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A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome

ABSTRACT: A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome

PROVIDER: PRJNA694854 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13529937_1.fastq.gz	Fastqsanger.gz
	SRR13529937_2.fastq.gz	Fastqsanger.gz
	SRR13529938_1.fastq.gz	Fastqsanger.gz
	SRR13529938_2.fastq.gz	Fastqsanger.gz
	SRR13529939_1.fastq.gz	Fastqsanger.gz

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A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome

Project description:Severe fever with thrombocytopenia syndrome (SFTS) is a new tick-borne infectious disease caused by a new SFTS virus (SFTSV). Due to its 12%-50% high fatality rate and the possibility of pandemic transmission, as well as no specific antiviral drugs for the treatment so far, SFTSV has been listed as one of the top 10 priority infectious diseases by the World Health Organization. Currently, there are rare studies of transcriptomic analysis for the patients infected with SFTSV, which makes it difficult to deeply understand the life cyle and pathogenicity of this virus. To explore the differences of transcripts after SFTSV infection, we performed a longitudinal sampling study to systematically investigate the chronological changes of viral load and transcriptomic and epigenetic characterization using white blood cells from SFTSV patients. The results showed significant changes in the expression of some genes from onset to recovery of SFTSV infection. Moreover, these differentially expressed genes showed good consistency in the three patients at different stages of treatment, which may contribute to the pathophysiology of SFTSV and thus lead to a breakthrough in SFTSV therapy. Moreover, by m6A-seq, we found some genes that might be regulated by m6A. This study in transcript changes and RNA modification may open a brand new direction to our understanding of SFTSV and play an important role in the drugs discovery for effective treatment.

2021-08-05 | GSE165518 | GEO

A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome.

Project description:Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne infectious disease caused by a new type of SFTS virus (SFTSV). Here, a longitudinal sampling study is conducted to explore the differences in transcript levels after SFTSV infection, and to characterize the transcriptomic and epigenetic profiles of hospitalized patients. The results reveal significant changes in the mRNA expression of certain genes from onset to recovery. Moreover, m6A-seq reveals that certain genes related with immune regulation may be regulated by m6A. Besides the routine tests such as platelet counts, serum ALT and AST levels testing, distinct changes in myocardial enzymes, coagulation function, and inflammation are well correlated with the clinical data and sequencing data, suggesting that clinical practitioners should monitor the above indicators to track disease progression and guide personalized treatment. In this study, the transcript changes and RNA modification may lend a fresh perspective to our understanding of the SFTSV and play a significant role in the discovery of drugs for effective treatment of this disease.

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Severe fever with thrombocytopenia syndrome virus

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Serum Proteomics of Severe Fever with Thrombocytopenia Syndrome Patients

Project description:Dabie bandavirus, also termed as severe fever with thrombocytopenia syndrome virus (SFTSV), was first isolated in China in 2010. At this time, the virus was found to have spread to South Korea, Japan, and other countries. A high case fatality rate is reported for SFTS, ranging from 12–50% within various sources. Several omics for clinical studies among SFTS patients as well as studies of cultured SFTSV have attempted to characterize the relevant molecular biology and epidemiology of the disease. However, a global serum proteomics analysis among SFTS patients has not yet been reported to date. Thrombocytopenia and multiple organ failure are the major immediate causes of death among SFTS patients. In this study, serum proteomic changes related to thrombocytopenia, abnormal immune response, and inflammatory activation were documented in SFTS patients. These findings provide useful information forunderstanding the clinical manifestations of SFTS.

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Ferret animal model of severe fever with thrombocytopenia syndrome phlebovirus for human lethal infection and pathogenesis

Project description:Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV), listed in the WHO most dangerous pathogens, has 12-30% fatality rates with a characteristic thrombocytopenia syndrome. With a majority of clinically diagnosed SFTSV patients older than ~50 years, age is a critical risk factor for SFTSV morbidity and mortality. Here, we report an age-dependent ferret model of SFTSV infection and pathogenesis that fully recapitulates the clinical manifestations of human infections. While young adult ferrets (≤2 years old) did not show any clinical symptoms and mortality, SFTSV-infected aged ferrets (≥4 years old) demonstrated severe thrombocytopenia, reduced white blood cells, and high fever with 93% mortality rate. Moreover, significantly higher viral load was observed in aged ferrets. Transcriptome analysis of SFTSV-infected young ferrets revealed strong interferon-mediated anti-viral signaling, whereas inflammatory immune responses were markedly upregulated and persisted in aged ferrets. Thus, this immunocompetent age-dependent ferret model should be useful for anti-SFTSV therapy and vaccine development.

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Expression profile and clinical significance of miRNAs at different stages of severe fever with thrombocytopenia syndrome (SFTS) in Chinese patients

Project description:In order to determine the microRNAs profile in peripheral blood mononuclear cell (PBMC) from severe febrile with thrombocytopenia syndrome virus infection and investigate possible diagnostic value of these differential microRNAs.

2023-05-01 | GSE130933 | GEO

Longitudinal blood transcriptome analysis of two patients with cyclic thrombocytopenia

Project description:Cyclic thrombocytopenia (CTP) is a rare disease of characterized by periodic platelet count oscillations of uncertain etiology. As part of a study that applied systems biology approaches to investigate two patients with CTP, we performed whole blood transcriptome analyses on semi-weekly collected sequential samples covering two platelet cycles. This blood transcriptome analysis revealed cyclical gene expression changes of platelet-specific genes that are in parallel with, and leading platelet count oscillations in both patients. In addition, erythrocyte-specific genes and neutrophil-specific genes also exhibited cyclic patterns which preceded platelet-specific genes. These findings revealed cyclical trilineage hematopoiesis, most pronounced in megakaryopoiesis in both patients with CTP.

2022-04-05 | GSE179076 | GEO

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Project description:The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. Linked cross omic data sets:Microbiome sequencing data associated with this study are available in the European Nucleotide Archive (ENA): accession number <a href='https://www.ebi.ac.uk/ena/browser/view/PRJEB37924' rel='noopener noreferrer' target='_blank'>PRJEB37924</a> and <a href='https://www.ebi.ac.uk/ena/browser/view/PRJNA612180' rel='noopener noreferrer' target='_blank'>PRJNA612180</a>.

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