Natasha Karassina

HaloTag: a novel protein labeling technology for cell imaging and protein analysis.

We have designed a modular protein tagging system that allows different functionalities to be linked onto a single genetic fusion, either in solution, in living cells, or in chemically fixed cells. The protein tag (HaloTag) is a modified haloalkane dehalogenase designed to covalently bind to synthetic ligands (HaloTag ligands). The synthetic ligands comprise a chloroalkane linker attached to a variety of useful molecules, such as fluorescent dyes, affinity handles, or solid surfaces. Covalent bond formation between the protein tag and the chloroalkane linker is highly specific, occurs rapidly under physiological conditions, and is essentially irreversible. We demonstrate the utility of this system for cellular imaging and protein immobilization by analyzing multiple molecular processes associated with NF-kappaB-mediated cellular physiology, including imaging of subcellular protein translocation and capture of protein--protein and protein--DNA complexes.

Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands.

Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins.

In vivo stable tumor-specific painting in various colors using dehalogenase-based protein-tag fluorescent ligands.

In vivo fluorescence cancer imaging is an important tool in understanding tumor growth and therapeutic monitoring and can be performed either with endogenously produced fluorescent proteins or with exogenously introduced fluorescent probes bound to targeting molecules. However, endogenous fluorescence proteins cannot be altered after transfection, thus requiring rederivation of cell lines for each desired color, while exogenously targeted fluorescence probes are limited by the heterogeneous expression of naturally occurring cellular targets. In this study, we adapted the dehalogenase-based protein-Tag (HaloTag) system to in vivo cancer imaging, by introducing highly expressed HaloTag receptors (HaloTagR) in cancer cells coupled with a range of externally injected fluorophore-conjugated dehalogenase-reactive reactive linkers. Tumor nodules arising from a single transfected cell line were stably labeled with fluorescence varying in emission spectra from green to near-infrared. After establishing and validating a SHIN3 cell line stably transfected with HaloTagR (HaloTagR-SHIN3), in vivo spectral fluorescence imaging studies were performed in live animals using a peritoneal dissemination model. The tumor nodules arising from HaloTagR-SHIN3 could be successfully labeled by four different fluorophore-conjugated HaloTag-ligands each emitting light at different wavelengths. These fluorophores could be alternated on serial imaging sessions permitting assessment of interval growth. Fluorescence was retained in histological specimens after fixation. Thus, this tagging system proves versatile both for in vivo and in vitro imaging without requiring modification of the underlying cell line. Thus, this strategy can overcome some of the limitations associated with the use of endogenous fluorescent proteins and exogenous targeted optical agents in current use.

Peptide phage display library as source for inhibitors of clostridial neurotoxins.

Clostridial neurotoxins are the most powerful toxins known. There are no available antidotes to neutralize neurotoxins after they have been internalized by neuronal cells. Enzymatic domains of clostridial neurotoxins are zinc-endopeptidases specific for protein components of the neuroexocytosis apparatus. Thus, attempts were made to find such antidotes among molecules possessing chelating properties. Subsequently, it was proposed that the process of interaction between clostridial neurotoxins and their substrates might be more complex than viewed previously and may include several separate regions of interaction. Phage display technology is free from bias toward any particular model. This technology in combination with recombinantly produced light chains of botulinum neurotoxins serotypes A, B, and C was used to identify potential inhibitors of clostridial neurotoxins. Identified sequences did not show substantial similarity with substrate proteins of clostridial neurotoxins. Nevertheless, three peptides chosen for further analysis were able to inhibit enzymatic activity of all clostridial neurotoxins tested. This work demonstrates that at least one of these peptides could not be cleaved by clostridial neurotoxin. Attempts to delete amino acid residues from this peptide resulted in dramatic loss of its inhibitory activity. Finally, this work presents a novel approach to searching for inhibitors of clostridial neurotoxins.

Abstract B49: Bioluminescent assays for measuring glycolytic rate and glucose homeostasis

We describe a set of bioluminescence assays for systematic evaluation of metabolic alterations in response to different growth conditions or treatments. These newly developed cell-based bioluminescence assays offer new methods to detect different metabolites such as NAD(P)/NAD(P)H, lactate, glutamate, glucose-6-phosphate, glucose and 2-deoxyglucose-6-phosphate (for glucose uptake). These assays address the need for more rapid, sensitive and easier to use approaches to quantify key metabolites in cell lysates and tissues. Using the glucose uptake assay, compounds altering translocation of glucose transporters can be screened and characterized rapidly. The lactate detection assay offers a sensitive and rapid approach for glycolytic rate measurements. The glucose detection assay provides information on glucose consumption rates. When these glucose consumption rates are correlated with lactate secretion, the results serve as an indicator of the metabolic status of the cells (e.g. a shift from oxidative phosphorylation to glycolysis). The glucose assay also provides a convenient and robust approach for studying activation or inhibition of gluconeogenesis or glycogenolysis. These bioluminescent assays are robust and sensitive with assay windows significantly larger than analogous fluorescent or colorimetric methods. The sensitivity (1-5pmol/sample) and wide dynamic range (maximum signal-to-background > 100 fold) of the assays allow simultaneous detection of multiple metabolites from the same set of samples. Most importantly, the assays incorporate rapid inactivation of endogenous enzymes, which overcomes the limitations of the deprotonization step required by other methods. The improved workflow in combination with the high sensitivity of luminescence enables measurement of intracellular metabolite levels by simply adding detection reagents directly to treated cells. Alternatively, small samples (2-5ul) can be removed from the media and used for multiple metabolite (lactate, glucose, glutamate) measurements. By consolidating dose- and time-dependent measurements, these assays conserve cells and reagents, streamline workflow, and produce internally controlled data sets. The assays can be used in various formats (e.g. 96- and 384-well plates), applied to various sample types (e.g. mammalian cells, tissues, and 3D microtissues), and multiplexed with other assays, including our new real time cell viability assay. The bioluminescent real time cell viability assay is a homogeneous, non-lytic method to measure cell viability in real time. It overcomes the limitations of standard end-point lytic assays by providing a comprehensive representation of changes in cell viability occurring in live cells over the entire length of an experiment. Changes in cell viability can be conveniently correlated with changes in metabolite levels. Citation Format: Jolanta Vidugiriene, Donna Leippe, Mary Sobol, Mike Valley, Natasha Karassina, Sarah Duellman, James Cali. Bioluminescent assays for measuring glycolytic rate and glucose homeostasis. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B49.

Abstract 1057: Bioluminescent assays for investigating cellular energy metabolism

Cellular energy metabolism is recognized to have a central role in many cell processes and is an increasingly important area of study in many research fields such as cancer, immunology, obesity, diabetes and neurology. To facilitate these studies, we have taken advantage of key features of bioluminescence, such as increased sensitivity and wide assay windows, to develop assays for measuring energy metabolites. These assays are easy-to-use plate-based assays with streamlined protocols that require minimal cell sample processing. The assays can be used to measure consumption of major fuel sources such as glucose and glutamine from the cell medium, as well as lactate and glutamate secretion. The sensitivity (1-5pmol/sample), broad linear range (0.1-100 uM) and wide dynamic range (maximum signal-to-background > 100 fold) allow all four metabolites to be measured from the same sample of medium and over time, with earlier detection from fewer cells compared to other methods. The assays are also sensitive enough to detect intracellular levels of glutamine, glutamate and lactate and changes in those levels. Additional assays have been developed to measure glucose uptake and NAD/NADH levels in cells. Analysis of these metabolites provides information regarding the energetic state of the cell. In this poster we provide examples demonstrating the utility of these assays to detect a glycolytic shift in cancer cells, monitor cell growth and differentiation with associated changes in glucose uptake and glycolysis, and evaluate insulin sensitivity in primary adipocytes. Citation Format: Donna M. Leippe, Mary Sobol, Mike Valley, Natasha Karassina, Sarah Duellman, Jolanta Vidugiriene, Jim Cali. Bioluminescent assays for investigating cellular energy metabolism. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1057.

Abstract 5440: Novel PD-1 blockade bioassay to assess therapeutic antibodies in PD-1 and PD-L1 immunotherapy programs

Programmed death receptor-1 (PD-1) and its ligand (PD-L1) are among the few important immunotherapy targets for cancer. Current PD1 assays measure cell proliferation or cytokine production in primary T cells which are tedious, have high assay variation and small assay window. To enable quantitative potency measurement for key anti-PD-1 drugs in the market or in clinical trials such as pembrolizumab and nivolumab, as well as anti-PD-L1 drugs in clinical trials such as MPDL3280A and BMS-936559, here we report the development of a robust bioluminescent cell-based PD1 blockade bioassay. For this, we built a PD-1 effector cells in Jurkat cells which stably express human PD-1 and a NFAT-RE-luciferase reporter, and a PD-L1 positive artificial Antigen Presenting Cells (PD-L1+ aAPC) in CHO-K1 cells which stably express PD-L1 and an engineered TCR activator. Once these two cell types were co-cultivated, transcriptional activation of NFAT pathway in PD-1 effector cells, mediated by binding of TCR complex with TCR activator in PD-L1+ aAPC, is significantly suppressed by PD-1/PD-L1 engagement. This inhibition can then be specifically reversed by co-incubation of PD-1 or PD-L1 blocking antibodies in dose-dependent manner, but not by the antibody for other immune checkpoint receptors such as anti-CTLA4 ipilimumab. We further developed both PD-1 effector cells and PD-L1+ aAPC in Thaw-and-Use format so the cells can be plated for assay without the need of cell culture. The resultant PD-1 assay using Thaw-and-Use cells brings the benefit of convenience, low day-to-day variation, and easy lab-to-lab assay transfer. We demonstrate the assay is able to measure relative potency for antibody biologics, and also can detect potency changes for stressed antibody samples. In summary, the reporter-based PD-1 blockade assay provides a valuable tool for both drug screening and characterization in early drug discovery, and lot release and stability study in drug manufacture for therapeutic antibody drug candidates in PD-1 and PD-L1 immunotherapy programs. Citation Format: Zhi-Jie Jey Cheng, Natasha Karassina, Jamison Grailer, Jim Hartnett, Frank Fan, Mei Cong. Novel PD-1 blockade bioassay to assess therapeutic antibodies in PD-1 and PD-L1 immunotherapy programs. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5440. doi:10.1158/1538-7445.AM2015-5440

Abstract 2555: A cell based bioluminescent reporter assay for rapid measuring function of PD-1 or PD-L1 therapeutic antibodies

Programmed death-1(PD-1) and its ligand (PD-L1) are important immunotherapy targets for cancer. PD-1 serves as a negative costimulatory receptor on various cell types, including T and B cells as well as myeloid-derived cells. Its ligand PD-L1 (B7-H1) is not expressed by normal epithelial tissues, but it is aberrantly expressed on a wide array of human cancers including melanoma, non-small cell lung carcinoma, breast cancer, pancreatic cancer, etc. Engagement of PD-1 by its ligands PD-L1 expressed on tumor cells associated with poorer prognosis by disabling the host antitumor response. The most recent investigational anti-PD-1 immunotherapy drugs such as nivolumab from BMS and lambrolizumab (MK-3475) from Merck have all demonstrated significant overall survival rate in patients with advanced melanoma. Here we developed a cell based bioluminescent reporter assay that can be used for rapid quantifying function of PD-1 or PD-L1 therapeutic antibodies as measured by activation of NFAT signaling pathway. For this, Jurkat T-cell line stably expressing NFAT-luciferase reporter and human PD-1 was generated. Raji stably expressing human PD-L1 was generated as antigen presenting cells (APC). by co-cultivating the two cell lines in the present of CD3 and IgG, Raji cells fully activate Jurkat NFAT pathway via CD28 binding to CD80 (B7-1) and CD86 (B7-2) endogenously expressed on Raji cells. PD-1 signaling in Jurkat cells following engagement of PD-L1 ectopically expressed on Raji cells inhibits T cell function, and results in NFAT pathway inhibition. Blockade of PD-L1 using anti-PD-L1 mAb reversed NFAT pathway activation. Citation Format: Mei Cong, Natasha Karassina, Jey Cheng, Frank Fan. A cell based bioluminescent reporter assay for rapid measuring function of PD-1 or PD-L1 therapeutic antibodies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2555. doi:10.1158/1538-7445.AM2014-2555

Abstract 151: Advancing pathway analysis using bioluminescent reporters

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL To enable investigation of key cellular signaling pathways, Promega has developed a portfolio of bioluminescent reporter gene assays using Firefly and Renilla luciferases. In combination with best-in-class luciferase detection reagents, these genetic reporter systems enable interrogation of important cellular responses involved in cancer, inflammation, and CNS disease. To address specialized customer needs in our industrial and research markets, Promega has a new custom assay service team dedicated to applying these enabling technologies through strategic external research collaborations. The performance of this technology portfolio is presented, including novel applications of luciferase reporters to interrogation of cytokine, stress, and toxicity pathway responses. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 151. doi:1538-7445.AM2012-151