Synthetic and Systems Biology Principles in the Design of Programmable Oncolytic Virus Immunotherapies for Glioblastoma

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Synthetic and Systems Biology Principles in the Design of Programmable Oncolytic Virus Immunotherapies for Glioblastoma NEUROSURGICAL FOCUS Neurosurg Focus 50 (2):E10, 2021 Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma *Dileep D. Monie, BA,1,6,7 Archis R. Bhandarkar, BS,6 Ian F. Parney, MD, PhD,1,3 Cristina Correia, PhD,5 Jann N. Sarkaria, MD,4 Richard G. Vile, PhD,1,2 and Hu Li, PhD5 Departments of 1Immunology, 2Molecular Medicine, 3Neurosurgery, 4Radiation Oncology, and 5Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; 6Mayo Clinic Alix School of Medicine; 7Mayo Clinic Graduate School of Biomedical Sciences; and Mayo Clinic College of Medicine and Science, Rochester, Minnesota Oncolytic viruses (OVs) are a class of immunotherapeutic agents with promising preclinical results for the treatment of glioblastoma (GBM) but have shown limited success in recent clinical trials. Advanced bioengineering principles from disciplines such as synthetic and systems biology are needed to overcome the current challenges faced in developing effective OV-based immunotherapies for GBMs, including off-target effects and poor clinical responses. Synthetic biol- ogy is an emerging field that focuses on the development of synthetic DNA constructs that encode networks of genes and proteins (synthetic genetic circuits) to perform novel functions, whereas systems biology is an analytical framework that enables the study of complex interactions between host pathways and these synthetic genetic circuits. In this review, the authors summarize synthetic and systems biology concepts for developing programmable, logic-based OVs to treat GBMs. Programmable OVs can increase selectivity for tumor cells and enhance the local immunological response using synthetic genetic circuits. The authors discuss key principles for developing programmable OV-based immunotherapies, including how to 1) select an appropriate chassis, a vector that carries a synthetic genetic circuit, and 2) design a syn- thetic genetic circuit that can be programmed to sense key signals in the GBM microenvironment and trigger release of a therapeutic payload. To illustrate these principles, some original laboratory data are included, highlighting the need for systems biology studies, as well as some preliminary network analyses in preparation for synthetic biology applications. Examples from the literature of state-of-the-art synthetic genetic circuits that can be packaged into leading candidate OV chassis are also surveyed and discussed. https://thejns.org/doi/abs/10.3171/2020.12.FOCUS20855 KEYWORDS synthetic biology; systems biology; oncolytic virus; cancer immunotherapy; glioblastoma LIOBLASTOMA (GBM) is the most common and tions for many cancer patients but, despite promising safe- lethal malignancy of the CNS. This devastating ty profiles, are not currently effective for those suffering disease has a median overall survival of 3 months from GBM.4 Gfrom the time of diagnosis in untreated patients.1 Despite Oncolytic viruses (OVs) are a class of immunotherapeu- the significant cost and morbidity associated with the stan- tic agents with an FDA-approved treatment for melanoma, dard of care, i.e., resection combined with adjuvant che- a solid tumor.5 OVs work by directly lysing tumor cells, motherapy and radiation, the median patient life expec- which then release tumor antigens in the context of danger tancy is only extended to about 14 months and the disease signals—both damage-associated (DAMPs) and pathogen- remains almost uniformly fatal.2,3 Yet, this is the best we associated (PAMPs) molecular patterns—that elicit antitu- can do for patients after hundreds of clinical trials over mor immunity (Fig. 1A).6 Since 1991, many attempts to use several decades. Immunotherapies are breakthrough op- OVs in GBM have had limited success. More than 20 clini- ABBREVIATIONS Ad5 = adenovirus serotype 5; CCN1 = cellular communication network factor 1; DAMP = damage-associated molecular pattern; dsDNA = double- stranded DNA; GBM = glioblastoma; GFAP = glial fibrillary acidic protein; GM-CSF = granulocyte-macrophage colony-stimulating factor; HSV-1 = herpes simplex virus type 1; hTERT = telomerase reverse transcriptase; IL = interleukin; miRNA = micro RNA; OV = oncolytic virus; PAMP = pathogen-associated molecular pattern; pCancer = cancer-selective promoter; PD-1 = programmed death–1; PD-L1 = programmed death–ligand 1; PDX = patient-derived xenograft; PPI = protein-protein interaction; scFv = single-chain variable fragment; sTRAIL = secreted tumor necrosis factor–related apoptosis-inducing ligand; VSV = vesicular stomatitis virus. SUBMITTED October 1, 2020. ACCEPTED December 4, 2020. INCLUDE WHEN CITING DOI: 10.3171/2020.12.FOCUS20855. * D.D.M. and A.R.B. contributed equally to this work. ©AANS 2021, except where prohibited by US copyright law Neurosurg Focus Volume 50 • February 2021 1 Unauthenticated | Downloaded 10/10/21 07:15 PM UTC Monie et al. FIG. 1. A: Mechanisms of OV immunotherapy for GBM. B: Sense-compute-actuate framework of programmable OV immunothera- py for GBM. C: Design-build-test-analyze development cycle of synthetic OVs for GBM blends systems and synthetic biology. 2 Neurosurg Focus Volume 50 • February 2021 Unauthenticated | Downloaded 10/10/21 07:15 PM UTC Monie et al. cal trials of 7 different OVs did not translate encouraging tropisms. To generate antitumor immunity, the innate im- preclinical results to patients with GBM.7 The root causes mune system must be activated at some point during OV of these failures can be traced to failed oncotropism, de- replication. This awakens the adaptive immune system spite neurosurgical delivery, and oncolysis mechanisms.7 to precisely target all cancerous cells, both infected and Therefore, advanced bioengineering methods are neces- uninfected.15 If the patient has been exposed to the viral sary to design and implement better armaments. chassis before, by either infection or vaccination, then this Synthetic biology involves the creation and manipula- may limit the efficacy of the OV. Host genome integra- tion of biological systems using rational, modular design tion (e.g., lentivirus) may be advantageous for persistent principles from electrical engineering, computer sci- antitumor effects but comes with the risk of genetic dam- ence, and related disciplines.8 The sense-compute-actuate age and chronic latent infection.16 Ultimately, however, the framework (Fig. 1B)9 is a guiding design principle in syn- immune system must be able to clear the OV infection, thetic biology, in which long stretches of synthetic DNA particularly in the CNS, to prevent chronic inflammation constructs that encode networks of genes and proteins and its sequelae. (synthetic genetic circuits) are designed to sense stimuli of interest, compute which environmental state a cell is in Neurotropic Viruses based on a permutation of stimuli, and actuate a response A chassis needs to target glioma cells, which arise from accordingly. In November 2019, the first living medicine healthy cells of the brain parenchyma and share many cell containing a synthetic genetic circuit entered phase 1 surface and metabolic features, so naturally occurring clinical trials in the form of a bacteria-based cancer im- neurotropic viruses are the obvious starting point. munotherapy.10 Such engineered genetic circuits are now primed to be packaged into OVs and programmed to co- Herpes Simplex Virus Type 1 ordinate local tissue responses, with preclinical studies Herpes simplex virus type 1 (HSV-1) is an enveloped demonstrating enhanced 1) tumor cell targeting and 2) virus with a linear 152-kilobase (Kb) double-stranded generation of antitumor immunity. DNA (dsDNA) genome.17 It is capable of carrying large Systems biology complements synthetic biology by en- payloads—as much as 20 Kb—making it particularly at- abling complex design and analysis of genetic circuits. Tu- tractive for synthetic biology applications. It is the first and mor microenvironment cell states can be defined by using only OV that has garnered FDA approval with talimogene single-cell multiomics data sets such as RNA sequencing laherparepvec, which has been engineered extensively to (RNA-seq) and mass cytometry. These high-dimensional target melanoma.18 Using HSV-1 against GBM was also data sets are amenable to machine learning11 and network- the first proposed OV with experimental success in a mu- based classification.12 Computation identifies biological rine model;19 therefore, HSV-1 is particularly promising as features unique to glioma cells,13 elucidates pathways a treatment for GBM. orthogonal to genetic circuit designs, and helps priori- The high prevalence of HSV-1 infection in humans, tize OV-based approaches.14 After the synthetic OVs are however, means that preexisting immunity (e.g., neutral- constructed and tested, further systems analyses ensure izing antibodies) poses a barrier to its application as an ef- that the OVs have predictable effects on the cells and the fective OV. Modulating this OV-host immune interaction greater tumor microenvironment, statistically accounting is a possibility with synthetic gene circuits.20 Additionally, for complex stochastic behavior. This knowledge is fed several molecular features of GBM have been identified back into the design of improved, next-generation OV ge- that influence the efficacy of HSV-1 OV in vitro and in netic circuits (Fig. 1C). vivo, including the integrin ligand cellular communication network factor 1 (CCN1) protein found in the extracellular Selection and Delivery of OV Chassis matrix
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