Epigenomic technologies for deciphering circulating tumor DNA.

Abstract:

:Tumor-derived DNA, found in body fluids (liquid biopsy) of cancer patients as part of cell-free DNA (cfDNA), lends itself for noninvasive cancer detection and monitoring. Advantages of cfDNA as analytical target have evoked a burst of sophisticated techniques, providing clinically relevant information. Each cell type carries a unique DNA modification profile consisting mainly of patterns of 5-methylcytosine in CpG dinucleotides, which are critical for establishing and maintaining cellular identity and which are frequently disturbed in cancer. Assessment of the tumor-derived cfDNA modifications combined with high-throughput analysis techniques holds promise for developing highly specific noninvasive diagnostic tests. This review highlights recent advances in locus-specific and whole-genome analysis of cfDNA, with a specific focus on epigenetic phenomena and their clinical value.

journal_name

Curr Opin Biotechnol

authors

Daniūnaitė K,Jarmalaitė S,Kriukienė E

doi

10.1016/j.copbio.2018.07.002

subject

Has Abstract

pub_date

2019-02-01 00:00:00

pages

23-29

eissn

0958-1669

issn

1879-0429

pii

S0958-1669(18)30033-8

journal_volume

55

pub_type

杂志文章,评审
  • Use of cell wall-less bacteria (L-forms) for efficient expression and secretion of heterologous gene products.

    abstract::In spite of many efforts and achievements to optimize the prokaryotic expression systems, there are still general and specific problems in obtaining sufficient yields of the functionally active gene products. The main problems concern the formation of inclusion bodies, incorrect folding, toxicity for the producer cell...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(98)80037-2

    authors: Gumpert J,Hoischen C

    更新日期:1998-10-01 00:00:00

  • Microbial biocatalyst developments to upgrade fossil fuels.

    abstract::Steady increases in the average sulfur content of petroleum and stricter environmental regulations concerning the sulfur content have promoted studies of bioprocessing to upgrade fossil fuels. Bioprocesses can potentially provide a solution to the need for improved and expanded fuel upgrading worldwide, because biopro...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2006.04.005

    authors: Kilbane JJ 2nd

    更新日期:2006-06-01 00:00:00

  • Patient-derived xenografts (PDXs) as model systems for human cancer.

    abstract::Patient-derived xenografts (PDXs) are obtained by transplanting fragments of a patient's tumour into immunodeficient mice. Growth and propagation of PDXs allows correlating therapeutic response in vivo with extensive, multi-dimensional molecular annotation, leading to identification of predictive biomarkers. PDXs are ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2020.01.003

    authors: Invrea F,Rovito R,Torchiaro E,Petti C,Isella C,Medico E

    更新日期:2020-06-01 00:00:00

  • Engineering yeast for utilization of alternative feedstocks.

    abstract::Realizing the economic benefits of alternative substrates for commodity chemical bioproduction typically requires significant metabolic engineering of common model organisms, such as Saccharomyces cerevisiae. A growing toolkit is enabling engineering of non-conventional yeast that have robust native metabolism for xyl...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2017.12.003

    authors: Yaguchi A,Spagnuolo M,Blenner M

    更新日期:2018-10-01 00:00:00

  • Dynamic covalent chemistry in aid of peptide self-assembly.

    abstract::Self-assembled peptide systems have been widely studied in the context of gaining understanding of the rules that govern biomolecular processes and increasingly as new bio-inspired nanomaterials. Such materials may be designed to be highly dynamic, displaying adaptive and self-healing properties. This review focuses o...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.copbio.2010.05.010

    authors: Sadownik JW,Ulijn RV

    更新日期:2010-08-01 00:00:00

  • Engineering a local microenvironment for pancreatic islet replacement.

    abstract::Intraportal islet transplantation has emerged as a promising treatment for type 1 diabetes mellitus (T1DM). Nevertheless, long-term efficacy has been limited to a marginal number of patients. Outcomes have been restricted, in part, by challenges associated with the transplant site, poor vascularization, and disruption...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2013.05.004

    authors: Coronel MM,Stabler CL

    更新日期:2013-10-01 00:00:00

  • Functional foods and strategies contrasting bacterial adhesion.

    abstract::Antibacterial strategies targeting bacterial adhesion to substrates are considered a valuable alternative to traditional antibiotic therapy, in view of the great advantage they bring in combating the infectious process at the very early stage without selecting for drug resistant cells. Amongst bioactive compounds with...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2011.08.006

    authors: Signoretto C,Canepari P,Stauder M,Vezzulli L,Pruzzo C

    更新日期:2012-04-01 00:00:00

  • The use of adenoviral vectors for gene therapy and gene transfer in vivo.

    abstract::Adenoviral vectors have proven to be excellent vehicles for gene delivery in vivo to a wide range of cell types. These vectors have been used to transfer genes such as CFTR to correct the defect in cystic fibrosis and, more recently, to supply serum blood factors and genetically modify tumors to enhance therapy. ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(95)80097-2

    authors: Bramson JL,Graham FL,Gauldie J

    更新日期:1995-10-01 00:00:00

  • Receptor-based assays.

    abstract::Recombinant DNA technology has expanded the potential of the targeted screening approach in drug discovery. The use of cloned and expressed receptors as targets for the evaluation of novel compounds can significantly simplify the structure affinity/activity process. However, the patenting of cloned receptors, as well ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(93)90038-x

    authors: Williams M

    更新日期:1993-02-01 00:00:00

  • The flux and impact of wastewater infrastructure microorganisms on human and ecosystem health.

    abstract::Wastewater infrastructure is designed, in part, to remove microorganisms. However, many microorganisms are able to colonize infrastructure and resist treatment, resulting in an enormous flux of microorganisms to urban adjacent waters. These urban-associated microorganisms are discharged through three primary routes 1)...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2019.03.015

    authors: Newton RJ,McClary JS

    更新日期:2019-06-01 00:00:00

  • Ultrafast laser nanosurgery in microfluidics for genome-wide screenings.

    abstract::The use of ultrafast laser pulses in surgery has allowed for unprecedented precision with minimal collateral damage to surrounding tissues. For these reasons, ultrafast laser nanosurgery, as an injury model, has gained tremendous momentum in experimental biology ranging from in vitro manipulations of subcellular struc...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2009.01.008

    authors: Ben-Yakar A,Bourgeois F

    更新日期:2009-02-01 00:00:00

  • Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors.

    abstract::Cytoskeletal molecular motors provide exciting proof that nanoscale transporters can be highly efficient, moving for microns along filamentous tracks by hydrolyzing ATP to fuel nanometer-size steps. For nanotechnology, such conversion of chemical energy into productive work serves as an enticing platform for re-purpos...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2016.10.011

    authors: DelRosso NV,Derr ND

    更新日期:2017-08-01 00:00:00

  • Genomic tools to assist breeding for drought tolerance.

    abstract::Water deficit or drought stress is a major limitation to crop production globally. Plant breeders have used a wide range of technologies to successfully breed varieties that perform well under the growth conditions for their target environments but they are always seeking new opportunities to enhance rates of genetic ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2014.11.027

    authors: Langridge P,Reynolds MP

    更新日期:2015-04-01 00:00:00

  • Polyphenols as antimicrobial agents.

    abstract::Polyphenols are secondary metabolites produced by higher plants, which play multiple essential roles in plant physiology and have potential healthy properties on human organism, mainly as antioxidants, anti-allergic, anti-inflammatory, anticancer, antihypertensive, and antimicrobial agents. In the present review the a...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2011.08.007

    authors: Daglia M

    更新日期:2012-04-01 00:00:00

  • Recombinant proteins for medical use: the attractions and challenges.

    abstract::Recombinant proteins that have survived the challenges of process development and clinical trials are becoming blockbuster medical products. Growth factors, enzymes and antibodies are being improved by mutational approaches, fused with other proteins, and even chemically modified in vitro. Drug development and testing...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(95)80112-x

    authors: Koths K

    更新日期:1995-12-01 00:00:00

  • T-cell receptor peptide-MHC interactions: biological lessons from structural studies.

    abstract::Fifteen years have passed since T-cell receptor (TCR) genes were identified (reviewed in [1]). Unlike the situation for antibodies, no direct structural information on the TCR proteins has been available for most of this time. Recently, however, the crystal structures of isolated alpha and beta chains were determined,...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(98)80004-9

    authors: Garcia KC,Teyton L

    更新日期:1998-08-01 00:00:00

  • Reconstruction of microbial transcriptional regulatory networks.

    abstract::Although metabolic networks can be readily reconstructed through comparative genomics, the reconstruction of regulatory networks has been hindered by the relatively low level of evolutionary conservation of their molecular components. Recent developments in experimental techniques have allowed the generation of vast a...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2003.11.002

    authors: Herrgård MJ,Covert MW,Palsson BØ

    更新日期:2004-02-01 00:00:00

  • Nucleic acids in the environment.

    abstract::The past year has witnessed several excellent advances in basic and applied research on nucleic acids in the environment. Improved methods for extracting nucleic acids from environmental samples have been published, as well as information on the use of reporter genes in bacteria, natural genetic transformation in soil...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(96)80040-1

    authors: Trevors JT

    更新日期:1996-06-01 00:00:00

  • The cellular response to unfolded proteins: intercompartmental signaling.

    abstract::Both prokaryotic and eukaryotic cells respond to the accumulation of unfolded proteins by increasing the transcription of genes encoding molecular chaperones and other stress-responsive proteins. Different sets of genes are activated when particular cellular compartments are burdened with unfolded proteins. Cells thus...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(94)90071-x

    authors: McMillan DR,Gething MJ,Sambrook J

    更新日期:1994-10-01 00:00:00

  • Synthetic gene networks in mammalian cells.

    abstract::The design and construction of synthetic gene circuits with complex spatiotemporal dynamics was pioneered in bacteria, but it took almost a decade until synthetic biologists were able to construct genetic circuits with complex spatiotemporal dynamics in mammalian cells. This review highlights the most recent advances ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2010.07.006

    authors: Weber W,Fussenegger M

    更新日期:2010-10-01 00:00:00

  • Measuring gene expression by quantitative proteome analysis.

    abstract::Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis for protein separation, visualization, and quantification and mass spectrometry for protein identification. Over the past year, exceptional progress has been made towards developing a new technology base for the p...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(00)00116-6

    authors: Gygi SP,Rist B,Aebersold R

    更新日期:2000-08-01 00:00:00

  • Novel methods for cloning and engineering genes using the polymerase chain reaction.

    abstract::Use of the polymerase chain reaction (PCR) has become increasingly widespread in virtually all aspects of molecular biology. Recently, novel ligation-independent methods have been developed for the cloning of DNA fragments amplified using PCR. Ligation-independent cloning utilizing the enzyme uracil DNA glycosylase (t...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(95)80006-9

    authors: Rashtchian A

    更新日期:1995-02-01 00:00:00

  • Targeted contrast agents for magnetic resonance imaging and ultrasound.

    abstract::The development of contrast agents that can be localized to a particular tissue or cellular epitope will potentially allow the noninvasive visualization and characterization of a variety of disease states. Recent advances have been made in the field of molecular imaging with magnetic resonance imaging and ultrasound a...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2004.11.001

    authors: Morawski AM,Lanza GA,Wickline SA

    更新日期:2005-02-01 00:00:00

  • Two-hybrid technologies in proteomics research.

    abstract::Given that protein-protein interactions (PPIs) regulate nearly every living process; the exploration of global and pathway-specific protein interaction networks is expected to have major implications in the understanding of diseases and for drug discovery. Consequently, the development and application of methodologies...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2008.06.005

    authors: Suter B,Kittanakom S,Stagljar I

    更新日期:2008-08-01 00:00:00

  • The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level.

    abstract::The Silicon Cell initiative aims to understand cellular systems on the basis of the characteristics of their components. As a tool to achieve this, detailed kinetic models at the network reaction level are being constructed. Such detailed kinetic models are extremely useful for medical and biotechnological application...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2005.05.003

    authors: Snoep JL

    更新日期:2005-06-01 00:00:00

  • Opportunities toward hydrogen production biotechnologies.

    abstract::Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2020.03.002

    authors: Swartz J

    更新日期:2020-04-01 00:00:00

  • High-density gridding: techniques and applications.

    abstract::Much progress has been made in the development of techniques for constructing dense grids either of ligands, such as peptides and oligonucleotides, or of cloned nucleic acids. Such arrays are finding practical applications in the analysis of sequence variation and gene expression. Methods for carrying out large number...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(96)80100-5

    authors: Southern EM

    更新日期:1996-02-01 00:00:00

  • Targets for sepsis therapies: tumor necrosis factor versus interleukin-1.

    abstract::Clinical testing of therapies for sepsis that target tumor necrosis factor and interleukin-1 is currently in progress. It is now clear from early clinical results that patients display a heterogeneous response to anti-cytokine therapies that may be related to the stage or severity of disease. Experimental results show...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(93)90055-2

    authors: Russell DA,Thompson RC

    更新日期:1993-12-01 00:00:00

  • Optimizing the fluorescent protein toolbox and its use.

    abstract::Fluorescent proteins (FPs) and fluorescent protein-derived biosensors are indispensable tools in life sciences. They make it possible to probe the location, activity, or interaction of molecules of interest from a subcellular to a multicellular scale. The desire for high-resolution and multidimensional information imp...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2019.04.006

    authors: Duwé S,Dedecker P

    更新日期:2019-08-01 00:00:00

  • Brave new proteins: what evolution reveals about protein structure.

    abstract::Synthetic proteins provide important information about the principles of protein structure. They illuminate the processes of natural protein evaluation, but are not limited by these processes. Here, we review studies of several mutant proteins and discuss the general principles that can be derived from them. ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0958-1669(91)90085-j

    authors: Pastore A,Lesk AM

    更新日期:1991-08-01 00:00:00