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frequency, and location of all off-target editing events, and assessment of genomic integrity including chromosomal rearrangements, large insertions or deletions, inte­gration of exogenous DNA, and potential oncogenicity or insertional mutagenesis. For gene-edited cell therapies, advances in single-cell DNA sequencing enabled more accurate and reliable characterization of these therapies. In-depth analysis of off-target editing and the assessment of large-scale chromosomal rearrangements that can result from inducing DSBs in DNA are also critical for safe CRISPR thera­pies [93].
The coming years are likely to see an increase in the use of CRISPR derivatives to treat a wider variety of diseases. This includes RNA editing systems for the treat­ment of RNA-mediated diseases and removal of RNA viruses, and CRISPR systems that can modify DNA without inducing DSBs, such as base, prime, PASTE, and epigenetic editing. The potentially increased safety proles of these systems may generate more public support for these advanced biologics they are used to create.
R. Kishton et al.
10.9.3 Regulatory Issues andDeveloping New Clinical
Frameworks forCRISPR Therapies
As the eld of CRISPR gene editing continues to grow, an increasing number of therapies are approaching clinical trials. Despite this progress, a key stumbling block remains in the form of the outdated clinical development pipeline; the current framework for developing a therapeutic product was simply not designed to accom­modate the novelty and complexity of next-generation CRISPR cell and gene thera­pies. Many CRISPR scientists have stated that an entirely new clinical framework should be developed by the FDA with these therapies in mind.
The FDA has recently voiced its support for CRISPR-based therapies, announc­ing several new draft guidance and initiatives for their improved development. This includes the bespoke Gene Therapy Consortium, which aims to provide clearer information on basic and clinical research, manufacturing, and regulatory require­ments in order to streamline the development of small-batch therapies [94]. As part of this initiative, the FDA also suggested that nancial incentives may be provided to encourage companies to generate gene therapies that may not otherwise be nan­cially viable, such as diseases with very small patient populations. Other FDA ini­tiatives include a gene therapy pilot program, which would provide real-time feedback to sponsors throughout development, and the INitial Targeted Engagement for Regulatory Advice on CBER producTs (INTERACT) program, which allows for informal meetings between the FDA’s Center for Biologics Evaluation and Research (CBER) and trial sponsors in the early stages of development [95]. The FDA’s increased commitment to ensuring the streamlined development and success of CRISPR-based therapies suggests that this eld will only continue to grow in the coming years, likely with more positive outcomes for patients.
10 CRISPR Technology andIts Application inTherapeutics
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R. Kishton et al.
Part VI
Fusion Proteins, Antibody Drug
Conjugates and Process Chemistry
Chapter 11
Fusion Proteins: Current Status andFuture Perspectives
StefanR.Schmidt
Abstract Fusion proteins, consisting of the joined peptide chains of two or more
proteins that are naturally not connected, are popular and highly successful recom­binant protein drugs with a wide range of different functionalities and therapeutic applications. This chapter summarizes the main features of this protein class and explains the general design principles. Typical building blocks comprise the con­stant domain of immunoglobulins, linkers with specic properties, and a second protein module that carries some extra functionality such as an enzyme for instance. In some cases, the inherent ability to form higher order complexes is utilized to generate oligomers with novel characteristics. As the articially combined protein subunits not necessarily share the same physicochemical characteristics, manufac­turing becomes challenging. Often even the orientation of the fusion partners has an effect on activity and yield. Therefore, some efforts were undertaken to optimize the constructs through protein engineering. These unnatural proteins are unknown to the human body and immune system, although their components are derived from existing proteins. This can lead to immunogenic reactions particularly through novel epitopes at the junction positions between linkers and fusion partners. The different therapeutic concepts rely on some specic features such as half-life exten­sion by either enlarging the diameter of the proteins to protect them from rapid kidney clearance or through recycling by Fc gamma receptor (FcRn). Both approaches have successfully been used to generate so-called biobetters with enhanced functions. The other important category of fusion proteins contains target­ing abilities often conferred trough antibody derivatives. Some proteins from that subtype are immunocytokines that deliver cytokines to specic cell types or organs to exert the corresponding pharmaceutical effect. Overall fusion proteins represent a highly successful but heterogeneous class of recombinant therapeutic.
S. R. Schmidt (*) evitria AG, Zurich, Switzerland e-mail: ssc@evitria.com
K. Gadamasetti, S. A. Kolodziej (eds.), Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry,
https://doi.org/10.1007/978-3-031-62007-2_11
287© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024
288
Keywords Fusion protein · Half-life extension · Glycosylation · Fc-fusion · Aggregation · Albumin · Stability · Cytokine · Protein engineering · Orientation · Biobetters
S. R. Schmidt

11.1 Introduction

11.1.1 Denition
This chapter focuses on fusion proteins engineered from two or more genes that code for separate proteins joined by genetic techniques. The result is a single poly­peptide sharing functional properties of both parent proteins. These recombinant proteins are combinations of unrelated domains that do not occur in nature. Therapeutic fusion proteins belong to the class of next generation biologicals as they are designed exclusively through human creativity and are not evolved from a natural process. Very often they represent so-called biobetters, molecules with improved functionalities such as, for instance, extended half-life.
Although this denition would also cover multi-epitope recombinant vaccines, they are excluded from the content of this chapter as well as naturally occurring fusion proteins resulting from chromosomal rearrangements that can be observed in many cancer cells or fusion tags utilized for protein afnity purication. Bispecic functionalities in antibodies have also become very popular in the last decade but are out of scope for this chapter as they typically are not forming a continuous poly­peptide, but rather come together via disulde bridges.
11.1.2 Categories
The simplest classication of these new proteins might be based on the function of their integrated domains. Typically, one fragment plays a role in molecular recogni­tion or binding, while the other fragment adds a specic function, such as half-life extension or stability, cytotoxicity, or new targeting or delivery pathways [1]. Most fusion proteins fulll three main goals, extend the half-life, and introduce a target­ing function or a specic bioactivity. At least two of these three elements coexist in the fusion protein. Interestingly, a natural molecule, the immunoglobulin G also known as antibody, incorporates all three elements in one molecule. Antibody deriv­atives, fragments, or domains are widely used as building blocks of fusion proteins, constituting a huge share of the protein portfolio discussed here. High afnity and selectivity for specic epitopes, which are key functions of antibodies, have been generated from many nonantibody constructs that can be used as a single module or by combining two units with different specicities [2]. Fusion proteins are very
11 Fusion Proteins: Current Status andFuture Perspectives
289
attractive due to several advantages. The combination of the two functions in a sin­gle molecule facilitates the production and delivery of drugs. Two molecules linked together automatically have the same biodistribution prole instead of two separate molecules with completely different proles. Interestingly new functions not found in natural or free proteins can be generated. This includes changes in half-life or targeting specicity [3]. There are also economic opportunities by creating new intellectual properties for novel and unnatural protein combinations. Therapeutic benets due to reduced side effects or longer dosing intervals together with enhanced activity are strong motifs for fusion protein production. However, in addition to these important benets, there are also many issues. In some cases, the combination of unrelated proteins can be difcult because the fusion partners have incompatible properties. For instance, misfolding or aggregation can occur for one domain while the same conditions might be perfect for the other domain. Although some fusion protein modules are elements of other well-established molecules such as antibod­ies, platform processes may not apply because other elements mightreplace the necessary domain. This can prohibit a successful formulation because of conicting features. In addition, it could be complicated to control and ne-tune the relative amounts of each component, making it difcult to administer in the optimal efcacy and safety window. Perhaps the most important issue is the high potential for immu­nogenicity due to the formation of new epitopes at the junctions between the fusion partners, even when using only human protein domains. A summary can be seen in Table11.1.
Table 11.1 Advantages and challenges of fusion proteins
Advantages Challenges Two functionalities in one molecule simplify
manufacture and drug delivery Truly identical bio-distribution prole for both entities Designing of novel „unnatural “functionalities with clear therapeutic benets (e.g., half-life and targeting) Potential of life cycle extension of products with expiring patents
Combination of two different proteins different properties (not always compatible) pH preferences, hydrophobicity,
glycosylation-isoforms, cellular
localization Sensitivity to virus inactivation method at low pH Typically lower expression level than antibodies No platform process (neither USP nor DSP) Rarely afnity chromatography applicable (exception: Fc and HSA-Fusions) Tendency to aggregate avoiding and removing aggregates Difcult ne tuning of functions (e.g., afnity) Immunogenicity risk