Recombinant CD1-Restricted T Cells And Methods

Abstract

T cells are transfected with a recombinant RNA molecule that encodes at least one of an alpha chain and a beta chain of a CD1b restricted T cell receptor. Preferably, the so prepared T cells are used as a cell-based therapeutic composition to treat tuberculosis.

Claims

1-38. (canceled)

39. A method of preparing primary T cells for use in the treatment of Mycobacterium tuberculosis-infected individuals, the method comprising: a. Obtaining primary T-cells; b. Stimulating the T-cells ex-vivo, wherein the T-cells are grown in a medium containing anti-CD3 and anti-CD28 antibodies or binding domains thereof, c. Transfecting stimulated T-cells with a recombinant RNA comprising alpha and beta chains of a CD1b restricted T cell receptor (TCR), wherein CD1b restricted TCR are expressed.

40. The method of claim 39, wherein the CD1b restricted T cell receptor is a clone 18 CD1b restricted T cell receptor.

41. The method of claim 39, wherein the recombinant RNA is a bi- or polycistronic RNA and includes at least one IRES sequence.

42. The method of claim 39, wherein the CD1b restricted T cell receptor comprises at least one of the sequences shown in Tables 1 and 2.

43. The method of claim 39, wherein the T cell is a primary T cell.

44. The method of claim 43, wherein the T cell is an autologous T cell.

45. The method of claim 39, wherein the recombinant RNA is at least temporarily coupled to a polymer particle, and wherein the polymer particle is optionally degradable within the T cell.

46. The method of claim 45, wherein the polymer particle lacks targeting moieties that specifically target the particle to a component of the T cell.

47. The method of claim 45, wherein the polymer of the polymer particle is a poly (β-amino ester) or a chitosan.

48. The method of claim 45, wherein the recombinant RNA is at least temporarily coupled to a polymer particle, and wherein the polymer particle is further coupled to a second mRNA that encodes an enzyme capable of degrading the polymer of the polymeric particle.

49. The method of claim 48, wherein the polymer of the polymer particle is a chitosan and wherein the enzyme is a chitosanase.

50. The method of claim 39, wherein the anti-CD3 antibody or binding domain thereof, and anti-CD28 antibody or binding domain thereof comprise modified beads.

51. The method of claim 39, wherein the transfection is performed such that at least 20% of all cells expressing the CD1b restricted T cell receptor are viable cells.

52. The method of claim 39, wherein the transfection is performed such that at least 40% of all cells expressing the CD1b restricted T cell receptor are viable cells.

53. The method of claim 39, wherein the transfection is performed such that at least 60% of all cells expressing the CD1b restricted T cell receptor are viable cells.

54. A method of treating an individual diagnosed with tuberculosis, comprising administering to the individual a plurality of genetically modified T cells according to claim 1 in an amount effective to treat tuberculosis.

55. The method of claim 54, wherein at least 10.sup.7 genetically modified T cells are administered.

56. A pharmaceutical composition, comprising: primary T-cells grown in a medium containing anti-CD3 and anti-CD28 antibodies or binding domains thereof, and subsequently transfected with one or more nucleic acids encoding the alpha chain and the beta chain of a CD1b restricted T cell receptor (TCR), wherein the primary T-cells express the CD1b restricted TCR; and and a liquid carrier suitable for injection of a plurality of genetically modified T cells.

57. The pharmaceutical composition of claim 56, wherein the composition comprises at least 10.sup.7 T-cells per transfusion unit.

58. The pharmaceutical composition of claim 56, wherein the liquid carrier has a pH of at least 7.0.

Description

BRIEF DESCRIPTION OF THE DRAWING

[0020] FIG. 1 is a graph depicting exemplary results for T cell transfections of stimulated and non-stimulated T cells using targeting and non-targeting PBAE nanoparticles.

[0021] FIG. 2 is a graph depicting exemplary results for T cell transfections of stimulated T cells using targeting and non-targeting PBAE nanoparticles.

[0022] FIG. 3 is a graph depicting exemplary results for T cell transfections of stimulated and non-stimulated primary T cells using targeting and non-targeting PBAE nanoparticles.

[0023] FIG. 4 is a graph depicting exemplary results for T cell stimulation using CD3-CD28 beads.

[0024] FIG. 5 is a graph depicting exemplary results for GFP expression in stimulated and non-stimulated primary T cells using targeting and non-targeting PBAE nanoparticles.

[0025] FIG. 6 is a graph depicting exemplary results for viability and GFP expression of stimulated and non-stimulated primary T cells using targeting and non-targeting PBAE nanoparticles.

[0026] FIG. 7 is an exemplary schematic of chitosan/chitosanase nanoparticle transfections.

[0027] FIG. 8 is one graph depicting exemplary results for viability and GFP expression in HEK293T cells using chitosan nanoparticles and various media.

[0028] FIG. 9 is another graph depicting exemplary results for viability and GFP expression in HEK293T cells using chitosan nanoparticles and various media.

[0029] FIG. 10 is a further graph depicting exemplary results for viability and GFP expression in HEK293T cells using chitosan nanoparticles and various media.

[0030] FIG. 11 is an exemplary vector map for generation of chitosanase mRNA.

[0031] FIG. 12 is a further graph depicting exemplary results for viability and GFP expression in HEK293T cells using various nanoparticles and media conditions.

[0032] FIG. 13 is yet another graph depicting exemplary results for viability and GFP expression in HEK293T cells using various nanoparticles and media conditions.

[0033] FIG. 14 depicts exemplary nucleic acid and protein sequences for a TCR 18 alpha chain.

[0034] FIG. 15 depicts exemplary nucleic acid and protein sequences for a TCR 18 beta chain.

DETAILED DESCRIPTION

[0035] The inventors have now discovered that expression of a functional CD1b restricted T cell receptor in T cells, and especially human primary T cells, can be used to generate a cell-based therapeutic for the treatment of tuberculosis. Notably, using various protocols as described in more detail below, T cells (particularly primary T cells or autologous T cells) can be transfected at relatively high rate and viability.

[0036] Most typically, but not necessarily, T cells for transfection are obtained from a patient that is acutely infected with Mycobacterium tuberculosis. T cells are in most cases isolated from whole blood following protocols using magnetic bead separation (e.g., coated with antibodies against CD2 and/or CD3), and such isolated T cells can be further cultivated to expand the cell population. Transfection is preferably performed using particle associated mRNA that encodes both the a and p chains of a CD1b restricted T cell receptor (TCR) with high specificity to mycolic acid. For example an especially suitable TCR is clone 18 (e.g., Nature Communications 2016, DOI: 10.1038/ncomms13257) T cell receptor. Upon transfection with the RNA, the T cells are further cultured (and optionally further stimulated) and then administered to the same patient.

[0037] Of course, it should be appreciated that the particular nature of the infection of the patient with Mycobacterium tuberculosis is not limiting to the inventive subject matter, and all forms of infection, including pulmonary tuberculosis (e.g., latent/dormant, acute, and chronic) as well as extrapulmonary tuberculosis (e.g., pleural infection, meningeal infection, genitourinary infection, and infection of the lymphatic system) are expressly contemplated herein. Moreover, it should be noted that the patient need not be a human, but indeed may be any mammal that is subject to infection with Mycobacterium tuberculosis.

[0038] Additionally, it is contemplated that the CD1b receptor need not necessarily be limited to binding of mycolic acid, but that all other ligands (and especially microbial lipids) for CD1b presentation are also deemed suitable. For example, suitable sequence variations and changes in specificity are described elsewhere (e.g., Nature Communications 2017, DOI: 10.1038/ncomms 13257). Therefore, numerous other microorganisms can also be targeted with the recombinant T cells as described herein. Likewise, it should be appreciated that numerous CD1 restricted TCR other than CD1b can be expressed in the T cells as noted herein, and especially contemplated subtypes include CD1a, CD1c, CD1 d, and CD1e. Therefore, it should be noted that all restricted TCRs can be expressed in the T cells in a manner as described herein to so add/expand the pool of ‘innate immunity’ in a patient.

[0039] In especially preferred examples, the recombinant TCR will have or include a sequence portion of the clone 18 CD1b restricted T cell receptor. Where the TCR will only include a portion of that sequence, any one or more of the Vα, Jα, Cα segments, and/or CDR1 and 2 in Vα and/or CDR3 for alpha chain are deemed suitable for use herein. Likewise, any one or more of the Vβ, Jβ, Dβ, Cβ segments, and/or CDR1 and 2 in Vβ and/or CDR3 for beta chain are deemed suitable for use herein. For example, particularly preferred sequences include those shown in FIGS. 14 and 15 (depicting SEQ ID Nos:1-4), or any portion thereof. Therefore, recombinant nucleic acids encoding the CD1b restricted TCR may include the alpha and/or beta chain of the clone 18 TCR, or have portions modified to adapt to specific lipid antigens (see e.g., Nature Communications 2017, DOI: 10.1038/ncomms 13257; or Nat Immunol. 2013 July; 14(7): 706-713).

[0040] Furthermore, it should be noted that the nature of the T cells may also vary considerably, and suitable T cells for transfection include autologous (with respect to the patient) T cells, primary T cells, cultivated T cells, T cells from T cell culture (which will typically be irradiated before administration), CD4+ T cells, CD8+ T cells, and T cells with tissue compatibility to a recipient. Therefore, the manner of T cell isolation may vary considerably and suitable isolation protocols will include isolations via magnetic beads or FACS using antibodies against CD23, CD3, CD4, and/or CD25. Further known protocols are described elsewhere (see e.g., J Vis Exp. 2010; (40): 2017).

[0041] In less preferred aspects, it is also contemplated that the host cells are cells other than T cells, and especially preferred alternative cells include various cytotoxic immune competent cells such as NK cells or iNK cells. However, in such case, these cells will require further genetic modification (via transfection of other genetic engineering) to enable co-expression of one or more of the CD3 gamma, delta, epsilon, and zeta chain.

[0042] Regardless of the particular type of cell for transfection, it is typically preferred that the recombinant nucleic acid is an RNA, preferably constructed as a bicistronic or polycistronic RNA that includes one or more IRES sequences for coordinated expression of the alpha and beta chain. However, monocistronic RNA is also deemed suitable, albeit less preferred. Also less preferred transfections include those with DNA (whether as gene edited modification, or as extrachromosomal). Still further contemplated transfection nucleic acids include viral vectors.

[0043] Preferably, transfection of the T cells is performed on stimulated (e.g., using CD3/CD28 dynabeads) T cells using one or more types of nanoparticles that are coupled to one or more RNA molecules. In particularly preferred aspects, the nanoparticles are degradable within the T cells, typically in an enzymatic manner. For example, especially preferred polymers of the nanoparticles are poly(β-amino esters) (see e.g., Methods Mol Biol. 2009; 480: 53-63) and chitosan (see e.g., Mol. Pharmaceutics 2017, 14, 2422-2436; or International Journal of Nanomedicine 2010:5 473-481). As will be readily appreciated, these nanoparticles can be targeted (e.g., with antibodies or fragments of antibodies binding CD3) or ‘naked’ (untargeted) as is discussed in more detail below. Alternatively, transfection of the T cells can also be performed using electroporation (see e.g., Molecular Therapy Vol. 13, No. 1, p 151-159, January 2006), or chemical transfection such as Nucleofactor or Amaxa kits (commercially available from Lonza, Allendale, N.J., USA).

[0044] Once transfected T cells are prepared, such cells are preferably formulated for transfusion to a patient, typically in an aqueous carrier suitable for injection. For example, a typical solution for transfusion will include at least 10.sup.6, or at least 10.sup.7, or at least 10.sup.8, or at least 109 transfected cells. Thus, pharmaceutical compositions comprising transfected T cells and use of such cells in pharmaceutical formulations (especially for treatment of (myco)bacterial infection) are deemed appropriate.

Examples

[0045] The following description provides the person of ordinary skill in the art exemplary guidance for preparation and use of the recombinant cells presented herein. However, the examples should not be construed as limiting the inventive subject matter.

[0046] To investigate the influence of T cell stimulation and type of transfection on the T cell response to various antigens, T cells were separately transfected with ‘naked’ non-targeting PBAE (poly(β-amino ester)) nanoparticles that were associated with two types of RNA: RNA encoding a clone 18 TCR (bicistronic construct with clone 18 TCR alpha and beta chain) and RNA encoding GFP (green fluorescent protein). Stimulation, in this case, was achieved by culturing isolated T cells with a cocktail of anti-CD3 and anti-CD28 antibodies (Immunocult Human CD3/CD28 T Cell Activator, Stemcell Technologies) for 24 hours followed by another 24 hours in unsupplemented culture medium prior to transfection. PBAE-RNA nanoparticles were prepared by first dissolving both PBAE and RNA separately in an acidic sodium acetate buffer, then adding the PBAE solution to the RNA solution at the appropriate ratio and rapidly mixing them by vortex. After allowing 5 minutes for nanoparticle formation they were added to the T cells in culture for 24 hours. These transfected T cells were then, in some cases, co-cultured with human peripheral blood monocyte-derived dendritic cells with the addition, in some additional cases, of ligands for the clone 18 TCR. These were either mycolic acid or an extract from Mycobacterium tuberculosis. Following approximately 24 hours of culture the amount of interferon gamma present in the culture media was measured by enzyme-linked immunosorbent assay (ELISA). As can be readily seen from FIG. 1, stimulation of the T cells had significant effect in terms of interferon gamma secretion by the transfected T cells with all tested CD1b ligands (top panels; mycolic acid and TB extract). No effect was seen on control peptide pp65. No effect with respect to interferon gamma secretion was also observed in the control transfection with GFP. Here, T only denotes T cells only as negative control; T+DC denotes T cells and dendritic cells; Myc Acid denotes addition of mycolic acid as a single identified Cd1b ligand, whereas TB extract denotes a complex mixture of M. tuberculosis. The pp65 peptide was used as a non-binding control.

[0047] The inventors also investigated whether targeting of the nanoparticles to the T cells (here CD3 targeting) had any effect of the ligand dependent interferon gamma secretion. Notably, as can be taken from FIG. 2, transfection of stimulated T cells using CD3 targeted nanoparticles (PBAE) provided similar effects for TB extracts, but a somewhat reduced effect for mycolic acid. More specifically, in order to target the nanoparticles, anti-CD3 monoclonal antibodies were chemically conjugated to polyanionic polyglutamic acid (PGA), and these conjugates were electrostatically adsorbed to the cationic naked PBAE-RNA particles. Thus, targeting did not provide a substantial advantage over untargeted transfection.

[0048] In yet further experiments, the inventors investigated effects of PBAE nanoparticle targeting where the T cells were stimulated or not stimulated. FIG. 3 depicts exemplary results in which stimulated T cells provided substantial interferon gamma secretion by the transfected T cells, with the same difference between targeted and non-targeted as observed in FIG. 2. Control transfections had no substantial differences between stimulated and unstimulated (albeit some IFN-7 secretion in isotarget transfection). More specifically, isotarget particles were prepared by replacing the anti-CD3 antibody with an isotype antibody, which should not specifically target any cell surface markers.

[0049] Stimulation of T cells was performed using CD3-CD28 dynabeads and resulted in similar responses for all types of transfections as can be seen in FIG. 4. More specifically, FIG. 4 shows the ELISA results from T cells that were treated with CD3-CD28 beads instead of CD1b/TB ligand presenting DCs, which was performed as a positive control to induce IFNγ production and to show that the T cells retained that functionality. Notably, only the stimulated cells responded even under these conditions.

[0050] Functional expression of the recombinant RNA was also confirmed using RNA encoding GFP in a set of experiments in which transfection was done using stimulated and non-stimulated T cells. Representative results are seen in FIG. 5 where ‘naked’ PBAE nanoparticles provided the strongest fluorescence signal. More specifically, T cells were collected 24 hours after transfection as above and run on a Life Technologies Attune NxT flow cytometer to measure GFP expression.

[0051] FIG. 6 depicts exemplary results from the same experiment as FIG. 5. Results for viability and transfection of T cells are shown, once more comparing stimulated T cells with non-stimulated T cells using PBAE nanoparticles and RNA encoding GFP. In the graph of FIG. 6, the first bar denotes the percentage of viable cells, while the second bar denotes the fraction of GFP expressing cells within the viable cell population.

[0052] To determine the influence of the type of nanoparticles, the inventors also tested chitosan nanoparticles with associated RNA, where the chitosan particles were further optionally coated with RNA encoding chitosanase. An exemplary schematic workflow for preparation of such particles is depicted in FIG. 7. Due to the positive charges of the chitosan, RNA readily associates with the chitosan during nanoparticle formation. Once formed (or during formation), the nanoparticle can be exposed to a second type of RNA (here RNA encoding chitosan) to so coat or otherwise associate the second RNA with the nanoparticle. It should be appreciated that such approach provides a nanoparticle that delivers the RNA to a cell where the RNA encodes the enzyme that degrades the nanoparticle. Thus, it should be appreciated that degradable nanoparticles can be prepared from a material that is selectively degradable by an enzyme. In such approach, the nanoparticle is then coated or otherwise associated with an RNA that encodes the material that is selectively degradable by the enzyme. Depending on the release kinetics of the RNA degradation kinetics of the nanoparticle can be controlled.

[0053] Exemplary results for nanoparticle RNA delivery using pure chitosan with single RNA (encoding GFP) and chitosan core/shell particles with GFP-encoding RNA comprising both the core and shell RNA component are shown in FIGS. 8-10 using HEK293T and T cells as indicated. More specifically, transfection efficiency and cell viability was compared by flow cytometry for transfections performed with a variety of nanoparticle and media conditions. Culture media used were phosphate buffered saline (PBS), OptiMEM (OM), and Stemcell Technologies' Immunocult-XF T Cell Expansion Medium (XF). The pH of the medium was also varied between 6 and 8. The N-to-P ratio of the chitosan-RNA complex was also varied 4 and 16 for both single complex and core/shell nanoparticles.

[0054] Chitosanase RNA was prepared by in vitro transcription reactions from a commercially available plasmid (pcDNA3.1+/c-(k)dyk) containing the chitosanase gene from Colletotrichum higginsianum IMI349063 (Gene Symbol: CH63R_01899) as is shown in FIG. 11.

[0055] Exemplary results for co-delivery of chitosanase mRNA with GFP mRNA via core/shell chitosan complex and separate delivery are illustrated in FIGS. 12-13. The results in FIG. 12 highlight the specific effects by media and nanoparticle composition, while the results in FIG. 13 illustrate exemplary differences between the nanoparticle systems. More specifically, transfection efficiency and cell viability was compared by flow cytometry for HEK 293T cells transfected with GFP or chitosanase encoding RNA, with either chitosan or PBAE as the carrier, as well as chitosan core/shell configurations where GFP RNA was the core RNA component and chitosanase RNA was the shell RNA component.

[0056] 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. 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. Where the specification claims refers 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.