Patent Application
20240132844
The field of the invention is cell-based therapeutics and related methods therefor, especially as they relate to memory-like cytokine enhanced NK cells (M-CENK) with improved cytotoxicity and expansion characteristics.
The background description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed invention, or that any publication specifically or implicitly referenced is prior art.
All publications and patent applications herein are incorporated by reference to the same extent as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Where a definition or use of a term in an incorporated reference is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply.
Natural killer (NK) cells constitute a group of innate immune cells, which are often characterized as cytotoxic lymphocytes that exhibit antibody dependent cellular toxicity via target-directed release of granulysin and perforin. Most NK cells have a specific cell surface marker profile (e.g., CD3−, CD56+, CD16+, CD57+, CD8+) in addition to a collection of various activating and inhibitory receptors. While more recently NK cells have become a significant component of certain cancer treatments, generation of significant quantities of NK cells (and especially autologous NK cells) has been a significant obstacle as the fraction of NK cells in whole blood is relatively low.
To obtain therapeutically meaningful quantities of NK and NK-like cells, NK cells can be generated from various precursor cells. For example, various stem cell factors (SCF), FLT3 ligand, interleukin (IL)-2, IL-7 and IL-15 have been reported in various in vitro approaches to induce and expand cord blood-derived cytokine-induced killer (CIK) cells (Anticancer Research 30: 3493-3500 (2010)). Similarly, CD34+ hematopoietic cells can be exposed to IL-12 and other agents as is reported in US 2018/0044636. In still other approaches, human hemangioblasts were sequentially exposed to two different cytokine cocktails as described in WO2011/068896, and different cytokine cocktails were used with post-embryonic hematopoietic stem cells as taught in WO2012/128622. While at least some of these methods provide a significant n-fold expansion of NK cells, methods and reagents for such expansion are both time and resource demanding. Still further, it should be noted that many of the known methods also require NK cell culture on a feeder cell layer, which is often problematic from a technical and a regulatory perspective.
In more simplified methods, acute myeloid leukemia (AML) cells can be exposed to TpoR agonists to so induce the AML cells to form NK cells. However, such approach is likely not viable as a source for therapeutic cell preparations. Alternative methods have also relied on culturing peripheral blood cells in the presence of various interleukins, stem cell factors, and FLT3 ligands as is disclosed in WO 2011/103882. In yet another method, US 2013/0295671 teaches methods of stimulating already existing NK cells with anti-CD16 and anti-CD3 antibodies along with cytokines. While procedurally simpler, such methods still require elaborate manipulation of the cells and add significant costs due to the specific reagent required.
In still further known methods, U.S. Pat. No. 10,125,351 describes use of cord blood or peripheral blood as a source of cells that are subject to density gradient separation to isolate nucleated cells that are then cultivated with a medium that contains interferon, interleukin, a CD3 antibody and human albumin. Most advantageously, such method is amenable to perfusion culture in a bioreactor and as such significantly reduces operational difficulties. Unfortunately, the yield of NK cells is still relatively low.
Regardless of the specific manner of production, cultivated NK cells will typically not exhibit memory like character, which is particularly desirable for cancer immune therapy. In at least some attempts to produce memory like NK cells, selected NK cells were exposed to IL-12, IL-15, and IL-18 and so exposed NK cells exhibited a memory like phenotype and correlated with the expression of CD94, NKG2A, NKG2C, and CD69 and a lack of CD57 and KIR (see Blood (2012) Vol. 120, No. 24; 4751-4760). Similarly, memory like NK cells were prepared by pre-activating NK cells using various stimulatory cytokines followed by contacting the pre-activated cells with PM21 particles, EX21 exosomes, or FC21 feeder cells as is described in WO 2018/089476 and U.S. Pat. No. 10,300,089. In yet another approach to generate memory like NK cells, freshly isolated NK cells were exposed to an IL-18/IL-12-TxM fusion protein complex as is described in WO 2018/165208. While such methods typically produced at least some NK cells with memory-like character, the cytotoxicity of such activated NK cells against selected target cells was still less than optimal, possibly due to lack or low expression of specific activating receptors and/or expression of specific inhibitory receptors.
In yet another known approach cytokine induced memory like NK cells (CIML NK) can be produced in the laboratory using patient blood. However, such method is typically limited in their usage due to the relatively limited number of CIML NK cells that can be produced. Hence, multiple samples must be taken multiple times from a patient to produce enough doses to cover a complete treatment regimen. In still another approach to generate CIML NK cells as described in WO2021/006876, cord or whole blood derived mononuclear cells are activated with anti-CD16 antibodies and N-803, and then expanded using a cytokine mix. While conceptually simplified, various difficulties nevertheless remain, including presence of CD3+ cells and sub-optimal cytotoxicity against at least some target cells.
Alternatively, NK cells can be isolated from an apheresis product using beads and so isolated cells are then directly induced to produce a CIML phenotype. While such approach allows reduction in CD3+ cells in the NK cell product, that approach also limits the ability to expand the cells. Moreover, the capability of freezing and later thawing such cells back to a therapeutically effective cell product is unknown. Finally, such isolated and induced NK cells tend to have relatively lower cytotoxic potential.
Thus, even though various systems and methods of targeted antiviral therapies and vaccines are known in the art, all or almost all of them suffer from several drawbacks. Among other difficulties, many CIML NK cell preparations can prepared only with a limited number of cells and may therefore not be therapeutically effective. Moreover, and especially where the memory phenotype is induced with multiple and distinct cytokines, expense and inconsistent activities of the cytokine mixtures may prevent production of reproducible therapeutic formulations with predictable activity. Therefore, there remains a need for compositions and methods for improved NK cell-based therapies, and especially for memory-like cytokine enhanced NK cell-based compositions and methods.
The inventive subject matter is directed to various compositions and methods of M-CENK cells and their generation and expansion, and various uses therefor. Notably, the M-CENK cells as presented herein have superior cytotoxicity, allowed for rapid and substantial expansion, and were therapeutically active after cryopreservation. Most advantageously, the M-CENK cells can be prepared from mononuclear cell-derived cytokine enhanced NK cells in a simple and effective manner in desirable quantities, and induction of the M-CENK phenotype is achieved with a single protein complex, preferably a TxM having IL-12/IL-15/IL-18 activity.
In one aspect of the inventive subject matter, the inventors contemplate a method of generating a memory-like cytokine enhanced natural killer (M-CENK) cell that includes a step of obtaining a plurality of mononuclear cells, and another step of contacting the plurality of mononuclear cells with a corticosteroid and optionally a cytokine. In still another step, the plurality of mononuclear cells are incubated in the presence of the corticosteroid and the optional cytokine to enrich the mononuclear cells in NK cells, and the enriched NK cells are then induced with a TxM fusion protein to generate the M-CENK cells, wherein the TxM fusion protein comprises a protein portion having IL-12 activity, a protein portion having IL-15 activity, and a protein portion having IL-18 activity.
In some embodiments, the plurality of mononuclear cells are cryopreserved before the step of incubating. In such embodiments, the cryopreserved mononuclear cells are preferably thawed and washed in a medium containing the corticosteroid and the optional cytokine. It is further contemplated that the step of incubating is performed over a period of between 14 and 21 days and/or until the NK cells are enriched to at least 65% of all live cells. Additionally, it is contemplated that the enriched NK cells are induced with the TxM at a concentration of between 1-25 μg/mL, typically over a period of between 12 and 16 hours.
While not limiting the inventive subject matter, it is generally preferred that the corticosteroid is hydrocortisone and that the optional cytokine is N-803. Moreover, it is also preferred that the step of incubating includes the optional cytokine. Contemplated methods will typically include a step of harvesting the M-CENK cells and formulating the harvested M-CENK cells for infusion. Where desired, the harvested M-CENK cells are cryopreserved before infusion. In further aspects of the inventive subject matter, the step of incubating is performed in an automated bioreactor.
Consequently, the inventors also contemplate a method of producing a memory-like cytokine enhanced natural killer (M-CENK) cell that includes a step of obtaining a plurality of mononuclear cell-derived cytokine enhanced NK cells (CENK), and a further step of inducing the enriched NK cells with a TxM fusion protein to generate the M-CENK cells, wherein the TxM fusion protein comprises a protein portion having IL-12 activity, a protein portion having IL-15 activity, and a protein portion having IL-18 activity.
Viewed from a different perspective, the inventors also contemplate a memory-like cytokine enhanced natural killer (M-CENK) cell produced by a method as presented herein. Most typically, the cells will be included into a pharmaceutical composition that includes a pharmaceutically acceptable carrier, which is or comprises in some embodiments a cryopreservation medium. It is further generally contemplated that the pharmaceutically acceptable carrier is formulated for infusion and/or may have a cell density of 0.5-1.5×10 7 cells/mL.
In still further embodiments, the inventors contemplate a method of treating an individual having cancer, comprising a step of administering the cells and compositions presented herein. Therefore, the compositions are also contemplated for use in the treatment of cancer. In one embodiment, the M-ceNK cells presented herein can be used, and may be administered to the patient, for killing cancer stem cells and mesenchymal cells.
Various objects, features, aspects and advantages of the inventive subject matter will become more apparent from the following detailed description of preferred embodiments, along with the accompanying drawing figures in which like numerals represent like components.
The inventors have discovered that M-CENK cells with superior cytotoxicity can be generated that can be expanded to a desirable quantity and that can be cryopreserved and thawed without compromising functional characteristics. Notably, and in contrast to protocols that produce CIML NK cells, the present methods do not require activation of NK cells in a mononuclear cell mixture using anti-CD16 antibodies. In contrast, the methods presented herein use hydrocortisone, preferably in combination with N-803 (or IL-15) and human AB serum. Moreover, it was unexpectedly observed that enrichment and expansion can be done from cryopreserved apheresis materials, and that the M-CENK cells can also be cryopreserved and thawed without loss in cytotoxicity.
Therefore, the inventors contemplate M-CENK (memory-like cytokine enhanced NK cells) and methods of their generation, as well as cell-based therapeutics comprising such cells, and especially cryopreserved M-CENK suspensions for infusion. Viewed from another perspective, it should be appreciated that selective enrichment and expansion of NK cells from (thawed) patient apheresis material can be achieved by inclusion of hydrocortisone (and typically N-803 or other cytokine or cytokine analog with IL-15 like activity) to the growth medium to so produce high quality NK cells from the apheresis product. The so obtained cells are then activated to produce a memory phenotype. Consequently, it should be appreciated that multiple doses of high-quality M-CENK cells can be prepared from cryopreserved material without the need of repeated blood collection from donor. Indeed, M-CENK cells produced in the processes presented herein can be cryopreserved in bespoke media for an off-the shelf product, and the freeze-thaw procedure developed for cryopreservation ensures preservation of cell characteristics and viability as is shown in more detail below.
For example, in one step of contemplated methods, a cryopreserved apheresis material intermediate is produced as follows: Leukapheresis product (MNC, apheresis) from a patient are processed and cryopreserved as an apheresis material intermediate (AMI) to enable the manufacture of M-CENK product. Cryoformulation media is formulated to ensure high viability of apheresis product post-thaw. Most preferably, the cryoformulation media comprises PlasmaLyte A, 5% Albumin (Human) USP, and DMSO. Freshly prepared media is filter sterilized using 0.2 μm, a PES filter unit. Cryoformulation media is mixed with the MNC apheresis product at 1:1 ratio (by volume) to so generate the AMI. Formulated product is filled in separate Cryo-bags. 10-20 bags can be made from each apheresis product. The filled cell bags are subsequently cryopreserved to equal or lower than −85° C. using a controlled-rate freezer (e.g., CryoMed freezer).
Enrichment and expansion of cytokine enhanced NK cells can then be done as follows. Cryopreserved apheresis material intermediate (AMI) is thawed in a 37° C. water bath and used for expansion. Thawed cells are washed, for example, using the Sepax C-Pro device or table top centrifuge, and re-suspended in growth media consisting of NK-MACS media containing 50-100 ng/mL N-803 and 0.2-2.0 μM Hydrocortisone and human AB serum. A strategy was developed where growth media was added to successfully enrich and expand NK cells for 20 days. For example,
Generation of M-CENK cells was then performed as follows: Once the culture reaches at least 85% CD56 positive cells up to expansion day 20 at a density of at least 1×106 cells/mL, fixed concentrations of N-803 (100-300 ng/mL), IL-12 (1-100 ng/mL) and IL-18 (5-250 ng/mL) are added to the culture. Cells are stimulated with the cocktail of cytokines for 14-16 hours which induces the memory like phenotype of the CD56 positive cells. After completion of the M-CENK induction stage, cells are washed using Sepax C-Pro device. Most typically, a 5% albumin (human) solution is used as washing and resuspension solution. For cryopreservation, M-CENK cells are formulated in media containing 5% Albumin (human) USP: CryoStor 10 (CS10) (1:1). M-CENK have enhanced ability to kill cancer cell targets through their increased IFN-γ production. In addition, these cells are phenotypically CD56+, CD25+, DNAM-1+, and NKP30+, NKG2D+, NKG2A+, and CD3−.
With respect to cytotoxicity, the inventors observed that the M-CENK cells had superior cytotoxic activity against a variety of target cells at a favorable effector to target ratio, even against MS-1 cells (see
Of course, it should be appreciated that numerous alternate methods or formulations can be used for freezing of apheresis material, or the apheresis material is not frozen or fresh material can be combined with previously frozen material prior to the step of enrichment and expansion. Similarly, it is contemplated that NK cells can also be purified first from whole blood, cord blood, or apheresis material and then be subjected to expansion. The so expanded cells can then be activated for memory phenotype. Likewise, it should be appreciated that while hydrocortisone is generally preferred for the step of enrichment and expansion, numerous hydrocortisone analogs and other corticosteroids (e.g., cortisol, corticosterone, cortisone, aldosterone, etc.) are also deemed suitable for use herein.
Additionally, it should be noted that the M-CENK cells can be frozen using different cryoformulation media and all known cryoformulation media are deemed appropriate for use herein. With respect to cryotreatment, it is also noted that the enriched and expanded NK cells may be frozen, and upon thawing, be subjected to activation for memory phenotype generation.
Manufacturing Process
General Description of an Exemplary Manufacturing Process: The manufacturing process starts with the receipt of an autologous leukapheresis product (MNC, apheresis) that is processed and cryopreserved as Apheresis Material Intermediate (AMI) to enable the manufacture of product on demand. Following thaw, AMI are processed for media change using Sepax C-Pro to remove cryoformulation media first with Plasmalyte A and eluted in NK-GM containing 10% human AB serum, N-803 and hydrocortisone and seeded in NANT 001 bioreactor for expansion and enrichment to CENK. When the desired number and purity of CENK cells are generated, the cells are treated with the cytokine cocktail containing N-803, IL-12 and IL-18 cytokines to generate cytokine-induced memory-like (CIML)-NK cells as M-CENK. Post induction, cells are harvested, concentrated and washed with 5% Albumin (Human) using Sepax C Pro and eluted in 5% Albumin (Human) and then mixed with CryoStor 10 (CS10) at a 1:1 ratio to the desired VCD (0.25-0.75×107 cells/mL) for a total of approximately 0.25-0.75×109 M-CENK cells/bag in 100 mL volume and cryopreserved.
Apheresis to Obtain Peripheral Blood Mononuclear Cells: The manufacturing of the Autologous M-CENK cells begins following the receiving of fresh apheresis material at the manufacturing site. Following the completion of chain of custody documentation, a sample is aseptically removed from the apheresis transfer pack to enable cell viability, total nucleated cell (TNC) enumeration and phenotype characteristics determination.
Cryopreservation of the Apheresis Material Intermediate (AMI): The cryopreservation and processing steps involved in between receiving the apheresis material at the manufacturing and thawing a patient specific mononuclear cells (MNC), Apheresis material Intermediate (AMI). The cryopreservation process of AMI is initiated by determining the total nucleated cell (TNC) count and the percent viability of the fresh MNC, apheresis product.
Cryoformulation Media is freshly prepared and is filter sterilize using 0.2 μm, a PES filter unit and store on ice until used. Cryoformulation media is prepared using a mixture of PlasmaLyte A and 5% Albumin (Human) USP, and DMSO. Apheresis material is transferred to an Erlenmeyer Flask and adjusted to a desired cell density. Cryoformulation media is mixed with MNC, apheresis product at 1:1 ratio and cells are formulated to generate Apheresis Material Intermediate (AMI). Formulated product is filled in separate Cryo-bags to achieve desired cell number (2-10×108 cells). Several (10-20) bags are made from each apheresis material. The filled cell bags are subsequently cryopreserved to ≤−85° C. using controlled-rate freezer (CryoMed freezer) and are then transferred to vapor phase liquid nitrogen (≤−120° C.) freezer for long-term storage.
Composition of the NK-Growth Media: The basal medium used in manufacturing of M-CENK is designated NK-Growth Medium (NK-GM). Media is prepared at the beginning of each study and then sterile filtered using 0.2 μm, a PES filter unit and stored on ice until used.
Throughout the process, different media supplements are added aseptically at specific steps of the process. (1) At the time of inoculation to NANT 001 bioreactor, thawed apheresis material intermediate (AMI) is suspended in NK-GM containing 50-100 ng/mL N-803 (0.8 nM) and 0.2-2.0 μM Hydrocortisone. (2) During subsequent media addition steps, NK-GM containing 50-100 ng/mL N-803 was added to the bioreactor. (3) Stimulation of memory phenotype is achieved by addition of NK-GM containing cytokine cocktail [N-803 (100-300 ng/mL), IL-12 (1-100 ng/mL) and IL-18 (5-250 ng/mL)]. Prior to each media addition step, the desired amount of NK-GM is mixed with fixed concentration of cytokine/supplements (N-803+hydrocortisone or N-803 alone or N-803+IL-12+IL-18), and are then filter sterilize using 0.2 μm, a PES filter unit. Prepared media is aseptically transferred to NANT 001 for cell expansion/stimulation.
Use of NANT 001 Platform for CENK Expansion: An overview of the process for the manufacture of M-CENK is illustrated below. The NANT 001 bioreactor platform system (ImmunityBio, Inc.) is a self-contained bioreactor that executes pre-programmed protocols that instruct automatic procedures and real time monitoring throughout the entirety of the recovery, enrichment, expansion, and M-CENK induction stages of the manufacturing process.
Programmable process parameters include pH monitoring, cell imaging, temperature, and rocking parameters. The NANT001 Bioreactor includes a thermostatic compartment, a touch-screen user interface, a barcode reader, a pH Estimation unit, an integrated imaging system, and a gas flow control. Components are easy to load, single-use closed-system design for safe and cGMP-compliant cell processing and include a waste bag, up to 4 L, an aseptic disconnector, a harvesting bottle, auxiliary bags ×2, up to 100 mL ea., aseptic connectors, a cell culture flask, 636 cm2, a media bag, up to 3 L, and a buffer bag, up to 3 L. Exemplary systems suitable for use herein are described, for example, in U.S. Pat. No. 10,801,005 and US 2017/0037357, incorporated by reference herein.
Thaw, Media Exchange and NANT 001 Inoculation of MNC, Apheresis—Cryopreserved Material Using Sepax C-Pro: First, the Sepax C-Pro device is initiated utilizing the CultureWash software program. Following the installation of a single use disposable kit, 1 L of Wash solution (PlasmaLyte A) and 100 mL of Resuspension solution (NK-GM containing 50-100 ng/mL N-803 and 0.2-2.0 μM Hydrocortisone) are attached to the device as per batch records. Cryopreserved apheresis material intermediate (AMI) is removed from cryostorage and the cryobag is inspected for visible signs of damage and immediately placed into a 37° C. water bath for rapid thawing.
Following thaw, a sample is aseptically removed for cell viability and TNC count determination prior to connecting the thawed cryobag material to the Sepax C-Pro device. The MNC Apheresis—Cryopreserved material is subsequently washed twice with wash solution (PlasmaLyte A) using the Sepax C-Pro device and re-suspended into a cell collection bag at ≥3.5×106 cells/mL in NK-GM containing 50-100 ng/mL N-803 and 0.2-2.004 Hydrocortisone. The cell collection bag is then removed from the Sepax C-Pro device. A sample is taken to confirm cell viability and cell number, and if required the cells are adjusted to a desired inoculation cell density (1.0-5.0×106 cells/mL) before transferring 50 mL of the inoculum into a NANT 001 bioreactor that contains a 100 mL of pre-warmed NK-GM containing the same concentration of N-803 (74 ng/mL) and Hydrocortisone (1 μM), in order to commence the NK cell enrichment and expansion stage. Initial cell culture volume in the NANT 001 bioreactor is 150 mL and cell density range is 0.5-1.5×106 cells/mL. Multiple AMI bags are thawed if more than one NANT 001 bioreactor inoculation from same patient is planned.
Cell Recovery, Enrichment and Expansion Using the NANT 001 Bioreactor: Following inoculation of a NANT 001 bioreactor unit with 1.20-1.80×108 thawed AMI cells, the culture is monitored daily using microscopy and is sampled at specific stages throughout the cell recovery, enrichment and expansion process stages. In-process monitoring (IPM) is performed to determine cell viability, cell count and the phenotype results (percentage of CD56 positive cells present). This testing is used to control the need for subsequent addition of fresh growth media containing N-803 (without hydrocortisone). Once the percentage of CD56 positive cells in the bioreactor reaches ≥85%, expansion day 20, total cell count exceeds >1×106 cells/mL, the culture is transitioned into the cytokine stimulation stage of the M-CENK manufacturing process. Samples are taken for Bioburden testing before cytokine stimulation stage.
In Process Monitoring (IPM): During each media and N-803 addition, the culture is visually inspected for any sign of turbidity or visible contamination. Viable cell density, cell viability and cell phenotype analysis are performed on specified days as per the batch record to obtain the NK enrichment profile, and it is ensured that the production bioreactors are within the desired VCD specifications.
Stimulation of CENK with Cytokine Cocktail (human IL-12, IL-18 and N-803): Once the NANT 001 bioreactor culture reaches ≥85% CD56 positive cells up to expansion day 20 at a density of ≥1×106 cells/mL, fixed concentrations of N-803 (100-300 ng/mL), IL-12 (1-100 ng/mL) and IL-18 (5-250 ng/mL) are added to the culture in fresh NK-GM up to a final total culture volume of approximately 650 mL. Cells are stimulated with the cocktail of cytokines for 14-16 hours which induces a memory like phenotype of the CD56 positive cells (M-CENK) contained within the NANT 001 bioreactor. This stimulation with cytokine cocktail stage in the bioreactor is then terminated by bulk cell harvesting of the culture using the NANT 001 auto-export feature. Samples are taken for mycoplasma testing prior to culture harvest.
NANT 001 Bioreactor: Cell Culture Harvest and Sepax Concentration, and Wash: After completion of the M-CENK induction stage, the NANT 001 is manually advanced to perform an automated auto-export harvest protocol. The auto-export harvest is conducted using a closed system utilizing direct sterile welds between the NANT 001 bioreactor and a collection bag. Following M-CENK export, NANT 001 bioreactor is flushed with NK-GM to retrieve any remaining cells.
After the completion of the auto-export harvest stage, the intermediate harvest bag, containing the M-CENK cells, is weighed and then directly welded to the Sepax C-Pro device for downstream processing and bulk drug substance formulation. The Sepax C-Pro from GE utilizes a single use disposable technology that allows a direct sterile weld to the BCH interim bag. Using a single use disposable kit and a designated wash and re-suspension program, the Sepax C-Pro initially performs a cell concentration step, followed by a two-chamber volume buffer exchange/wash step using 5% albumin (human) solution. Finally, the cells are concentrated and eluted into an attached 300 mL cell collection bag in an approximate volume of 50 mL of 5% human albumin solution at an anticipated cell density of 0.1-2.5×107 cells/mL. The collection bag/vessel containing M-CENK is then removed from the device and QC samples are aliquoted to determine cell viability, cell density and endotoxin. M-CENK can be pooled if multiple NANT 001 bioreactors contained the same patient MNCs as the seeding inoculum.
M-CENK Drug Product Formulation: M-CENK preparation generated from multiple NANT 001 bioreactors inoculated with the same patient AMI are pooled at this stage and volume correction is made to achieve the VCD of 0.5-1.5×107 cells/mL. M-CENK in 5% human albumin is subsequently mixed with equivalent volume (1:1) of the CryoStor® CS10 in a flask on ice to prepare the formulated drug product. Formulated cells are transferred into CellFreeze® infusion bags (CF-750) on ice to prepare multiple drug product bags and small QC bags. The filled infusion bags are subsequently frozen to equal or lower than −85° C. using a controlled-rate freezer. The frozen drug product is then transferred to vapor phase of LN2 freezer (equal or lower than −120° C.) for long-term storage. QC and Sterility testing is performed on QC bags at thaw. The process flow for the expansion and harvest of M-CENK cells using NANT 001 bioreactor is shown below.
An overview of the M-CENK-DS manufacturing process using NANT 001 Bioreactor is shown in
IL-12/IL-18/N-803 Induced M-CENK
Viability and Viable Cell Density: One measure reflective of M-CENK cell structural integrity is percent viability. Viability is used as a routine in process and final product release measurement and is indicative of product quality. The following experiments describe exemplary tests to ascertain product characteristics and quality.
CD56 Expression: The neural cell adhesion molecule (NCAM1), also known as CD56, is a member of the immunoglobulin superfamily. NK cells are characterized by the expression of CD56 in the absence of CD3. PB-NK-derived M-CENK cells retain the CD56 expression.
IFN-γ Expression: NK cells are cytolytic and cytokine-producing effector cells of the innate immune system. They are a major source of IFN-gamma (IFN-γ) that interferes in tumor activity. A flow cytometry based intracellular cytokine staining assay was used to analyze IFN-γ production. As can be seen from
Phenotype Analysis: (A) DNAM-1: is a cell surface glycoprotein that functions as an adhesion molecule to synergize with activating receptors and trigger NK cell mediated cytotoxicity. DNAM-1+ve NK cells produces higher IFNγ than their DNAM-1-ve counterparts following stimulation with IL-12 and IL-18. DNAM-1 is upregulated on M-CENK cells as observed in the phenotyping assay described below. (B) TIGIT: is a checkpoint receptor that may negatively influence NK cell cytotoxicity activity. M-CENK generation showed no significant change in TIGIT expression. TIGIT expression was analyzed in the phenotyping assay described below. (C) CD25: Natural killer cells express IL-2Rα—chain (p55), identified as CD25 for the formation of the high-affinity IL-2R. CD25 is upregulated on M-CENK cells. (D) CD16: is present on select CD56+ peripheral blood NK cells. Upon recognition of antibody-coated cells it delivers a potent signal to NK cells, which eliminate targets through direct killing and cytokine production.
GSH Cell Vitality: One measure reflective of M-CENK cell health status is the intracellular reducing power available to the cell or percent vitality. Expression of intracellular reduced thiols (glutathione; GSH) can be analyzed by staining the cell line with a specific dye (VitaBright-48™, VB48) which reacts with thiols forming a fluorescent product in combination with Acridine Orange (AO) and Propidium Iodide (PI) to stain nucleated cells and dead cells, respectively. The stained sample is subsequently analyzed by NucleoCounter® NC3000™ imaging cytometer. M-CENK cells from different culture batches expanded in NANT 001 bioreactor displayed characteristics of healthy cells with high vitality (GSH+ve, PI-ve) and were comparable to each other as can be seen from the exemplary results in
Annexin V Cell Health: Another measure reflective of M-CENK cell health is the presence of apoptotic, pre-apoptotic and necrotic cells in culture. Annexin V assay enables detection of translocalisation of phosphatidylserine to the outer cell membrane layer indicating early apoptosis. Quantification of early apoptotic cells can be achieved by staining the cells with an Annexin V-AF488 conjugate along with Hoechst 33342 and PI to stain nucleated cells and dead cells, respectively. The stained sample is subsequently analyzed by NucleoCounter® NC3000™ imaging cytometer. M-CENK cells from different culture batches expanded in NANT 001 bioreactor displayed characteristics of a healthy cells (Annexin negative PI negative) and were comparable to each other, and exemplary results are shown in
M-CENK Cytotoxicity Against MS-1 Cells: An important functional assay used to measure the activity of M-CENK cells is to assess cytotoxicity against the MS-1 target cell line, a cell line that is relatively resistant to general NK cell cytotoxicity. As an example of extended characterization, the graph in
Cytotoxicity of M-CENK Cells Against K562 Cells: Testing for the natural cytotoxicity of M-CENK cells towards the K562 cell line is part of extended characterization of M-CENK cells. The graph in
TxM Induced M-CENK Cells
The TxM used in the studies below was obtained from ImmunityBio, Inc. and is a fusion protein as shown in
The production of CENK from mononuclear cells was described as above, however, in the present process the induction/stimulation of CENK with the cytokine cocktail (human IL-12, IL-18 and N-803) was replaced by induction/stimulation with a TxM as described immediately above. In this context, it should be noted that the TxM used herein had equimolar ratios of IL-15 analog (N-803) to IL-18 to IL12 (single chain) of 1:1:1. Notably, the molar ratio of components in the TxM is substantially distinct from the molar ratio of the cytokine cocktail.
Moreover, it should be noted that the TxM had all three cytokine function associated in close proximity and as such provides contemporaneous activation, whereas induction/stimulation of CENK with a cytokine cocktail (human IL-12, IL-18 and N-803) will allow for spatially and temporally separate activation events. Surprisingly, the TxM allowed for substantially identical, If not even improved formation of M-CENK as compared to use of the cytokine cocktail. In addition, as the TxM is provided as a single protein complex and requires only a single addition to the CENK cells (as opposed to three additions), the risk of contamination is significantly reduced. Furthermore, inconsistencies in potency of individual cytokine preparations (e.g., lot-to-lot variations) can be entirely avoided as the TxM is provided as a single protein complex.
For comparison with the TxM induced cells, N-803 enriched NK cells (CENK, Cytokine-enhanced NK cells) were incubated with cytokine cocktail containing fixed concentrations of N-803 (175 ng/mL), IL-12 (10 ng/mL) and IL-18 (50 ng/mL) or with TxM (9.8 μg/mL) alone. Cells were stimulated for 14-16 hours, which induced a memory like phenotype of the CD56 positive cells (M-CENK) as is shown in more detail below.
Post-harvest, M-CENK cells from both treatment experiments were evaluated in various assay for memory cell characteristics. Cytokine priming is generally required for NK cell proliferation and function. However, cytokines may also lead to a dose dependent death of NK cells. Viability of N-803 expanded NK cells was therefore evaluated before and after TxM stimulation. As can be seen form the Table below, TxM induced M-CENK cells showed high viability that was comparable to the CENK cells (>90%).
M-CENK cells are major IFN-gamma producers. To evaluate if TxM induced M-CENK cells develop IFN-gamma producing capacity, a flow cytometry based staining method was employed. As can be seen from
With respect to cytotoxicity, various experiments were performed to establish that TxM induced M-CENKS cells had significant cytotoxicity against various cell lines.
In one set of experiments, TxM induced M-CENK cell cytotoxicity was tested against MS-1 cell. MS-1 is a skin carcinoma cells with a resistance to general NK cell cytotoxicity. Cytotoxicity of M-CENK cells against MS-1 cell line was measured over a wide range of Effector to Target (E:T) cell ratios in the cytotoxicity assay. Notably, M-CENK but not CENK cells induced significant lysis of MS-1 cells, suggesting that the generated product gained potent cytotoxicity activity against resistant tumor cells. In particular,
M-CENK cells from both treatments were then compared in a cytotoxicity assay. Here, cells produced from either treatment induced potent and comparable cytotoxicity against MS-1 suggesting that the TxM can serve a replacement for the cytokine cocktail.
To evaluate if TxM induced M-CENK cells retain NK cell natural cytotoxic activity, M-CENK cells were mixed with K562 target cells in a calcein-based cytotoxicity assay. Effector and target cells were mixed together at varying ratio. M-CENK produced from either treatment induced potent and comparable cytotoxicity against K562, suggesting that the NK cell natural cytotoxicity was retained in the activation process using TxM.
In a further experiment, M-CENK cell from both treatments (TxM induced and cytokine cocktail induced) were compared for their potential to produce IFN-gamma. Remarkably, M-CENK generated from either treatment induced potent IFN-gamma as observed in the flow cytometry-based assay. In particular,
It is well known that NK cell activating receptors play a key role in triggering the anti-tumor response of NK cells. The inventors therefore investigated whether TxM treatment would influence the expression of one or more NK-specific receptors. Notably, comparable expression of NKG2D, NKp30, NKp44, NKG2A, and NKG2C were observed on cells generated from either treatment as is shown in the exemplary results of
To establish that the TxM-treated CENK cells will indeed differentiate to an M-CENK phenotype, the inventors assayed the treated cells for the presence of specific memory-type associated markers. More specifically, differentiation of CENK to M-CENK is generally accompanied by changes in specific receptors expression including DNAM-1 (DNAX Accessory Molecule-1), CD25, and CD16. To that end, changes in the expression status of these receptors was detected using a flow cytometry-based assay. Once more, M-CENK cells from either treatment showed comparable expression of these receptors.
In view of the above, the experimental results clearly and unexpectedly demonstrate that a TxM fusion protein can serve as a replacement for an IL-12/IL-18/N-803 cocktail for induction of an NK memory phenotype in CENK cells (M-CENK). These cytokines may also serve as a replacement for other NK cell activating cytokines (e.g., IL-21) that often increase cytotoxicity but will cause apoptosis at high concentrations.
M-ceNK Cells Provide Enhanced Cytotoxic Effect
The inventors also discovered that where various NK cells were treated with an N-803 (or a TxM having an IL15 receptor scaffold as presented herein) containing cytokine cocktail, such cells had superior cytotoxicity against a variety of cancer cells, and even against those that had undergone EMT (endothelial to mesenchymal transition). Notably, thusly treated cells exhibited a phenotype that was CD56bright, CD16low, had high NKp44 expression, and low TIGIT expression relative to untreated cells.
The NK cell lysis assay comprised NK Cell Effectors such as ceNK, M-ceNK, Healthy donor NK cells (2 donors), and Healthy donor NK cells pre-treated with N-803 (2 donors). The tumor cells comprised SCLC—H69 & H841, Ovarian—OVCAR3 & SK-OV-3, Breast—MDA-MB-231, NSCLC—H441. NK and tumor cells were co-cultured for 6-hour duration, cell counts collected via Celigo system. E:T ratios of 20:1, 10:1, and 5:1 assessed. The results are shown in
An overview of NK receptors assessed via flow cytometry may be found in Chan. C et al, Cell Death & Differen., 2016, which is incorporated by reference herein in its entirety. CD56/CD16 Profile of NK Cells-CD56/CD16 profile of healthy donor NK cells differs greatly from that of ImmunityBio NK cells, with the latter being highly CD56+, as shown in
Apheresis Material Intermediate Stability in LN2 and Cryopreserved M-CENK Cellular Product Stability are shown in
Fusion Protein Scaffold 18/12/TxM Activates the IL-12, IL-15, and IL-18 Receptors to Induce Human Memory-Like Natural Killer Cells
In one embodiment, Fehniger and colleagues describe the creation of a novel triple-cytokine fusion molecule, 18/12/TxM, containing an IL-15 superagonist backbone (N-803) fused to IL-18 and IL-12. This trimeric molecule retained specific and unique IL-12, IL-15, and IL-18 activities, and generated potent human memory-like natural killer cells in vitro and in vivo. See Cubitt C C, et al, “A novel fusion protein scaffold 18/12/TxM activates the IL-12, IL-15, and IL-18 receptors to induce human memory-like natural killer cells”, Molecular Therapy: Oncolytics (2022), which is incorporated by reference in its entirety.
Natural killer (NK) cells are cytotoxic innate lymphoid cells that are emerging as a cellular immunotherapy for various malignancies. NK cells are particularly dependent on interleukin-15 (IL-15) for their survival, proliferation, and cytotoxic function. NK cells differentiate into memory-like cells with enhanced effector function after a brief activation with IL-12, IL-15, and IL-18. N-803 is an IL-15 superagonist comprised of an IL-15 mutant (IL-15N72D) bound to the sushi domain of IL-15Rα fused to the Fc region of IgG1, which results in physiological transpresentation of IL-15. Here, we describe the engineering of a novel triple-cytokine fusion molecule, 18/12/TxM, using the N-803 scaffold fused to IL-18 via the IL-15N72D domain and linked to a heteromeric single-chain IL-12 p70 by the sushi domain of the IL-15Rα. This molecule displays trispecific cytokine activity through its binding and signaling through the individual cytokine receptors. Compared to activation with the individual cytokines, 18/12/TxM induces similar short-term activation and memory-like differentiation of NK cells on both the transcriptional and protein level, and identical in vitro and in vivo anti-tumor activity. Thus, N-803 can be modified as a functional scaffold for the creation of cytokine immunotherapies with multiple receptor specificities to activate NK cells for adoptive cellular therapy.
Natural killer (NK) cells are cytotoxic innate lymphoid cells that make up approximately 5-20% of circulating blood lymphocytes and are important in the elimination of virally infected and malignantly transformed cells. NK cell function is tightly regulated by a balance of germ-line encoded activating, co-stimulatory, and inhibitory receptors expressed at the cell surface. Through these receptors, NK cells are able to recognize and spontaneously kill cells through the loss of self-identifying molecules such as major histocompatibility complex (MHC) class I that bind to inhibitory receptors on NK cells (detection of ‘missing self’) or by upregulating ligands recognized by activating receptors on NK cells that can overcome inhibitory signals. Human NK cells are identified by surface expression of CD56 and the absence of CD3 and can be categorized based on relative CD56 expression into the distinct CD56bright and CD56dim subsets, where CD56dim NK cells typically express the FcγRIII (CD16), while CD56bright NK cells have low or no expression.
NK cells constitutively express a number of cytokine receptors, and are particularly dependent on IL-15 for development, homeostasis, and function. IL-15 signaling has been shown to promote the survival, proliferation, and priming (at higher doses) of CD56bright NK cells, and to enhance the cytotoxicity of the CD56dim subset. There are three receptor subunits for IL-15 receptor forms: IL-15Rα (CD25), IL-15Rβ (CD122), and IL-15R (CD132). The signaling components of the IL-15 receptor are not private, with its β subunit shared with IL-2 and its γ subunit (common γ chain) with IL-2, IL-4, IL-7, IL-9, and IL-21. Physiologically, IL-15 mediates its effects through trans-presentation, whereby the high affinity IL-15Rα is expressed on the surface of accessory cells (such as dendritic cells and monocytes/macrophages) that present IL-15 to NK cells bearing the IL-15Rβγc. In addition to the effects mediated by IL-15, the cytokines IL-12 and IL-18 are also important for NK cell survival and function. The primary effect of IL-12 on NK cells occurs via STAT4-mediated signaling and include interferon-γ (IFN-γ) and tumor necrosis factor (TNF) production. IL-18 transduces signals that lead to MAPK and NF-kB activation and has been described to function synergistically with IL-12 and IL-15, while also priming NK cells for IFN-γ production. Indeed, paradigm-shifting studies have demonstrated that combined activation with IL-12, IL-15, and IL-18 induces a memory-like NK cells defined by enhanced proliferation, expression of the high-affinity IL-2 receptor αβγ (IL-2Rαβγ) and increased IFN-γ production after restimulation with cytokines, tumors, or via activating receptors. These cytokine-induced memory-like (ML) NK cells represent a promising NK cell therapy and have shown encouraging results in first-in-human clinical trials for relapsed/refractory AML patients.
N-803 is an IL-15 superagonist comprised of an IL-15 mutant (IL-15N72D) bound to the N-terminal structural (sushi) domain of IL-15Rα fused to the Fc region of IgG1. This results in accessory cell-independent trans-presentation of IL-15, prolonged in vivo pharmacokinetics, increased in vivo biological activity, and increased effector functions compared to IL-15. Given the potent functional effects induced by the combined stimulation of IL-12, IL-15, and IL-18, we hypothesized that the construction of a single molecule that could signal through all three cytokine pathways would be beneficial for generating memory-like NK cells for both research and clinical applications. As such, we constructed a fusion protein, 18/12/TxM, employing N-803 as a scaffold, linking IL-18 to the IL-15N72D domain and a heteromeric single-chain IL-12 p70 to the sushi domain of IL-15Rα, which is already linked to the Fc domain of human IgG1. This non-covalently associated, heterodimeric homodimer, triple-cytokine fusion protein retained specific and unique IL-18, IL-12, and IL-15 activities in vitro and in vivo.
The stability of the N-803 structure provides a biochemical strategy to decorate the ‘backbone’ with additional components, while maintaining IL-15 based signals. Here we investigated the ability of the novel 18/12/TxM fusion protein to generate memory-like NK cells, compared to the combination of individual recombinant human IL-12, IL-15, and IL-18. This included in vitro examination of individual activity of each cytokine receptor signaling, short term effector function, and ability to generate memory-like NK cells.
The Fusion 18/12/TxM Superkine Induces Signaling Via all Targeted Cytokine Receptors
We first sought to construct a fusion protein consisting of human IL-18, IL-12, and IL-15 to replace individual use of the recombinant cytokines. To this end, N-803 (an IL-15 superagonist formerly known as ALT-803) was linked to IL-18 via the IL-15N72D domain and linked to heteromeric single-chain IL-12 p70 by the sushi domain of the IL-15Rα connected to the Fc domain of human IgG1 (
Short Term Activation with 18/12/TxM Superkine Results in NK Cell Activation
Short-term activation of human NK cells with IL-12, IL-15, and IL-18 leads to increased expression of the IL-2 receptor α (IL-2Rα, CD25) and enhanced production of IFN-γ. To evaluate the optimal concentration for 18/12/TxM activation, purified human NK cells were activated for 16 hours with increasing concentrations of 18/12/TxM or IL12/15/18. Induction of an activated phenotype was assessed as increased cell surface CD25 expression and intracellular IFN-γ, as compared to control, resting NK cells, as determined by flow cytometry (
Activation with 18/12/TxM Superkine Stimulates NK Cell Proliferation
Previous studies have demonstrated that activation with IL-12, IL-15, and IL-18 leads to a memory-like phenotype that includes robust proliferation and expansion of NK cells. To address the ability of 18/12/TxM to induce proliferation, purified human NK cells were labeled with Carboxyfluorescein succinimidyl ester (CF SE), activated for 16 hours with 18/12/TxM (38.8 nM), IL12/15/18, or low-dose IL-15 (LD IL15). After activation, NK cells (including both CD56dim and CD56bright subsets) were washed and rested in LD IL15 for 6 days. In agreement with previous data, activation with IL-12/15/18 or 18/12/TxM induced robust proliferation, as compared to those activated with low-dose IL-15 (
Multidimensional Phenotypic Changes are Similar Between IL12/15/18 and 18/12/TxM Induced Memory-Like NK Cells
Memory-like NK cells undergo dramatic changes in a large number of cell surface and intracellular markers both immediately after activation with IL12/15/18 and 6 days after differentiation. A custom mass cytometry panel was previously developed including markers for NK cells lineage, maturation, and functional capacity (
18/12/TxM Induces Functional Memory-Like NK Cells In Vitro
Previous studies have shown that ML NK cells can be induced ex vivo following overnight stimulation of purified NK cells with saturating amounts of IL12/15/18. These cells exhibit ML properties such as 1) enhanced proliferation, 2) expression of IL-2Rα, 3) increased IFN-γ production, and 4) augmented cytotoxicity mediated by perforin and granzymes. To demonstrate generation of ML NK cells by 18/12/TxM, primary human NK cells were activated with 18/12/TxM (38.8 nM), IL12/15/18 or LD IL15 for 16 hours, washed, and supported in low-dose IL-15 for 6 days to allow memory-like differentiation (
18/12/TxM Activation Induces a Molecular Program Similar to IL-12, IL-15, and IL-18
To complement the phenotypic and functional similarities induced by 18/12/TxM and IL12/15/18, we performed bulk RNA sequencing. Purified NK cells from three different donors were isolated, and RNA was isolated before (baseline), after overnight activation (D1), and six days supported by IL-15 (D6) after activation with either 18/12/TxM, IL12/15/18, or IL-15. Analysis of transcript counts revealed a similar gene expression profile on D1 after activation between IL12/15/18 and 18/12/TxM activated NK cells, when contrasted to LD IL-15. Analysis of the genes that were significantly differentially expressed (p<0.05) on D1 following IL12/15/18 or 18/12/TxM stimulation demonstrated that the vast majority (5,812 genes) of changes were shared after either treatment, with 808 unique genes expressed in the TxM condition, and 332 unique genes following IL12/15/18 treatment (
18/12/TxM Induces Memory-Like NK Cell Anti-Tumor Activity In Vivo
To confirm that the molecular and phenotypic changes induced in vitro by 18/12/TxM would also translate to enhanced in vivo functionality, we compared the anti-tumor activity in NOD-SCID-IL2Rg−/− (NSG) mice engrafted with leukemia. Briefly, NSG mice were engrafted with luciferase-expressing K562 tumor cells (0.5×106 cells/mouse) and injected 4 days later with NK cells (3-5×106 cells/mouse) that had been pre-activated with 18/12/TxM, IL-2/15/18, or LD IL-15 (
The novel fusion protein 18/12/TxM was constructed using N-803 as a scaffold, linking IL-18 to the IL-15N72D domain and linking heteromeric single-chain IL-12 p70 to the sushi domain of IL-15Rα, which is already linked to the Fc domain of human IgG1. This non-covalently associated, heterodimeric homodimer, triple-cytokine fusion protein retained specific and unique IL-18, IL-12, and IL-15 activities in vitro, as measured by activation, proliferation, and signaling through cognate receptors. Furthermore, 18/12/TxM exhibited functions equivalent to the combination of the individual cytokines when used at the appropriate concentration on primary NK cells ex vivo after overnight stimulation and after 6 days of in vitro differentiation into memory-like NK cells and in vivo in NSG mice. The ability of 18/12/TxM to induce this memory-like phenotype was confirmed at the protein and transcriptional level using high-dimensional methods including mass cytometry phenotyping and bulk RNA-sequencing. These phenotypic changes translated to equivalent cytotoxic effector functions in vitro and similar tumor control in vivo. Thus, 18/12/TxM is an alternative to IL-12, IL-15 and IL-18 for the generation of memory-like NK cells.
Interestingly, activation with 18/12/TxM resulted in greater levels of proliferation in purified NK cells than the individual cytokines combined. This finding suggests that there may be distinct biological outcomes resulting from simultaneous engagement of the IL-12, IL-15, and IL-18 receptors on the same cell rather than sequential activation of the receptors on the same or different cells. Another possibility is that the spatial linking of the cytokines on the scaffold that results in enhanced membrane clustering of cytokine receptors and signaling molecules as a result of binding from the trimeric molecule. It may also be possible that the Fc portion of 18/12/TxM is activating NK cells via downstream signaling events following engagement with the FcγRIII receptor (CD16). However, given the observation that the increased proliferation occurred in both CD56dim (CD16+) and CD56bright (CD16−) NK cells, it may also be possible that Fc-FcR interactions allow CD16+ NK cells to readily trans-present the 18/12/TxM to nearby NK cells. Further investigation using an FcR null variant of the 18/12/TxM would be required to clarify this potential contribution.
Minimal differences in gene expression were observed between LD IL15 and IL12/15/18-activated NK cells at Day 6. This is consistent with previous observations that only some NK cells are able to fully undergo memory-like differentiation, therefore making it difficult to identify their gene signatures with bulk RNA-sequencing methods and following extensive IL-15-supported culture in vitro. Further studies using more in-depth sequencing methods such as single-cell RNA-sequencing will be essential for characterizing the unique transcriptional changes in memory-like differentiated NK cells. It is also possible that memory-like differentiation is orchestrated predominantly by epigenetic changes, which can be clarified with methods such as ATAC-seq.
IL-15 has been used as an ideal candidate for clinical immunotherapy combinations due to its ability to stimulate NK cell (and CD8+ T cell) activation. However, physiological activation with IL-15 requires binding to the IL-15Rα-chain prior to activating target cells, which limits the research and clinical roles of free IL-15. N-803, consists of human IgG1 Fc fused to two IL-15Rα subunits bound to an IL-15 superagonist (N72D mutation that enhances biological activity), resulting in higher biological activity and longer serum half-life compared with free IL-15. Previous studies have demonstrated that preactivation of NK cells with IL12/15/18 results in ML NK cell differentiation that represents a promising approach to enhancing adoptive allogenic NK cell therapy. However, the use of these individual cytokines alone or in combination for research and clinical purposes can be subject to production issues and lot variability. Additionally, this superkine presents a promising platform for exchanging out different NK cell activating cytokines (IL-2, IL-21) or tumor targeting molecules (e.g., CD20, EGFR, HER2 or CD34) to direct activated NK cells to kill tumor cells. Indeed, N-803 has been used as a functional scaffold fused with CD20 targeting antibody components and demonstrated superior anti-tumor activity than the individual components alone. Other studies have demonstrated enhanced anti-tumor activity when N-803 is used in combination with either tumor targeting or checkpoint inhibitory antibodies, which represents a promising avenue for the development of additional fusion proteins.
In this disclosure, it is demonstrated that the fusion of three distinct cytokines via a human IgG1Fc connection induced equivalent activity to the individual cytokines combined, in vitro and in vivo. While these studies used 18/12/TxM to pre-activate NK cells in vitro before infusion, the Fc backbone confers additional in vivo half-life that could support its use in vivo in other contexts. Additionally, the use of the N-803 protein scaffold linked to three distinct cytokine targets represents a novel method to expand and stimulate NK cells for adoptive cell therapy.
Materials and Methods
Recombinant Proteins: hIL18/IL12/TxM protein, lot #305-86(1) and N-803 protein, lot #01062016 were manufactured and purified at Altor BioScience, Miramar, FL. Endotoxin-free, recombinant human (rh)IL-12 (Biolegend), IL-15 (Miltenyi), IL-18 (InVivoGen) and IL-2 (R&D Systems, Minneapolis, MN) were used in these studies.
Flow cytometry antibodies: The following Beckman Coulter antibodies were used: CD3 (clone UCHT1, CD45 (clone A96416), CD56 (clone N901), NKG2A (clone Z199.1), NKp46 (clone BAB281). The following BD antibodies were used: CD16 (clone 3G8), IFN-□(clone B27), CD107a (clone H4A3), CD57 (NK-1) CD69 (FN50), CD137 (clone 4-1BB), Perforin (clone dG9), Ki67 (clone B56), ERK1/2 (pT202, pY204), AKT (pS473), STAT4 (38/p-Stat4), STAT5 (47/Stat5, pY694), p38 (pT290/pY182), p65 (pS529). The following Biolegend antibodies were used: NKG2D (clone 1D11), NKp30 (clone P30-15). NKp44 (clone P44-8), IgG1 control (clone MG1-45). The following eBioscience antibodies were used: Granzyme B (GB12), TNF (clone Mal) 11).
Cell lines: K562 cells (ATCC, CCL-243) were obtained from ATCC in 2008, viably cryopreserved, thawed for use in these studies, and maintained for no more than 2 months at a time in continuous culture as described. Prior to our studies, the K562 cells were authenticated by confirming cell growth morphology (lymphoblast), growth characteristics, and functionally as NK-cell—sensitive targets in 2014 and 2015. Cells were cultured in RPMI1640 supplemented with L-glutamine, HEPES, NEAA, sodium pyruvate, and Pen/Strep/Glutamine containing 10% FBS (Hyclone/GE Healthcare, Logan, UT).
HEK-BlueIL-18 cells (Interleukin-18 sensor cells) and HEK-Blue IL-12 cells (Interleukin-12 sensor cells) from Invivogen (San Diego, CA) were cultured in complete HEK-Blue media (I10 media) consisting of IMDM, 10% FBS (HyClone/GE Healthcare, Logan, UT); 1× penicillin-streptomycin-glutamine (Thermo Fisher Scientific, Dallas, TX); 100 ug/ml normacin, and 1X HEK-Blue selection (InvivoGen, San Diego, CA). 32D-IL2/15Rβ (32D13) cells were constructed at Altor BioScience (Miramar, FL), cultured in complete 32Dβ media containing IMDM-10 media plus 25 ng/ml rh IL-2, and maintained at a cell density between 1.5×104-2×106 cells/ml at 37° C. and 5% CO2.
NK-cell purification and cell culture: Human platelet apheresis donor PBMCs were obtained by ficoll centrifugation. NK cells were purified using RosetteSep (StemCell Technologies, ≥95% CD56+CD3−) and used for selected experiments. Cells were plated at 3-5×106 cells/mL and preactivated for 16 hours using 38.8 nM 18/12/TxM (9.5 ug/mL), rhIL-12 (10 ng/mL)+rhIL-18 (50 ng/mL)+rhIL-15 (50 ng/mL) or control conditions (rhIL-15, 1 ng/mL). Cells were washed 3 times to remove cytokines, and cultured for 6 days in HAB10 complete media containing RPMI 1640 medium+10% human AB serum (Sigma-Aldrich, St. Louis, MO) supplemented with rhIL-15 (1 ng/mL) to support survival, with 50% of the medium being replaced every 2-3 days with fresh rhIL-15.
Assessment of IL-18 and IL12 activity: HEK-Blue IL-18 and HEK-Blue IL-12 cells were maintained in complete HEK-Blue Media at 37° C. and 5% CO2. HEK-Blue Selection was added to the growth media after two passages, as per the manufacturers' cell handling recommendations. Growth media was renewed twice a week and cells were passaged when 70-80% confluency was reached. To measure activity of IL-18 or IL12, the respective sensor cells were detached in PBS and resuspended in Complete HEK-Blue assay media at 280,000 cells/ml. Twenty microliters of half-log serially diluted cytokine control and hIL18/IL12/TxM (in the concentration range described below) was added to a flat bottom 96 well plate, followed by addition of 180 uL of cells, for a final cell count of ˜50,000 cells in 200 uL. The plates were incubated for ˜20 hours at 37° C. and 5% CO2. To assess the activity of IL-18 or IL-12, the resulting secreted alkaline phosphatase was quantified using QUANTI-Blue detection reagent (Invivogen, San Diego, CA). QUANTI-Blue reagent was prepared as per the manufacturers' instructions. After warming QUANTI-Blue to room temperature, 180 uL was added to 20 uL of culture supernatant in a 96 well flat bottom plate and incubated for 18 hours at 37° C. and 5% CO2. Absorbance was then measured at 650 nm to determine cell activation based on reduction of QUANTI-Blue by secreted alkaline phosphatase. The EC50 of IL-18 or IL-12 bioactivity of 18/12/TxM was determined from the dose response curve generated using non-linear regression variable slope curve fitting with GraphPad Prism 7.
Concentration Range: For detection of IL-18 activity, half-log serial dilution ranging from 10 ng/ml (556 pM) to 0.05 pg/ml (0.0028 pM) for IL-18 and 3350 ng/ml (13673 pM) to 0.0167 ng/ml (0.0683 pM) for 18/12/TxM was performed. This corresponds to final pM concentrations of 56 pM to 0.00028 pM for the IL-18 cytokine and 1367 pM to 0.00683 pM for 18/12/TxM. For detection of IL-12 activity, half-log serial dilutions ranging from 1000 ng/ml (17483 pM) to 5 pg/ml (0.0875 pM) for IL-12 and 85.7 ug/ml (349,796 pM) to 0.428 ng/ml (1.748 pM) for 18/12/TxM was performed. This corresponds to final pM concentrations of 1748.3 to 0.00875 pM for IL-12 cytokine and 34,979.6 to 0.1748 pM for 18/12/TxM molecule.
Assessment of IL-15 activity: To measure IL-15 activity, the assay plate was prepared as follows: 100 uL of IMDM-10 media was added to each well in a 96 well, flat bottom plate. Next 100 uL of 4× concentration of N-803 (225 ng/ml; ˜2400 pM) or IL18/IL12/TxM (18,000 ng/ml; ˜73468 pM) was added to column 1. The drugs were 2-fold serially diluted to column 10, leaving 100 uL in each well. The cells were washed 3× with IMDM-10 media, resuspended at a density 1×105 cell/ml in IMDM-10 media, and 100 uL of the cells was added to the assay plate from column 1 to 11, for a total assay volume of 200 uL. One hundred uL of IMDM-10 was added to column 12. The assay plate was placed at 37° C. and 5% CO2 for ˜72 hours. To assess the activity of IL-15, 20 uL of 10× PrestoBlue Cell Viability Reagent was added directly to the assay plate after ˜72 hours, and the plate is placed at 37° C. and 5% CO2 for an additional ˜4 hours. Absorbance was measured at 570 nm and at 600 nM for normalization. Using column 11 (cells with no drug) as a negative control, the EC50 of IL-15 bioactivity of hIL18/IL12/TxM was determined from the dose response curve generated using non-linear regression variable slope curve fitting with GraphPad Prism 7.
Phosphorylation assays: Freshly isolated human NK cells were incubated in HAB10 media without cytokines at 37° C. for 30 min. Individual cytokines (IL-12, IL-15, or IL-18) were added to wells at the indicated concentration for varying time intervals (2-hour stimulation for STAT4, 1 hour stimulation for Akt and ERK, and 15 minute stimulation for NF-□3-P65, STAT5, and P38 detection). After incubation, cells were fixed with 4% paraformaldehyde (PFA) and incubated at room temperature for 10 minutes. The cells were then pelleted and resuspended in cold 100% methanol and incubated and 4° C. for 30 minutes. Cells were washed 3 times with FACs buffer (PBS, 0.5% BSA, 2 mM EDTA). After washing, cells were suspended in surface antibody master mix (CD3, CD16, CD56, CD45) as well as the appropriate phosphoflow antibodies and stained overnight at 4° C. The next morning, cells were washed twice, and samples were acquired on a BeckmanCoulter Gallios flow cytometer and analyzed using FlowJo Version 9.3.2 (TreeStar) software.
Functional assays to assess cytokine production: Control and memory-like NK cells were harvested after a rest period of 6 days to allow memory-like NK cell differentiation to occur. Cells were then restimulated in a standard functional assay. Briefly, cells were incubated for 6 hours with K562 leukemia targets at an effector to target (E:T) ratio of 5:1 unless otherwise noted, in presence of CD107a. After 1 hour of stimulation, Brefeldin A and Monensin (GolgiStop/GolgiPlug, BD) were added, and 5 hours later the cells were stained for CD45, CD3, CD56, CD25. Cells were fixed (Cytofix/Cytoperm, BD) and permeabilized (Perm/Wash, BD) before the staining of intracellular IFN-□ and TNF. Cells were acquired on a Gallios 3 flow cytometer and analyzed using FlowJo Version 9.3.2 (TreeStar) software.
Assessment of Specific Killing: On D6 or D7 post-activation, control or ML-NK cells were re-suspended in 1 ng/mL IL-15 and challenged with K562 targets at various E:T ratios, in a standard four-hour 51Chromium release assay. 51Cr release was detected on a Wallac Microbeta Tri-lux Scintillation Counter. The percent specific lysis was calculated by: [(cpmexp−cpmspontaneous)/cpmmax−cpmspontaneous)]*100.
Flow cytometric analysis: Cell staining was performed as described previously, and data were acquired on a Gallios flow cytometer (Beckman Coulter, Indianapolis, IN) and analyzed using Kaluza Version 1.2 (Beckman Coulter) or FlowJo Version 9.3.2 (TreeStar) software. Statistical analysis were done using GraphPad Version 7.0 software.
RNA-sequencing: One million purified NK cells were frozen in Trizol at −80° C. until RNA isolation using the Direct-zol RNA MicroPrep kit (Zymo Research). NextGen RNA sequencing was performed using an Illumina Hi Seq 2500 sequencer. RNASeq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount version 1.4.5. Analysis of sequencing data was performed using Phantasus, a browser-based gene expression analysis software. Differential expression analysis was performed using the LIMMA package to analyze for differences between conditions and the results were filtered for only those genes with false-discovery rate adjusted p values less than or equal to 0.05.
Mass cytometry: All mass cytometry data were collected on a CyTOF2 mass cytometer (Fluidigm) and analyzed using Cytobank. Mass cytometry data were analyzed using previously described methods, and sample staining and data collection was performed as previously described.
NSG xenograft model and BLI imaging: K562-expressing luciferase tumor cells (1×106) were injected intravenously (i.v.) via tail vein into 8-12-week-old male and female NOD-SCID-IL2Rγ−/− (NSG) mice (The Jackson Laboratory, Bar Harbor, ME) on day 0. All mice were irradiated with 2.5 cGy 2 days before tumor injection. At day 3, BLI was performed to confirm leukemia cells engraftment. On Day 4, 5×106 control (NK cells in 1 ng/mL IL-15) or NK cells activated with IL-12/15/18 (10 ng/mL IL-12, 50 ng/mL IL-15, 50 ng/mL IL-18), or 18/12/TxM (38 nM) were administered retro-orbitally to the mice (total 9-10 mice per group from 2 independent experiments). The mice were treated with rhIL-2 (50,000 IU per mouse) every other data and monitored weekly for tumor burden (BLI).
In vivo BLI imaging was performed on an IVIS 50, (1-60 sec exposure, bin8, FOV12 cm, open filter) (Xenogen, Alameda, CA). For this, mice were injected intraperitoneally with D-luciferin (150 mg/kg in PBS, Gold Biotechnology, St. Louis, MO) and imaged under anesthesia with isoflourane (2% vaporized in O2). Total photon flux (photons/sec) was measured from fixed regions of interest over the entire mouse using the Living Image 2.6 software program.
In some embodiments, the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term “about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. The recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein.
As used herein, the term “administering” a pharmaceutical composition or drug refers to both direct and indirect administration of the pharmaceutical composition or drug, wherein direct administration of the pharmaceutical composition or drug is typically performed by a health care professional (e.g., physician, nurse, etc.), and wherein indirect administration includes a step of providing or making available the pharmaceutical composition or drug to the health care professional for direct administration (e.g., via injection, infusion, oral delivery, topical delivery, etc.). It should further be noted that the terms “prognosing” or “predicting” a condition, a susceptibility for development of a disease, or a response to an intended treatment is meant to cover the act of predicting or the prediction (but not treatment or diagnosis of) the condition, susceptibility and/or response, including the rate of progression, improvement, and/or duration of the condition in a subject.
All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided with respect to certain embodiments herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.
As used in the description herein and throughout the claims that follow, the meaning of “a,” “an,” and “the” includes plural reference unless the context clearly dictates otherwise. Also, as used in the description herein, the meaning of “in” includes “in” and “on” unless the context clearly dictates otherwise. As also used herein, and unless the context dictates otherwise, the term “coupled to” is intended to include both direct coupling (in which two elements that are coupled to each other contact each other) and indirect coupling (in which at least one additional element is located between the two elements). Therefore, the terms “coupled to” and “coupled with” are used synonymously.
It should be apparent to those skilled in the art that many more modifications besides those already described are possible without departing from the inventive concepts herein. The inventive subject matter, therefore, is not to be restricted except in the scope of the appended claims. Moreover, in interpreting both the specification and the claims, all terms should be interpreted in the broadest possible manner consistent with the context. In particular, the terms “comprises” and “comprising” should be interpreted as referring to elements, components, or steps in a non-exclusive manner, indicating that the referenced elements, components, or steps may be present, or utilized, or combined with other elements, components, or steps that are not expressly referenced. Where the specification or claims refer to at least one of something selected from the group consisting of A, B, C . . . and N, the text should be interpreted as requiring only one element from the group, not A plus N, or B plus N, etc.
This application claims priority to our co-pending US provisional applications with the serial numbers 63/156,269, filed Mar. 3, 2021, and Ser. No. 63/217,097, filed Jun. 30, 2021, each of which is incorporated by reference herein in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US22/18290 | 3/1/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63217097 | Jun 2021 | US | |
| 63156269 | Mar 2021 | US |
