All Publications

  • Context-specific functions of chromatin remodellers in development and disease. Nature reviews. Genetics Gourisankar, S., Krokhotin, A., Wenderski, W., Crabtree, G. R. 2023


    Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.

    View details for DOI 10.1038/s41576-023-00666-x

    View details for PubMedID 38001317

    View details for PubMedCentralID 1474054

  • Author Correction: Rewiring cancer drivers to activate apoptosis. Nature Gourisankar, S., Krokhotin, A., Ji, W., Liu, X., Chang, C. Y., Kim, S. H., Li, Z., Wenderski, W., Simanauskaite, J. M., Yang, H., Vogel, H., Zhang, T., Green, M. R., Gray, N. S., Crabtree, G. R. 2023

    View details for DOI 10.1038/s41586-023-06543-1

    View details for PubMedID 37596490

  • Rewiring cancer drivers to activate apoptosis. Nature Gourisankar, S., Krokhotin, A., Ji, W., Liu, X., Chang, C., Kim, S. H., Li, Z., Wenderski, W., Simanauskaite, J. M., Yang, H., Vogel, H., Zhang, T., Green, M. R., Gray, N. S., Crabtree, G. R. 2023


    Genes that drive the proliferation, survival, invasion and metastasis of malignant cells have been identified for many human cancers1-4. Independent studies have identified cell death pathways that eliminate cells for the good of the organism5,6. The coexistence of cell death pathways with driver mutations suggests that the cancer driver could be rewired to activate cell death using chemical inducers of proximity (CIPs). Here we describe a new class of molecules called transcriptional/epigenetic CIPs (TCIPs) that recruit the endogenous cancer driver, or a downstream transcription factor, to the promoters of cell death genes, thereby activating their expression. We focused on diffuse large B cell lymphoma, in which the transcription factor B cell lymphoma 6 (BCL6) is deregulated7. BCL6 binds to the promoters of cell death genes and epigenetically suppresses their expression8. We produced TCIPs by covalently linking small molecules that bind BCL6 to those that bind to transcriptional activators that contribute to the oncogenic program, such as BRD4. The most potent molecule, TCIP1, increases binding of BRD4 by 50% over genomic BCL6-binding sites to produce transcriptional elongation at pro-apoptotic target genes within 15min, while reducing binding of BRD4 over enhancers by only 10%, reflecting a gain-of-function mechanism. TCIP1 kills diffuse large B cell lymphoma cell lines, including chemotherapy-resistant, TP53-mutant lines, at EC50 of 1-10nM in 72h and exhibits cell-specific and tissue-specific effects, capturing the combinatorial specificity inherent to transcription. The TCIP concept also has therapeutic applications in regulating the expression of genes for regenerative medicine and developmental disorders.

    View details for DOI 10.1038/s41586-023-06348-2

    View details for PubMedID 37495688

  • Chemical Inhibitors of a Selective SWI/SNF Function Synergize with ATR Inhibition in Cancer Cell Killing. ACS chemical biology Chory, E. J., Kirkland, J. G., Chang, C. Y., D'Andrea, V. D., Gourisankar, S. n., Dykhuizen, E. C., Crabtree, G. R. 2020


    SWI/SNF (BAF) complexes are a diverse family of ATP-dependent chromatin remodelers produced by combinatorial assembly that are mutated in and thought to contribute to 20% of human cancers and a large number of neurologic diseases. The gene-activating functions of BAF complexes are essential for viability of many cell types, limiting the development of small molecule inhibitors. To circumvent the potential toxicity of SWI/SNF inhibition, we identified small molecules that inhibit the specific repressive function of these complexes but are relatively nontoxic and importantly synergize with ATR inhibitors in killing cancer cells. Our studies suggest an avenue for therapeutic enhancement of ATR/ATM inhibition and provide evidence for chemical synthetic lethality of BAF complexes as a therapeutic strategy in cancer.

    View details for DOI 10.1021/acschembio.0c00312

    View details for PubMedID 32369697

  • Formation of Small Gold Nanoparticle Chains with High NIR Extinction through Bridging with Calcium Ions LANGMUIR Stover, R. J., Moaseri, E., Gourisankar, S. P., Iqbal, M., Rahbar, N. K., Changalvaie, B., Truskett, T. M., Johnston, K. P. 2016; 32 (4): 1127–38


    The self-assembly of citrate-capped Au nanoparticles (5 nm) resulted in branched nanochains by adding CaCl2 versus spherical nanoclusters for NaCl. These assemblies were formed between 1 s to 30 min by tuning the electrostatic repulsion and the interparticle bridging attraction between the cations and citrate ligands as a function of electrolyte concentration. For dilute Ca(2+), strong interparticle bridging favored particle attachment at chain ends. This resulted in the formation of small, branched chains with lengths as short as 20 nm, due to the large Debye length for the diffuse counterions. Furthermore, the bridging produced very small interparticle spacings and sintering, as evident in high-resolution TEM despite the low temperature. This morphology produced a large red shift in the surface plasmon resonance, as characterized by a broad extinction peak with NIR absorption out to 1000 nm, which is unusual for such small particles. Whereas these properties were seen for primary particles with partial citrate monolayers, the degrees of sintering and NIR extinction were small in the case of citrate multilayers. The ability to design the size and shape of nanoparticle clusters as well as the interparticle spacing by tuning bridging and electrostatic interactions may be expected to be quite general and of broad applicability in materials synthesis.

    View details for DOI 10.1021/acs.langmuir.5b03639

    View details for Web of Science ID 000369472000023

    View details for PubMedID 26735290

  • Quenched Assembly of NIR-Active Gold Nanoclusters Capped with Strongly Bound Ligands by Tuning Particle Charge via pH and Salinity JOURNAL OF PHYSICAL CHEMISTRY C Stover, R. J., Murthy, A. K., Nie, G. D., Gourisankar, S., Dear, B. J., Truskett, T. M., Sokolov, K. V., Johnston, K. P. 2014; 118 (26): 14291–98


    Gold nanospheres coated with a binary monolayer of bound citrate and cysteine ligands were assembled into nanoclusters, in which the size and near-infrared (NIR) extinction were tuned by varying the pH and concentration of added NaCl. During full evaporation of an aqueous dispersion of 4.5 ± 1.8 nm Au primary particles, the nanoclusters were formed and quenched by the triblock copolymer polylactic acid (PLA)(1K)-b-poly(ethylene glycol) (PEG)(10K)-b-PLA(1K), which also provided steric stabilization. The short-ranged depletion and van der Waals attractive forces were balanced against longer ranged electrostatic repulsion to tune the nanocluster diameter and NIR extinction. Upon lowering the pH from 7 to 5 at a given salinity, the magnitude of the charge on the primary particles decreased, such that the weaker electrostatic repulsion increased the hydrodynamic diameter and, consequently, NIR extinction of the clusters. At a given pH, as the concentration of NaCl was increased, the NIR extinction decreased monotonically. Furthermore, the greater screening of the charges on the nanoclusters weakened the interactions with PLA(1K)-b-PEG(10K)-b-PLA(1K) and thus lowered the amount of adsorbed polymer on the nanocluster surface. The generalization of the concept of self-assembly of small NIR-active nanoclusters to include a strongly bound thiol and the manipulation of the morphologies and NIR extinction by variation of pH and salinity not only is of fundamental interest but also is important for optical biomedical imaging and therapy.

    View details for DOI 10.1021/jp408715p

    View details for Web of Science ID 000338693600025

    View details for PubMedID 25061496

    View details for PubMedCentralID PMC4096191

  • Plasmonic biodegradable gold nanoclusters with high NIR-absorbance for biomedical imaging Stover, R., Murthy, A., Gourisankar, S., Nie, G., Martinez, M., Truskett, T., Sokolov, K., Johnston, K., Parak, W. J., Osinski, M., Yamamoto, K. I. SPIE-INT SOC OPTICAL ENGINEERING. 2014

    View details for DOI 10.1117/12.2040289

    View details for Web of Science ID 000337284100014

  • Charged Gold Nanoparticles with Essentially Zero Serum Protein Adsorption in Undiluted Fetal Bovine Serum JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Murthy, A. K., Stover, R. J., Hardin, W. G., Schramm, R., Nie, G. D., Gourisankar, S., Truskett, T. M., Sokolov, K. V., Johnston, K. P. 2013; 135 (21): 7799–7802


    The adsorption of even a single serum protein molecule on a gold nanosphere used in biomedical imaging may increase the size too much for renal clearance. In this work, we designed charged ~5 nm Au nanospheres coated with binary mixed-charge ligand monolayers that do not change in size upon incubation in pure fetal bovine serum (FBS). This lack of protein adsorption was unexpected in view of the fact that the Au surface was moderately charged. The mixed-charge monolayers were composed of anionic citrate ligands modified by place exchange with naturally occurring amino acids: either cationic lysine or zwitterionic cysteine ligands. The zwitterionic tips of either the lysine or cysteine ligands interact weakly with the proteins and furthermore increase the distance between the "buried" charges closer to the Au surface and the interacting sites on the protein surface. The ~5 nm nanospheres were assembled into ~20 nm diameter nanoclusters with strong near-IR absorbance (of interest in biomedical imaging and therapy) with a biodegradable polymer, PLA(1k)-b-PEG(10k)-b-PLA(1k). Upon biodegradation of the polymer in acidic solution, the nanoclusters dissociated into primary ~5 nm Au nanospheres, which also did not adsorb any detectable serum protein in undiluted FBS.

    View details for DOI 10.1021/ja400701c

    View details for Web of Science ID 000319856700003

    View details for PubMedID 23565806

    View details for PubMedCentralID PMC3891907

  • Equilibrium Gold Nanoclusters Quenched with Biodegradable Polymers ACS NANO Murthy, A. K., Stover, R. J., Borwankar, A. U., Nie, G. D., Gourisankar, S., Truskett, T. M., Sokolov, K. V., Johnston, K. P. 2013; 7 (1): 239–51


    Although sub-100 nm nanoclusters of metal nanoparticles are of interest in many fields including biomedical imaging, sensors, and catalysis, it has been challenging to control their morphologies and chemical properties. Herein, a new concept is presented to assemble equilibrium Au nanoclusters of controlled size by tuning the colloidal interactions with a polymeric stabilizer, PLA(1k)-b-PEG(10k)-b-PLA(1k). The nanoclusters form upon mixing a dispersion of ~5 nm Au nanospheres with a polymer solution followed by partial solvent evaporation. A weakly adsorbed polymer quenches the equilibrium nanocluster size and provides steric stabilization. Nanocluster size is tuned from ~20 to ~40 nm by experimentally varying the final Au nanoparticle concentration and the polymer/Au ratio, along with the charge on the initial Au nanoparticle surface. Upon biodegradation of the quencher, the nanoclusters reversibly and fully dissociate to individual ~5 nm primary particles. Equilibrium cluster size is predicted semiquantitatively with a free energy model that balances short-ranged depletion and van der Waals attractions with longer-ranged electrostatic repulsion, as a function of the Au and polymer concentrations. The close spacings of the Au nanoparticles in the clusters produce strong NIR extinction over a broad range of wavelengths from 650 to 900 nm, which is of practical interest in biomedical imaging.

    View details for DOI 10.1021/nn303937k

    View details for Web of Science ID 000314082800028

    View details for PubMedID 23230905

    View details for PubMedCentralID PMC3880307