Research
Radiation-induced DNA damage response
Radiation-induced clustered DNA lesions are becoming recognized as a determinant in activation of various DNA repair pathways. Clustered DNA lesions are defined as spatial clusters of various forms of direct DNA damage: base damage (BD), single strand breaks (SSBs), and double strand breaks (DSBs). Formation of radiation-induced clustered DNA lesions directly correlates with linear energy transfer (LET). Low-LET radiation, such as x-ray or high-energy proton beams, induces relatively few clustered DNA lesions. Most of the damage is caused indirectly via reactive oxygen species (ROS). These damages are repaired mainly through base excision repair (BER), SSB repair, and non-homologous end-joining repair (NHEJR).
Unlikely, high-LET radiation, such as low-energy proton and heavy ion beams (He, C, and O), is less affected by hypoxic conditions because it directly induces numerous clustered DNA lesions that have significantly slower repair kinetics and arrest cells in the G2 phase of the cell cycle. The physical proximity of clustered DNA lesions is thought to trigger cell cycle arrest and make NHEJR less efficient making cells rely more on homologous recombination repair (HRR). Thus, clustered DNA damage induced by proton and heavy ion beams make cells to rely more on HRR. To measure the efficiency of HRR and NHEJR for different types of therapeutic radiation we are using time lapsed confocal microscopy imaging of live cells in proton and heavier ion beams in conjunction with fluorescent nuclear track detectors to measure radiation at the nanoscopic scale in live cells in real time. In addition we use Monte Carlo simulations to understand how radiation energy is deposited in subcellular compartments.
Collaborators: Asaithamby Aroumougame, Ph.D., from UTSW, Steffan Greilich, Ph.D., from DKFZ, Teruaki Konishi, Ph.D., from NIRS
Relevant Publications:
C.H. McFadden, T. Hallacy, D.B. Flint, D.A. Granville, A. Asaithamby, N. Sahoo, G.O. Sawakuchi, "Co-localization of DNA damage and particle tracks at the single cell level in real time," Int. J. Radiat. Oncol., Biol., Phys. 96, 221-227 (2016).
G.O. Sawakuchi, F.A. Ferreira, C.H. McFadden, T. Hallacy, D.A. Granville, N. Sahoo, M.S. Akselrod, "Nanoscale measurements of proton tracks using fluorescent nuclear track detectors," Med. Phys. 43, 2485-2490 (2016).
Transformative discoveries often require technologies that surpass current limitations. Our lab is dedicated to developing and applying innovative methods to dissect the complexity of cancer biology. We have a track record of developing new methods to explore biology at unprecedented resolution. We developed the highly-sensitive STAR ChIP-seq method, which requires as few as ~200 cells, to profile the epigenetic landscape in mouse embryos. We also devised a multimodal assay that simultaneously measures chromatin marks and cell surface proteins within individual cells. Cell identity is represented not only by the transcriptome but also by the epigenome, proteome and beyond. To fully capture all existing cell states in cancer, including transitional states, we continue to invent methods that capture multiple layers of information from each cell, enabling us to detect critical cell states that were previously "invisible."
Cancer Plasticity
Cancer is characterized by remarkable cellular plasticity, which enables cancer cells to reprogram and adapt to new environments, making tumors more aggressive and harder to eradicate. Using our single-cell multiomic toolkit, we aim to capture the dynamic continuum of cellular states and map how cancer cells switch from one state to another. For example, we might look at how a tumor cell could gain stem-like traits or activate a previously silent program under stress. We are particularly interested in the epigenetic mechanisms driving these shifts. By unraveling how cancer plasticity works, we aim to identify key points where medical intervention can be most effective.
Interpatient Variability in Cancer Treatment
A long-standing question in cancer therapy is why patients respond so differently to the same treatment. Our lab is excited to explore whether epigenetics — the dynamic regulatory layer controlling gene expression beyond the genetic code — could be the missing piece of this puzzle. Epigenetic mechanisms not only dictate a cell’s current behavior but also influence how it may respond to future stimuli. By pairing baseline epigenetic states with drug treatment responses, our lab seeks to determine whether inherent epigenomic differences could explain the interpatient variability observed in cancer treatment. We aim to pinpoint epigenetic signatures that can predict drug sensitivity.