Cell and gene therapy: OVERVIEW, CURRENT LANDSCAPE AND FUTURE TRENDS

by Akanksha Gupta, Ph.D. and Steven Anderson, Ph.D.

Overview

Background on cell and gene therapies Many diseases are caused by alterations in the genome that impact a specific cell type (or even multiple cell types). Such mutations can be either inherited, such as the faulty cystic fibrosis transmembrane conductance regulator (CFTR) gene that causes cystic fibrosis, or acquired, as in the case of many cancers. Whether inherited or acquired, the result of these disease-causing mutations is generally the same: a loss of the normal function of the proteins encoded by them. The ability to restore gene function through cell and gene therapies has transformed medicine such that we may now be at a turning point in our ability to treat diseases with a precise, personalized medicine approach.

Cell and gene therapies share an overlapping modality that involves the transfer of new genetic material to a patient’s cells. Examples include restoring the normal expression and function of proteins affected by genetic alterations or directing immune cells against the patient’s cancer. Both aim to treat (and potentially cure) diseases caused by genetic alterations, including cancers that arise through aberrant genetic activity. Transferring new genetic material to cells clearly differs significantly from conventional therapeutic approaches.1

Gene therapy generally involves the use of a vector to deliver specific genetic sequences to a cell, either in vivo or ex vivo, to replace, disrupt, or change a faulty gene.1 In contrast, cell therapy involves the transfer of whole, functioning, but modified ‘living’ cells that supplement or replace the activity of the original cells.2 These cells may originate from the patient themselves (autologous cells), or from a donor (allogeneic cells), and are also genetically modified in a specific manner.1,2

In practice, cell and gene therapy techniques are often considered together, but they differ in their specifics and applications.3 For example, cancer therapies may utilize cells removed from a patient that are then genetically modified ex vivo and returned to the patient. One example of this technology is an innovative therapy that utilizes CAR (chimeric antigen receptor) T-cells; these genetically-modified T cells can now express an antigen-specific, non-major histocompatibility complex (MHC)‑restricted receptor that engages antigens on target cells and initiates mechanistic signalling pathways. This approach harnesses the power of T-cells, the workhorses of one’s immune response, and has elicited remarkable therapeutic effects in patients with hematological cancers and holds great promise for the future.4,5 Key features of adoptive cell and gene replacement therapies are outlined in Table 1.

Early efforts, innovations, and setbacks

Some of the earliest conceptual studies into the use of cells and genes to correct disorders were published nearly 50 years ago.1 While these early reports identified several theoretical considerations that would be necessary for successful gene therapy,9 it was not until the early 1990s that technological advances made clinical studies possible. The first successful use of cell and gene therapy as a therapeutic approach in humans occurred in 1990, in a study in which patients with advanced melanoma were administered tumor‑infiltrating lymphocytes (TILs). The treatment persisted in the patients’ circulation and tumor deposits for up to several months during which they experienced no side effects, clearly demonstrating the clinical feasibility of administrating genetically modified cells.10 This first attempt was quickly followed by a number of other efforts to address specific diseases, including treatments for adenosine deaminase‐deficient – severe combined immunodeficiency (ADA‑SCID)11,12 and familial hypercholesterolaemia.13

However, the initial enthusiasm for gene therapy diminished following the death of a patient owing to an immune response to the vector delivering the gene therapy in a clinical trial for ornithine transcarbamylase deficiency in 1999.14 This event, and the discovery that several individuals who received gene therapy for X-linked SCID had subsequently developed leukemia, led the FDA to review the ethical concerns and safety risk associated with gene therapy trials.15,16

Despite these early setbacks, the new millennium saw renewed interest and growth in the development of cell and gene therapies, primarily due to the rapid advancements in drug delivery technology, genetic engineering methods, and synthetic biology models, as well as in our understanding of genomics and biology of disease. This progress has led to the development of a variety of techniques to manipulate genes and refinements in ways to deliver genetic information to cells.

Recent therapeutic applications of cell and gene therapies

Over the last decade, research has accelerated and resulted in several approvals for gene and cell therapies for a broad variety of indications. More recently, these include the FDA approvals for brexucabtagene autoleucel for mantle cell lymphoma (MCL; Tecartus™), axicabtagene ciloleucel for B-cell lymphoma, (BCL; Yescarta®), tisagenlecleucel for acute lymphoblastic leukemia (ALL; Kymriah®), onasemnogene abeparvovec-xioi for spinal muscular atrophy (SMA; Zolgensma®), and voretigene neparvovec-rzyl for inherited retinal diseases (Luxturna®).6

All these therapies offer significant clinical benefit and show great promise in the treatment of these diseases. For example, in a Phase 2 trial involving 75 children and young adults with pre-treated CD19+ ALL, a remarkable 81% of patients were in remission at 3 months following a single infusion of tisagenlecleucel (Kymriah, a preparation of CAR T-cells expressing an anti-CD19 receptor). Event-free survival was 73% and 50% at 6 and 12 months, indicating durable efficacy in this difficult-to-treat population.4 Similarly, in an open-label study involving 22 children (mean age 3.7 months) with Type 1 spinal muscular atrophy, patients received onasemnogene abeparvovec-xioi (Zolgensma), an adeno-associated virus (AAV) vector-based gene therapy carrying a functional copy of the human survival motor neuron (SMN) gene. After a single infusion, over 90% of patients were still alive without permanent ventilation two years later. Without treatment, only around 25% remain alive without permanent breathing support at age 14 months.17 The potential of these therapies in either preventing disease progression or providing a curative benefit highlights the clinical value compared to existing therapies that are often geared towards symptomatic treatment.

These recent successes illustrate increased interest in cell and gene therapy over the past few years, partly due to the rapid advancements in vector biology, drug delivery technology and precision medicine: areas which have until recently limited the application of cell and gene therapies.1 Additionally, cell and gene therapies are typically developed for smaller, underserved patient populations with rare diseases and cancers, and the potential for substantially enhancing these patients’ lives is high.

As such, shorter development timelines and accelerated regulatory approvals are possible.18 Indeed, so far, the FDA has issued forty-four Regenerative Medicine Advanced Therapy (RMAT) designations, designed to streamline and expedite the approval process for promising cell and gene therapy products for serious or life-threatening disorders.19 These accelerated pathways are shifting the clinical trials paradigm by enabling innovative designs including novel surrogate endpoints and potential for registrational approval as early as Phase II.

Gene editing mediated approaches

Technological advancements in vector biology along with genetic engineering platforms enabling gene editing or correction, gene addition, or gene disruption have significantly improved our ability to modify the genome. Gene editing or correction technologies based on engineered or bacterial nucleases are providing more flexible approaches to alter the genome. These techniques include TALEN (transcription activator-like effector nucleases), CRISPR/Cas9- , zinc finger-, or mega-nucleases that can alter a cell’s DNA with expected precision at the nucleotide level, without affecting other off target sequences that may impact expression of the gene or other genes. Genome editing can be performed on cells ex vivo or the editing machinery can be delivered in vivo.24

In addition to gene editing, the above cited nucleases can also be used for gene disruption if knockdown or knockout of a gene is desired. For example, this technology can be used to modify the T-cell genomes by knocking out negative T-cell regulators through specific gene disruption as well as by adding transgenes. Knock-down/out technologies are particularly useful for treating diseases caused by gene overexpression, including many cancers.

Another application of this technology is in the modification of allogeneic donor cells wherein the immunogenic sequence can be eliminated to render these cells less immunogenic to the host receiving them. Gene editing technologies are also being applied to gene replacement therapy approaches in diseases such as sickle cell anemia, inherited retinal degenerative disorders, cystic fibrosis and others.

Gene therapy delivery via viruses

Another advancement in the field has been the successful delivery of the genetically modified material using either a viral or non-viral based approach. The majority of the gene therapy trials utilize an engineered adeno-associated virus (AAV) or lentivirus (‘lenti’) vector due to the inherent ability of viruses to introduce genetic material into host cells and their ease of manipulation.1,31 Although these properties make viruses an obvious choice for delivery of cell and gene therapies, such delivery methods have disadvantages that include the potential for immunogenicity and malignancies caused by vector-mediated insertional activation of oncogenes. Active research and focus on non‑viral methods for delivery is ongoing, and non-viral vectors such as the PiggyBac™ (PB) system that delivers DNA via a transposon are currently under clinical investigation.

CAR T-cell therapy

The field of CAR T-cell therapy has also evolved with refinements in CAR design to prompt immune system activation, enhance signalling and proliferation of T-cells, and an improved safety profile. The backbone of the approved CAR T-cell therapies feature a second generation CAR that consists of additional co-stimulatory molecules such as CD-28 or 4-1BB. Since then, CARs have evolved to third and fourth generation versions to address autoimmune issues and tumor‑mediated immunosuppresion. For instance, the fourth‑generation CAR T, referred to as TRUCKs (T-cells redirected for universal cytokine‑mediated killing) are genetically “armored” with antitumor activity maximized through additional genetic modification, including knock-out or knock-in of different genes that can control CAR expression and activity.

Additional focus areas in the cell therapy space include induced pluripotent stem cells (iPSCs), Natural killer (NK) cells, TILs and T-cell receptor (TCR) immunotherapy approaches.

Biomarkers enabling cell-based therapies

Another aspect that has played a key role in the evolution of these cell-based therapies are biomarkers that can be used to assess and monitor pharmacokinetics of the treatment dosing, level of the target cell population, and other indicators of treatment efficacy and safety. In the context of CAR T-cell therapy, functional and phenotypic characterization provides insight into the potential effectiveness of the product. As these therapies entail the use of a ‘living drug’, assessing the immunological fitness and the status of immune activation and differentiation, memory response, and survival capacity during manufacturing and in the final product is critical.

In addition, incorporation of biomarker assessments in CAR T-cell clinical trials are beneficial in determining cellular kinetics, including expansion and persistence of CAR T-cells post administration, efficacy endpoints including minimum residual disease (MRD), and the impact on immune system activation. Safety related biomarkers (e.g., inflammatory markers such as C-reactive protein (CRP) levels and cytokines such as IL-6, IL-15, IFNγ, GM-CSF, IL-8, MIP-1, among others) have provided insights in predicting cytokine release syndrome (CRS), a condition that presents a serious and potentially life-threatening safety risk for patients. A summary of biomarker applications in CAR T-cell therapies is shown in Figure 1.

Current Landscape of biomarker applications in CAR T-cell therapies

Future Trends

Cell and gene therapies have progressed substantially since their conceptual beginning in the 1970s. Many setbacks have been addressed following the first successful human trials in the early 1990s, and the last decade has yielded some remarkable advancements in these technologies.2 The momentum of activity is attracting more biopharmaceutical companies to the cell and gene technology space. In fact, over 1,000 active cell and gene therapy trials are ongoing; the majority are Phase 1 or 2 trials for oncology indications, but others span a range of therapeutic areas including metabolic diseases, ophthalmologic disorders, as well as musculoskeletal and immunological disorders.7,20 More to the point, this burgeoning branch of precision medicine now includes multiple approvals, and hundreds of companies globally are supporting development and moving forward with a significant and growing pipeline of therapeutic candidates.

The current cell and gene therapy approvals6 bode well for the future of cell and gene therapies. In due time, cell and gene therapies will take their place as pillars of precision medicine with the potential to transform the lives of those affected by genetic diseases and many types of cancer – conditions for which treatments have so far been unattainable.2 The numbers of clinical trials and regulatory approvals for cell and gene therapies are expected to rise over the coming years: the FDA anticipates that by 2025 it will approve 10–20 cell and gene therapy products per year,21 and separate estimates suggest that by 2030 half a million patients in the US alone will have been treated with 40–60 approved gene or cell therapy products.22

Additional research and operational developments are needed if cell and gene therapies are to become more widely available to the patients who need them. Improvements in vector biology, manufacturing, and delivery mechanisms are needed to make these therapies more broadly available and cost effective. Consortia involving government, academic, and industry participants will be critical to these efforts. For example, vector systems that are more universal might improve the scalability of manufacturing. Such improvements may also allow enhancements in the tissue specificity of the administered therapy. The paucity of safe, delivery systems that are both therapeutically and cost-effective is a headwind to the clinical application of cell and gene technologies,23 and potentially prevents some novel therapies from progressing past early research phases.20

Advances in nanotechnology, nucleic acid engineering, and molecular biology may lead to novel non-viral vectors being developed that overcome the limitations with existing delivery methods.23 Furthermore, reverse genetics is now possible for almost all viruses, and this has vastly expanded the virus types that can be evaluated as potential vectors. In addition to AAVs, poxviruses, herpesviruses and some non-human viruses are now being studied for their potential as vaccine and gene therapy vectors; some of these viral vectors may provide options that offer better safety and efficacy profiles compared with current delivery methods.25

The ability to use allogeneic versus autologous donors will also allow for potential scalability of adoptive cell therapies.20 Improvements in patient stratification through the identification of more therapeutic and prognostic biomarkers may further improve cell and gene therapies by matching patients with therapies that maximize efficacy and minimize side effects.26 A combination of methods, along with a systems biology approach for data analytics, will add considerably to our ability to use biomarkers more effectively in patient management.27 A summary of these and other future trends is outlined in Table 2. We look forward to advances in these critical areas and our understanding of disease biology to drive the expansion of these modalities beyond current applications in rare diseases and oncology to other therapeutic areas and clinical indications.

 

Akanksha Gupta, PhD Head of Immunology, Biomarker Solution Center

Dr. Akanksha Gupta leads the immunology therapeutic team for the Biomarker Solution Center, a team that delivers biomarker solutions and strategy to clients, leveraging the laboratory resources of both Covance and LabCorp. Her strategic leadership provides scientific direction on biomarker strategies integrating innovative technologies, emerging scientific knowledge, clinical feasibility and regulatory requirements for a precision medicine approach across multiple therapy areas including immuno-inflammation, immuno-oncology, respiratory, dermatology and other auto-immune disorders. Dr. Gupta draws more than 15 years of pharmaceutical industry experience in drug development, translational research and supporting development strategies for early to late stage assets. She shares her experience as author or co-author of multiple peer-reviewed research publications, abstracts and patent submissions.

 

 

Steven Anderson, Ph.D. Chief Scientifi c Offi cer, Covance Drug Development

Steven Anderson is senior vice president and chief scientific officer for Covance Drug Development. He has worked for LabCorp for 30 years and has held a variety of positions, including director of operations for ViroMed Laboratories, director of operations for Monogram Biosciences, director of operations for the Center for Molecular Biology and Pathology, director of operations for Integrated Oncology and Integrated Genetics, national director of research and development, and global head of LabCorp Clinical Trials. His research interests include Molecular Pathology and Oncology based biomarkers, and that work has resulted in the development and validation of multiple companion diagnostics and pharmacogenomic assays in clinical use today. He holds a doctorate in genetics from Iowa State University and was an American Cancer Society postdoctoral fellow at the Waksman Institute of Microbiology at Rutgers University.

 

 

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