Microfluidics for low input epigenomic analysis and application to oncology and brain neuroscience

Microfluidics is a versatile tool with many applications in biology. Its ability to manipulate small volumes of liquid precisely has led to the development of many microfluidic assay platforms. They could handle small amounts of samples and carry out analysis with high sensitivity and throughput. Microfluidic assays have provided new insights into scarce biological samples at higher resolution. In this thesis, we developed microfluidic tools to conduct low input ChIP-seq and ChIRP-seq. We applied them to a variety of samples profiling different targets. The native MOWChIP-seq platform was developed to map RNA polymerase II, transcription factors and histone deacetylase binding in 1,000-50,000 cells. We examined mouse prefrontal cortex and cerebellum using this technology. We found extensive differences that correlated with distinct neurological functions of the brain regions. The same platform and workflow were used to profile five key histone modifications in human lung tumor and normal tissue samples. Integrative analysis with gene expression data revealed extensive chromatin remodeling in lung tumor. Spatial histone modification mapping was conducted in mouse neocortex in a similar fashion. We generated an epigenomic tomography that demonstrated the molecular state of the brain in 3D. Lastly, we developed a microfluidic version of the ChIRP-seq process which successfully conducted the assay using only 500K cells. This improvement makes ChIRP-seq in tissue samples feasible.

Name thesis:degree_name

Doctor of Philosophy

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Biomedical Engineering

Department dc:contributor.department

Department of Biomedical Engineering and Mechanics

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2023

Author dc:creator

• Liu, Zhengzhi

Chair dc:contributor.committeechair

• Lu, Chang

Committee members dc:contributor.committeemember

• Li, Liwu
• Verbridge, Scott
• Chen, Zhen Bouman
• Davalos, Rafael V.

• microfluidics
• epigenome
• chromatin immunoprecipitation
• next generation sequencing
• histone modification
• RNA polymerase II
• transcription factor
• chromatin isolation by RNA purification
• epigenomic tomography
• non-small cell lung cancer

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Language dc:language.iso

en

Dc Identifier Other

vt_gsexam:37059

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/116243