA) genes in plants, greatly promoting the study of miRNA function. However, due to its propensity for generating small insertions and deletions, Cas9 is not well-suited for achieving a complete knockout of miRNA genes. By contrast, CRISPR-Cas12a nuclease generates larger deletions, which could significantly disrupt the secondary structure of pre-miRNA and prevent the production of mature miRNAs. Through the case study of OsMIR390 in rice, we confirmed that Cas12a is a more efficient tool than Cas9 in generating knockout mutants of a miRNA gene. To further demonstrate CRISPR-Cas12a-mediated knockout of miRNA genes in rice, we targeted nine OsMIRNA genes that have different spaciotemporal expression and have not been previously investigated via genetic knockout approaches. With CRISPR-Cas12a, up to 100% genome editing efficiency was observed at these miRNA loci. The resulting larger deletions suggest Cas12a robustly generated null alleles of miRNA genes. Transcriptome profiling of the miRNA mutants, as well as phenotypic analysis of the rice grains revealed the function of these miRNAs in controlling gene expression and regulating grain quality and seed development. This study established CRISPR-Cas12a as an efficient tool for genetic knockout of miRNA genes in plants.

Mutation-Specific CRISPR Targeting with SaCas9 and AsCas12a Restores Therapeutic Sensitivity in Treatment-Resistant Melanoma.

Background: Melanoma remains one of the most challenging cancers to treat effectively with drug resistant remaining a constant concern, primarily with activating BRAF mutations. Mutations in the BRAF gene appear in approximately 50% of patients, 90% of which are V600E. Two frontline BRAF inhibitors (BRAFi), vemurafenib and dabrafenib, are frequently used to treat unresectable or metastatic BRAF V600E melanoma. Initial response rates are high, but soon thereafter, 70-80% of patients develop resistance to treatment within a year. A major mechanism of resistance is the generation of a secondary Q61K mutation in the NRAS gene. Methods: We have developed an approach in which a CRISPR-Cas complex can be designed to distinguish between mutant genes enabling resistance to standard care in tumor cells and normal genomes of healthy cells. For the first time, we demonstrated the utility of two CRISPR-directed mutation-specific editing approaches to restore BRAFi sensitivity in BRAFV600E/NRASQ61K resistant A375 cells. Results: We utilize an AsCas12a protospacer adjacent motif site created by the NRAS Q61K mutation and the Q61K mutation in the critical seed region of an SaCas9 sgRNA for Q61K-selective targeting. We show here that both approaches allow for effective NRAS targeting of only mutated-Q61K and after CRISPR-directed Q61K-targeting, previously resistant A375 cells are re-sensitized to BRAFi treatment. Conclusion: Our data support the feasibility of the development of CRISPR-Cas therapeutic approaches to the treatment of melanoma. Successful therapeutic CRISPR-directed gene editing would enable both specific and efficient editing of a mutation-specific targeting approach eliminate concern for on- and off-target damage to the genomes of healthy cells.

The functional roles of zebrafish HoxA- and HoxD-related clusters in the pectoral fin development

The paralogs 9–13 Hox genes in mouse HoxA and HoxD clusters are critical for limb development. When both HoxA and HoxD clusters are deleted in mice, significant limb truncation is observed compared to the phenotypes of single and compound mutants of Hox9-13 genes in these clusters. In zebrafish, mutations in hox13 genes in HoxA- and HoxD-related clusters result in abnormal morphology of pectoral fins, homologous to forelimbs. However, the effect of the simultaneous deletions of entire HoxA- and HoxD-related clusters on pectoral fin development remains unknown. Here, we generated mutants with several combinations of hoxaa, hoxab, and hoxda cluster deletions and analyzed the pectoral fin development. In hoxaa−/−;hoxab−/−;hoxda−/− larvae, the endoskeletal disc and the fin-fold are significantly shortened in developing pectoral fins. In addition, we show that this anomaly is due to defects in the pectoral fin growth after the fin bud formation. Furthermore, in the surviving adult mutants, micro-CT scanning reveals defects in the posterior portion of the pectoral fin which is thought to represent latent regions of the limb. Our results further support that the functional role of HoxA and HoxD clusters is conserved in the paired appendage formation in bony fishes.

Activated single nucleotide mismatch determination through toehold-embedded hairpin-mediated strand displacement reaction alongside CRISPR-Cas12a for detection of TP53 point mutation

The CRISPR-Cas12a-based diagnostic platform is renowned for its high sensitivity and, when coupled with the toehold-mediated strand displacement (TMSD) reaction, enables the detection of single nucleotide mismatch (SNM). However, conventional TMSD with the CRISPR-Cas12a system suffers from signal leakage due to overlapping activator sequences and low displacement efficiency. Here, we propose a toehold-embedded hairpin-mediated strand displacement (THMSD) method and leverage the magnesium attenuation effect of CRISPR-Cas12a for selective single-point mutation detection in the TP53 gene. This approach effectively mitigates signal leakage as the hairpin DNA retains partial crRNA targeting sequences within its loop, preventing sequence overlap with the trigger and direct Cas12a activation. Additionally, the magnesium attenuation effect reduces background signal and enhances selectivity. We investigated toehold length and mismatch position to detect SNM with a high discrimination factor (DF). This high DF allows the THMSD/CRISPR-Cas12a system to differentiate between TP53 R273H mutant and TP53 wildtype genes for cancer screening at low abundances, down to 0.1 % with a concentration of 20 pM. When used for screening between H1975 and WI38 cells, the statistically significant difference was attainable with polymerase chain reaction (PCR) template loading as low as 4 ng. These results pave the way for developing CRISPR-Cas12a-based methods to effectively detect TP53 mutations as lung cancer biomarkers.

Uveal melanoma: molecular-genetic mechanisms of arising and the therapeutic approaches

Uveal melanoma (UM) is a tumor of neuroectodermal origin, which results from malignant transformation of melanocytes of the eye vasculature: iris, ciliary body and chorioidea. UM represents up to 5% of all melanoma cases, but it is extremely aggressive, since half of patients with UM develop metastases within the first 1‒2 years after the tumor appearance. Molecular mechanisms of uveal melanoma carcinogenesis are poorly understood, and have already been shown to be different from those of skin melanoma. Activating mutations in the GNAQ and GNA11 genes, encoding the large G protein subunits Gq and G11, respectively, are found in 90% of UM patients. The main signaling cascade leading to the transformation of melanocytes of the uveal tract is the signaling pathway Gaq/PKC/MAPK, and the major regulators of this cascade are targets for the development of drugs. The development of the metastatic form of UM is most often associated with mutations in the genes BAP1, EIF1AX, GNA11, GNAQ, and SF3B1. A combination of a commercial expression test panel of 15 genes and a mutation panel of 7 genes, supplemented with data on the size of the primary tumor, has been shown to be highly effective prognostic signature in prediction the risk of metastases. The risk of metastases determines the choice of therapy and patient follow-up regimen. At the same time, no systemic therapy for the treatment of metastatic UM has been developed to date; new drugs undergoing clinical trials mostly refer to either targeted therapy aimed at inhibiting the protein products of mutant genes, or immunotherapy designed to stimulate an immune response against specific antigens. In addition to these approaches, the review also considers potential therapeutic targets of epigenetic regulation of UM development.

Clinicopathological and molecular genetic insights into EBV-positive inflammatory follicular dendritic cell sarcoma

Epstein-Barr virus (EBV)-positive inflammatory follicular dendritic cell (FDC) sarcoma (EBV + IFDCS) is a rare entity, and its histopathological characteristics have not been fully described. This study aimed to investigate the clinical characteristics, pathological features, and molecular genetic profiles of EBV + IFDCS to improve our understanding of these lesions. A total of 12 EBV + IFDCS specimens were obtained from patients in our pathology diagnostic center. The clinical data, morphology, immunohistochemistry, in situ hybridization, and high-throughput DNA-targeted sequencing data were collected, and follow-up data were analyzed. These data were compared with those of 6 patients with traditional FDCS. The patients with EBV + IFDCS ranged from 21 to 84 years old, with a mean age of 52.3 years and a male-to-female ratio of 1:5. At the last follow-up, all patients were alive, with 2 experiencing recurrence and metastasis. In these cases, four were classified as the classical subtype, four as the angiomatoid/sclerosing subtype, and four as the lymphoma-like subtype, with two cases also exhibiting epithelioid granulomas. All patients exhibited heterogeneous expression of follicular dendritic cell markers (CD21, CD23, CD35, and CXCL13) alongside the fibroblast marker SMA, with significantly higher expressions of IgG4, EBER, and SMA in EBV + IFDCS patients compared to FDCS patients (P < 0.05). Conversely, SSTR2, EGFR, and STAT3 expression were significantly lower in the EBV + IFDCS group (P < 0.05). The average value of EBER was significantly higher in the classical subtype group (P = 0.022). Among the four cases of EBV + IFDCS analyzed for molecular genetic features, one patient exhibited germline mutations in the CDKN1C, PDGFRA, MSH2, FANCG, MLH1, ALK, and RUNX1 genes; three exhibited simultaneous SNP variations in the MTHFR gene; and two exhibited simultaneous SNP variations in the NQO1 gene. We conducted KEGG pathway analysis on the mutant genes, revealing significant enrichment in the cAMP signaling pathway, which plays a crucial role in tumor development. Survival analysis demonstrated that the median PFS rates were not reached (NR) for EBV + IFDCS patients, compared to 5 months (HR = 7.76) for FDCS patients. The 3-year PFS rates were 66.67% and 16.67%, respectively. Compared with the FDCS group, EBV + IFDCS patients had a significantly longer median PFS time (p < 0.05). In conclusion, EBV + IFDCS represents a group of tumors with unique clinical, morphological, immunological, prognostic, and molecular cytogenetic characteristics.

Small Molecules Inducing Autophagic Degradation of Expanded Polyglutamine Protein through Interaction with Both Mutant ATXN3 and LC3.

Polyglutamine (polyQ)-mediated spinocerebellar ataxia (SCA), including SCA1, 2, 3, 6, 7, and 17, are caused by mutant genes with expanded CAG repeats, leading to the intracellular accumulation of aggregated proteins, the production of reactive oxygen species, and cell death. Among SCA, SCA3 is caused by a mutation in the ATXN3 (ataxin-3) gene. In a circumstance of polyQ aggregation, the autophagic pathway is induced to degrade the aggregated proteins, thereby suppressing downstream deleterious effects and promoting neuronal survival. In this study, we tested the effects of synthetic indole (NC009-1, -2, -3, -6) and coumarin (LM-022, -031) derivatives as chemical chaperones to assist mutant ATXN3-Q75 folding, as well as autophagy inducers to clear aggregated protein. Among the tested compounds, NC009-1, -2, and -6 and LM-031 interfered with Escherichia coli-derived ATXN3-Q75 aggregation in thioflavin T binding and filter trap assays. In SH-SY5Y cells expressing GFP-fused ATXN3-Q75, these compounds displayed aggregation-inhibitory and neurite growth-promoting potentials compared to untreated cells. Furthermore, these compounds activated autophagy by increasing the phosphatidylethanolamine-conjugated LC3 (microtubule associated protein 1 light chain 3)-II:cytosolic LC3-I ratio in these cells. A biochemical co-immunoprecipitation assay by using a mixture of HEK 293T cell lysates containing recombinant ATXN3-Q75-Venus-C-terminus (VC) or Venus-N-terminus (VN)-LC3 protein indicated that NC009-1 and -2 and LM-031 served as an autophagosome-tethering compound (ATTEC) to interact with ATXN3-Q75 and LC3, and the interaction was further confirmed by bimolecular fluorescence complementation analysis in cells co-expressing both ATXN3-Q75-VC and VN-LC3 proteins. The study results suggest the potential of NC009-1 and -2 and LM-031 as an ATTEC in treating SCA3 and, probably, other polyQ diseases.

Genome analysis of Streptomyces recifensis SN1E1 to investigate mechanisms for inhibiting fire blight disease.

Fire blight, attributed to the bacterium Erwinia amylovora, significantly damages economically important crops, such as apples and pears. Conventional methods for managing fire blight involve the application of chemical pesticides, such as streptomycin and oxytetracycline. Nevertheless, apprehensions are increasing regarding developing antibiotic and pesticide-resistant strains, compounded by documented instances of plant toxicity. Here, we present that Streptomyces recifensis SN1E1 has exhibited remarkable efficacy in suppressing apple fire blight disease. This study aims to unravel the molecular-level antimicrobial mechanisms employed by the SN1E1 strain. We identified four antimicrobial-associated biosynthetic gene clusters within the genomics of S. recifensis SN1E1. To validate antimicrobial activity against E. amylovora, knock-out mutants of biosynthetic genes linked to antimicrobial activity were generated using the CRISPR/Cas9 mutagenesis system. Notably, the whiE4 and phzB deficient mutants displayed statistically reduced antibacterial activity against E. amylovora. This research establishes a foundation for environmental and biological control studies. The potential utilization of environmentally friendly microbial agents derived from the SN1E1 strain holds promise for the biological control of fire blight disease.

Rhodopseudomonas palustris Atp2 Protein Exerts Antifungal Effects by Targeting the Ribosomal Protein MoRpl12 in Magnaporthe oryzae.

Rice blast is one of the most hazardous diseases affecting rice production. Previously, we discovered that the Atp2 protein of Rhodopseudomonas palustris could significantly inhibit the appressorium formation and pathogenicity of Magnaporthe oryzae. However, the molecular mechanism of this fungus has remained unknown. This study revealed that Atp2 can enter the cell and interact with the ribosomal protein MoRpl12 of M. oryzae, directly affecting the expression of the MoRpl12 protein. Silencing the MoRPL12 gene can affect cell wall integrity, growth, conidiogenesis, and fungal pathogenicity. The quantitative reverse transcription PCR results showed significant changes in the expression of conidiation-related genes in the MoRPL12 gene-silenced mutants or in the Atp2 protein-treated plants. We further found that Atp2 treatment can influence the expression of ribosomal-related genes, such as RPL, in M. oryzae. Our study revealed a novel antifungal mechanism by which the Atp2 protein binds to the ribosomal protein MoRpl12 and inhibits the pathogenicity of rice blast fungus, providing a new potential target for rice blast prevention and control.