4.7 Article

Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-months recovery of COVID-19

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

The cGAS-STING pathway drives type I IFN immunopathology in COVID-19

Jeremy Di Domizio et al.

Summary: This study reveals the mechanism behind aberrant type I interferon responses in COVID-19 through the cGAS-STING pathway and demonstrates its importance in severe cases. By using animal and lung-on-chip models, the study provides insights into host-directed therapeutic strategies for COVID-19.

NATURE (2022)

Article Biochemistry & Molecular Biology

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal et al.

Summary: ReMap 2022 provides manually curated, high-quality catalogs of regulatory regions from Human, Arabidopsis, Mouse, and Fly, including hundreds of transcription factors and regulators. The update also introduces new regulatory catalogs for Mouse and Fly, enriching research resources for scientists. Users can browse the four regulatory catalogs through track hubs at UCSC, Ensembl, and NCBI genome browsers.

NUCLEIC ACIDS RESEARCH (2022)

Letter Gastroenterology & Hepatology

Six-month follow-up of gut microbiota richness in patients with COVID-19

Yanfei Chen et al.

Article Immunology

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells

Ying Yin et al.

Summary: The study suggests that coronavirus infections can lead to increased retrotransposon expression, potentially causing genome instability and more severe symptoms, especially in cancer patients and the elderly. Additionally, the interaction between coronaviruses and retrotransposons may result in viral fragment invasion of the human genome, leading to more severe disease outcomes.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2021)

Article Cell & Tissue Engineering

Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3

Vidya Padmanabhan Nair et al.

Summary: Elevated HERV-K (HML-2) transcription is detrimental to the development and function of cortical neurons, with dopaminergic neurons being unaffected. The effects are associated with hyperactivation of NTRK3 expression, revealing a cell-type-specific role for HERV-K (HML-2) in cortical neuron development.

CELL STEM CELL (2021)

Article Multidisciplinary Sciences

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Toni M. Delorey et al.

Summary: This study using single-cell and spatial atlases revealed the impact of COVID-19 infection on lung, kidney, liver, and heart tissues, showing structural remodeling and viral RNA enrichment. Differences in lung inflammatory responses and transcriptional alterations in heart tissue of COVID-19 patients were also identified, along with cell types and genes associated with disease severity.

NATURE (2021)

Article Nutrition & Dietetics

Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery

Yu Tian et al.

Summary: Recent studies suggest that COVID-19 may lead to intestinal tissue infection and alter the gut microbiota, with these changes potentially not fully restored in recovered patients. Differences in bacterial diversity, species, and relative abundance were observed between recovered COVID-19 male patients and healthy controls.

FRONTIERS IN NUTRITION (2021)

Article Cell Biology

A cohort autopsy study defines COVID-19 systemic pathogenesis

Xiao-Hong Yao et al.

Summary: The study profiles 26 COVID-19 autopsy cases from Wuhan and determines the systemic distribution of SARS-CoV-2 in critically ill patients. It reveals that SARS-CoV-2 may invade multiple organs and utilize physiological barriers as entry ports for systemic dissemination, shedding light on novel COVID-19 treatment development.

CELL RESEARCH (2021)

Review Multidisciplinary Sciences

The role of retrotransposable elements in ageing and age-associated diseases

Vera Gorbunova et al.

Summary: The article discusses the impact of transposons on aging and age-related diseases in complex metazoan organisms, focusing on the activity of retrotransposons in particular. Research has shown that the activity of retrotransposons in somatic tissues during an individual's lifespan influences health and well-being, intersecting with our own physiology.

NATURE (2021)

Article Multidisciplinary Sciences

The trans-omics landscape of COVID-19

Peng Wu et al.

Summary: The authors conducted blood sampling and multi-omics analysis on COVID-19 patients of various disease severities, reporting a trans-omics landscape of COVID-19. The study found differences in characteristics between patients with different disease severities, suggesting potential clues for pathophysiology and therapeutic strategies of COVID-19.

NATURE COMMUNICATIONS (2021)

Article Oncology

Blood DNA methylation and COVID-19 outcomes

Joseph Balnis et al.

Summary: The study compared DNA CpG methylation in blood samples from COVID-19 patients and healthy controls collected before the pandemic, revealing differentially methylated regions associated with acute illness and autoimmune disorders. The results also showed a correlation between hyper-methylation in COVID-19 patients and worse outcomes, suggesting that DNA methylation may influence the expression of genes that regulate COVID-19 progression.

CLINICAL EPIGENETICS (2021)

Review Immunology

The cGAS-STING pathway as a therapeutic target in inflammatory diseases

Alexiane Decout et al.

Summary: The cGAS-STING signaling pathway plays a crucial role in inflammation in infection, cellular stress, and tissue damage settings. It has the ability to sense and regulate cellular responses to DNA and has the potential to be targeted in the treatment of various inflammatory diseases.

NATURE REVIEWS IMMUNOLOGY (2021)

Article Medicine, General & Internal

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Chaolin Huang et al.

LANCET (2020)

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

Article Medicine, General & Internal

Clinical Characteristics of Coronavirus Disease 2019 in China

W. Guan et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Biochemistry & Molecular Biology

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Daniel Blanco-Melo et al.

Article Biochemistry & Molecular Biology

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

Bo Shen et al.

Article Multidisciplinary Sciences

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

Denisa Bojkova et al.

NATURE (2020)

Article Multidisciplinary Sciences

Deep learning of immune cell differentiation

Alexandra Maslova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

Ludovico Cantuti-Castelvetri et al.

SCIENCE (2020)

News Item Medicine, General & Internal

Long covid: How to define it and how to manage it

Nikki Nabavi

BMJ-BRITISH MEDICAL JOURNAL (2020)

Article Multidisciplinary Sciences

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Yingyao Zhou et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

Michelle Percharde et al.

Article Multidisciplinary Sciences

Intact piRNA pathway prevents L1 mobilization in male meiosis

Simon J. Newkirk et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Biochemistry & Molecular Biology

The role of the mtDNA set point in differentiation, development and tumorigenesis

Xin Sun et al.

BIOCHEMICAL JOURNAL (2016)

Article Multidisciplinary Sciences

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

Edward J. Grow et al.

NATURE (2015)

Article Biochemistry & Molecular Biology

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Shihao Shen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

Anas Fadloun et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Altuna Akalin et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Felix Krueger et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

A novel member of the IκB family, human IκB-ζ, inhibits transactivation of p65 and its DNA binding

G Totzke et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Multidisciplinary Sciences

Accelerated chemokine receptor 7-mediated dendritic cell migration in Runx3 knockout mice and the spontaneous development of asthma-like disease

O Fainaru et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Critical Care Medicine

Short-term outcome of critically ill patients with severe acute respiratory syndrome

CD Gomersall et al.

INTENSIVE CARE MEDICINE (2004)

Article Genetics & Heredity

LINE-mediated retrotransposition of marked Alu sequences

M Dewannieux et al.

NATURE GENETICS (2003)