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Center for Chromatin NanoImaging in Cancer (NIH U54)

The National Cancer Institute has awarded CPGE a prestigious five-year U54 grant to establish the Center for Chromatin NanoImaging in Cancer. This mission of the Center is to develop, optimize, test, and deploy new nanoimaging technologies, integrated with state-of-the-art molecular and computational methods, to address some of the long-standing questions related to the origin of cancer stem cells and their ability to adapt to chemotherapies. Addressing these fundamental knowledge and technology gaps may help identify new therapeutic strategies that prevent tumor resistance to therapeutics and relapse after treatment.


Cancer stem cells (CSCs) represent a small population of cells within tumors that have the ability to self-renew, differentiate, and initiate tumors in vivo. CSCs are resistant to chemotherapy and responsible for tumor relapse after conventional treatment. The transcriptional program of CSCs is tightly regulated by epigenetic events and chromatin features that keep the stemness pathways active and repress differentiation programs. As sequencing and chromatin mapping technologies have advanced, transcriptional analysis of rare cells such as CSCs has become possible.

However, understanding the CSC-specific chromatin structure and how its 3D conformations determine the transcriptional state of these rare cells has not been feasible due to the lack of high-resolution chromatin imaging tools. We propose to elucidate this knowledge gap by integrating a cutting-edge chromatin imaging and analysis (nano-ChIA) platform with molecular genomic features. Our ultimate goal is to define the structural basis of CSC-specific chromatin conformations and integrate this with molecular genomic features (transcriptional and epigenomic profiles) in an ovarian cancer (OC) model. We will elucidate how 3D physical chromatin structure is associated with and potentially drives stemness and chemo-resistance in ovarian cancer.

A number of biological questions remain controversial and unanswered in the field of cancer stem cells: Can non-CSCs transition to a CSC state under select pressure? What are the transcriptional, epigenomic, and chromatin-dependent drivers facilitating cellular plasticity in and out of the CSC state? Can CSCs be reprogrammed to undergo differentiation and permanently exit the CSC state? Can the state of chromatin predict stemness? Are epigenetic mechanisms driving the transcriptional state of stem cells? To answer these questions, the Center for Chromatin NanoImaging in Cancer at CPGE integrates the fields of physical, computational, and biomolecular sciences by imaging chromatin structure and defining molecular states in the context of genomic and transcriptional events that drive the survival and tumorigenic functions of CSCs.

Technology Development

An ongoing revolution in our understanding of the relationship between chromatin structure, epigenetic states, and transcriptional rewiring, in particular those processes involved in the function of cancer stem cells (CSCs), has been to a large extent driven by access to new technologies, notably, cellular nanoimaging. A barrier to fully elucidating the behavior of CSCs lies in the complexity of the multi-directional relationship among the three-dimensional (3D) structure of chromatin, epigenetic states, and transcription. In addition to genome mapping and sequencing methods, it is imperative to visualize the spatio-temporal relationship among these structural and molecular facets, a capability that only nanoscale imaging can provide.

Chromatin imaging must address three critical challenges:

  1. The multi-scale challenge stems from the fact that chromatin regulates gene expression across a wide range of scales, from the diameter of DNA (~2 nm) to the size of nucleosomes (~10 nm) to chromatin domains (~100 nm) to cell nuclei (~10 μm) and to the population of cells to account for intercellular heterogeneity. Electron microscopy (EM) has the requisite resolution but a small field of view. Optical super-resolution breaks the diffraction-limited resolution of optical microscopy, from ~200 to sub-20 nm, and provides the needed molecular contrasts based on fluorescent labels, but imaging of the chromatin polymer with the requisite ~1 nm resolution remains unresolved.
  2. The multiplexed molecular imaging challenge arises due to a large number of critical genes and molecular regulators that need to be co-registered with the 3D chromatin structural data. The existing multi-color optical microscopy (2-3 distinct labels) cannot satisfy the expected need for co-registering >10 molecular species.
  3. The temporal dynamics challenge: changes in chromatin conformation may take as little as minutes, whereas CSC (de)differentiation and the emergence of chemoresistance may take weeks. Live cells need to be imaged over these time scales under minimally perturbing conditions, which would ideally stipulate low light intensities and label-free contrast.

No single technique satisfies all three requirements. The CPGE team has developed a suite of EM, optical super-resolution, and spectroscopic nanosensing technologies (Nanoscale Chromatin Imaging and Analysis platform, or Nano-ChIA) that respectively are capable of imaging chromatin structure with sub-3 nm resolution, providing molecular localizations, and work with live cells or tissue sections. The Center for Chromatin NanoImaging in Cancer will build upon the strengths of nano-ChIA and develop a unified Multi-scale NanoImaging Platform that co-registers chromatin scanning transmission EM (ChromSTEM), spectroscopic single-molecule localization microscopy (sSMLM), and partial wave spectroscopic (PWS) nanosensing microscopy that addresses all three critical challenges in chromatin imaging. The Center will also bridge the Imaging Platform with predictive modeling of the role of chromatin structure in transcriptional reprogramming in CSCs, and state-of-the-art computational genomics and genome mapping technologies.

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