The growing demand to unravel complex cellular processes has fueled rapid expansion in the field of proteomics. As researchers strive to understand proteins in their native context, traditional tools such as antibody-based fluorescence and mass spectrometry present significant challenges. These methods often lack the sensitivity, scalability, or specificity needed to accurately capture the dynamics of endogenous protein behavior. As a result, there is an increasing need for innovative solutions that can overcome these limitations and provide more precise, physiologically relevant insights into protein function and regulation.
Lost in Lysis: The Limits of Conventional Protein Tools
Studying protein function within living cells presents significant challenges due to limitations in current detection technologies. While mass spectrometry and antibody-based protein detection are valuable tools, both approaches have drawbacks that restrict their effectiveness in analyzing endogenous proteins in real time. These limitations have created a need for a robust and scalable method that allows researchers to monitor protein expression and interactions in their native cellular environment without the need for destructive sample preparation.
Figure 1. Traditional methods to detect and study subcellular proteomics. These methods typically require cell lysis, overexpression and/or other processes that alter endogenous protein dynamics. (Credit: Christopher et al. Nature Reviews Methods Primers. 2021)
Mass spectrometry struggles with detecting low-abundance proteins, making it less effective for comprehensive protein analysis. Additionally, it requires extensive sample preparation and sophisticated instrumentation, which are costly and time-consuming. Antibody-based methods, such as Western blotting or immunofluorescence microscopy, rely on highly protein-specific antibodies that may not always be available for all targets (even available ones aren't always particularly good), limiting their broader application. Especially since both techniques necessitate cell lysis, the ability to analyze proteins dynamically over time within their physiological context is impossible. Plasmid-based overexpression systems provide an alternative, but these methods rarely accurately reflect endogenous protein levels and can introduce experimental artifacts. After all, adding foreign expression systems are, by definition, altering normal biological processes and are quite likely to affect responses to experimental treatments.
CRISPR/Cas9 Meets HiBiT: A Breakthrough in Protein Analysis
To address these challenges, researchers have increasingly turned to genome editing technologies, particularly CRISPR/Cas9, to integrate protein tags directly into the genome. One of the most effective tagging approaches involves the insertion of the 11-amino acid bioluminescent HiBiT tag into endogenous loci. HiBiT tagging offers a highly quantitative method for studying protein expression and dynamics while preserving the native cellular environment. By circumventing the need for traditional cloning, overexpression, and external reporters, this technique enables real-time protein analysis with high specificity and minimal disruption to natural cellular processes.
Figure 2. CRISPR-mediated tagging of endogenous proteins with a luminescent peptide. (Credit: Schwinn et al. ACS Chemical Biology. 2017)
Recent research has significantly expanded the application of this technology beyond initial proof-of-concept studies. Previous work demonstrated the successful integration of HiBiT tags in a small number of proteins within a single signaling pathway, providing an early indication of the method’s potential. However, critical questions remained regarding the scalability of this approach, its broader applicability across various protein classes, and whether it could accurately preserve native cellular biology.
The Protein Revolution Will Be Bioluminescent
A more extensive investigation into HiBiT knock-in efficiency has now been conducted, encompassing a diverse set of proteins across multiple cell lines. This study examined nearly 100 target proteins that vary widely in size, subcellular localization, physiological function, and expression levels. Researchers found that HiBiT tagging was successful in over 80% of these targets, demonstrating the method’s versatility and scalability. Importantly, this approach eliminates the need for extensive antibody libraries, which would otherwise be required for equivalent studies using Western blotting, and ensures that even proteins lacking commercially available antibodies can be analyzed.
Beyond simply tagging proteins, this study validated the expression, size, and localization of HiBiT-labeled proteins using advanced detection methods such as HiBiT-specific blotting and bioluminescence imaging. These techniques provide high-sensitivity, multi-format analysis without the drawbacks of traditional Western blotting or immunofluorescence microscopy. Unlike fluorescence-based reporters, which may suffer from photobleaching or autofluorescence interference, bioluminescence offers exceptional sensitivity and a wide dynamic range, making it well-suited for quantitative studies of protein abundance and localization.
Figure 3. Workflow for large-scale HiBiT endogenous tagging. (a) Schematic showing integration of HiBiT sequence immediately upstream of native stop codon to generate C-terminal protein fusion. (b) Diagram of editing and validation procedure for large-scale knockin of HiBiT. (Credit: Schwinn et al. Scientific Reports. 2020)
Minimizing Artifacts with Endogenous Protein Analysis
Further comparisons between endogenous HiBiT-tagged proteins and overexpression models revealed a critical advantage: only endogenous tagging accurately captured dynamic protein behavior in live cells. Unlike overexpression systems, which can artificially amplify protein levels and disrupt cellular processes, endogenous HiBiT tagging preserves the native regulatory environment. This ensures that cellular signaling pathways and protein interactions can be studied under physiologically relevant conditions. Additionally, HiBiT-tagged proteins maintain normal regulatory mechanisms, including post-translational modifications, degradation pathways, and spatial localization, which are often altered in overexpression models.
From Discovery to Disease: The Broad Impact of HiBiT Tagging
The broader implications of this research extend into multiple areas of biological investigation. The ability to conduct real-time, quantitative protein analysis in live cells has the potential to accelerate drug discovery efforts by enabling researchers to measure target engagement, protein stability, and dynamic interactions in disease-relevant models. Additionally, in disease modeling, HiBiT knock-in technology can provide insights into the effects of genetic mutations on protein function and localization, improving our understanding of various pathological mechanisms. Functional genomics studies also benefit from this approach, as it allows for systematic interrogation of protein networks without the need for exogenous expression constructs.
Figure 4. Applications of the HiBiT protein tagging system. (Credit: Promega)
Future-Proofing Proteomics: The Path Forward is Bright
As the demand for high-throughput, physiologically relevant protein analysis continues to grow, the scalability and sensitivity of HiBiT knock-in technology make it an invaluable tool for the research community. By overcoming the limitations of traditional protein detection methods, this approach enables a deeper understanding of cellular biology and molecular mechanisms. With further research and continued advancements in genome editing and bioluminescent technologies, CRISPR/Cas9 HiBiT knock-in is poised to become a standard method for real-time, quantitative protein analysis in live-cell environments. Its potential applications extend beyond basic research, with promising implications for biopharmaceutical development, personalized medicine, and synthetic biology.
Figure 5. A simplified workflow to build HiBiT knock-in cells through EditCo's high-throughput CRISPR platform. (Credit: EditCo Bio)
The continued evolution of genome-editing technologies will further enhance the precision and efficiency of protein tagging strategies. Future studies may explore ways to improve knock-in efficiency across diverse cell types, refine detection methods for even greater sensitivity, and integrate this technology with emerging fields such as artificial intelligence-driven data analysis. As HiBiT-based protein tagging becomes increasingly adopted, researchers will gain unprecedented insights into the complexities of cellular function, paving the way for groundbreaking discoveries in the life sciences.
