Literature DB >> 31338502

Microfluidic epigenomic mapping technologies for precision medicine.

Chengyu Deng1, Lynette B Naler1, Chang Lu1.   

Abstract

Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.

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Mesh：

Year:  2019        PMID： 31338502      PMCID： PMC6697104          DOI： 10.1039/c9lc00407f

Source DB:  PubMed          Journal:  Lab Chip        ISSN： 1473-0189            Impact factor:   6.799


  243 in total

Review 1.  Family and twin strategies as a head start in defining prodromes and endophenotypes for hypothetical early-interventions in schizophrenia.

Authors:  I I Gottesman; L Erlenmeyer-Kimling
Journal:  Schizophr Res       Date:  2001-08-01       Impact factor: 4.939

2.  Accurate multiplex gene synthesis from programmable DNA microchips.

Authors:  Jingdong Tian; Hui Gong; Nijing Sheng; Xiaochuan Zhou; Erdogan Gulari; Xiaolian Gao; George Church
Journal:  Nature       Date:  2004-12-23       Impact factor: 49.962

3.  Genomic maps and comparative analysis of histone modifications in human and mouse.

Authors:  Bradley E Bernstein; Michael Kamal; Kerstin Lindblad-Toh; Stefan Bekiranov; Dione K Bailey; Dana J Huebert; Scott McMahon; Elinor K Karlsson; Edward J Kulbokas; Thomas R Gingeras; Stuart L Schreiber; Eric S Lander
Journal:  Cell       Date:  2005-01-28       Impact factor: 41.582

4.  Epigenetic differences arise during the lifetime of monozygotic twins.

Authors:  Mario F Fraga; Esteban Ballestar; Maria F Paz; Santiago Ropero; Fernando Setien; Maria L Ballestar; Damia Heine-Suñer; Juan C Cigudosa; Miguel Urioste; Javier Benitez; Manuel Boix-Chornet; Abel Sanchez-Aguilera; Charlotte Ling; Emma Carlsson; Pernille Poulsen; Allan Vaag; Zarko Stephan; Tim D Spector; Yue-Zhong Wu; Christoph Plass; Manel Esteller
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-11       Impact factor: 11.205

5.  Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases.

Authors:  Bodo Brueckner; Regine Garcia Boy; Pawel Siedlecki; Tanja Musch; H Christian Kliem; Piotr Zielenkiewicz; Sandor Suhai; Manfred Wiessler; Frank Lyko
Journal:  Cancer Res       Date:  2005-07-15       Impact factor: 12.701

6.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

7.  Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors.

Authors:  M Esteller; J M Silva; G Dominguez; F Bonilla; X Matias-Guiu; E Lerma; E Bussaglia; J Prat; I C Harkes; E A Repasky; E Gabrielson; M Schutte; S B Baylin; J G Herman
Journal:  J Natl Cancer Inst       Date:  2000-04-05       Impact factor: 13.506

Review 8.  FDA drug approval summary: azacitidine (5-azacytidine, Vidaza) for injectable suspension.

Authors:  Edvardas Kaminskas; Ann T Farrell; Yong-Cheng Wang; Rajeshwari Sridhara; Richard Pazdur
Journal:  Oncologist       Date:  2005-03

9.  Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer.

Authors:  Mario F Fraga; Esteban Ballestar; Ana Villar-Garea; Manuel Boix-Chornet; Jesus Espada; Gunnar Schotta; Tiziana Bonaldi; Claire Haydon; Santiago Ropero; Kevin Petrie; N Gopalakrishna Iyer; Alberto Pérez-Rosado; Enrique Calvo; Juan A Lopez; Amparo Cano; Maria J Calasanz; Dolors Colomer; Miguel Angel Piris; Natalie Ahn; Axel Imhof; Carlos Caldas; Thomas Jenuwein; Manel Esteller
Journal:  Nat Genet       Date:  2005-03-13       Impact factor: 38.330

10.  Hypermethylation of multiple genes in tumor tissues and voided urine in urinary bladder cancer patients.

Authors:  Michael W Y Chan; Lun W Chan; Nelson L S Tang; Joanna H M Tong; Kwok W Lo; Tin L Lee; Ho Y Cheung; Wai S Wong; Peter S F Chan; Fernand M M Lai; Ka F To
Journal:  Clin Cancer Res       Date:  2002-02       Impact factor: 12.531
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  4 in total

1.  Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.

Authors:  Yi Xu; Steven R Doonan; Tamas Ordog; Ryan C Bailey
Journal:  Anal Chem       Date:  2020-06-04       Impact factor: 6.986

2.  Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics.

Authors:  Chengyu Deng; Travis W Murphy; Qiang Zhang; Lynette B Naler; Alice Xu; Chang Lu
Journal:  Anal Chem       Date:  2020-10-01       Impact factor: 6.986

Review 3.  Extracellular Vesicle Identification Using Label-Free Surface-Enhanced Raman Spectroscopy: Detection and Signal Analysis Strategies.

Authors:  Hyunku Shin; Dongkwon Seo; Yeonho Choi
Journal:  Molecules       Date:  2020-11-09       Impact factor: 4.411

Review 4.  Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis.

Authors:  Jialang Zhuang; Qin Huo; Fan Yang; Ni Xie
Journal:  Front Genet       Date:  2020-10-29       Impact factor: 4.599
  4 in total

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