The development of tools which allow for the precise alterations of the epigenetic landscape in desired genomic locations presents exciting possibilities toward further understanding how gene expression is regulated and opportunities to harness these properties for therapeutic purposes. In contrast to gene knockout strategies, targeted epigenome modifications, such as editing of DNA methylation, can mediate gene expression modulation without changing the genomic sequence. Thereby, in a therapeutic context, this strategy may offer a safer route as compared to gene disruption using designer nucleases that, to reach high efficiencies, relies on the occurrence of random mutations to inactivate the target gene. In addition, therapeutic benefit is influenced not only by the intrinsic safety and efficacy of the tools used but also by methods that allow efficient and non-toxic transfer of the selected reagents in the target cells. Here, we describe a detailed protocol, for safe delivery of TALE-based designer epigenome modifiers in the form of in vitro transcribed mRNA into primary human CD4 T cells to efficiently silence the expression of an exemplary human gene (i.e., CCR5).
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http://dx.doi.org/10.1007/978-1-4939-7774-1_9 | DOI Listing |
Mol Psychiatry
January 2025
Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland.
Childhood maltreatment exposure (CME) increases the risk of adverse long-term health consequences for the exposed individual. Animal studies suggest that CME may also influence the health and behaviour in the next generation offspring through CME-driven epigenetic changes in the germ line. Here we investigated the associated between early life stress on the epigenome of sperm in humans with history of CME.
View Article and Find Full Text PDFCancer Cell
December 2024
Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address:
Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer's underlying biology, bringing hope to inform a patient's prognosis and treatment plan. However, most approaches used in the discovery of subtypes are not suitable for assigning subtype labels to new cancer specimens from other studies or clinical trials. Here, we address this barrier by applying five different machine learning approaches to multi-omic data from 8,791 TCGA tumor samples comprising 106 subtypes from 26 different cancer cohorts to build models based upon small numbers of features that can classify new samples into previously defined TCGA molecular subtypes-a step toward molecular subtype application in the clinic.
View Article and Find Full Text PDFPLoS Pathog
December 2024
Institute of Human Genetics, School of Medicine, University Bonn & University Hospital Bonn, Bonn, Germany.
Courses of SARS-CoV-2 infections are highly variable, ranging from asymptomatic to lethal COVID-19. Though research has shown that host genetic factors contribute to this variability, cohort-based joint analyses of variants from the entire allelic spectrum in individuals with confirmed SARS-CoV-2 infections are still lacking. Here, we present the results of whole genome sequencing in 1,220 mainly vaccine-naïve individuals with confirmed SARS-CoV-2 infection, including 827 hospitalized COVID-19 cases.
View Article and Find Full Text PDFNat Commun
December 2024
Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
High-dimensional cytometry (HDC) is a powerful technology for studying single-cell phenotypes in complex biological systems. Although technological developments and affordability have made HDC broadly available in recent years, technological advances were not coupled with an adequate development of analytical methods that can take full advantage of the complex data generated. While several analytical platforms and bioinformatics tools have become available for the analysis of HDC data, these are either web-hosted with limited scalability or designed for expert computational biologists, making their use unapproachable for wet lab scientists.
View Article and Find Full Text PDFCrit Rev Clin Lab Sci
December 2024
Department of Molecular Endocrinology, National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research, Mumbai, India.
Polycystic ovary syndrome (PCOS) is a complex multifactorial endocrinopathy affecting reproductive aged women globally, whose presentation is strongly influenced by genetic makeup, ethnic, and geographic diversity leaving these affected women substantially predisposed to reproductive and metabolic perturbations. Sophisticated techniques spanning genomics, proteomics, epigenomics, and transcriptomics have been harnessed to comprehensively understand the enigmatic pathophysiology of PCOS, however, conclusive markers for PCOS are still lacking today. Metabolomics represents a paradigm shift in biotechnological advances enabling the simultaneous identification and quantification of metabolites and the use of this approach has added yet another dimension to help unravel the strong metabolic component of PCOS.
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