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Genes Jan 2024Stalk rot caused by fungi is one of the most widespread and devastating diseases of maize, and the introduction of resistant genotypes is one of the most effective...
Stalk rot caused by fungi is one of the most widespread and devastating diseases of maize, and the introduction of resistant genotypes is one of the most effective strategies for controlling the disease. Breeding genotypes with genetically determined resistance will also allow less use of crop protection products. The aim of the research was to identify molecular markers and associated candidate genes determining maize plant resistance to Fusarium stalk rot. The plant material for this study consisted of 122 maize hybrids. The experiment was conducted in two localities: Smolice and Kobierzyce. The Fusarium stalk rot values ranged from 1.65% (for genotype G01.10) to 31.18% (for genotype G03.07) in Kobierzyce and from 0.00% (for 58 genotypes) to 6.36% (G05.03) in Smolice. The analyzed genotypes were simultaneously subjected to next-generation sequencing using the Illumina platform. Illumina sequencing identified 60,436 SilicoDArT markers and 32,178 SNP markers (92,614 in total). For association mapping, 32,900 markers (26,234 SilicoDArT and 6666 SNP) meeting the criteria (MAF > 0.25 and the number of missing observations <10%) were used. The results of the observation of the degree of infection and sequencing were used for association mapping, which ultimately resulted in the selection of ten molecular markers important at both places. Among the identified markers, two SNP markers that are located inside candidate genes play an important role. Marker 4772836 is located inside the serine/threonine-protein kinase bsk3 gene, while marker 4765764 is located inside the histidine kinase 1 gene. Both genes can be associated with plant resistance to Fusarium stalk rot, and these genes can also be used in breeding programs to select resistant varieties.
Topics: Fusarium; Plant Breeding; Genotype; High-Throughput Nucleotide Sequencing; Technology; Zea mays
PubMed: 38254995
DOI: 10.3390/genes15010106 -
Haematologica May 2024
Topics: Humans; Translocation, Genetic; Prognosis; Chromosome Aberrations; Female; Male; Proto-Oncogene Proteins c-maf; Middle Aged; Aged; Adult; Myelodysplastic Syndromes
PubMed: 38235518
DOI: 10.3324/haematol.2023.284666 -
Journal of the Neurological Sciences Feb 2024Mitochondrial DNA (mtDNA) is a 16,569 base pairs, double-stranded, circular molecule that contains 37 genes coding for 13 subunits of the respiratory chain plus 2 rRNAs...
Mitochondrial DNA (mtDNA) is a 16,569 base pairs, double-stranded, circular molecule that contains 37 genes coding for 13 subunits of the respiratory chain plus 2 rRNAs and 22 tRNAs. Mutations in these genes have been identified in patients with a variety of disorders affecting every system in the body. The advent of next generation sequencing technologies has provided the possibility to perform the whole mitochondrial DNA sequencing, allowing the identification of disease-causing pathogenic variants in a single platform. In this study, the whole mtDNA of 100 patients from South Italy affected by mitochondrial diseases was analyzed by using an amplicon-based approach and then the enriched libraries were deeply sequenced on the ION Torrent platform (Thermofisher Scientific Waltham, MA, USA). After bioinformatics analysis and filtering, we were able to find 26 nonsynonymous variants with a MAF <1% that were associated with different pathological phenotypes, expanding the mutational spectrum of these diseases. Moreover, among the new mutations found, we have also analyzed the 3D structure of the MT-ATP6 A200T gene variation in order to confirm suspected functional alterations. This work brings light on new variants possibly associated with several mitochondriopathies in patients from South Italy and confirms that deep sequencing approach, compared to the standard methods, is a reliable and time-cost reducing strategy to detect all the variants present in the mitogenome, making the possibility to create a genomics landscape of mitochondrial DNA variations in human diseases.
Topics: Humans; Mutation; DNA, Mitochondrial; Mitochondria; Genomics; Italy; High-Throughput Nucleotide Sequencing
PubMed: 38215527
DOI: 10.1016/j.jns.2024.122869 -
International Journal of Molecular... Dec 2023Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) are the most common types of cancers in the head and neck region (HNSCC). Despite...
Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) are the most common types of cancers in the head and neck region (HNSCC). Despite very aggressive treatment modalities, the five-year survival rate has not changed for decades and is still around 60%. The search for potential specific biomarkers of aggressiveness or outcome indicators could be of great benefit in improving the treatment of these patients. One of the potential biomarkers is survivin, the protein product of the gene. In this study, we investigated the occurrence of gene polymorphisms in 48 patients with OSCC and OPSCC compared with healthy controls. A total of 18 polymorphisms were found, 11 of which occurred in HNSCC with a minor allele frequency (MAF) of more than 5%. Five polymorphisms (rs3764383, rs9904341, rs2071214, rs2239680, rs2661694) were significantly associated with tumor size, tumor stage, and advanced regional disease, but had no impact on survival.
Topics: Humans; Biomarkers; Carcinoma, Squamous Cell; Head and Neck Neoplasms; Mouth Neoplasms; Papillomavirus Infections; Polymorphism, Genetic; Squamous Cell Carcinoma of Head and Neck; Survivin
PubMed: 38139318
DOI: 10.3390/ijms242417490 -
International Journal of Molecular... Dec 2023Group-specific component macrophage-activating factor (GcMAF) is the vitamin D-binding protein (DBP) deglycosylated at Thr. The protein is believed to exhibit a wide...
Group-specific component macrophage-activating factor (GcMAF) is the vitamin D-binding protein (DBP) deglycosylated at Thr. The protein is believed to exhibit a wide range of therapeutic properties associated with the activation of macrophagal immunity. An original method for GcMAF production, DBP conversion to GcMAF, and the analysis of the activating potency of GcMAF was developed in this study. Data unveiling the molecular causes of macrophage activation were obtained. GcMAF was found to interact with three CLEC10A derivatives having molecular weights of 29 kDa, 63 kDa, and 65 kDa. GcMAF interacts with high-molecular-weight derivatives via Ca-dependent receptor engagement. Binding to the 65 kDa or 63 kDa derivative determines the pro- and anti-inflammatory direction of cytokine mRNA expression: 65 kDa-pro-inflammatory (TNF-α, IL-1β) and 63 kDa-anti-inflammatory (TGF-β, IL-10). No Ca ions are required for the interaction with the canonical 29 kDa CLEC10A. Both forms, DBP protein and GcMAF, bind to the 29 kDa CLEC10A. This interaction is characterized by the stochastic mRNA synthesis of the analyzed cytokines. Ex vivo experiments have demonstrated that when there is an excess of GcMAF ligand, CLEC10A forms aggregate, and the mRNA synthesis of analyzed cytokines is inhibited. A schematic diagram of the presumable mechanism of interaction between the CLEC10A derivatives and GcMAF is provided. The principles and elements of standardizing the GcMAF preparation are elaborated.
Topics: Anti-Inflammatory Agents; Macrophage-Activating Factors; Macrophages; RNA, Messenger; Humans; Vitamin D-Binding Protein
PubMed: 38139225
DOI: 10.3390/ijms242417396 -
Wellcome Open Research 2023CD4 Th1 cells producing IFN-γ are required to eradicate intracellular pathogens, however if uncontrolled these cells can cause immunopathology. The cytokine IL-10 is...
BACKGROUND
CD4 Th1 cells producing IFN-γ are required to eradicate intracellular pathogens, however if uncontrolled these cells can cause immunopathology. The cytokine IL-10 is produced by multiple immune cells including Th1 cells during infection and regulates the immune response to minimise collateral host damage. In this study we aimed to elucidate the transcriptional network of genes controlling the expression of and proinflammatory cytokines, including in Th1 cells differentiated from mouse naive CD4 T cells.
METHODS
We applied computational analysis of gene regulation derived from temporal profiling of gene expression clusters obtained from bulk RNA sequencing (RNA-seq) of flow cytometry sorted naïve CD4 T cells from mouse spleens differentiated into Th1 effector cells with IL-12 and IL-27 to produce and compared to IL-27 alone which express only or IL-12 alone which express and no or medium control driven-CD4 T cells which do not express effector cytokines Data were integrated with analysis of active genomic regions from these T cells using an assay for transposase-accessible chromatin with sequencing (ATAC)-seq, integrated with literature derived-Chromatin-immunoprecipitation (ChIP)-seq data and the RNA-seq data, to elucidate the transcriptional network of genes controlling expression of and pro-inflammatory effector genes in Th1 cells. The co-dominant role for the transcription factors, (encoding Blimp-1) and (encoding c-Maf) in cytokine gene regulation in Th1 cells, was confirmed using T cells obtained from mice with T-cell specific deletion of these transcription factors.
RESULTS
We show that the transcription factors Blimp-1 and c-Maf each have unique and common effects on cytokine gene regulation and not only co-operate to induce gene expression in IL-12 plus IL-27 differentiated mouse Th1 cells, but additionally directly negatively regulate key proinflammatory cytokines including , thus providing mechanisms for reinforcement of regulated Th1 cell responses.
CONCLUSIONS
These data show that Blimp-1 and c-Maf positively and negatively regulate a network of both unique and common anti-inflammatory and pro-inflammatory genes to reinforce a Th1 response in mice that will eradicate pathogens with minimum immunopathology.
PubMed: 38074197
DOI: 10.12688/wellcomeopenres.19680.2 -
International Journal of Molecular... Nov 2023The nuclear factor erythroid 2-related factor 2 (Nrf2) is a pivotal regulator of antioxidant gene expression in mammals, forming heterodimer complexes with small Maf...
The nuclear factor erythroid 2-related factor 2 (Nrf2) is a pivotal regulator of antioxidant gene expression in mammals, forming heterodimer complexes with small Maf proteins through its BZip domain. However, the underlying mechanism of Nrf2 action in molluscs remains poorly understood. The thick shell mussel, , represents a model organism for the marine environment and molluscs interaction research. In this study, we used in silico cloning to obtain a small Maf homologue called from . MafF_G_K possesses a typical BZip domain, suggesting its affiliation with the traditional small Maf family and its potential involvement in the Nrf2 signaling pathway. Transcriptional analysis revealed that MafF_G_K exhibited a robust response to benzo[a]pyrene (Bap) in the digestive glands. However, this response was down-regulated upon interference with MafF_G_K-siRNA. Interestingly, the expression levels of Nrf2, NAD(P)H: quinone oxidoreductase (NQO-1), and Glutathione Peroxidase (GPx), which are key players in oxidative stress response, showed a positive correlation with MafF_G_K in digested adenocytes of . Furthermore, in vitro analysis of antioxidant capacity in digestive gland cells demonstrated that Bap exposure led to an increase in reactive oxygen species (ROS) levels, accompanied by an elevation in total antioxidant capacity (T-AOC), potentially counterbalancing the excessive ROS. Strikingly, transfection of MafF_G_K siRNA resulted in a significant rise in ROS level and a down-regulation of T-AOC level. To validate the functional relevance of MafF_G_K, a glutathione S-transferase (GST) pull-down assay confirmed its interaction with Nrf2, providing compelling evidence of their protein interaction. This study significantly contributes to our understanding of the functional role of MafF_G_K in the Nrf2 signaling pathway and sheds light on its potential as a target for further research in oxidative stress response.
Topics: Animals; Antioxidants; NF-E2-Related Factor 2; Reactive Oxygen Species; Oxidative Stress; Bivalvia; RNA, Small Interfering; Mammals
PubMed: 38069123
DOI: 10.3390/ijms242316800 -
Journal of Clinical Medicine Dec 2023Histamine intolerance arises when there is a disparity between the production of histamine and the body's ability to break it down. In the gastrointestinal tract, the...
Histamine intolerance arises when there is a disparity between the production of histamine and the body's ability to break it down. In the gastrointestinal tract, the primary enzyme responsible for metabolizing ingested histamine is diamine oxidase (DAO), and a shortage of this enzyme has been associated with some diseases related to the respiratory, cardiovascular, nervous, muscular, and digestive systems, in addition to migraines. The treatment of migraines typically revolves around the utilization of both anti-migraine and anti-inflammatory drugs, but their interaction with DAO is not thoroughly understood. In this study, we examined the impact of nonsteroidal anti-inflammatory drugs (NSAIDs) and anti-migraine medications on DAO activity through in vitro experiments. We also investigated their effects on the human intestinal cell line Caco-2, assessing changes in DAO expression (both at the mRNA and protein levels) as well as DAO activity. The tested drugs, including ibuprofen, acetylsalicylic acid, paracetamol, a combination of acetylsalicylic acid with paracetamol and caffeine, zolmitriptan, and sumatriptan, did not inhibit DAO activity or reduce their levels. However, naproxen reduced DAO protein levels in human enterocyte cultures while not affecting DAO activity. These results suggest that combining anti-inflammatory and anti-migraine drugs with DAO enzyme supplementation for migraine patients with DAO deficiency could be beneficial for healthcare professionals in their daily practice.
PubMed: 38068554
DOI: 10.3390/jcm12237502 -
Gut Feb 2024Metastasis is the major cause of cancer death. However, what types of heterogenous cancer cells in primary tumour and how they metastasise to the target organs remain...
OBJECTIVE
Metastasis is the major cause of cancer death. However, what types of heterogenous cancer cells in primary tumour and how they metastasise to the target organs remain largely undiscovered.
DESIGN
We performed single-cell RNA sequencing and spatial transcriptomic analysis in primary colorectal cancer (CRC) and metastases in the liver (lCRC) or ovary (oCRC). We also conducted immunofluorescence staining and functional experiments to examine the mechanism.
RESULTS
Integrative analyses of epithelial cells reveal a stem-like cell cluster with high () and () expression as the metastatic culprit. This cell cluster comprising distinct subpopulations shows distinct liver or ovary metastatic preference. Population 1 (P1) cells with high and expression are enriched in primary CRC and oCRC, thus may be associated with ovarian metastasis. P3 cells having a similar expression pattern as cholangiocytes are found mainly in primary CRC and lCRC, presuming to be likely the culprits that specifically metastasise to the liver. Stem-like cells interacted with cancer-associated fibroblasts and endothelial cells via the DLL4-NOTCH signalling pathway to metastasise from primary CRC to the ovary. In the oCRC microenvironment, myofibroblasts provide cancer cells with glutamine and perform a metabolic reprogramming, which may be essential for cancer cells to localise and develop in the ovary.
CONCLUSION
We uncover a mechanism for organ-specific CRC metastasis.
Topics: Female; Humans; Colorectal Neoplasms; Endothelial Cells; Liver Neoplasms; Gene Expression Profiling; Signal Transduction; Gene Expression Regulation, Neoplastic; Neoplasm Metastasis; Tumor Microenvironment; Basic Helix-Loop-Helix Transcription Factors
PubMed: 38050068
DOI: 10.1136/gutjnl-2023-330243 -
RMD Open Nov 2023To assess the safety, immunogenicity and cellular responses following the Moderna Spikevax primary series in rheumatic disease. (Clinical Trial)
Clinical Trial
COVID-19 Vaccine in Immunosuppressed Adults with Autoimmune rheumatic Diseases (COVIAAD): safety, immunogenicity and antibody persistence at 12 months following Moderna Spikevax primary series.
OBJECTIVE
To assess the safety, immunogenicity and cellular responses following the Moderna Spikevax primary series in rheumatic disease.
METHODS
We conducted a 12-month, prospective, non-randomised, open-label, comparative trial of adults with either rheumatoid arthritis (RA, n=131) on stable treatment; systemic lupus erythematosus (SLE, n=23) on mycophenolate mofetil (MMF); other rheumatic diseases on prednisone ≥10 mg/day (n=8) or age-matched/sex-matched controls (healthy control, HC, n=58). Adverse events (AEs), humoral immune responses (immunogenicity: IgG positivity for anti-SARS-CoV-2 spike protein and its receptor binding domain, neutralising antibodies (NAbs)), cellular responses (ELISpot) and COVID-19 infection rates were assessed.
RESULTS
Frequency of solicited self-reported AEs following vaccination was similar across groups (HC 90%, RA 86%, SLE 90%); among them, musculoskeletal AEs were more frequent in RA (HC 48% vs RA 66% (Δ95% CI CI 3 to 32.6)). Disease activity scores did not increase postvaccination. No vaccine-related serious AEs were reported. Postvaccination immunogenicity was reduced in RA and SLE (RA 90.2%, SLE 86.4%; for both, ΔCIs compared with HC excluded the null). Similarly, NAbs were reduced among patients (RA 82.6%, SLE 81.8%). In RA, age >65 (OR 0.3, 95% CI 0.1 to 0.8) and rituximab treatment (OR 0.003, 95% CI 0.001 to 0.02) were negative predictors of immunogenicity. ELISpot was positive in 16/52 tested RA and 17/26 HC (ΔCI 11.2-53.3). During the study, 11 HC, 19 RA and 3 SLE patients self-reported COVID-infection.
CONCLUSION
In COVID-19 Vaccine in Immunosuppressed Adults with Autoimmune Diseases, the Moderna Spikevax primary series was safe. MMF, RA age >65 and rituximab were associated with reduced vaccine-induced protection.
Topics: Adult; Humans; 2019-nCoV Vaccine mRNA-1273; Autoimmune Diseases; COVID-19; COVID-19 Vaccines; Lupus Erythematosus, Systemic; Mycophenolic Acid; Prospective Studies; Rheumatic Diseases; Rituximab
PubMed: 38030231
DOI: 10.1136/rmdopen-2023-003400