Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70503—Immunoglobulin superfamily
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70503—Immunoglobulin superfamily
  • C07K14/70521—CD28, CD152
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70503—Immunoglobulin superfamily
  • C07K14/70532—B7 molecules, e.g. CD80, CD86
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70575—NGF/TNF-superfamily, e.g. CD70, CD95L, CD153, CD154
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/62—DNA sequences coding for fusion proteins
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
  • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/70—Fusion polypeptide containing domain for protein-protein interaction
  • C07K2319/74—Fusion polypeptide containing domain for protein-protein interaction containing a fusion for binding to a cell surface receptor

Definitions

• the present invention relates to fusion proteins comprising (a) an extracellular domain containing a polypeptide derived from PD-1 or CD40L at its N-terminus; (b) a transmembrane domain; and (c) an intracellular domain containing a polypeptide derived from 4-1 BB or CD28 at its C-terminus. Also, fusion proteins with CD28 at the N-terminus and CD40L at the C-terminus are envisaged.
• the present invention also relates to nucleic acid molecules encoding such fusion proteins, vectors containing such nucleic acid molecules, and host cells containing such vectors. The present invention further relates to methods for producing such host cells.
• the present invention relates to pharmaceutical compositions comprising such fusion proteins, nucleic acid molecules, vectors, and/or host cells, particularly for treating diseases or disorders associated with PD-1/PD-L2 or CD40 binding and/or PD-L1/PD-L2 or CD40 expression such as cancer and chronic viral infection.
• TILs tumor infiltrating Lymphocytes
• T cells show short survival, and lose their function in patients (Janicki et al., Cancer Res (2008), 68: 2993-3000; Bai et al., PNAS USA (2008), 105: 13003-13008; Bendle et al., Cancer Res (2004), 64: 8052-8056; Anderson et al., J Immunol (2007), 178: 1268-1276).
• Co-stimulation of the TCR signalling cascade with co-stimulatory receptors such as CD28 can enhance proliferation, survival and cytotoxicity of the T cells (Chen et al., Nat Rev Immunol (2013), 13: 227-242).
• chimeric co-stimulatory receptors were created. They consist of the extracellular domain of the co-inhibitory receptor PD-1 (also known as CD279) and the signalling domain of CD28 (Ankri et al., J Immunol (2013), 4121-4129; Prosser et al., Mol Immunol (2012), 263-272; WO 2013/019615).
• tumor specific T cell express PD-1 on the surface which then binds to its ligand PD-L1 expressed on tumor cells. This binding results in blocking of TCR-signalling and T cell activation, thus leading to inhibition of the tumor specific T cells.
• stimulation of CD28 would be necessary; see above.
• Chimeric co-stimulatory receptors comprising PD-1 and CD28 domains shall exhibit the relevant functions of both, the extracellular receptor function of PD-1 on the one hand, and the intracellular signalling function of CD28 on the other hand.
• the transmembrane domains were taken from the respective signalling molecule.
• the present invention relates to a fusion protein comprising
• ECD extracellular domain
• TMD transmembrane domain
• ICD intracellular domain
• the intracellular domain contains a polypeptide derived from 4-1 BB at its C-terminus and vice versa.
• the extracellular domain contains a polypeptide derived from CD40L at its N-terminus
• the intracellular domain contains a polypeptide derived from CD28 at its C-terminus and vice versa.
• fusion proteins with an ECD derived from CD40L and an ICD derived from CD28, it is also possible that the ICD is located N-terminally of the TMD, while the TMD is located at the very C-terminus of the fusion protein; cf. fusion proteins as exemplarily (and non-limiting) shown in Figure 8.
• the extracellular domain (a) contains a polypeptide derived from PD-1 at its N-terminus and a polypeptide derived from 4-1 BB at its C-terminus.
• 4-1 BB (CD137) is a co-stimulatory receptor present on a subset of T cells capable of augmenting TCR signaling.
• 4-1 BB is a member of the tumor necrosis factor receptor (TNFR) superfamily and is absent in naive T cells but induced following T cell stimulation and differentiation into effector cells (Cheuk at al., Cancer Gene Ther (2004), 1 1 : 215-226).
• TNFR tumor necrosis factor receptor
• the intracellular domain of 4-1 BB contains the QEE motif, which, upon ligation with 4-1 BBL, expressed on APCs, recruits TNFR associated factor 2 (TRAF2) (Arch et al., Mol Cell Biol (1998), 18: 558-565; Nam et al., J Immunol (2005), 174: 1898-1905).
• TRAF2 activates MAPK pathways including ERK and activates nuclear translocation of NFKB (Watts, Annu Rev Immunol (2005), 23: 23-68). It thereby enhances cytokine production and T cell survival.
• the present invention provides fusion (also termed herein "chimeric") proteins comprising or consisting of the extracellular domain (ECD) of PD-1 and the intracellular signaling domain (ICD) of 4-1 BB.
• a fusion protein which comprises an ICD derived from CD28 at its N-terminus, a fragment of an ICD derived from CD40L, the TMD of CD40L, and the ECD from CD40L at its C-terminus ( Figure 8).
• the fusion protein comprises or consists of the amino acid sequence shown in SEQ ID NO: 29.
• the present invention provides a fusion (chimeric) protein comprising the extracellular domain (ECD) of CD40L and the intracellular signaling domain (ICD) of CD28.
• ECD extracellular domain
• ICD intracellular signaling domain
• this chimeric protein exerts dual function when interacting with cells expressing its receptor CD40:
• T cell In the T cell it is supposed to initiate the co-stimulatory pathway providing survival and enhanced effector activity (cis effect).
• cis effect In the interacting CD40 cells (trans effect), i.e. tumor cells, tumor endothelium it is supposed to cause cell death, and in the case that the interacting cell is an antigen presenting cells it is supposed to be able to induce secretion of cytokines (e.g., IL-12) that further supports T cell activity (Figure 7).
• cytokines e.g., IL-12
• fusion proteins comprising or consisting of the extracellular domain (ECD) derived from PD- 1 , a transmembrane domain (TMD), and the intracellular domain (ICD) derived from 4-1 BB are also referred to herein as "PD-1 :4-1 BB" or "PD-1 :BB”.
• fusion proteins comprising or consisting of the extracellular domain (ECD) derived from PD-1 , a transmembrane domain (TMD), and the intracellular domain (ICD) derived from CD28 are also referred to herein as "PD-1 :CD28”.
• fusion proteins comprising or consisting of the extracellular domain (ECD) derived from CD40L, a transmembrane domain (TMD), and the intracellular domain (ICD) derived from CD28 are also referred to herein as "CD40L:CD28” or “CD28:CD40L” (also referred to herein as “CD40L:CD28i” or “CD40L:CD28i” because of the inversed ICD of CD28; cf. also exemplary fusion protein embodiments as shown as variant 3) in Figure 7 and evaluated in Figures 8 to 1 1 ) where the ICD of CD28 forms the N-terminus and the ECD of CD40L forms the C-terminus of the fusion protein.
• ECD extracellular domain
• TMD transmembrane domain
• ICD intracellular domain
• TM or " tm” in context with fusion proteins indicate which transmembrane domain is used for the respective construct.
• PD-1TM:BB or “PD-1 tm :BB” means that the fusion protein comprises the transmembrane domain of PD-1
• PD-1 :BBTM or “PD-1 :BB tm” means the fusion protein comprises the transmembrane domain of 4-1 BB.
• CD28:CD40L tm “ or “CD40L tm :CD28” means that the fusion protein comprises the transmembrane domain of CD40L
• CD40L:CD28TM or means the fusion protein comprises the transmembrane domain of CD28.
• a fusion protein which comprises the extracellular domain (ECD) of PD-1 or CD40L (e.g., PD-1 ), a transmembrane domain (TMD), and the intracellular domain (ICD) of 4-1 BB.
• ECD extracellular domain
• TMD transmembrane domain
• ICD intracellular domain
• the CD40L:CD28 fusion proteins expressed on T cells were able to activate B cells (trans effect; Figure 10) as well as to support T cell functions (cis effect) such as increased IFN- ⁇ secretion (cf. Figure 1 1 A) and cytotoxicity (Figure 1 1 B).
• a fusion product comprising the ICD of 4-1 BB exhibits superior effects in form of increased proliferation rates compared to constructs comprising the ICD of CD28 when expressed in T cells, e.g., in human melanoma xenograft.
• the ECD of the fusion protein described and provided in context with the present invention having an ECD derived from PD-1 preferably has the function to bind to PD-L1/2 on the surface of tumor cells which express PD-L1 as part of an escape mechanism as known in the art.
• the ICD of the fusion protein - comprising a polypeptide derived from 4-1 BB - preferably acts as activating signalling molecule, thus increasing proliferation of the host cell (e.g., T cell such as CD8 + T cell) and/or cytokine secretion.
• the ECD of the fusion protein described and provided in context with the present invention having an ECD derived from CD40L preferably has the function to bind to CD40 on the surface of tumor cells which express CD40 as part of an escape mechanism as known in the art.
• the ICD of the fusion protein - comprising a polypeptide derived from CD28 - preferably acts as activating signalling molecule, thus increasing proliferation and/or survival of the host cell (e.g., T cell such as CD8 + T cell) and/or cytokine secretion and/or cytotoxicity .
• the fusion protein provided in accordance with the present invention may further comprise a ⁇ 3 ⁇ domain. This may particularly be applicable for cases where the fusion protein is not expressed in a T cell or generally in a TCR negative cell or in cases where TCR and/or CAR are not co-transduced (or generally co-expressed) in the cell expressing the fusion construct of the present invention.
• the ICD amino acid sequence of ⁇ 3 ⁇ can be taken from data base known in the art (NP_932170). Generally, ⁇ 3 ⁇ may preferably be introduced after the ICD of the 4-1 BB or CD28 protein.
• the fusion proteins provided herein may particularly comprise at the N-terminus an ECD containing a polypeptide derived from PD-1 , preferably the ECD of PD-1 (e.g., human or murine, preferably human PD-1 ), or from CD40L.
• the term "derived from” particularly means that the polypeptide contained in the ECD comprises at least a part of PD- 1 (e.g., human or murine, preferably human PD-1 ), preferably the ECD of PD-1 , or CD40L, respectively.
• the term "derived from” PD-1 or CD40L also allows that up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid are substituted, deleted, and/or inserted compared to a native sequence of PD-1 (human or murine, preferably human PD-1 ) or CD40L, or part thereof (e.g., ECD).
• ECD e.g., ECD
• the ECD may comprise or consist of the ECD highlighted in SEQ ID NO: 30 of Figure 1 .
• it may be the soluble part of CD40L (e.g., amino acids 1 13-261 of SEQ ID NO: 30; Figure 8).
• the signal peptide sequence (as recognizable for those of skill in the art and as also depicted in specific SEQ ID NOs. referred to herein) is usually cut off in the mature protein before, during or after integration of the fusion protein in the membrane. It is also possible in accordance with the present invention that if the ECD is derived from CD40L, the signal peptide may be derived from PD-1 ( Figure 8). That is, when referring to fusion proteins or host cells expressing the fusion proteins as described and provided herein, it is always also encompassed in accordance with the present invention that the ECD of the fusion protein may lack the respective signal peptide.
• the fusion protein comprises an ECD containing a polypeptide derived from PD-1 or CD40L comprises an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of the ECD of human or murine PD-1 , e.g., of human PD-1 as depicted in SEQ ID NO: 2 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 2) or CD40L (as highlighted in SEQ ID NO: 30 in Figure 1 ; as full polypeptide according to SEQ ID NO: 30 or only the soluble fragment (amino acids 1 13-261 of SEQ ID NO: 30), wherein said fusion protein exhibits PD-L1/2 or CD40 binding affinity, respectively.
• binding affinity may be compared to the binding affinity of native PD-1 (e.g., human PD-1 ) or CD40L to its respective ligand PD-L1/2 or CD40.
• native PD-1 e.g., human PD-1
• CD40L ligand PD-L1/2 or CD40.
• a polypeptide having a binding affinity to native human PD-L1/2 or CD40 which is as least 0.8-fold, preferably at least 0.9-fold, or more preferably at least 1.0-fold as high compared to binding affinity of native human PD-1 to PD-L1/2 or CD40L to CD40 is considered to exhibit binding affinity to PD-L1/2 or CD40, respectively.
• the binding affinity of a given polypeptide to PD-L1/2 or CD40 can be measured by methods known in the art and usually and preferably comprises the measurement of the K D value (dissociation constant) which is expressed as a molar concentration.
• K D value dissociation constant
• Such methods for measuring protein interactions in terms of K D are well known in the art and comprise, e.g., ELISA, flow cytometry, surface plasmon resonance, biacore measurement, and the like.
• the fusion protein comprises an ECD comprising or consisting of the amino acid sequence of the ECD of PD-1 according to SEQ ID NO: 2 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 2).
• the fusion protein comprises an ECD comprising or consisting of the amino acid sequence of the ECD of CD40L as highlighted in SEQ ID NO: 30 in Figure 1 (as full polypeptide according to SEQ ID NO: 30 or only the soluble fragment according to amino acids 1 13-261 of SEQ ID NO: 30).
• the ECD of the fusion protein described and provided herein may further comprise a hinge- and/or a linker region at the C-termimus of the ECD (e.g., between the ECD and TMD of the fusion protein, or between the ECD and the ICD of the fusion protein where the TMD is located C-terminally of the ICD) in order to allow more flexibility to the ECD.
• a hinge- and/or a linker region at the C-termimus of the ECD e.g., between the ECD and TMD of the fusion protein, or between the ECD and the ICD of the fusion protein where the TMD is located C-terminally of the ICD
• Typical hinge- or linker regions are known in the art and comprise those derived from the constant region (Fc) of antibodies (e.g., lgG1 , CD8alpha) (see, e.g., Shirasu et al., Anticancer Res (2012), 32: 2377-2383 and Cartellieri et al., J Biomed Biotechnol (2010), 956304) (e.g., IgGFc spacers), Gly/Ser linkers, or filamin (e.g., Fil3 spacers).
• Fc constant region
• linker- or hinge regions may also cause side effects due to activation of NK cells which secrete high amounts of inflammatory cytokines
• the fusion proteins described and provided herein do not comprise linker- or hinge regions. That is, in one embodiment of the present invention, the ECD of the fusion protein does not comprise a linker- or hinge region.
• the ECD is derived from CD40L and the ICD is derived from CD28
• linker- or hinge regions C-terminally of the ECD e.g., a Gly/Ser linker plus an Fc spacer (e.g., IgGFc spacer) and/or a filamin linker (e.g., Fil3), e.g. as highlighted accordingly in SEQ ID NOs. 27 or 28 of Figure 1 .
• the fusion proteins provided herein further comprise a TMD operably linked between the ECD and the ICD or linked C-terminally of the ICD (e.g. where the ECD is derived from CD40L and the ICD is derived from CD28).
• a TMD operably linked between the ECD and the ICD or linked C-terminally of the ICD (e.g. where the ECD is derived from CD40L and the ICD is derived from CD28).
• the TMD is not limited to a specific TMD.
• the TMD allows stable anchorage of the fusion protein in the membrane of a cell expressing the fusion protein (e.g., a T cell) and further allows binding of the ECD to PD-L1/2 or CD40, respectively, and, upon binding to PD-L1/2 or CD40, allows signaling induction of the ICD containing a polypeptide derived from 4-1 BB, CD28 or CD40L as described and exemplified herein.
• TMDs may inter alia comprise those derived from CD8(alpha), CD28, ICOS, PD-1 , or 4-1 BB.
• the TMD is derived from CD28 (CD40L:CD28 tm ) or from CD40L (CD28:CD40L tm ).
• the fusion protein comprises or consists of an amino acid sequence shown in SEQ ID NOs 27, 28 or 29.
• the TMDs may generally be of any origin, but are preferably murine or human, more preferably human.
• the TMD of the fusion protein is not derived from CD8(alpha), and/or ICOS. If the ECD is derived from PD-1 and the ICD is derived from 4-1 BB, the TMD is in one embodiment also not derived from CD28.
• the TMD of the fusion protein comprises a polypeptide derived from PD-1 , 4-1 BB (e.g., human or murine), particularly where the ECD is from PD-1 and the ICD is from 4-1 BB, or the TMD is derived from CD28, particularly where the ECD is from CD40L and the ICD is from CD28 (e.g., as highlighted in SEQ ID NOs: 27 or 28 of Figure 1 ).
• the TMD of the fusion protein comprises a polypeptide derived from PD-1 , e.g., human or murine PD-1 , particularly human PD-1.
• the term "derived from” particularly means that the polypeptide contained in the TMD comprises at least a part of PD-1 , 4-1 BB (e.g., human or murine, preferably human PD-1 or 4-1 BB) or CD28, preferably the TMD of PD-1 or 4-1 BB (e.g., PD- 1 ), particularly where the ECD is from PD-1 and the ICD is from 4-1 BB.
• 4-1 BB e.g., human or murine, preferably human PD-1 or 4-1 BB
• CD28 preferably the TMD of PD-1 or 4-1 BB (e.g., PD- 1 ), particularly where the ECD is from PD-1 and the ICD is from 4-1 BB.
• the term "derived from" PD-1 , 4-1 BB, or CD28 also allows that up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid are substituted, deleted, and/or inserted compared to a native sequence of PD-1 , 4-1 BB (human or murine, preferably human PD-1 or 4-1 BB), or CD28, or part thereof (e.g., TMD).
• fusion proteins having an ICD derived from 4-1 BB generally exhibit superior proliferation rates of the host cells (e.g., T cells such as CD8 + T cells) compared to similar constructs having an ICD derived from CD28 and an ECD from PD-1. Furthermore, fusion proteins comprising a TMD derived from PD-1 lead to an even higher secretion rate of cytokines (e.g., IFNy or IL-2) in transduced T cells compared to fusion proteins comprising a TMD derived from 4-1 BB. Accordingly, in a specific embodiment of the present invention, the TMD of the fusion protein comprises or consists of a polypeptide derived from PD-1 , e.g., human or murine PD-1 , particularly human PD-1.
• the fusion protein comprises a TMD containing a polypeptide derived from 4-1 BB comprising an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of the TMD of human or murine 4-1 BB, e.g., of human 4-1 BB as depicted SEQ ID NO: 6, wherein said fusion protein is capable of increasing the proliferation rate of a CD8 + T cell when retrovirally transduced into a said CD8 + T cell upon stimulation of said CD8 + T cell with a PD-L1/2 + target cell as described and exemplified herein.
• Proliferation can be quantified by CFSE dye dilution, i.e. reduction of CFSE fluorescence intensity measured by flow cytometry (as exemplified in Figure 5 and Method description "Proliferation of TCR-D1 15 T cells.", or any other suitable method known in the art to determine proliferation, e.g., H 3 thymidin incorporation, BrdU incorporation, etc.
• the proliferation difference can be calculated as the ratio of mean fluorescence activity (MFI) between T cells without chimeric receptor (mock) and T cells expressing a PD-1 :BB or PD-1 :CD28 variant.
• MFI mean fluorescence activity
• the fusion protein comprises a TMD comprising or consisting of the amino acid sequence of the TMD of 4-1 BB according to SEQ ID NO: 6, particularly where the ECD is derived from PD-1 and the ICD is derived from 4- 1 BB.
• the fusion protein comprises a TMD (which may be located at the N- or C-terminal of the ICD, preferably at the N-terminal of the ICD) containing a polypeptide derived from CD28 comprising an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of the TMD of CD28 as highlighted in SEQ ID NO: 27 or 28 of Figure 1 , wherein said fusion protein is capable of increasing the activation rate of B cells when expressed on TCR-T58 cells as shown in Figure 10.
• TMD which may be located at the N- or C-terminal of the ICD, preferably at the N-terminal of the ICD
• a polypeptide derived from CD28 comprising an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid
• the fusion protein is considered capable of increasing activation.
• the fusion protein comprises a TMD (which may preferably be located between the ICD and the ECD) containing a polypeptide derived from CD40L comprising an amino acid sequence with up to
• fusion protein is capable of increasing the activation rate of B cells when expressed on TCR- T58 cells as shown in Figure 10. If the activation increase of the B cell-is greater 1 .2-fold, preferably at least 1 .3-fold, more preferably at least 1.5-fold compared to the B cell activation rate with TCR-T58 cells which were not transduced with the fusion protein, the fusion protein is considered capable of increasing activation.
• the fusion protein comprises a TMD containing a polypeptide derived from PD-1 comprising an amino acid sequence with up to 0,
• amino acid substitutions preferably conservative or highly conservative substitutions
• deletions and/or insertions compared to the amino acid sequence of the TMD of human or murine PD-1 , e.g., of human PD-1 as depicted SEQ ID NO: 8, wherein said fusion protein is capable of increasing secretion of I FNY and/or IL-2 when retrovirally transduced into a CD8 + T cell upon stimulation of said CD8 + T cell with a PD-L1/2 + target cell.
• the IFNy and/or IL-2 secretion level of a CD8 + T cell retrovirally transduced with said fusion protein is compared to the IFNy and/or IL-2 secretion level of a comparable CD8 + T cell not transduced with said fusion protein.
• both CD8 + T cells are stimulated with a PD-L1/2 + target cell as described and exemplified herein followed by measuring the secretion level of IFNy and/or IL-2.
• the CD8 + T cell transduced with the fusion protein and the non-transduced control CD8 + T cell are usually derived from the same donor.
• transgenic human T cells may be retrovirally transduced to express the fusion protein containing said polypeptide derived from 4-1 BB, then cultured with HEK/Tyr or HEK/Tyr/PD-L1 cells at a 1 :2 ratio.
• Co-culture supernatants may then be harvested after 16 h and analyzed by sandwich ELISA (BD) or Bio-Plex (Bio-Rad) according to the manufacturer's protocol.
• the amount of measured cytokine can be normalized to the percentage of TCR + CD8 + T cells within the cell suspension (determined by flow cytometry), applying the following formula: cytokine concentration measured
• IFNy and IL-2 are well known in the art and also exemplified herein and comprise, inter alia, ELISA, Bio-Plex, intracellular flow cytometry (ICS), or the like. If the IFNy and/or IL-2 secretion level of the CD8 + T cell retrovirally transduced with the given fusion protein is at least 1.2-fold, preferably at least 1 .3-fold, more preferably at least 1.5-fold higher compared to the CD8 + T cell which was not transduced with the fusion protein, the fusion protein is considered capable of increasing secretion of IFNy and/or IL-2.
• the fusion protein comprises a TMD comprising or consisting of the amino acid sequence of the TMD of PD-1 according to SEQ ID NO: 8.
• the fusion protein comprises a TMD (which may be located at the N- or C-terminal of the ICD, preferably at the N-terminal of the ICD), the TMD comprises or consists of the amino acid sequence of the TMD of CD28 as highlighted in SEQ ID NO: 27 or 28 of Figure 1.
• the fusion protein comprises a TMD (which may preferably be located between the ICD and the ECD), the TMD comprises or consists of the amino acid sequence of the TMD of CD40L as highlighted in SEQ ID NO: 29 of Figure 1.
• the fusion proteins provided herein further comprise an ICD operably linked to the C- terminus of the TMD (particularly for fusion proteins where the ECD is from PD-1 and the ICD is from 4-1 BB), or operably linked to the C- or N-terminus of the TMD (particularly for fusion proteins where the ECD is from CD40L and the ICD is from CD28).
• the ICD of the inventive fusion proteins contains a polypeptide which is derived from 4-1 BB (CD137) or CD28.
• the term "derived from” particularly means that the polypeptide contained in the ICD comprises at least a part of 4-1 BB (e.g., human or murine, preferably human 4-1 BB), preferably the ICD of (human) 4-1 BB, or CD28.
• 4-1 BB e.g., human or murine, preferably human 4-1 BB
• the term “derived from” 4-1 BB or CD28 also allows that up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid are substituted, deleted, and/or inserted compared to a native sequence of 4-1 BB (human or murine, preferably human 4-1 BB) or CD28, or part thereof (e.g., ICD).
• the ICD of the fusion protein comprises a polypeptide derived from the ICD of 4-1 BB, e.g., human or murine 4-1 BB, particularly human 4-1 BB.
• the fusion protein comprises a polypeptide derived from the ICD of CD28, for example comprising or consisting of an amino acid sequence highlighted in SEQ ID NO: SEQ ID NO: 27, 28, or 29 of Figure 1 (according to SEQ ID NO: 27 or 28 particularly for cases where the ECD is located at the N-terminus of the fusion protein and the ICD is located at the C-terminus (C- or N-terminally of the TMD, preferably C-terminally of the TMD) of the fusion protein; and according to SEQ ID NO: 29 particularly for cases where the ICD is located at the N-terminus of the fusion protein and the ECD is located at the C-terminus of the fusion protein;
• the fusion protein comprises an ICD containing a polypeptide derived from 4-1 BB comprising an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of the ICD of human or murine 4-1 BB, e.g., of human 4-1 BB as depicted in SEQ ID NO: 4, wherein said fusion protein is capable of increasing the proliferation rate of a CD8+ T cell when retrovirally transduced into said CD8 + T cell upon stimulation of said CD8 + T cell with a PD-L1/2 + target cell as described and exemplified herein.
• the fusion protein comprises an ICD containing a polypeptide derived from CD28 comprising an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of the ICD of CD28 as highlighted in SEQ ID NO: SEQ ID NO: 27, 28, or 29 of Figure 1 (according to SEQ ID NO: 27 or 28 particularly for cases where the ECD is located at the N-terminus of the fusion protein and the ICD is located at the C-terminus (C- or N- terminally of the TMD, preferably N-terminally of the TMD) of the fusion protein; and according to SEQ ID NO: 29 particularly for cases where the ICD is located at the N-terminus of the fusion protein and the ECD is located at the C-terminus of the fusion protein), wherein said fusion protein is capable of increasing the activation rate of B cells when expressed on TCR-T58 cells as shown
• the fusion protein is considered capable of increasing activation.
• the fusion protein comprises an ICD comprising or consisting of the amino acid sequence of the ICD of 4-1 BB according to SEQ ID NO: 4.
• the fusion protein provided and described herein comprises or consists of an ECD derived from PD-1 , a TMD derived from 4- 1 BB, and an ICD derived from 4-1 BB. In one embodiment, all domains are derived from corresponding human domains.
• the fusion protein of the present invention comprises or consists of an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of SEQ ID NO: 22 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 22), wherein said fusion protein exhibits PD-L1/2 binding affinity as described herein, and wherein said fusion protein is capable of increasing the proliferation rate of a CD8+ T cell when retrovirally transduced into said CD8 + T cell upon stimulation of said CD8 + T cell with a PD- L1/2 + target cell as described and exemplified herein.
• the fusion protein comprises or consists of an amino acid according to SEQ ID NO: 22 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 22).
• fusion protein provided and described herein comprises or consists of an ECD derived from CD40L, a TMD derived from CD28 or CD40L (CD28 where the ECD is located at the N-terminus of the fusion protein and the ICD is located at the C-terminus (C- or N-terminally of the TMD, preferably N-terminally of the TMD) of the fusion protein; CD40L where the ICD is located at the N-terminus of the fusion protein and the ECD is located at the C-terminus of the fusion protein), and an ICD derived from CD28.
• all domains are derived from corresponding human domains.
• the fusion protein of the present invention comprises or consists of an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of SEQ ID NOs: 27, 28, or 29 (for SEQ ID NOs.
• the fusion protein comprises or consists of the amino acid sequence of SEQ ID NOs: 27, 28, or 29 (with or without the signal peptide as depicted in Figure 1 for 27, 28, or 29).
• the fusion protein provided and described herein comprises or consists of an ECD derived from PD-1 , a TMD derived from PD-1 , and an ICD derived from 4-1 BB.
• all domains are derived from corresponding human domains.
• the fusion protein of the present invention comprises or consists of an amino acid sequence with up to 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions (preferably conservative or highly conservative substitutions), deletions and/or insertions compared to the amino acid sequence of SEQ ID NO: 24 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 24), wherein said fusion protein exhibits PD-L1/2 binding affinity as described herein, and whereinsaid fusion protein is capable of increasing secretion of IFNy and/or IL-2 when retrovirally transduced into a CD8 + T cell upon stimulation of said CD8 + T cell with a PD-L1/2 + target cell as described and exemplified herein.
• a given fusion protein in order to assess whether a given fusion protein is capable of increasing the proliferation rate of a CD8+ T cell as well as increasing the IFNy and/or IL-2 secretion level of said CD8 + T cell retrovirally transduced with said fusion protein is compared to the proliferation rate/the IFNy and/or IL-2 secretion level of a comparable CD8 + T cell not transduced with said fusion protein.
• Methods for assessing proliferation and I FNY /IL-2 secretion rates are known in the art and described and exemplified herein above and below.
• the fusion protein comprises or consists of an amino acid according to SEQ ID NO: 24 (with or without the signal peptide as depicted in Figure 1 for SEQ ID NO: 24).
• polypeptide is equally used herein with the term “protein”. Proteins (including fragments thereof, preferably biologically active fragments, and peptides, usually having less than 30 amino acids) comprise one or more amino acids coupled to each other via a covalent peptide bond (resulting in a chain of amino acids).
• polypeptide as used herein describes a group of molecules which typically comprise more than 10 amino acids. Polypeptides may further form multimers such as dimers, trimers and higher oligomers, i.e. consisting of more than one polypeptide molecule. Polypeptide molecules forming such dimers, trimers etc. may be identical or non-identical.
• heteromultimer is an antibody molecule, which, in its naturally occurring form, consists of two identical light polypeptide chains and two identical heavy polypeptide chains.
• polypeptide and protein also refer to naturally modified polypeptides/proteins wherein the modification is effected e.g. by post-translational modifications like glycosylation, acetylation, phosphorylation and the like. Such modifications are well known in the art.
• amino acid typically refers to an amino acid having its art recognized definition such as proteinogenic amino acid selected from the group consisting of: alanine (Ala or A); arginine (Arg or R); asparagine (Asn or N); aspartic acid (Asp or D); cysteine (Cys or C); glutamine (Gin or Q); glutamic acid (Glu or E); glycine (Gly or G); histidine (His or H); isoleucine (He or I): leucine (Leu or L); lysine (Lys or K); methionine (Met or M); phenylalanine (Phe or F); pro line (Pro or P); serine (Ser or S); threonine (Thr or T); tryptophan (Trp or W); tyrosine (Tyr or Y); and valine (Val or V), although modified, synthetic, or rare amino acids
• amino acids can be grouped as having a nonpolar side chain (e.g., Ala, Cys, He, Leu, Met, Phe, Pro, Val); a negatively charged side chain (e.g., Asp, Glu); a positively charged sidechain (e.g., Arg, His, Lys); or an uncharged polar side chain (e.g. , Asn, Cys, Gin, Gly, His, Met, Phe, Ser, Thr, Trp, and Tyr).
• a nonpolar side chain e.g., Ala, Cys, He, Leu, Met, Phe, Pro, Val
• a negatively charged side chain e.g., Asp, Glu
• a positively charged sidechain e.g., Arg, His, Lys
• an uncharged polar side chain e.g. , Asn, Cys, Gin, Gly, His, Met, Phe, Ser, Thr, Trp, and Tyr.
• fusion protein relates to a protein which is made of polypeptide parts from different sources. Accordingly, it may be also understood as a “chimeric protein", a “chimeric construct”, “fusion construct”, or the like.
• fusion proteins are proteins created through the joining of two or more genes (or preferably cDNAs) that originally coded for separate proteins. Translation of this fusion gene (or fusion cDNA) results in a single polypeptide, preferably with functional properties derived from each of the original proteins.
• Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics. Further details to the production of the fusion protein of the present invention are known in the art and described and exemplified herein.
• the present invention further relates to a nucleic acid molecule encoding the fusion protein provided and described herein.
• the present invention also relates to nucleic acid molecules which only encode parts of the fusion protein described and provided herein, e.g., which encode only the ECD, the TMD, and/or the ICD of the fusion protein.
• the present invention relates to nucleic acid molecules according to SEQ ID NOs. 1 , 3, 5, 7, 21 , or 23, or combinations thereof linked via nucleic acid bonds, provided a fusion protein according to the present invention or a part thereof (e.g., the ECD, TMD and/or ICD) is encoded.
• the present invention also relates to nucleic acid molecules where 30, 27, 24, 21 , 18, 15, 12, 9, 6, 3, or 0 nucleotides have been substituted (preferably silent mutations which do not result in a change of translated amino acid), deleted or inserted compared to nucleic acid molecules according to SEQ ID NOs. 1 , 3, 5, 7, 21 , or 23, or combinations thereof linked via nucleic acid bonds, provided a fusion protein according to the present invention or a part thereof (e.g., the ECD, TMD and/or ICD) is encoded.
• the present invention preferably relates to nucleic acids encoding fusion proteins specifically described and embodied herein. Generally, SEQ ID NOs.
• FIG. 13 and 14 show the human nucleic acid and amino acid sequence of CD28, respectively, where the predominant transcript of CD28 is depicted. Yet, given that CD28 also exists in further splice variants (e.g., in-frame donor splice variants or variants lacking an in-frame coding exon), such variants or parts thereof (particularly TMD thereof) are also encompassed to be part of the fusion protein described and provided herein. Generally, SEQ ID NOs. 13 and 14 show the human nucleic acid and amino acid sequence of CD28, respectively, where the predominant transcript of CD28 is depicted.
• splice variants e.g., in-frame donor splice variants or variants lacking an in-frame coding exon
• SEQ ID NOs. 13 and 14 show the human nucleic acid and amino acid sequence of CD28, respectively, where the predominant transcript of CD28 is depicted.
• nucleic acid or “nucleic acid molecule” is used synonymously with “oligonucleotide”, “nucleic acid strand”, “polynucleotide”, or the like, and means a polymer comprising one, two, or more nucleotides.
• nucleic acid molecule relates to the sequence of bases comprising purine- and pyrimidine bases which are comprised by polynucleotides, whereby said bases represent the primary structure of a nucleic acid molecule.
• nucleic acid molecule includes all kinds of nucleic acid, including DNA, cDNA, genomic DNA, RNA, synthetic forms of DNA and mixed polymers comprising two or more of these molecules, and preferably relates to DNA and cDNA.
• nucleic acid sequences provided herein represent sequences of DNA and also comprise corresponding RNA sequences where T is replaced by U.
• nucleic acid molecule generally comprises sense and antisense strands.
• Nucleic acid molecule may further comprise non- natural or derivatized nucleotide bases as well as natural or artificial nucleotide analogues, e.g., in order to protect the nucleic acid molecule against endo- and/or exonucleases as will be readily appreciated by those skilled in the art.
• the present invention further relates to a vector comprising the nucleic acid molecule described and provided herein.
• vector generally comprises all kinds of linear or circular nucleic acid molecules which can replicate autonomously is a suitable host cell.
• Such vectors comprise, but are not limited to, plasmids, cosmids, phages, virus (e.g., adeno-, adeno- associated-, lenti-, or preferably retroviral vectors), and other vectors or shuttles known in the art which are suitable to carry and transfer genes into host cells in order to allow stable or transient translation and constitutive or conditional expression of the inventive fusion protein in the host cell.
• the vector is usually not integrated into the cell genome, but may also be integrated.
• Vectors according to the present invention which comprise nucleic acid molecules as described and provided herein preferably allow stable expression of the fusion protein of the present invention in the host cell (expression vector).
• Vectors of the present invention may further comprise marker genes, promoter and/or enhancer sequences (operably linked to the nucleic acid molecule of the present invention), replication origin suitable for the respective host cell, restriction sited, multiple cloning sites, labels and further functional units as known in the art.
• the vectors may inter alia be transferred into host cells via a shuttle such as a virus (which may itself be considered a vector), or be nakedly transformed or transduced into host cells.
• the vector is preferably adapted to suit to the respective host cell where it is to be transformed or transduced into.
• the vector (plasmid) pGEM is a suitable vector for transformation into bacterial cells
• the retroviral vector pMP71 is suitable for transduction into eukaryotic cells (e.g., T cells).
• the vector of the present invention is a viral vector, e.g., a retroviral or lentiviral vector, e.g., a retroviral vector.
• retroviral vectors include, e.g., pMP71-PRE (Leisegang, K Mol Med (2008), 86(5): 573-583), SAMEN CMV/SRa, LZRS-id3-IHRES (Heemskerk et al., J. Exp. Med. 186 (1997), 1597-1602), FeLV (Neil et al., Nature 308 (1984), 814-820), SAX (Kantoff et al., Proc.
• the vector is pMP71 -PRE or pMP71.
• the present invention further relates to a host cell comprising the nucleic acid molecule or the vector as described and provided herein.
• the host cell of the present invention is transduced or transformed with the nucleic acid molecule or the vector as described and provided herein.
• transduced or “transformed” (as well as “transduction” or “transformation”) or the like may be used interchangeably and generally mean any kind of transfer of a nucleic acid molecule and/or vector into a host cell, regardless of the kind of host cell and regardless of the way of transfer (e.g., (chemical) transformation, (viral) transduction, electroporation, transfection, etc.).
• the nucleic acid molecule and/or the vector may be stably integrated into the genome of the host cell, or be extrachromosomal ⁇ i.e. transient expression). Examples for suitable methods for achieving transient expression in a host cell are known in the art and comprise mRNA transfection. In one embodiment, the nucleic acid molecule and/or the vector is stably integrated into the genome.
• the host cell described and provided in context with the present invention comprising the nucleic acid molecule or the vector as described and provided herein is preferably able to stably or transiently (e.g., stably) express (either constitutively or conditionally ) the fusion protein of the present invention.
• the host cell may generally be transduced or transformed by any method with any suitable nucleic acid molecule or vector.
• the host cell is transduced with a retroviral or lentiviral (e.g., retroviral) vector comprising a nucleic acid molecule encoding the fusion protein of the present invention or parts thereof (e.g., ECD, TMD, and/or ICD) as described above.
• the host cell of the present invention is transduced with a retroviral vector comprising a nucleic acid molecule encoding the fusion protein of the present invention or parts thereof (e.g., ECD, TMD, and/or ICD) as described above and stably expresses (either constitutively or conditionally) the fusion protein or part thereof.
• the host cell then stably expresses the fusion protein in its membrane, with the ECD of the fusion protein of the present invention directed to the surface, the TMD being (largely) embedded in the membrane, and the ICD directed to the cytoplasm.
• the host cell comprising the nucleic acid molecule or the vector as described and provided herein relates to a genetically modified cell where said nucleic acid molecule or said vector was transduced, transformed or otherwise introduced into the host cell.
• the host cell of the present invention may be a cell which transiently or stably expresses the fusion protein of the present invention.
• the nucleic acid molecule encoding the fusion protein of the present invention can be stably integrated into the genome of the cell by retroviral or lentiviral (e.g., retroviral) transduction.
• the PD-1-BB fusion protein is expressed in the membrane of the herein provided transduced cell.
• the detection of the ECD of the PD-1 polypeptide can be carried out by using an antibody or other binding molecule specifically binding the ECD of PD-1 as described herein, e.g., by ELISA or by flow cytometry, or microscopy.
• the transduced cell of the present invention may be, e.g., CD8 + T cells, CD4 + T cells, double- negative ⁇ / ⁇ T cells, NK (natural killer) cells, ⁇ T cells, macrophages, dendritic cells, as well as cells suitable store and/or reproduce the nucleic acid molecule or vector of the present invention, including bacterial cells (e.g., E. coli) and further eukaryotes.
• the host cell of the present invention is a T cell, e.g., a CD8 + T cell.
• the host cell of the present invention may be transduced with a nucleic acid molecule or a vector encoding the fusion protein as described and provided herein.
• the host cell provided and described herein may be co-transduced with further nucleic acid molecules, e.g. with a nucleic acid molecule encoding a T cell receptor (TCR) or a chimeric antigen receptor (CAR).
• TCR T cell receptor
• CAR chimeric antigen receptor
• suitable host cells include, but are not limited to, T cells, e.g. CD8 + T cells, CD4 + T cells, TCR such as (but not limited to) TCR-T58 or TCR-D1 15 T cells, double-negative ⁇ / ⁇ T cells, NK (natural killer) cells, ⁇ T cells, macrophages, dendritic cells, as well as cells suitable store and/or reproduce the nucleic acid molecule or vector of the present invention, including bacterial cells (e.g., E. coli) and further eukaryotes.
• the cells may be autologous or non-autologous, but are preferably autologous. Also, the cells may be allogeneic or non-allogeneic as readily clear for the skilled person.
• the host cell of the present invention is a CD8 + T cell.
• the present invention also relates to a method of preparing a host cell of the present invention as described and provided herein, said method comprising
• step (1 ) transducing or transforming a host cell as described above with a nucleic acid molecule or a vector as described and provided herein; (2) cultivating the transduced host cell of step (1 ) in a suitable medium allowing growth of the cell and expression of the fusion protein encoded by said nucleic acid molecule or said vector;
• the host cell is transduced or transformed outside the human body.
• Methods for obtaining, isolating and culturing cells e.g., T cells such as CD8 + T cells, CD4 + T cells, TCR such as (but not limited to) TCR-T58 or TCR-D1 15 T cells
• donors e.g., human donors
• T cells such as CD8 + T cells, CD4 + T cells, TCR such as (but not limited to) TCR-T58 or TCR-D1 15 T cells
• the host cell may be transduced or transformed or otherwise be provided with a nucleic acid molecule or a vector as described and provided herein by any method known in the art. Such methods comprise, inter alia, (chemical) transformation, (viral) transduction, electroporation, transfection, and the like. In one embodiment, the host cell is transduced with a retroviral vector.
• the host cell to be prepared in accordance with the present invention may be any host cell as described herein.
• the host cell is a T cell, for example a CD8 + T cell, CD4 + T cell, TCR such as (but not limited to) TCR-T58 or TCR-D1 15 T cell.
• the present invention also relates to a host cell obtainable by the preparation method provided herein.
• the present invention further relates to a pharmaceutical composition comprising a fusion protein, a nucleic acid molecule, a vector, and/or a host cell as described and provided by the present invention.
• a pharmaceutical composition comprising a fusion protein, a nucleic acid molecule, a vector, and/or a host cell as described and provided by the present invention.
• Such pharmaceutical composition is suitable to be administered to patient (preferably, human patient), particularly to the donor of the host cells as described above.
• the present invention also relates to methods for treating a disease or disorder by administering comprising a pharmaceutical composition comprising a fusion protein, a nucleic acid molecule, a vector, and/or a host cell as described and provided by the present invention.
• the pharmaceutical composition of the present invention may further comprise a pharmaceutically acceptable carrier and further components, e.g., for galenic.
• the pharmaceutical composition is particularly useful for treating diseases or disorders associated with the expression of PD-1 ligands (e.g., PD-L1 or PD-L2) and/or CD40.
• Such diseases and disorders are known to the skilled person and comprise particularly (but not limited to) different types of cancer such as lung cancer, gastric cancer, renal cell cancer, colon cancer, breast cancer, ovarian cancer, urothelial cancer, melanoma, pancreatic cancer, myeloma, Hodkin's lymphoma, retinoblastoma, leukemia, cervical cancer, esophageal cancer, glioma, non-Hodkin's lymphoma, hepatocellular cancer, oral cancer, and others.
• Further diseases and disorders which may be treated by the pharmaceutical compositions provided herein comprise (chronic) viral infections and (chronic) inflammations, particularly for cases where PD-L1/L2 and/or CD40 is expressed.
• the present invention further relates to a kit or kit-in-parts comprising a fusion protein, a nucleic acid molecule, a vector, and/or a host cell as described and provided in context with the present invention.
• the present invention further relates to the following items:
• a fusion protein comprising
• transmembrane domain comprises a polypeptide derived from PD-1 or 4-1 BB, preferably from PD-1 .
• polypeptide derived from PD-1 comprised by said extracellular and/or by said transmembrane domain is a polypeptide derived from human PD-1.
• polypeptide derived from 4-1 BB comprised by said transmembrane and/or by said intracellular domain is a polypeptide derived from human 4-1 BB.
• said fusion protein exhibits PD-L1/2 binding affinity.
• fusion protein of any one of the preceding items, wherein said intracellular domain containing a polypeptide derived from 4-1 BB comprises an amino acid sequence with 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions, deletions, and/or insertions compared to the amino acid sequence of SEQ ID NO: 4,
• said fusion protein is capable of increasing the proliferation rate of a CD8 + T cell when retrovirally transduced into a said CD8 + T cell upon stimulation of said CD8 + T cell with a PD-L1/2 + target cell.
• transmembrane domain containing a polypeptide derived from PD-1 comprises an amino acid sequence with 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions, deletions, and/or insertions compared to the amino acid sequence of SEQ ID NO: 8,
• said fusion protein is capable of increasing secretion of IFNy and/or IL-2 when retrovirally transduced into a CD8 + T-cell upon stimulation of said CD8 + T-cell with a PD-L1/2 + target cell.
• the fusion protein of any one of the preceding items, wherein said extracellular domain comprises the amino acid sequence of SEQ ID NO: 2.
• the fusion protein of any one of the preceding items, wherein said intracellular domain comprises the amino acid sequence of SEQ ID NO: 4.
• transmembrane domain comprises the amino acid sequence of SEQ ID NO: 8.
• a nucleic acid molecule encoding the fusion protein of any one of the preceding items is provided.
• a vector comprising the nucleic acid molecule of item 13.
• a host cell comprising the nucleic acid molecule of item 13 or the vector of item 14.
• the host cell of item 15 which is transduced with the nucleic acid molecule of item 13 or the vector of item 14.
• the host cell of item 16 or 17 which is transduced via retroviral transduction.
• the host cell of any one of items 15 to 18 stably expressing a fusion protein encoded by the nucleic acid molecule of item 13.
• a method of preparing a host cell of any one of items 15 to 20 comprising
• step (1 ) cultivating the transduced host cell of step (1 ) in a suitable medium allowing growth of the cell and expression of the fusion protein encoded by said nucleic acid molecule or said vector;
• a host cell obtainable by the method of item 21.
• a pharmaceutical composition comprising a fusion protein of any one of items 1 to 12, a nucleic acid molecule of item 13, a vector of item 14, and/or a host cell of any one of items 15 to 20 or 22.
• kit or kit-in-parts comprising a fusion protein of any one of items 1 to 12, a nucleic acid molecule of item 13, a vector of item 14, and/or a host cell of any one of items 15 to 20 or 22.
• Figure 1 SEQ ID NO 1 : nucleic acid sequence ECD human PD-1
• SEQ ID NO: 2 amino acid sequence ECD human PD-1
• SEQ ID NO: 3 nucleic acid sequence ICD human 4-1 BB
• SEQ ID NO: 4 amino acid sequence ICD human 4-1 BB
• SEQ ID NO: 5 nucleic acid sequence TMD human 4-1 BB
• SEQ ID NO: 6 amino acid sequence TMD human 4-1 BB
• SEQ ID NO: 7 nucleic acid sequence TMD human PD-1
• SEQ ID NO: 8 amino acid sequence TMD human PD-1
• SEQ ID NO: 9 nucleic acid sequence human PD-1
• SEQ ID NO: 10 amino acid sequence human PD-1
• SEQ ID NO: 1 1 nucleic acid sequence human 4-1 BB
• SEQ ID NO: 12 amino acid sequence human 4-1 BB
• SEQ ID NO: 13 nucleic acid sequence human CD28
• SEQ ID NO: 14 amino acid sequence human CD28
• SEQ ID NO: 15 nucleic acid sequence murine PD-1
• SEQ ID NO: 16 amino acid sequence murine PD-1
• SEQ ID NO: 17 nucleic acid sequence murine 4-1 BB
• SEQ ID NO: 18 amino acid sequence murine 4-1 BB
• SEQ ID NO: 19 nucleic acid sequence murine CD28
• SEQ ID NO: 20 amino acid sequence murine CD28
• SEQ ID NO: 21 nucleic acid sequence human PD-1 :BBTM
• SEQ ID NO: 22 amino acid sequence human PD-1 :BBTM
• SEQ ID NO: 23 nucleic acid sequence human PD-1TM:BB
• SEQ ID NO: 24 amino acid sequence human PD-1TM:BB
• SEQ ID NO: 25 nucleic acid sequence human PD-1 :CD28TM
• SEQ ID NO: 26 amino acid sequence human PD-1 :CD28TM
• SEQ ID NO: 27 amino acid sequence CD40L:CD28 tm with Gly/Ser (G/S) linker and IgGFc spacer:
• SEQ ID NO: 28 amino acid sequence CD40L:CD28 tm with Gly/Ser (G/S) linker and Fil3 spacer:
• PD1 SP signal peptide from PD-1 , first underlined sequence part
• ECD from CD40L aa 1 13-261 261 from SEQ ID NO: 30
• SEQ ID NO: 29 CD28:CD40L tm with inverted CD28 ICD at N-terminus, short CD40 ICD-fragment, TMD from CD40L and ECD from CD40L at C-terminus
• SEQ ID NO: 30 native CD40L sequence
• Figure 2 Design of chimeric PD-1 co-stimulatory receptors
• amino acids (aa) correspond to the respective human parental proteins. Note that for the PD-1 ECD, the signal peptide sequence is removed and thus the mature protein is depicted
• FIG. 3 Chimeric receptor expression on TCR-T58+ CD8+ T cells after retroviral transduction
• Human T cells which stably express the HLA-A2 restricted tyrosinase-specific T cell receptor TCR-T58, were retrovirally transduced with vectors encoding indicated chimeric receptors. T cells were frozen 15 days after transduction for later use. Receptor expression on the T cell surface was evaluated by flow cytometry after defrosting T cells and before T cells were used in co-culture experiments (3 days culture in medium containing 50 U/ml IL-2). Shown are representative FACS histograms demonstrating surface expression of PD- 1 :28 tm , PD-1 :BB tm and PD-1 tm :BB as determined by anti-PD-1 staining. Numbers are the % of receptor-positive cells and the corresponding MFI. Black line histograms and black numbers correspond to isotype staining, red line histograms and red numbers correspond to the PD-1 staining.
• Figure 5 Effect of chimeric receptors on T cell proliferation in the milieu of human melanoma xenografts in NSG mice
• SK-Mel23 human melanoma cells expressing the peptide-MHC complex (pMHC) for TCR-D1 15 T cells (HLA-A2/tyrosinase) were injected s.c. into the flank of immuno-deficient NSG mice.
• T cells CD8 + , CD4 + and CD4 CD8 " double- negative (dbl ) cells
• TCR-D1 15 + CD8 + T cells can be activated by the tumor cells and acquire a dbl " phenotype due to activation.
• CD8 + and dbl " T cells demonstrated comparable CFSE dilution and are represented as one population.
• CD4 + T cells cannot recognize the melanoma cells and, therefore, cannot undergo pMHC-specific proliferation.
• CFSE dilution in CD4 + T cells was not seen until 6 days after T cell injection and most likely occurred due to cytokines produced by the activated CD8 + T cells (not shown).
• CD87dbl " T cells that co- expressed the chimeric receptor PD-1 tm :BB had lower CFSE intensity compared to CD8 + /dbl " T cells without chimeric receptor or expressing the PD- 1 :CD28 tm receptor, respectively.
• CD8 + dbl " T cells displayed comparable CFSE dilution independent of chimeric receptor expression (not shown). The early dilution of CFSE by PD-1 tm :BB expressing T cells indicates that these T cells reacted with the tumor cells more strongly and initiated proliferation earlier than T cells without chimeric receptor or T cells expressing the chimeric receptor PD-1 :CD28 tm .
• FIG. 6 SK-Mel23 human melanoma cells expressing the peptide-MHC complex
• TCR-D1 15 and TCR-T58 T cells HLA-A2/tyrosinase
• CFSE-labelled TCR- D1 15 T cells without co-receptor expression (Mock) and those expressing the chimeric receptor PD-1 tm :BB were injected intratumorally into established xenografts (802 mm3, SEM ⁇ 83, ca. 17 days).
• TCR-D1 15/PD-1 tm :BB T cells reached much higher intratumoral cell numbers on day 2 than T cells without chimeric receptor, and numbers were still elevated at day7. Concomitantly with higher cell numbers, TCR-D1 15/PD- 1 tm :BB T cells achieved good tumor control with reduction in tumor volume compared to starting volume at day 2, and still better tumor control at day 7 (mean fold-change in tumor volume of 1.7 compared to 2 at day 7) (B).
• Figure 7 Projected effects of CD40L:28 chimeric proteins expressed in human T cells.
• trans-effect on transgene-expressing T cells Ligation of the fusion protein on T cells induces CD28 signaling and thus supports TCR signals, CTL effector function, and survival, leading to better tumor killing.
• trans-effect on antigen presenting cells (APC) CD40 activation on APCs will stimulate APC to secrete cytokines (IL-12) and chemokines that will enhance CTL effector function.
• trans-effect on endothelium ligation of CD40 expressed on tumor endothelium will cause endothelial apoptosis, thus destroying the tumor's vascular support.
• trans-effect on tumor cells ligation of CD40 expressed on tumor cells will cause tumor cell apoptosis.
• Figure 8 3 different constructs are created with different linker and orientation of the domains.
• CD40LFc 28; 2) CD40LFil:28; 3) CD40L:28i
• FIG. 9 Expression characteristics of CD40L:28 constructs on human T cells after stable retroviral transduction.
• T cells were co-cultured with primary B cells at 1 :1 ratio for 24 h. Thereafter, cells were harvested and analyzed for CD86 and Fas by flow cytometry. Bars depict the mean fluorescence intensity of analyzed marker on B cells.
• the CD40L-ECD of the chimeric proteins was functionally active as demonstrated by observed higher CD86 and Fas expression on B cells. Similar effect was seen for CD83, another marker of B cell activation (not shown).
• the 3 different constructs showed graded activity, similar or higher than the native CD40L protein.
• TCR-T58 transgenic T cells without chimeric protein (crtl) or TCR-T58 transgenic T cells expressing native CD40L or chimeric proteins after retroviral transduction were co-cultured with melanoma cell lines (SK-Mel23, FM86, positive for the TCR ligand and CD40).
• T cells expressing the chimeric proteins secreted more IFN- ⁇ and exhibited higher cytotoxicity against the tumor cells compared to Ctrl.
• the CD28-ICD of the chimeric proteins is functionally active, i.e. enhancing effector activity of chimeric protein expressing T cells.
• Chimeric receptor sequences were ordered at Geneart, Life Technologies. They were delivered as a lyophilized powder and dissolved in nuclease-free water at a concentration of 0.5 pg/ ⁇ .
• TOP10 or MACH1 E.coli were chemically transformed with the Geneart constructs, following standard plasmid preparation methods.
• Chimeric receptor sequences were cloned into pGEM for ivtRNA preparation. Cloning into the pGEM vector (provided by S. Milosevic, Medigene GmbH, Martinsried, Germany) was achieved using Hindlll or Hindll and EcoRI (New England Biolabs). IvtRNA was generated from pGEM plasmids using the mMESSAGEmMACHINE Kit (Ambion) according to the manufacturer's protocol. Human primary T cells were electroporated with 20 pg ivtRNA at 900 V for 2.3 ms using Gene Pulser Xcell (Bio-Rad).
• Chimeric receptor sequences were cloned into pMP71 -PRE vector (Leisegang 2008, loc. Cit, for retroviral transduction). Retroviral transduction of T cells was achieved as described (Leisegang 2008, loc. cit.).
• Human PBMCs from healthy donors were plated into 24-well plates at a cell density of 1x106/ml per well in RPMI1640 supplemented with 10% human serum, 1 % L-glutamine, 1 % non-essential amino acids, 1 % sodium pyruvate and 1 % penicillin/streptomycin (all Invitrogen) plus 100 U/ml IL-2 (Cancernova) and activated with 5 pg/ml OKT3 (provided by E.
• PBMCs which were activated for 2 days, were added to virus-coated plates for 24 h, then split to freshly virus-coated plates and cultivated for another 3 days. Transduced PBMCs were transferred to uncoated plates and cultivated for at least 12 additional days reducing the amount of IL-2 to 50 U/ml. Receptor expression was determined at day 12 after transduction using anti-PD-1 antibody (BioLegend).
• HEK/Tyr and HEK/Tyr/PD-L1 were generated by transducing HLA-A2+ HEK293 cells to express tyrosinase (HEK Tyr) or tyrosinase and PD-L1 (HEK/Tyr/PD-L1 ). After transduction, HEK293 cells were single-cell cloned and clones selected for comparable HLA-A2 and tyrosinase expression.
• SK-Mel23 gift from M.C.
• HEK/Tyr and HEK/Tyr/PD-L1 were grown in RPMI-1640 supplemented with 1 % L-glutamine, 1 % nonessential amino acids, 1 % sodium pyruvate, 1 % penicillin/streptomycin (RMPI basic) plus 12% FCS.
• LSRII LSRII
• PBS Invitrogen
• human serum 2% human serum
• 0.1 % sodium azide 1% sodium azide
• 2 mM EDTA both Sigma-Aldrich
• Expression of human chimeric receptors and transgenic TCRs was analyzed using anti-CD3-PE-Cy7, anti-mouse TCR ⁇ -constant region-PB (both BioLegend), anti-CD4- APC-A780, anti-PD-1 -APC (both eBioscience), anti-CD8-V500 (BD) and 7-AAD (Sigma- Aldrich).
• HEK293 cells were analyzed using anti-HLA-A2 (ATCC HB54) plus anti-mouse lgG1-A488 (Invitrogen), anti-PD-L1-FITC (BD), anti-tyrosinase (Upstate) plus anti-mouse lgG2a-A647 (Invitrogen) and 7-AAD.
• T cells after injection into xenograft tumors were analyzed using CFSE, anti-CD45-PE-Cy7, anti-CD8-PB (BD), CD4-APC-A780, anti-PD-1 -APC and 7-AAD.
• CD45+ leukocytes were selected and CFSE intensity was analyzed in CD8 + , CD4 + and dbl- cells after gating on viable and single cells. Data were analyzed using FlowJo 8.8.7 software.
• BD sandwich ELISA
• Bio-Rad Bio-Plex
• the amount of measured cytokine was normalized to the percentage of TCR + CD8 + T cells within the cell suspension (determined by flow cytometry). The following formula was applied:
• NSG mice were obtained from Charles River. NOD/scid IL2Rgnull (NSG) mice were bred on the genetic background of non-obese diabetic (NOD) mice characterized by reduced innate immunity. NSG mice carry the prkdcscid mutation, a loss-of-function mutation in the PRKDC gene, leading to defective repair of DNA strand breaks during V(D)J recombination in the development of B and T cells. This severe combined immunodeficiency (scid) is characterized by a major reduction of T and B cells. Additionally, NSG mice carry a null mutation in the IL-2 receptor gamma chain (IL2Rgnull) blocking NK cell differentiation. The impairment of innate immunity and absence of adaptive immunity render NSG mice a good model system for adoptive T cell therapy of human tumor xenografts.
• NSG mice NOD/scid IL2Rgnull
• mice were injected s.c. with 5 x 106 HLA-A2+ tyrosinase + human melanoma cells SK-Mel23 (gift of Monica C. Panelli, NIH, Bethesda, USA).
• This melanoma line was selected because it expresses PD-L1/L2 as well as HLA-A2 and tyrosinase, which are required to form the ligand for TCR-D1 15 and TCR-T58 (Wilde et al., Blood (2009), 1 14: 2131 -2139).
• T cells expressing TCR-D1 15 were selected for the mouse experiment as they can recognize SK-Mel23 with low avidity which is not sufficient to eradicate established tumors.
• Cell tracer dyes i.e CFDA-SE
• CFDA-SE Cell tracer dyes
• CFSE fluorescent carboxyfluorescein succinimidyl esters
• TCR-D1 15 T cells without or with chimeric receptor expression were labeled with 0.15 ⁇ CFDA-SE for 8 minutes at 37°C.
• the reaction was stopped with FCS, T cells were washed twice with PBS and re-suspended in PBS at a concentration of 10 x 107 cells per ml.
• Tumors were harvested 1 , 2, 4, 6 and 1 1 days after i.t. injection.
• Single cell suspensions were prepared by mechanical and enzymatic digestion (Prinz et al., J Immunol (2012), 188: 5990-6000) and used for flow cytometry analysis.

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