profiling analysis
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2021 ◽  
Author(s):  
Chen Huang ◽  
Min Deng ◽  
Dongliang Leng ◽  
Elaine Lai-Han Leung ◽  
Baoqing Sun ◽  
...  

Current scoring systems for prognosis of breast cancer are available but usually consider only one prognostic feature. We aim to develop a novel prognostic scoring system based on both immune-infiltration and metastatic features to not only assess the patient prognoses more accurately but also guide therapy for patients with breast cancer. Computational immune-infiltration and gene profiling analysis identified a 12-gene panel firstly characterizing immune-infiltrating and metastatic features. Neural network model yielded a precise prognostic scoring system called metastatic and immunogenomic risk score (MIRS). The influence of MIRS on the prognosis and therapy of breast cancer was then comprehensively investigated. MIRS significantly stratifies patients into high risk-group (MIRShigh) and low risk-group (MIRSlow) in both training and test cohorts. The MIRSlow patients exhibit significantly improved survival rate compared with MIRShigh patients. A series of analyses demonstrates that MIRS can well characterize the metastatic and immune landscape of breast cancer. Further analysis on the usage of MIRS in chemotherapy suggests that MIRShigh patients may benefit from three chemotherapeutic drugs (Cisplatin, Tamoxifen and Vincristine). Higher immune infiltration and significantly prolonged survival are observed in MIRSlow patients, indicating a better response in immune checkpoint inhibitor therapy. Our analysis demonstrates that MIRS could effectively improve the accuracy of prognosis for patients with breast cancer. Also, MIRS is a useful webtool, which is deposited at https://lva85.github.io/MIRS/, to help clinicians in designing personalized therapies for patients with breast cancer.


2021 ◽  
Author(s):  
Yaowen Chang ◽  
Xuhui Zhang ◽  
Alastair I.H. Murchie ◽  
Dongrong Chen

Abstract Background: Aminoglycosides are not only antibiotics but also have wider and diverse non-antibiotic cellular functions. No genome-wide study focusing on the changes of gene expression by aminoglycosides in E.coli has been reported. Here, we report transcriptome-profiling analysis of E.coli with or without Kanamycin B to elucidate the understanding of non-antibiotic cellular functions. Results: The differentially expressed genes (DEGs) at two given concentrations of Kanamycin B were identified. The results indicated that Kanamycin B does not affect the expression of the majority of the genes. Functional classification of the DEGs revealed that they were mainly related to microbial metabolism including two-component systems, biofilm formation, oxidative phosphorylation and nitrogen metabolism in diverse environments. Conclusions: Kanamycin B treatment causes diverse changes in the transcriptional profile of E. coli JM109, that are not directly associated with the antibiotic activity of Kanamycin B.


2021 ◽  
pp. 1-15
Author(s):  
Mohammad Tahseen Al Bataineh ◽  
Ayman Alzaatreh ◽  
Rima Hajjo ◽  
Bayan Hassan Banimfreg ◽  
Nihar Ranjan Dash

BACKGROUND: Age-related alterations in the composition and function of gut microbiota may influence human health and disease mechanisms. However, connections between compositional changes in gut bacterial and fungal communities, and their role in the aging process, remain poorly understood. OBJECTIVE: Compare the gut microbiota and mycobiota composition in different age groups and evaluate the functionality. METHODS: In this study, we performed 16S rRNA and ITS2 gene-based microbial profiling analysis and shotgun metagenomics using the NextSeq platform. RESULTS: We observed a shift in compositional changes of human gut microbiota with age. Older individuals revealed a significantly different gut microbiota profile compared to younger individuals. For example, gut microbiota composition of the older individuals showed increase in genera Bacteroides, Blautia, Ruminococcaceae, and Escherichia coli. Additionally, older individuals had significant reduction in fungi belonging to saccharomyces cerevisiae and candida albicans in comparison to their younger counterparts. Moreover, metagenomics functional profiling analysis using shotgun metagenomics sequencing data showed substantial differences in the enrichment of 48 pathways between the young and older age groups. Metabolic pathways such as amino acid biosynthesis, carbohydrate metabolism, cell structure biosynthesis and vitamin biosynthesis were declined in the older age group, in comparison with the younger individuals. CONCLUSIONS: The identified differences provide a new insight to enrich our understanding of age-related changes in gut microbiota, their metabolic capabilities, and potential impact on health and disease conditions.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ming Chen ◽  
Siqi Zhou ◽  
Huasong Shi ◽  
Hanwen Gu ◽  
Yinxian Wen ◽  
...  

Abstract Background The componential and structural change in the meniscus with aging would increase the tissue vulnerability of the meniscus, which would induce meniscus tearing. Here, we investigated the molecular mechanism of age-related meniscus degeneration with gene expression profiling analysis, and validate pivotal genes in vivo and in vitro models. Methods The GSE45233 dataset, including 6 elderly meniscus samples and 6 younger meniscus samples, was downloaded from the Gene Expression Omnibus (GEO) database. To screen the differential expression of mRNAs and identify the miRNAs targeting hub genes, we completed a series of bioinformatics analyses, including functional and pathway enrichment, protein–protein interaction network, hub genes screening, and construction of a lncRNA–miRNA–mRNA network. Furthermore, crucial genes were examined in human senescent menisci, mouse senescent meniscus tissues and mouse meniscus cells stimulated by IL-1β. Results In total, the most significant 4 hub genes (RRM2, AURKB, CDK1, and TIMP1) and 5 miRNAs (hsa-miR-6810-5p, hsa-miR-4676-5p, hsa-miR-6877-5p, hsa-miR-8085, and hsa-miR-6133) that regulated such 4 hub genes, were finally identified. Moreover, these hub genes were decreased in meniscus cells in vitro and meniscus tissues in vivo, which indicated that hub genes were related to meniscus senescence and could serve as potential biomarkers for age-related meniscus tearing. Conclusions In short, the integrated analysis of gene expression profile, co-expression network, and models detection identified pivotal genes, which elucidated the possible molecular basis underlying the senescence meniscus and also provided prognosis clues for early-onset age-related meniscus tearing.


Author(s):  
F.M. Colles ◽  
S.J. Hedges ◽  
R. Dixon ◽  
S.G. Preston ◽  
P. Thornhill ◽  
...  

Campylobacter from contaminated poultry meat is a major source of human gastroenteritis worldwide. To date, attempts to control this zoonotic infection with on-farm biosecurity measures have been inconsistent in outcome. A cornerstone of these efforts has been the detection of chicken infection with microbiological culture, where Campylobacter is generally not detectable until birds are at least 21 days old. Using parallel sequence based bacterial 16S profiling analysis and targeted sequencing of the porA gene, Campylobacter was identified at very low levels in all commercial flocks at less than 8 days old that were tested from the UK, Switzerland, and France. These young chicks exhibited a much greater diversity of porA types than older birds testing positive for Campylobacter by culture or qPCR. This suggests that, as the bacteria multiply sufficiently to be detected by culture methods, one or two variants, as indicated by porA type, dominate the infection. The findings that: (i) most young chicks carry some Campylobacter and (ii) not all flocks become Campylobacter positive by culture, suggest that efforts to control infection, and therefore avoid contamination of poultry meat, should concentrate on how to limit Campylobacter to low levels by the prevention of the overgrowth of single strains. Importance: Our results demonstrate the presence of Campylobacter DNA amongst faecal samples from a range of commercially reared meat chicks that are less than 8 days of age, consistent across 3 European countries. The recently developed, sensitive detection method indicates that infection occurs on commercial farms much earlier and more widely than previously thought, which opens-up new opportunities to control Campylobacter contamination at the start of the food-chain, and reduce the unacceptably high levels of human disease.


Author(s):  
Davide Nardone ◽  
Angelo Ciaramella ◽  
Mariangela Cerreta ◽  
Salvatore Pulcrano ◽  
Gian C. Bellenchi ◽  
...  

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1315
Author(s):  
Foteini Vasilopoulou ◽  
Carmen Escolano ◽  
Mercè Pallàs ◽  
Christian Griñán-Ferré

I2-IR have been found dysregulated in patients with neurodegenerative diseases, such as Alzheimer’s disease (AD), in which the importance of neuroinflammation in the establishment and maintenance of cognitive decline is well-documented. To research the implication of I2-IR in neuroinflammatory pathways altered in AD, we determined the expression profile of genes associated with inflammation in the 5XFAD model treated with LSL60101, a well-established I2-IR ligand. Thus, we performed a qPCR array containing 84 inflammation-related genes. Hierarchical clustering analysis revealed three gene clusters, suggesting that treatment with LSL60101 affects the gene expression associated with inflammation in the 5XFAD model. Furthermore, we evaluated the functions of the three clusters; thereby performing a pathway enrichment analysis using the GO database. As we expected, clusters 2 and 3 showed alterations in the inflammatory response, chemotaxis and the chemokine-mediated signaling pathway, among others. To validate previous results from the gene profiling analysis, the expression levels of a representative subset of mRNAs were selected according to the intensity of the observed changes and their biological relevance. Interestingly, changes induced by LSL60101 in the 5XFAD model were validated for several genes. These results suggest that treatment with LSL60101 in the 5XFAD model reverses the inflammatory process during the development of AD.


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