Project description:Although several dysregulated miRNAs have been reported in liver diseases of different etiologies, no genome-wide analyses of hepatic miRNAs from patients with chronic hepatitis C (CHC) of HCV genotype 3 have been reported. With the aim of determining miRNAs associated with CHC pathogenesis, we present a comprehensive catalogue of the hepatic miRNAome of CHC-infected and control liver tissues obtained using next-generation sequencing. The study design was divided into discovery and validation phases. In the initial NGS-based discovery phase, 10 liver tissues (CHC-positive: 8, controls: 2) were subjected to miRNA-sequencing, using illumina HiSeq 2000. The expression of selected deregulated miRNAs was validated using qRT-PCR in a validation cohort comprising of 123 treatment-naive CHC patients of the HCV genotype 3 and 60 healthy controls. Furthermore, a comprehensive computational workflow incorporating miRNA–mRNA interaction analysis, was established to determine the functional significance of dysregulated miRNA–mRNA pairs in CHC infection.
Project description:The global impact of Plasmodium vivax has been largely underestimated for several decades due to lower mortality rates compared to P. falciparum. However, in recent times, the parasite has become a serious threat to public health due to its ability to cause severe malaria with fatal outcomes. Its unique biology makes it resilient to control measures and poses a challenge to available diagnostic methods. Diagnosis by RDTs is further restricted due to inadequate P. vivax specific antigens for species identification. Therefore, there is an urgent need to develop tests that employ antigens unique to the parasite. This study represents the first in-depth proteomics analysis of human plasma and parasite isolates to identify P. vivax protein biomarkers that can be tested for use in RDTs while developing diagnostics for malaria. Here we report 39 P. vivax proteins in human plasma and 103 highly expressed P. vivax proteins from parasite isolates with high confidence. Interestingly, five proteins, found to be unique to P. vivax were detected in both sources, representing the best candidates for evaluation as diagnostic markers. Moreover, targeted proteomics assays were used to validate some of these proteins. This study represents the first step in the development of new diagnostic assays for P. vivax malaria.
Project description:Little is known about the impact of DNA methylation on the evolution/progression of chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. While only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared to controls, ~6,500 differentially methylated CpG sites were found in cells from BC-CML patients. In the majority of affected CpG sites methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes which were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared to CP-CML-derived cells. Several of them are well-known tumor suppressor genes or regulators of cell proliferation. 5-aza-2 -deoxycytidine treatment of CML cells resulted in gene re-expression and in a dose-dependent cell growth reduction. Single nucleotide variants of certain epigenetic modifiers during CML progression were not found. Together, our results demonstrate that methylation changes occur frequently during CML progression and may provide a useful basis for revealing new targets of therapy in advanced CML.
Project description:Little is known about the impact of DNA methylation on the evolution/progression of chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. While only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared to controls, ~6,500 differentially methylated CpG sites were found in cells from BC-CML patients. In the majority of affected CpG sites methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes which were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared to CP-CML-derived cells. Several of them are well-known tumor suppressor genes or regulators of cell proliferation. 5-aza-2 -deoxycytidine treatment of CML cells resulted in gene re-expression and in a dose-dependent cell growth reduction. Single nucleotide variants of certain epigenetic modifiers during CML progression were not found. Together, our results demonstrate that methylation changes occur frequently during CML progression and may provide a useful basis for revealing new targets of therapy in advanced CML.
Project description:Compared to whole serum miRNAs, miRNAs in serum small extracellular vesicles (sEVs) are well protected form RNA enzymes, thus provide a consistent source of miRNA for disease biomarker detection. Serum sEVs and their miRNA cargos released by injured liver cells could be promising biomarkers for diagnosis of liver diseases. We were very interested to find out the effects of liver injury on serum extracellular vesicles as well as the small RNA components they transported, if there is any difference between acute and chronic injury. Study in this regard will help us to identify new serum biomarkers for liver injury, and to find out if there are specific markers for acute or chronic liver injury. To identify potential biomarker for liver injury based on serum sEVs miRNAs, we established the carbon tetrachloride (CCL4) induced acute and chronic liver injury mice model, and examined the dynamic changes of small RNA components, especially miRNAs, in serum sEVs.
Project description:The aim of the present project is to assess the effects of the chronic diseases and their associated treatments chronic paediatric diseases (CPD), to further understand their impact on physical fitness for public health perspectives. This is an innovative approach in the treatment of chronic paediatric diseases . This project should yield results that help improving treatments for children and adolescents with chronic paediatric diseases throughout physical activity as therapy, reduced pain, fatigue and inflammation, and improvement in physical fitness and life quality. The originality and novelty of this project is to combine architectural, functional and metabolic components of skeletal muscle to further understand the impact of chronic paediatric diseases as a function of treatment, disease activity and maturation status (prepubertal, pubertal or post pubertal).
This study will aim at assessing muscular function (force production capacity and fatigability) in specific or ecologic situations so as to get information about muscle functioning on isolated muscle group (here knee extensors) or during whole body exercise. Moreover, results arising from muscle architecture or quality will allow understanding the decrease in strength or endurance reported in the literature. The data collected will allow us to further understand the impact of the disease on structural, functional and metabolic parameters. Finally, the understanding of these alterations will provide information enabling to establish recommendations in physical activity (PA) to reduce or even counter the effect of the chronic inflammation and prevent at long-term overweight and cardiovascular risks.
The long-term objective is to contribute establishing recommendations or guidelines for prescribing physical activity during medical therapy. Values obtained in pathological children will be compared to those of control children matched for gender and maturation.
Project description:We report the application of high throughput Illumina sequencing for profiling of small RNAs in saliva of patients who were diagnosed with chronic periodontitis as compared to healthy controls. To date, there is no published literature on salivary microRNA profiling done using the high throughput next-generation sequencing analysis in patients diagnosed with chronic periodontitis. Also, this is the first study of its kind done in an Indian population. The objectives of the study were to profile microRNAs expressed in saliva of patients diagnosed with chronic periodontitis, to identify differentially expressed microRNAs between chronic periodontitis and healthy patients and to identify putative salivary microRNAs which can serve as biomarkers for periodontal disease.