Addressing common challenges of biotherapeutic protein peptide mapping using recombinant trypsin

Peptide mapping is the key method for characterization of primary structure of biotherapeutic proteins. This method relies on digestion of proteins into peptides that are then analyzed for amino acid sequence and post-translational modifications. Owing to its high activity and cleavage specificity, trypsin is the protease of choice for peptide mapping. In this study, we investigated critical requirements of peptide mapping and how trypsin affects these requirements. We found that the commonly used MS-grade trypsins contained non-specific, chymotryptic-like cleavage activity causing generation of semi-tryptic peptides and degradation of tryptic-specific peptides. Furthermore, MS-grade trypsins contained pre-existing autoproteolytic peptides and, moreover, additional autoproteolytic peptides were resulting from prominent autoproteolysis during digestion. In our long-standing quest to improve trypsin performance, we developed novel recombinant trypsin and evaluated whether it could address major trypsin drawbacks in peptide mapping. The study showed that the novel trypsin was free of detectable non-specific cleavage activity, had negligible level of autoproteolysis and maintained high activity over the course of digestion reaction. Taking advantage of the novel trypsin advanced properties, especially high cleavage specificity, we established the application for use of large trypsin quantities to digest proteolytically resistant protein sites without negative side effects. We also tested trypsin/Lys-C mix comprising the novel trypsin and showed elimination of non-specific cleavages observed in the digests with the commonly used trypsins. In addition, the improved features of the novel trypsin allowed us to establish the method for accurate and efficient non-enzymatic PTM analysis in biotherapeutic proteins.

Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines

Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.

Monitoring PROTAC interactions in biochemical assays using Lumit immunoassays

The discovery of new PROTAC molecules is dependent on robust and high-throughput assays to measure PROTAC-protein interactions and ternary complex formation. Here we present the optimization and execution of Lumit Immunoassays to measure PROTAC binding and ternary complex formation in a biochemical format. We demonstrate how Lumit can be used to rank order affinities of small molecules and PROTACs to BRD4(BD1, BD2) and how to measure PROTAC-mediated ternary complex formation of BRD4(BD1, BD2) and E3 Ligase VHL. Results from both biochemical assays correlate with live and lytic cell assays, indicating that Lumit Immunoassays can be used as a high-throughput compatible screening methodology to test new small molecules.

The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation

Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (D_max), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.

A homogeneous bioluminescent immunoassay for parallel characterization of binding between a panel of antibodies and a family of Fcγ receptors

Fc engineering efforts are increasingly being employed to modulate interaction of antibodies with variety of Fc receptors in an effort to improve the efficacy and safety of the therapeutic antibodies. Among the various Fc receptors, Fc gamma receptors (FcγRs) present on variety of immune cells are especially relevant since they can activate multiple effector functions including antibody dependent cellular cytotoxicity (ADCC) and antibody dependent cellular phagocytosis (ADCP). Depending on the desired mechanism of action (MOA) of the antibody, interactions between Fc domain of the antibody and FcγR (denoted as Fc/FcγR) may need to be enhanced or abolished. Therefore, during the antibody discovery process, biochemical methods are routinely used to measure the affinities of Fc/FcγR interactions. To enable such screening, we developed a plate based, simple to use, homogeneous immunoassays for six FcγRs by leveraging a luminescent protein complementation technology (NanoBiT). An added advantage of the NanoBiT immunoassays is their solution-based format, which minimizes well known surface related artifacts associated with traditional biosensor platforms (e.g., surface plasmon resonance and biolayer interferometry). With NanoBiT FcγRs assays, we demonstrate that assays are specific, report IgG subclass specific affinities and detect modulation in Fc/FcγR interactions in response to the changes in the Fc domain. We subsequently screen a panel of therapeutic antibodies including seven monoclonal antibodies (mAbs) and four polyclonal intravenous immunoglobulin (IVIg) products and highlight the advantages of parallel screening method for developing new antibody therapies.

Development of no-wash, rapid Fcγ Receptor Binding Immunoassays using NanoBiT® Technology

Antibody driven therapies including monoclonal antibodies (mAbs), intravenous IgG (IVIG), subcutaneous IgG (SCIG), and vaccines have made a significant impact in the treatment of many diseases including multiple cancers and autoimmune, metabolic, viral, and infectious diseases. A key mechanism of action (MOA) that makes antibody-based therapies so effective is the ability of the Fc domain of the antibody to recruit immune effector cells through their interaction with a variety of Fc receptors (FcγR). However, assessing the combined impact of interaction of the Fc domain of various antibody isotypes with diverse FcγRs (Fc/FcγR interaction) on the efficacy of the drug is challenging, primarily due to the lack of simple to use and reproducible Fc/FcγR binding assays. Furthermore, existing technologies like SPR can introduce artifacts based on assay format, sensor chip characteristics, and immobilization methods.

To meet the need for reliable, simple to use assays, we have developed a suite of bioluminescent biochemical assays for the following receptors: Lumit™ FcγRI Binding ImmunoassayLumit™ FcγRIIA (H131) Binding ImmunoassayLumit™ FcγRIIA (R131) Binding ImmunoassayLumit™ FcγRIIIA (V158) Binding ImmunoassayLumit™ FcγRIIIA (F158) Binding Immunoassay

These assays are homogeneous, meaning no immobilization or washing steps are required. In addition, they are rapid, easy to use in a 96-well format, and require a simple luminometer. These assays can enable better understanding of antibody MOA and hence better therapies.

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that can simultaneously recruit target proteins and E3 ligases to form a ternary complex, promoting target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities and enabling targeting of previously “undruggable” proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC-induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by cereblon (CRBN)-based PROTACs by leveraging available structural information of the CRL4A ligase complex (CRBN/DDB1/CUL4A/Rbx1/NEDD8/E2/Ub). We generated ternary complex ensembles with Rosetta, modeled multiple CRL4A ligase complex conformations, and predicted ubiquitination efficiency by separating the ternary ensemble into productive and unproductive complexes based on the proximity of the ubiquitin to accessible lysines on the target protein. We validated our CRL4A ligase complex models with published ternary complex structures and additionally employed our modeling workflow to predict ubiquitination efficiencies and sites of a series of cyclin-dependent kinases (CDKs) after treatment with TL12–186, a pan-kinase PROTAC. Our predictions are consistent with CDK ubiquitination and site-directed mutagenesis of specific CDK lysine residues as measured using a NanoBRET ubiquitination assay in HEK293 cells. This work structurally links PROTAC-induced ternary formation and ubiquitination, representing an important step toward prediction of target “degradability.”

Bioluminescent Bridging Immunoassay for Anti-Drug Antibody (ADA) Detection

Any immune reaction to therapeutic antibodies will impact the drug efficacy and can have serious consequences for patient safety. Therefore, detection and reporting of anti-drug antibodies (ADA) during clinical trials is required by regulatory agencies during drug approval process. We have developed a bioluminescent bridging immunoassay for ADA detection, which uses an extremely bright NanoLuc enzyme as a reporter. The assay is sensitive with a wide dynamic range and meets the FDA drug tolerance guideline of detecting 100 ng/ml of ADA in the presence of 500-fold excess of free drug. We describe detailed protocols for development of ADA assays using therapeutic Trastuzumab as a model drug and an anti-Trastuzumab antibody as an example of immune response.

Deciphering the Interaction between Neonatal Fc Receptor and Antibodies Using a Homogeneous Bioluminescent Immunoassay

Long half-life of therapeutic Abs and Fc fusion proteins is crucial to their efficacy and is, in part, regulated by their interaction with neonatal Fc receptor (FcRn). However, the current methods (e.g., surface plasmon resonance and biolayer interferometry) for measurement of interaction between IgG and FcRn (IgG/FcRn) require either FcRn or IgG to be immobilized on the surface, which is known to introduce experimental artifacts and have led to conflicting data. To study IgG/FcRn interactions in solution, without a need for surface immobilization, we developed a novel (to our knowledge), solution-based homogeneous binding immunoassay based on NanoBiT luminescent protein complementation technology. We optimized the assay (NanoBiT FcRn assay) for human FcRn, mouse FcRn, rat FcRn, and cynomolgus FcRn and used them to determine the binding affinities of a panel of eight Abs. Assays could successfully capture the modulation in IgG/FcRn binding based on changes in Fc fragment of the Abs. We also looked at the individual contribution of Fc and F(ab)₂ on the IgG/FcRn interaction and found that Fc is the main driver for the interaction at pH 6. Our work highlights the importance of using orthogonal methods to validate affinity data generated using biosensor platforms. Moreover, the simple add-and-read format of the NanoBiT FcRn assay is amenable for high-throughput screening during early Ab discovery phase.

Targeted Protein Degradation Phenotypic Studies Using HaloTag CRISPR/Cas9 Endogenous Tagging Coupled with HaloPROTAC3

To assess the role of a protein, protein loss phenotypic studies can be used, most commonly through mutagenesis RNAi or CRISPR knockout. Such studies have been critical for the understanding of protein function and the identification of putative therapeutic targets for numerous human disease states. However, these methodological approaches present challenges because they are not easily reversible, and if an essential gene is targeted, an associated loss of cell viability can potentially hinder further studies. Here we present a reversible and conditional live‐cell knockout strategy that is applicable to numerous proteins. This modular protein‐tagging approach regulates target loss at the protein, rather than the genomic, level through the use of HaloPROTAC3, which specifically degrades HaloTag fusion proteins via recruitment of the VHL E3 ligase component. To enable HaloTag‐mediated degradation of endogenous proteins, we provide protocols for HaloTag genomic insertion at the protein N or C terminus via CRISPR/Cas9 and use of HaloTag fluorescent ligands to enrich edited cells via Fluorescence‐Activated Cell Sorting (FACS). Using these approaches, endogenous HaloTag fusion proteins present in various subcellular locations can be degraded by HaloPROTAC3. As detecting the degradation of endogenous targets is challenging, the 11‐amino‐acid peptide tag HiBiT is added to the HaloTag fusion to allows the sensitive luminescence detection of HaloTag fusion levels without the use of antibodies. Lastly, we demonstrate, through comparison of HaloPROTAC3 degradation with that of another fusion tag PROTAC, dTAG‐13, that HaloPROTAC3 has a faster degradation rate and similar extent of degradation. © 2020 The Authors.

Basic Protocol 1: CRISPR/Cas9 insertion of HaloTag or HiBiT‐HaloTag

Basic Protocol 2: HaloPROTAC3 degradation of endogenous HaloTag fusions

CDK Family PROTAC Profiling Reveals Distinct Kinetic Responses and Cell Cycle-Dependent Degradation of CDK2

Targeted protein degradation using heterobifunctional proteolysis-targeting chimera (PROTAC) compounds, which recruit E3 ligase machinery to a target protein, is increasingly becoming an attractive pharmacologic strategy. PROTAC compounds are often developed from existing inhibitors, and assessing selectivity is critical for understanding on-target and off-target degradation. We present here an in-depth kinetic degradation study of the pan-kinase PROTAC, TL12-186, applied to 16 members of the cyclin-dependent kinase (CDK) family. Each CDK family member was endogenously tagged with the 11-amino-acid HiBiT peptide, allowing for live cell luminescent monitoring of degradation. Using this approach, we found striking differences and patterns in kinetic degradation rates, potencies, and Dmax values across the CDK family members. Analysis of the responses revealed that most of the CDKs showed rapid and near complete degradation, yet all cell cycle-associated CDKs (1, 2, 4, and 6) showed multimodal and partial degradation. Further mechanistic investigation of the key cell cycle protein CDK2 was performed and revealed CDK2 PROTAC-dependent degradation in unsynchronized or G1-arrested cells but minimal loss in S or G2/M arrest. The ability of CDK2 to form the PROTAC-mediated ternary complex with CRBN in only G1-arrested cells matched these trends, despite binding of CDK2 to TL12-186 in all phases. These data indicate that target subpopulation degradation can occur, dictated by the formation of the ternary complex. These studies additionally underscore the importance of profiling degradation compounds in cellular systems where complete pathways are intact and target proteins can be characterized in their relevant complexes.

High-Throughput Cellular Profiling of Targeted Protein Degradation Compounds using HiBiT CRISPR Cell Lines

Targeted protein degradation compounds, including molecular glues or proteolysis targeting chimeras, are an exciting new therapeutic modality in small molecule drug discovery. This class of compounds induces protein degradation by bringing into proximity the target protein and the E3 ligase machinery proteins required to ubiquitinate and ultimately degrade the target protein through the ubiquitin-proteasomal pathway (UPP). Profiling of target protein degradation in a high-throughput fashion, however, remains highly challenging given the complexity of cellular pathways required to achieve degradation. Here we present a protocol and screening strategy based on the use of CRISPR/Cas9 endogenous tagging of target proteins with the 11 amino acid HiBiT tag which complements with high affinity to the LgBiT protein, to produce a luminescent protein. These CRISPR targeted cell lines with endogenous tags can be used to measure compound induced degradation in either real-time, kinetic live cell or endpoint lytic modes by monitoring luminescent signal using a luminescent plate-based reader. Here we outline the recommended screening protocols for the different formats, and also describe the calculation of key degradation parameters of rate, Dmax, DC50, Dmax50, as well as multiplexing with cell viability assays. These approaches enable rapid discovery and triaging of early stage compounds while maintaining endogenous expression and regulation of target proteins in relevant cellular backgrounds, allowing for efficient optimization of lead therapeutic compounds.

Abstract 6409: Targeted degradation of endogenously tagged proteins for phenotypic studies using HaloPROTAC3 and HaloTag technologies

To understand a protein's function inside the cell, studies are often done to remove it using CRISPR-mediated knockout or RNAi knockdown methods. These approaches have challenges in either obtaining efficient or complete loss, are not possible if the protein target is essential for cell growth, and are genetic methods, not directly protein loss. To overcome these hurdles, we have employed a highly precise and temporally controlled target protein degradation strategy utilizing HaloPROTAC, a HaloTag Proteolysis-targeting chimera small molecule which will specifically degrade HaloTag fusion proteins in live cells. HaloPROTAC3, developed by Prof. Craig Crews at Yale University, recruits HaloTag fusion proteins to VHL E3 ligase complexes, resulting in ubiquitination and degradation of the HaloTag fusion via the ubiquitin-proteasomal pathway. For phenotypic studies, removal of the endogenous proteins is often required, therefore we have developed efficient protocols for the introduction of HaloTag via CRISPR/Cas9 gene editing into either the endogenous N- or C-terminal loci of any target protein. We have additionally appended the 11 amino acid HiBiT to the HaloTag-target protein, allowing for highly quantitative and kinetic monitoring of degradation to be tracked in live cells without the use of antibodies. Shown here are several key therapeutic proteins, BRD4 and B-catenin, which have been endogenously tagged with HiBiT-HaloTag via CRISPR/Cas9 and show rapid and sustained degradation (80-90% loss) after treatment with HaloPROTAC3. For BRD4, this loss was similar to what was observed using a BET-family specific PROTAC. For B-catenin, further phenotypic studies were done to show a muted response to Wnt3a stimulation and TCF/LEF promoter gene activation after degradation of endogenous B-catenin. These examples demonstrate that the technologies can be used readily to elicit robust degradation of target proteins, with control over the protein level and the time frame for which the protein will be lost, in order to more fully understand protein function. Together, these provide new opportunities for phenotypic studies based directly on control of protein levels and loss, with the ability to study the roles of essential proteins not amenable to genetic knockout or knockdown approaches.

Citation Format: Elizabeth A. Caine, Sarah Mahan, Kristin Riching, Nancy Murphy, Mark McDougall, Cesear Corona, Chris Heid, Danette L. Daniels, Marjeta Urh. Targeted degradation of endogenously tagged proteins for phenotypic studies using HaloPROTAC3 and HaloTag technologies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6409.

Abstract 5230: Real-time monitoring of PROTAC and molecular glue targeted degradation in living cells

The emergence of targeted protein degradation as a broad, new therapeutic modality has greatly expanded the opportunities for treatments of many diseases. Currently, small molecule degrader compounds fall under two major categories; molecular glues and heterobifunctional PROTACs. The two types of compounds both facilitate and induce a ternary complex consisting of an E3 ligase-degrader-target protein, bringing into proximity the machinery proteins required to ubiquitinate and ultimately degrade the target protein. Significant challenges exist in characterization and rank-ordering of degradation compounds in live cells given the differences in dynamics of protein loss and recovery among compounds. Currently, the availability of technologies to interrogate real-time protein degradation is severely lacking. Here, we present a live-cell, luminescence-based technology platform with these capabilities. We employ CRISPR/Cas9 endogenous tagging of target proteins with the small peptide, HiBiT, which has high affinity for and can complement with the LgBiT protein to produce NanoBiT luminescence. This allows for sensitive detection of endogenous protein levels in living cells, and can also serve as a BRET energy donor to study protein:protein or protein:small molecule interactions. We demonstrate the power of this technology in continuous 24-hour monitoring of endogenous target protein levels, and the ability to quantify key degradation parameters for compound ranking including rate, Dmax, and DMax50. We further show the ability to measure the mechanistic steps important for the degradation including kinetics of PROTAC- or molecular glue-induced ternary complex formation and target ubiquitination. These studies facilitate discernment of individual parameters required for successful degradation, ultimately enabling chemical design strategies for optimization and rank ordering of therapeutic degradation compounds.

Citation Format: Neal C. Cosby, Kristin M. Riching, Sarah Mahan, Elizabeth A. Caine, Danette L. Daniels, Marjeta Urh. Real-time monitoring of PROTAC and molecular glue targeted degradation in living cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5230.

Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation

The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biology and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.

Monitoring and deciphering protein degradation pathways inside cells

A new series of therapeutic modalities resulting in degradation of target proteins, termed proteolysis targeting chimeras (PROTACs), hold significant therapeutic potential with possible prolonged pharmacodynamics, improved potency, and ability to target proteins previously thought of as "undruggable". PROTACs are heterobifunctional small molecules consisting of a target binding handle bridged via a chemical linker to an E3 ligase handle which recruit the E3 ligase and ubiquitin machinery to target proteins, resulting in subsequent ubiquitination and degradation of the target. With the generation of small molecule PROTAC compound libraries for drug discovery, it becomes essential to have sensitive screening technologies to rapidly profile activity and have assays which can clearly inform on performance at the various cellular steps required for PROTAC-mediated degradation. For PROTAC compounds, this has been particularly challenging using either biochemical or cellular assay approaches. Biochemical assays are highly informative for the first part of the degradation process, including optimization of compound binding to targets and interrogation of target:PROTAC:E3 ligase ternary complex formation, but struggle with the remaining steps; recruitment of ternary complex into larger active E3 ligase complexes, ubiquitination, and proteasomal degradation. On the other hand, cellular assays are excellent at determining if the PROTAC successfully degrades the target in its relevant setting but struggle as early development PROTAC compounds are often poorly cell-permeable given their high molecular weight. Additionally, if degradation is not observed in a cellular assay, it is difficult to deconvolute the reason why or at which step there was failure. In this review we will highlight the current approaches along with recent advances to overcome the challenges faced for cellular PROTAC screening, which will enable and advance drug discovery of therapeutic degradation compounds.

Quantitative Live-Cell Kinetic Degradation and Mechanistic Profiling of PROTAC Mode of Action

A new generation of heterobifunctional small molecules, termed proteolysis targeting chimeras (PROTACs), targets proteins for degradation through recruitment to E3 ligases and holds significant therapeutic potential. Despite numerous successful examples, PROTAC small molecule development remains laborious and unpredictable, involving testing compounds for end-point degradation activity at fixed times and concentrations without resolving or optimizing for the important biological steps required for the process. Given the complexity of the ubiquitin proteasomal pathway, technologies that enable real-time characterization of PROTAC efficacy and mechanism of action are critical for accelerating compound development, profiling, and improving guidance of chemical structure-activity relationship. Here, we present an innovative, modular live-cell platform utilizing endogenous tagging technologies and apply it to monitoring PROTAC-mediated degradation of the bromodomain and extra-terminal family members. We show comprehensive real-time degradation and recovery profiles for each target, precisely quantifying degradation rates, maximal levels of degradation ( D_max), and time frame at D_max. These degradation metrics show specific PROTAC and family member-dependent responses that are closely associated with the key cellular protein interactions required for the process. Kinetic studies show cellular ternary complex stability influences potency and degradation efficacy. Meanwhile, the level of ubiquitination is highly correlated to degradation rate, indicating ubiquitination stemming from productive ternary complex formation is the main driver of the degradation rate. The approaches applied here highlight the steps at which the choice of E3 ligase handle can elicit different outcomes and discern individual parameters required for degradation, ultimately enabling chemical design strategies and rank ordering of potential therapeutic compounds.

Abstract 4426: Automated miRNA purification from plasma, serum or exosomes

Introduction: MicroRNAs (miRNAs) are endogenous small noncoding RNAs 18-24 nucleotides in size that play important roles involving gene regulation associated with cancer, disease control and gene silencing. Because of the impact on disease progression, miRNA research is rapidly shifting towards biomarker discovery. Many of the commercially available miRNA purification methods involve organic extraction during preprocessing. Here, we describe a novel chemistry that enables RNA purification including smaller RNA such as miRNA. This chemistry offers significant advantages with a simple automated workflow, no organic extraction and minimal preprocessing.

Method: In this study we show successful purification of small RNA, including miRNA, from 100uL to 500uL liquid samples utilizing a novel chemistry on the Maxwell® RSC instrument, which can process between 1 and 16 samples. Proteinase K and Lysis Buffer C are added to the liquid samples and incubated before being transferred to the Maxwell cartridge for miRNA isolation. Sample types tested include plasma, serum and isolated exosomes. The miRNA were evaluated using RT-qPCR including miR-16, miR-21, and let-7a.

Results: The eluates had high levels of small RNA including miRNA at levels comparable to manual competitor methods that require organic extraction. Quantitative PCR showed that the eluates had little or no detectable DNA contamination. Integration of the chemistry onto this automated platform reduced hands-on time while maintaining high quality needed for use in downstream RT-qPCR amplification assays.

Summary: This novel chemistry and method enables purification of small RNA from a range of samples types and volumes. The purified RNA has little or no detectable DNA contamination. Phenol extraction is not required, improving safety and simplifying waste disposal. Also, the automation of this workflow decreases manual hands-on time, saving scientist time and reducing the risk of RNase contamination.

Citation Format: Michelle Mandrekar, Jami English, Douglas Horejsh, Chris Moreland, Herly Karlen, Marjeta Urh. Automated miRNA purification from plasma, serum or exosomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4426.

A Multidimensional Analytical Comparison of Remicade and the Biosimilar Remsima

In April 2016, the Food and Drug Administration approved the first biosimilar monoclonal antibody (mAb), Inflectra/Remsima (Celltrion), based off the original product Remicade (infliximab, Janssen). Biosimilars promise significant cost savings for patients, but the unavoidable differences between innovator and copycat biologics raise questions regarding product interchangeability. In this study, Remicade and Remsima were examined by native mass spectrometry, ion mobility, and quantitative peptide mapping. The levels of oxidation, deamidation, and mutation of individual amino acids were remarkably similar. We found different levels of C-terminal truncation, soluble protein aggregates, and glycation that all likely have a limited clinical impact. Importantly, we identified more than 25 glycoforms for each product and observed glycoform population differences, with afucosylated glycans accounting for 19.7% of Remicade and 13.2% of Remsima glycoforms, which translated into a 2-fold reduction in the level of FcγIIIa receptor binding for Remsima. While this difference was acknowledged in Remsima regulatory filings, our glycoform analysis and receptor binding results appear to be somewhat different from the published values, likely because of methodological differences between laboratories and improved glycoform identification by our laboratory using a peptide map-based method. Our mass spectrometry-based analysis provides rapid and robust analytical information vital for biosimilar development. We have demonstrated the utility of our multiple-attribute monitoring workflow using the model mAbs Remicade and Remsima and have provided a template for analysis of future mAb biosimilars.

Antibody Labeling with Fluorescent Dyes Using Magnetic Protein A and Protein G Beads

Antibodies labeled with small molecules like fluorescent dyes, cytotoxic drugs, and radioactive tracers are essential tools in biomedical research, immunodiagnostics and more recently as therapeutic agents. Traditional methods for labeling antibodies with small molecules require purified antibodies at relatively high concentration, involve multiple dialysis steps and have limited throughput. However, several applications, including the field of Antibody Drug Conjugates (ADCs), will benefit from new methods that will allow labeling of antibodies directly from cell media. Such methods may allow antibodies to be screened in biologically relevant assays, for example, the receptor-mediated antibody internalization assay in the case of ADCs. Here, we describe a method (on-bead method) that enables labeling of small amounts of antibodies directly from cell media. This approach utilizes high capacity magnetic Protein A and Protein G affinity beads to capture antibodies from the cell media followed by labeling with small molecules using either amine or thiol chemistry and subsequent elution of the labeled antibodies. Taking fluorescent dyes as surrogates for small molecules, we demonstrate the on-bead labeling of three different mouse antibodies directly from cell media using both amine and thiol labeling chemistry. The high binding affinity of antibodies to Protein A and Protein G ensures high recoveries as well as high purity of the labeled antibodies. In addition, use of magnetic beads allows multiple samples to be handled manually, thereby significantly improving labeling throughput.

Abstract 1966: Automated miRNA purification without the use of organic solvents

MicroRNAs (miRNAs) are endogenous small non-coding RNAs 18-24 nucleotides in size that play important roles involving gene regulation associated with cancer, disease control and gene silencing. Because of the impact on disease progression, miRNA research is rapidly shifting towards biomarker discovery. Many of the commercially available miRNA purification methods involve organic extraction during pre-processing. Here, we describe a novel chemistry that enables total RNA purification including smaller RNA such as miRNA. This chemistry offers significant advantages with a simple automated workflow, no organic extraction and minimal pre-processing.

In this study, we successfully show purification of miRNAs from a range of solid and liquid sample types including frozen tissue, whole blood, plasma, exosomes, mammalian cell lines, saliva, bone and FFPE samples. Absorbance yield, absorbance ratios, RINs, and amplification of miRNA show equivalence with organic solvent-based purification methods. The miRNA studied included miR-21, let-7a, miR-141, and miR-125b, depending on starting sample type. Next generation sequencing (NGS) analysis shows equivalent sequence diversity when compared pairwise with a manual, organic pre-processing method.

This novel chemistry and method enables purification of small and large RNA from a range of sample types. The purified RNA has little or no detectable DNA contamination and does not require phenol extraction, thus improving safety. Also, the automation of this workflow decreases manual hands on time, saving scientist time and reducing the risk of RNase contamination.

Citation Format: Jami D. English, Doug Horejsh, Chris Moreland, Marjeta Urh. Automated miRNA purification without the use of organic solvents. [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 1966.

Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy

The histone acetyltransferases CBP/p300 are involved in recurrent leukemia-associated chromosomal translocations and are key regulators of cell growth. Therefore, efforts to generate inhibitors of CBP/p300 are of clinical value. We developed a specific and potent acetyl-lysine competitive protein-protein interaction inhibitor, I-CBP112, that targets the CBP/p300 bromodomains. Exposure of human and mouse leukemic cell lines to I-CBP112 resulted in substantially impaired colony formation and induced cellular differentiation without significant cytotoxicity. I-CBP112 significantly reduced the leukemia-initiating potential of MLL-AF9(+) acute myeloid leukemia cells in a dose-dependent manner in vitro and in vivo. Interestingly, I-CBP112 increased the cytotoxic activity of BET bromodomain inhibitor JQ1 as well as doxorubicin. Collectively, we report the development and preclinical evaluation of a novel, potent inhibitor targeting CBP/p300 bromodomains that impairs aberrant self-renewal of leukemic cells. The synergistic effects of I-CBP112 and current standard therapy (doxorubicin) as well as emerging treatment strategies (BET inhibition) provide new opportunities for combinatorial treatment of leukemia and potentially other cancers.

Abstract C158: A chemoproteomics strategy for target identification and lead compound optimization using chloroalkane derivatized compounds

The Identification and validation of drug targets is an industry wide challenge. There is a very clear and urgent need for technologies that can identify the interaction partners of small molecules. Chemical proteomics is one technology that has attracted attention as a solution to the drug target identification problem. Here we present a new approach utilizing a chloroalkane (CA) moiety capture handle, which can be chemically attached to small molecules to isolate their respective protein partners. In general derivatization of small molecules with the CA moiety does not impact their cell permeability and has limited impact on potency, allowing for phenotypic assays of the derivatized compound to be performed. The retention of cell permeability also allows for the capture process to be performed from live cells treated with the CA-compound. This process is also compatible with competition assays, which can be used to evaluate and compare other compounds exhibiting a similar mode of action.

Here we present a study using Dasatinib-CA, a modified kinase inhibitor and potent anti-cancer drug which binds to a broad range of kinases. First we performed target enrichment experiments by incubating K562 cells with the modified Dasatinib (Dasatinib-CA). Cells were lysed and the Dasatinib-CA, together with the bound targets, was rapidly captured onto magnetic resin coated with HaloTag. Unmodified compound was used to competitively elute putative interacting proteins. Secondly using the same assay format we evaluated the relative target affinities of Dasatinib-CA versus competing molecules. Competition assays were performed by incubating multiple mixtures of Dasatinib analogues and Dasatinib-CA at varying relative concentrations.

Eluted proteins were processed using SDS-PAGE and in-gel digestion. For target identification experiments peptides were analyzed using label free mass spectrometry. For the competition assays digested material was labeled with Tandem Mass Tags (TMT) 10plex reagents. Peptides were analyzed using nanoscale LC-MS/MS coupled with a Q Exactive mass spectrometer (Thermo). Protein identification and quantitation was performed with MaxQuant (MaxQuant.org) and data validation and visualization was performed using Perseus (Perseus-framework.org).

Using this approach we identified over 30 kinases, including known membrane associated and membrane protein targets. This work presented here highlights a new method for chemical proteomics and demonstrates utility of the platform to enable target identification and to evaluate competitor molecules.

Citation Format: Michael Ford, Richard Jones, Ravi Amunugama, Danette Daniels, Rachel Ohana, Sergiy Levin, Thomas Kirkland, Marjeta Urh, Keith Wood. A chemoproteomics strategy for target identification and lead compound optimization using chloroalkane derivatized compounds. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C158.

Abstract LB-B10: Chemical Proteomic Analysis of BTK and PI3K Using Chloroalkane-Derivatized Small Molecule Inhibitors

Chemical proteomics is a rapidly evolving technology that allows for drug target identification for small molecule inhibitors. Here we present an approach utilizing a chloroalkane (CA) moiety capture handle, which can be chemically attached to small molecules and used to pull-down protein binding partners using the HaloTag technology. CA-modified compounds are cell permeable and have minimal impact on potency, allowing for phenotypic assays of the derivatized compound to be recapitulated.

Here we present a study looking at the targets of two compounds - a Brutons Tyrosine Kinase (BTK) small molecule inhibitor and a Phospho-inositol 3 Kinase (PI3K) small molecule inhibitor. BTK is a non-receptor tyrosine kinase expressed in most hematopoietic cells except T cells, it is essential for B cell receptor (BCR) signaling in B cells and as such is the therapeutic focus in many autoimmune diseases, including rheumatoid arthritis (RA) and lupus. Upon binding to growth factor receptor, PI3K is activated which initiates a signaling cascade involving AKT and mTOR that promotes cell cycle progression and cell proliferation. Mutations of the catalytic subunit of PI3KA are observed in several types of cancers. Inhibition of PI3K is therefore an important therapeutic focus.

Taselisib, a selective inhibitor of PIK3CA, and G02599124, an inhibitor of BTK, were derivitized with the CA linker. Phenotypic screens compared to the parental compound showed comparable IC50 values. Both CA-compounds showed good binding to HaloTag and were cell permeable in a U2OS stable cell line. Control and test experiments were performed with BTK-CA compound using Jurkat (T cells) and Ramos (B cells) cell lines. Taselib-CA was studied after 1h and 8h treatment in the HCC1954 cell line. Cells were lysed and the CA compounds, together with the bound targets, were rapidly captured onto magnetic resin coated with HaloTag. Unmodified compound was used to competitively elute interacting proteins. Eluted proteins were processed using SDS-PAGE and in-gel digestion. Peptides were analyzed using nanoscale LC-MS/MS coupled with an Orbitrap Velos Pro mass spectrometer.

Using this approach we were able to specifically isolate BTK when compared to control experiments in T cells. In the Taselib-CA experiment, we were able to specifically isolate the PIK3CA catalytic subunit and PIK3R1 and PIK3R2 regulatory subunits. Observation of the wild type and mutant forms of PI3KCA will be discussed.

Citation Format: Victoria Pham, James Crawford, Steve Saben, Michael Ford, Richard Jones, Danette Daniels, Thomas Kirkland, Marjeta Urh, Jennie Lill. Chemical Proteomic Analysis of BTK and PI3K Using Chloroalkane-Derivatized Small Molecule Inhibitors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B10.

HaloTag technology for specific and covalent labeling of fusion proteins

Appending proteins of interest to fluorescent protein tags such as GFP has revolutionized how proteins are studied in the cellular environment. Over the last few decades many varieties of fluorescent proteins have been generated, each bringing new capability to research. However, taking full advantage of standard fluorescent proteins with advanced and differential features requires significant effort on the part of the researcher. This approach necessitates that many genetic fusions be generated and confirmed to function properly in cells with the same protein of interest. To lessen this burden, a newer category of protein fusion tags termed "self-labeling protein tags" has been developed. This approach utilizes a single protein tag, the function of which can be altered by attaching various chemical moieties (fluorescent labels, affinity handles, etc.). In this way a single genetically encoded protein fusion can easily be given functional diversity and adaptability as supplied by synthetic chemistry. Here we present protein labeling methods using HaloTag technology; comprised of HaloTag protein and the collection of small molecules designed to bind it specifically and provide it with varied functionalities. For imaging purposes these small molecules, termed HaloTag ligands, contain distinct fluorophores. Due to covalent and rapid binding between HaloTag protein and its ligands, labeling is permanent and efficient. Many of these ligands have been optimized for permeability across cellular membranes allowing for live cell labeling and imaging analysis. Nonpermeable ligands have also been developed for specific labeling of surface proteins. Overall, HaloTag is a versatile technology that empowers the end user to label a protein of interest with the choice of different fluorophores while alleviating the need for generation of multiple genetic fusions.

Abstract 4846: Automated RNA and DNA purification from FFPE samples

Formalin-fixed, paraffin-embedded (FFPE) samples are commonly used for archiving pathology samples for use by many researchers including clinical research labs. These samples provide a valuable tool for retrospective studies of diseases such as cancer. Traditional methods for the purification of DNA or RNA from FFPE tissue samples are often labor intensive, include the use of hazardous organic reagents, and involve difficult pre-processing steps. Here, we describe development of automated methods for the purification of RNA or DNA from FFPE tissue sections using the Maxwell® RSC Instrument, which can process between 1 and 16 samples. DNA was purified from FFPE mouse brain, liver, lung, skin and spleen as well as FFPE human colon. RNA was purified from FFPE mouse brain, liver, lung, skin and spleen as well as FFPE human breast tissue. Eluates were tested for inhibition in qPCR or RT-qPCR. A comparison with another automated method was performed with FFPE mouse spleen and skin and a human tissue. The Maxwell RSC methods produced high quality amplifiable DNA or RNA from a variety of sample types with little or no inhibition. In addition, these methods simplified pre-processing, minimized hands-on time, and did not use hazardous organics.

Citation Format: Michelle Mandrekar, Douglas Horejsh, Samantha Lewis, Chris Moreland, Marjeta Urh. Automated RNA and DNA purification from FFPE samples. [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 4846. doi:10.1158/1538-7445.AM2015-4846

Abstract 2003: Investigating the cellular interactions of BIRB796 analogues using a novel chloroalkane capture tag

Identifying the targets of a bioactive compound is often the rate limiting step toward understanding the molecular mechanism of drug action. Current approaches rely on linking the bioactive compound to a surface or an affinity handle, permitting selective capture of interacting proteins for identification by mass spectrometry. A major consideration with these methods is insuring that the chemical derivatization of the bioactive compound does not disrupt the binding interactions with the cellular targets. We have developed a method based on a novel chloroalkane capture tag that minimally affects compound potency and cell permeability. This allows verification of the pharmacological activity of the modified compound, thus increasing the confidence in the biological relevance of captured proteins. In addition, by allowing the chloroalkane-modified compound to bind the targets within living cells, the cellular architecture during the binding step is preserved and better represents the conditions that the unaltered compound would normally engage these targets. Following binding with the tagged compound in live cells, the cells are lysed and the chloroalkylated compound and its associated targets are rapidly captured onto immobilized HaloTag protein and then released by competitive elution. The identified targets are then validated for direct binding relationship with the bioactive compound by bioluminescence energy transfer. We tested this target capture/target validation work flow using the interaction of MAPK kinases with two allosteric kinase inhibitors (BIRB796 and a BIRB analog exhibiting 100-fold lower potency).

RESULTS: Using the two BIRB-chloroalkane derivatives to selectively enrich for targets from HEPG2 cells, we identified and validated multiple relevant MAPK kinases as well as additional off-targets. Interestingly, all the discovered off-targets bind purines. Kinase inhibitors such as BIRB796 which acts by binding to the kinase ATP binding site can interact in a similar manner with other purine binding proteins. Using bioluminescence energy transfer we interrogated the affinity and residence time of the two BIRB compounds to multiple MAPK kinases inside living cells. Our results indicates that the BIRB796 analog exhibits 30-1000 fold reduced affinity to multiple MAPK kinases as well as significant shorter residence time compared to BIRB796. Taken together these results indicate that our workflow can reveal the direct binding relationships between bioactive compounds and their cellular targets and contribute to further understanding of these interactions.

Citation Format: Rachel Friedman Ohana, Robin Hurst, Thomas Kirkland, Carolyn Woodroofe, Sergiy Levin, Paul Otto, Tetsuo Uyeda, Michael Ford, Richard Jones, Danette Daniels, Marjeta Urh, Keith Wood. Investigating the cellular interactions of BIRB796 analogues using a novel chloroalkane capture tag. [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 2003. doi:10.1158/1538-7445.AM2015-2003

Abstract 2439: Multiplexed chemoproteomic profiling as a tool to decipher the intracellular interactions between proteins and small molecules

Chemoproteomic profiling is the qualitative and quantitative study of small molecule protein interactions using mass spectrometry. Chemoproteomics approaches typically involve four steps 1) modification of the bait drug molecules with the addition of an affinity tag, e.g. biotin, 2) incubation of the bait molecule with cells, cell lysates or tissue homogenates, 3) recovery of the bait molecule using the added affinity mechanism, e.g. streptavidin and 4) identification of proteins interacting with the bait molecule by liquid chromatography and tandem mass spectrometry (LC-MS/MS). To obtain value from chemoproteomics experiments any identified small molecule protein interactions need to be representative of the underlying biology and not artifacts of the chemoproteomics process.

Chemoproteomic workflows offer a relatively simple method to generate a large volume of extremely valuable data about the behavior of a molecule, its analogs and its competitors. As such the number of samples generated for analysis can be significant. One method for maintaining throughput in chemoproteomics workflows is multiplexed proteomics with chemical labeling. This approach enables the pooling of multiple experimental conditions for analysis in a single LC-MS/MS experiment thus helping to reduce potential bottle necks associated with instrument capacity.

Here we report a multiplexed chemoproteomics workflow based on a novel chloroalkane (CA) ligand that minimally affects compound potency and cell permeability using a p38 MAPKinase inhibitor. We show changes in protein interaction profiles by titrating cells with different mixtures of parent inhibitor + modified inhibitor-CA compound at varying relative concentrations. These changes in profiles can be monitored using cells transfected with NanoLuc fusion proteins of known inhibitor targets and show increasing capture correlated with increasing concentrations of modified inhibitor CA-compound. Overall interactions profiles can be more thoroughly analyzed by chemical labeling and combing this approach with 8plex iTRAQ labeling techniques. This multiplexing approach allows for many titrations points to be studies at once, yielding information about the dynamics of interactions between small molecules and their protein targets. The ability to study these differences after treatment of live cells aids in the understanding of the differing interaction targets of many given small molecule inhibitor.

Citation Format: Michael Ford, Richard Jones, Ravi Amunugama, Danette Daniels, Rachel Ohana, Thomas Kirkland, Marjeta Urh. Multiplexed chemoproteomic profiling as a tool to decipher the intracellular interactions between proteins and small molecules. [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 2439. doi:10.1158/1538-7445.AM2015-2439

Abstract 3383: Correlation of mutations detected in liquid and tissue biopsies

Circulating cell-free DNA (ccfDNA) in plasma can be used to detect biomarkers that show great promise for diagnosis and monitoring of cancer, giving rise to the possibility of liquid biopsies that obviate the need for invasive tissue collection. The low concentration and highly fragmented nature of ccfDNA, coupled with the low frequency of potential oncogenic biomarkers, presents challenges and will require a purification method that is efficient and highly reproducible.

Here we describe a method for purifying nucleic acids based on novel surface and binding chemistries. The combination of these two approaches allows for increased binding of fragmented DNA. The method can be partially automated to ensure highly reproducible results. Up to 4mls of plasma can be processed and eluted in as little as 15ul, giving DNA concentrations of 1-10ul. This greatly facilitates use in Next Generation Sequencing.

Using the automated method, ccfDNA was purified from the plasma of 7 patients who had previously undergone surgical resection for malignancy. DNA was also purified from the FFPE malignant tissue off of slides, following macrodissection, from the same patients. NGS was used to interrogate both sample types for potentially oncogenic variants. Several laboratory developed tests, all including COLD-PCR, were also employed to verify the presence or absence of variants. The two types of samples showed excellent correlation on mutations, suggesting that use of a less invasive liquid biopsy has the potential to enable actionable mutation detection without using more invasive solid tumor biopsy means.

Citation Format: Douglas H. White, Douglas Horejsh, Molly Accola, William Rehrauer, Marjeta Urh. Correlation of mutations detected in liquid and tissue biopsies. [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 3383. doi:10.1158/1538-7445.AM2015-3383

Abstract 2446: Decoding phenotypic drug screening targets using a novel chloroalkane capture tag

Phenotypic screening has become increasingly common to the drug discovery workflow. Yet, productive outcomes remain hindered by the challenging task of identifying the underlying cellular targets mediating the desired phenotype. Current approaches rely on linking the bioactive compound to a surface or an affinity handle allowing selective capture of interacting proteins for identification by mass spectrometry. These methods can be constrained by ineffective capture of low affinity and low abundance proteins. In addition, for these methods to provide meaningful results, it is critical that the chemical derivatization of the bioactive compound would not disrupt the binding interactions with the cellular targets. Consequently, there is preference for methods compatible with living cells because they allow verification of the pharmacological activity of the modified compound. We have developed such a method based on a novel chloroalkane capture tag that minimally affects compound potency and cell permeability. Following binding with the tagged compound in live cells, the cells are lysed and the chloroalkylated compound, together with the bound targets, is rapidly captured onto immobilized HaloTag protein. The in-situ target engagement combined with rapid covalent capture allows for isolation of difficult targets with low affinity and/or low abundance. The putative targets identified by mass spectrometry are then validated for direct binding relationship with the bioactive compound by bioluminescence energy transfer. We tested this target capture/target-validation workflow using the interaction of histone deacetylases (HDACs) class I/IIb and the inhibitor SAHA (Vorinostat).

RESULTS: Treatment of K562 cells with SAHA or SAHA-chloroalkane revealed high cellular potency against HDAC class I/IIb with minimal impact of the chloroalkane modification on the drug potency. Using the SAHA-chloroalkane to selectively enrich for SAHA targets from K-562 cells, we identified and validated all the known targets of SAHA (i.e., HDAC 1, 2, 3, 6, 8 and 10) regardless of their abundance or affinity (nM to low μM). In addition, we also identified and validated two previously undescribed targets of SAHA (CPPED1 and ADO), both metalloenzymes. Because SAHA binds to HDACs by chelating to a bound zinc ion, it may interact by a similar mechanism with other metalloenzymes. The discovery of ADO may also provide insight to a potential novel mode of action for SAHA in neurodegenerative diseases. Other experiments showed that replacing the chloroalkyl group in the SAHA-chloroalkane with biotin significantly reduced drug potency and consequently enrichment efficiency (only HDAC6 was isolated), further demonstrating the advantages provided by the relatively inert chloroalkane tag. Taken together these results indicate that our workflow can reveal the direct binding relationships between bioactive compounds and their cellular targets.

Citation Format: Rachel Friedman Ohana, Thomas Kirkland, Carolyn Woodroofe, Sergiy Levin, Robin Hurst, Paul Otto, Tetsuo Uyeda, Michael Ford, Richard Jones, Danette Daniels, Marjeta Urh, Keith Wood. Decoding phenotypic drug screening targets using a novel chloroalkane capture tag. [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 2446. doi:10.1158/1538-7445.AM2015-2446

Abstract 1872: A novel method for efficient and hands-free purification of circulating DNA from human plasma

Circulating or Cell-Free DNA in plasma can be used to detect biomarkers that show great promise for diagnosis and monitoring of cancer, and is already being used as a non-invasive method to detect trisomy in fetuses. There is currently great interest in the discovery of new cancer biomarkers and their potential clinical application. However, reproducible and efficient purification of these highly fragmented and low-concentration species represents a major challenge. Here we will present a novel method which is completely automated and allows parallel purification of circulating nucleic acid from plasma and serum using a medium-throughput robot. Sixteen samples can be processed simultaneously. The method was optimized to produce high-quality DNA that is suitable for use in quantitative PCR and next generation sequencing. In addition, the absence of any pre-processing steps improves reproducibility and lowers the risk of contamination.Initial characterization on plasma from pregnant women showed that fetal DNA could be detected as early as 4 weeks into gestation and could be tracked throughout pregnancy. Further characterization showed that the system was able to reliably detect less than 25 copies/ml plasma of fragmented DNA that was spiked into the sample. Subsequent work on plasma from patients with colorectal cancer showed that the system was able to detect DNA containing both wild-type and mutated EGFR, suggesting that this method can be a useful tool when screening plasma samples for biomarkers of interest.

Citation Format: Douglas White, Douglas Horejsh, Zhiyang Zeng, Tetsuo Uyeda, Poncho Meisenheimer, Marjeta Urh. A novel method for efficient and hands-free purification of circulating DNA from human plasma. [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 1872. doi:10.1158/1538-7445.AM2014-1872

Discovering protein interactions and characterizing protein function using HaloTag technology

Research in proteomics has exploded in recent years with advances in mass spectrometry capabilities that have led to the characterization of numerous proteomes, including those from viruses, bacteria, and yeast.  In comparison, analysis of the human proteome lags behind, partially due to the sheer number of proteins which must be studied, but also the complexity of networks and interactions these present. To specifically address the challenges of understanding the human proteome, we have developed HaloTag technology for protein isolation, particularly strong for isolation of multiprotein complexes and allowing more efficient capture of weak or transient interactions and/or proteins in low abundance.  HaloTag is a genetically encoded protein fusion tag, designed for covalent, specific, and rapid immobilization or labelling of proteins with various ligands. Leveraging these properties, numerous applications for mammalian cells were developed to characterize protein function and here we present methodologies including: protein pull-downs used for discovery of novel interactions or functional assays, and cellular localization. We find significant advantages in the speed, specificity, and covalent capture of fusion proteins to surfaces for proteomic analysis as compared to other traditional non-covalent approaches. We demonstrate these and the broad utility of the technology using two important epigenetic proteins as examples, the human bromodomain protein BRD4, and histone deacetylase HDAC1.  These examples demonstrate the power of this technology in enabling  the discovery of novel interactions and characterizing cellular localization in eukaryotes, which will together further understanding of human functional proteomics.              

TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS

This paper identifies the N-acetylglucosamine transferase OGT as binding partner for TET2/3 proteins. Their genome-wide chromatin binding and the characterization of the Set1/COMPASS complex as OGT target implies coordinated gene regulation.

TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O-GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3–OGT co-localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3–OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step-wise model, involving TET–OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation.

HaloTag, a Platform Technology for Protein Analysis

Understanding protein function and interaction is central to the elucidation of biological processes. Systematic analysis of protein interactions have shown that the eukaryotic proteome is highly interconnected and that biological function frequently depends on the orchestrated action of many proteins. Perturbation of these functions or interactions can lead to various disease states and pharmacologic intervention can result in corrective therapies. The fact that proteins rarely act in isolation, but rather comprise complex machines that stably and/or transiently interact with many different partners at different times, demands the need for robust tools that allow comprehensive global analyses of these events. Here we describe a powerful protein fusion technology, the HaloTag platform, and how it enables the study of many facets of protein biology by offering a broad choice of applications. We review the development of the key aspects of the technology and it's performance in both in vitro and in vivo applications. In particular, we focus on HaloTag's multifunctional utility in protein imaging, protein isolation and display, and in the study of protein complexes and interactions. We demonstrate it's potential to help elucidate important facets of proteomic biology across complex biological systems at the biochemical, cell-based and whole animal level.

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.

Examining the complexity of human RNA polymerase complexes using HaloTag technology coupled to label free quantitative proteomics

Efficient determination of protein interactions and cellular localization remains a challenge in higher order eukaryotes and creates a need for robust technologies for functional proteomics studies. To address this, the HaloTag technology was developed for highly efficient and rapid isolation of intracellular complexes and correlative in vivo cellular imaging. Here we demonstrate the strength of this technology by simultaneous capture of human eukaryotic RNA polymerases (RNAP) I, II, and III using a shared subunit, POLR2H, fused to the HaloTag. Affinity purifications showed successful isolation, as determined using quantitative proteomics, of all RNAP core subunits, even at expression levels near endogenous. Transient known RNAP II interacting partners were identified as well as three previously uncharacterized interactors. These interactions were validated and further functionally characterized using cellular imaging. The multiple capabilities of the HaloTag technology demonstrate the ability to efficiently isolate highly challenging multiprotein complexes, discover new interactions, and characterize cellular localization.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

Background

Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays. To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells.

Results

In analysis of CREB genome-wide binding events using a comprehensive DNA microarray of human promoters, we observe for the first time that CREB has a strong preference for binding at bidirectional promoters and unlike unidirectional promoters, these binding events often occur downstream of transcription start sites. Comparison between HaloCHIP-chip and ChIP-chip data reveal this to be true for both methodologies, indicating it is not a bias of the technology chosen. Transcriptional data obtained from promoter-luciferase reporter arrays also show an unprecedented, high level of activation of CREB-bound promoters in the presence of the co-activator protein TORC1.

Conclusion

These data suggest for the first time that TORC1 provides directional information when CREB is bound at bidirectional promoters and possible pausing of the CREB protein after initial transcriptional activation. Also, this combined approach demonstrates the ability to more broadly characterize CREB protein-DNA interactions wherein not only DNA binding sites are discovered, but also the potential of the promoter sequence to respond to CREB is evaluated.

HaloTag7: a genetically engineered tag that enhances bacterial expression of soluble proteins and improves protein purification

Over-expression and purification of soluble and functional proteins remain critical challenges for many aspects of biomolecular research. To address this, we have developed a novel protein tag, HaloTag7, engineered to enhance expression and solubility of recombinant proteins and to provide efficient protein purification coupled with tag removal. HaloTag7 was designed to bind rapidly and covalently with a unique synthetic linker to achieve an essentially irreversible attachment. The synthetic linker may be attached to a variety of entities such as fluorescent dyes and solid supports, permitting labeling of fusion proteins in cell lysates for expression screening, and efficient capture of fusion proteins onto a purification resin. The combination of covalent capture with rapid binding kinetics overcomes the equilibrium-based limitations associated with traditional affinity tags and enables efficient capture even at low expression levels. Following immobilization on the resin, the protein of interest is released by cleavage at an optimized TEV protease recognition site, leaving HaloTag7 bound to the resin and pure protein in solution. Evaluation of HaloTag7 for expression of 23 human proteins in Escherichia coli relative to MBP, GST and His(6)Tag revealed that 74% of the proteins were produced in soluble form when fused to HaloTag7 compared to 52%, 39% and 22%, respectively, for the other tags. Using a subset of the test panel, more proteins fused to HaloTag7 were successfully purified than with the other tags, and these proteins were of higher yield and purity.

Methods for detection of protein-protein and protein-DNA interactions using HaloTag

HaloTag is a protein fusion tag which was genetically engineered to covalently bind a series of specific synthetic ligands. All ligands carry two groups, the reactive group and the functional/reporter group. The reactive group, the choloroalkane, is the same in all the ligands and is involved in binding to the HaloTag. The functional reporter group is variable and can carry many different moieties including fluorescent dyes, affinity handles like biotin or solid surfaces such as agarose beads. Thus, HaloTag can serve either as a labeling tag or as a protein immobilization tag depending on which ligand is bound to it. Here, we describe a procedure for immobilization of HaloTag fusion proteins and how immobilized proteins can be used to study protein-protein and protein-DNA interactions in vivo and in vitro.

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.

Assemblies of replication initiator protein on symmetric and asymmetric DNA sequences depend on multiple protein oligomerization surfaces

The pi35.0 protein of plasmid R6K regulates transcription and replication by binding a DNA sequence motif (TGAGR) arranged either asymmetrically into 22 bp direct repeats (DRs) in the gamma origin, or symmetrically into inverted half-repeats (IRs) in the operator of its own gene, pir. The binding patterns of the two natural forms of the pi protein and their heterodimers revealed that the predominant species, pi35.0 (35.0 kDa), can bind to a single copy of the DR as either a monomer or a dimer while pi30.5 (30.5 kDa) binds only as a dimer. We demonstrate that only one subunit of a pi35.0 dimer makes specific contact with DNA. Electron microscopic (EM) analysis of the nucleoprotein complexes formed by pi35.0 and DNA fragments containing all seven DRs revealed coupled ("hand-cuffed") DNA molecules that are aligned in a parallel orientation. Antiparallel orientations of the DNA were not observed. Thus, hand-cuffing depends on a highly ordered oligomerization of pi35.0 in such structures. The pi protein (pi35.0, pi30.5) binds to an IR as a dimer or heterodimer but not as a monomer. Moreover, a single amino acid residue substitution, F200S (pir200), introduced into pi30.5 severely destabilizes dimers of this protein in solution and concomitantly prevents binding of this protein to the IR. This mutation also changes the stability of pi35.0 dimers but it does not change the ability of pi35.0 to bind IRs. To explain these observations we propose that the diverse interactions of pi variants with DNA are controlled by multiple surfaces for protein oligomerization.