Northwestern University Center for Chromatin NanoImaging in Cancer (NU-CCNIC)

Overall: PROJECT SUMMARY
Cancer stem cells (CSCs) play a critical role in fostering tumor resistance to therapies and relapse after
treatment. This presents a crucial barrier to the development of successful anti-cancer therapeutics.
Transcriptional reprogramming and plasticity play a critical role in and out of the CSC state, which in turn are
interdependent on the regulatory function of the three-dimensional (3D) structure of chromatin, epigenetic states,
and other molecular events. Our understanding of fundamental CSC biology has been hampered by the need
for cellular nanoscale imaging technologies that provide both highly detailed structural information regarding 3D
chromatin organization and highly multiplexed molecular imaging of the many molecular regulators and events
involved in CSC processes. We propose to establish the Northwestern University Center for Chromatin
Nanoimaging in Cancer (NU-CCNIC) to address this fundamental technology gap in cellular nanoscale imaging
and deploy the new technologies to address the fundamental knowledge gap in CSC biology. The Center
converges experts in cellular nanoscale imaging, computational imaging, molecular modeling, computational
genomics, CSC biology, and oncology. The Center will develop, test, validate, iterate, and deploy an integrated
and co-registered Multi-scale Chromatin Nanoimaging Platform that will comprise three “nested-doll” imaging
techniques: chromatin scanning transmission electron microscopy, optical spectroscopic super-resolution
nanoscopy, and optical spectroscopic nanosensing. The Nanoimaging Platform will enable quantitative imaging
of chromatin structure and highly multiplexed molecular and gene-specific localization, at the most fundamental
length-scale approaching 1 nm resolution, including the imaging of statistically significant cell populations and
live cells with high temporal resolution over prolonged temporal follow-up times. The Nanoimaging Platform will
be bridged to computational genomics, epigenomics, genome mapping, and predictive transcriptional modeling
datasets. These technologies will be deployed to answer several long-standing open questions in CSC biology.
We will elucidate whether CSCs can originate from non-CSCs via transcriptional reprogramming, test the role of
chromatin structure in fostering transcriptional plasticity in CSC processes, and explore the possibility of
transcriptionally reprogramming CSCs to exit the stem-state as a new therapeutic strategy. All aspects of the
technology development will be guided by the needs of the CSC biology testbed through a series of research
feedback loops. In the long term, such single-cell nanoimaging technologies will help comprehensive
understanding of the complex interplay between structural, physico-chemical, and molecular genomic events.
We anticipate that these convergence studies will provide new insights into CSC biology, which are impossible
to reveal with the use of any single method, and open new opportunities for identifying therapeutic strategies.

Grant Number: 5U54CA268084-04
NIH Institute/Center: NIH
Principal Investigator: Vadim Backman