Means and methods for producing high affinity antibodies
10344076 ยท 2019-07-09
Assignee
Inventors
- Tim Beaumont (Ouderkerk a/d Amstel, NL)
- Mark Jeroen Kwakkenbos (Amsterdam, NL)
- Hergen Spits (Amsterdam, NL)
- Adrianus Quirinus Bakker (Hoorn, NL)
Cpc classification
C07K16/1027
CHEMISTRY; METALLURGY
C07K2317/76
CHEMISTRY; METALLURGY
C07K2317/14
CHEMISTRY; METALLURGY
C07K2317/92
CHEMISTRY; METALLURGY
C07K16/00
CHEMISTRY; METALLURGY
International classification
C12N15/63
CHEMISTRY; METALLURGY
C07K17/00
CHEMISTRY; METALLURGY
C07K16/00
CHEMISTRY; METALLURGY
Abstract
The invention provides means and methods for modulating the occurrence of somatic hypermutations in antibody producing plasmablast-like B-cells.
Claims
1. A method of antibody production, the method comprising: introducing an exogenous nucleic acid molecule encoding Bcl 6 into a B cell; introducing an exogenous anti-apoptotic nucleic acid molecule into said B cell, thus generating an antibody producing plasmablast-like B cell with functional AID activity; selecting an antibody producing plasmablast-like B cell that produces an antibody of interest; and reducing expression and/or activity of AID in said B cell thereby reducing the occurrence of somatic hypermutations in said B-cell.
2. The method according to claim 1, wherein the expression and/or activity of AID is reduced in said B cell by introduction of a molecule that interferes with the homo- or heterodimerization of E47 and/or E12.
3. The method according to claim 1, wherein the expression and/or activity of AID is reduced in said B cell by introduction of an exogenous nucleic acid molecule encoding an ID protein.
4. The method according to claim 1, wherein the expression and/or activity of AID is reduced in said B cell by introduction of an antisense nucleic acid or ribozyme directed against E12 and/or E47.
5. The method according to claim 1, wherein the expression and/or activity of AID is reduced in said B cell by introduction of a dsRNA molecule that induces E12 or E47 mRNA degradation.
6. The method according to claim 1, wherein the expression and/or activity of AID is reduced in said B cell by introduction of a zinc-finger protein that has been modified to be able to bind to the promoter region of AID and which is coupled to a transcriptional repressor domain.
7. The method according to claim 1, wherein the anti-apoptotic nucleic acid comprises a gene of the BCL2 family.
8. The method according to claim 7, wherein the gene of the BCL2 family is Bcl-xL or Mcl 1, or a functional part thereof.
9. The method according to claim 1, wherein the B-cell is cultured in the presence of IL21 and CD40L.
Description
FIGURE LEGENDS
(1)
(2)
(3)
(4)
(5)
(6)
(7)
(8)
(9)
(10) Transduction of human IgG+ memory B cells with BCL6, Bcl-xL and MCL-1. Shown are FACS analysis of the percentage of GFP (BCL6 or BCL6 and Bcl-xL) and NGFR (Bcl-xL or MCL-1) expressing cells 4 days and 21 days after transduction.
(11)
(12)
(13)
(14)
(15)
(16) Relative expansion of number of double transduced cells. Cultures of BCL6, Bcl-xL and MCL1 co-transduced cells were taken 21 days post transduction and were started with equal cell numbers and were set to 1. BCL6/Bcl-xL and BCL6/MCL-1 culture are 100% double transduced at day 21. BCL6/Bcl-xL and MCL-1 was 86% double transduced at day 21 and approximately 96% at day 43. Expansion of BCL6/Bcl-xL and MCL-1 transduced cells is equal to the expansion of BCL6 Bcl-xL transduced cells. Numbers of cells expand at least till day 43 post transduction.
(17)
(18)
EXAMPLES
(19) Methods
(20) B-cell isolation. We obtained B-cells from peripheral blood (huffy coats from Sanquin) by Ficoll separation and CD22 MACS microbeads (Miltenyi Biotech). Subsequently we sorted these cells for CD19.sup.+ CD3.sup.CD27.sup.+ IgM.sup.IgA.sup. (IgG memory cells) or CD19.sup.+ CD3.sup.CD27.sup.+ IgG.sup.IgA.sup. (IgM memory cells) on a FACSAria (Becton Dickinson).
(21) Tonsil B-cell sorting. We obtained Tonsil B-cells from routine tonsillectomies performed at the Department of Otolaryngology at the Academic Medical Center, Amsterdam, The Netherlands. We separated B-cells by Ficoll and sorted the CD19+CD3CD44IgD GC population. The use of these tissues was approved by the medical ethical committees of the institution.
(22) Cell culture. We maintained B-cells (210.sup.5 cells ml.sup.1) in IMDM (Gibco) culture medium containing 8% FBS (Gibco), penicillin/streptomycin (Roche) supplemented with recombinant mouse IL 21 (25 ng ml.sup.1, R&D systems) and co-cultured them on .gamma.-irradiated (50Gy) mouse L cell fibroblasts stably expressing CD40L (CD40L-L cells, [[0.10.sup.5]]10.sup.5 cells ml.sup.1). We tested cells routinely by PCR for the presence of mycoplasma and EBV.
(23) Retroviral transduction. The BCL6, ID2 and ID3 retroviral constructs were described previously (Shvarts, A. et al. Genes Dev 16, 681-6 (2002); Jaleco, A. C. et al. Blood 94, 2637-46 (1999); Spits H. et al. J Exp Med 192, 1775-83 (2000)). In brief, we have constructed bicistronic vectors with a gene of interest linked to a downstream internal ribosomal entry site (IRES) and a marker gene that allow independent translation of the products of both genes in the transduced target cells. The ID3 coding sequence was cloned from the pCDNA-Id3 plasmid (gift of Dr C. Murre, University of California at San Diego, San Diego, Calif.). The product was ligated between the Xho I and SnaBI site of the polylinker from our plasmid LZRS-linker-IRES-GFP and/or YFP to obtain the retroviral vector LZRS-Id3-IRES-GFP.
(24) The coding sequence of human ID2 was cut from the pSG5-Id2 vector (a gift of Dr. R. de Groot, University of Utrecht, Utrecht, Netherlands) with Not1 and was ligated in the Not1 site of polylinker from our plasmid LZRS-linker-IRES-GFP and/or YFP. A codon optimized sequence of the phosphorylation-site mutant (S159A) of human MCL-1 (Maurer, U. et al. Mol Cell 21, 749-760 (2006)) was ordered from GeneArt (Regensburg Germany) and cloned into the LZRS retroviral vector. Human Bcl-xL cDNA was cloned into the LZRS retroviral vector and helper-free recombinant retroviruses were produced after transfection into a 293T-based amphotropic retroviral packaging cell line, Phoenix (Kinsella, T. M. et al Hum Gene Ther 7, 1405-1413 (1996)). Human memory B-cells were co-transduced by the different retroviruses after activation on CD40L-L cells in the presence of rmIL-21 for 36 hrs as before (Diehl, S. A. et al. J Immunol 180, 4805-15 (2008)), but in addition cells and virus were centrifuged at room temperature for 60 min at 360g (1800 RPM).
(25) Flow cytometry. We analyzed stained cells on an LSRII (BD) and processed flow cytometry data with FlowJo software (Tree Star). We purchased the following mAbs against the human molecules from BD-Pharmingen unless otherwise indicated CD3 (SK7), CD10 (HI10a), CD19 (SJ25C1), CD20 (B9E9; Beckman Coulter), CD21 (B-ly4), CD22 (B-ly8; IQ Products), CD25 (BC96; eBioscience), CD27 (0323; eBioscience), CD30 (BerH8), CD38 (HB7), CD40 (MAB89; Beckman Coulter), CD70 (Ki24), CD71 (YDJ1.2.2; Beckman Coulter), CD80 (L307.4), CD86 (2331), CD95 (DX2), CD132 (TUGh4), CD184 (CXCR4, 12G5), CD271 (LNGFR; ME20.4-1.H4; Miltenyi Biotech), CD275 (MIH12; eBioscience), HLA-DR (L243), IgA (F(ab)2; DAKO), IgD (IA6-2), IgG (G18-145), IgM (G20-127) (BD), IL-21R (152512; R&D systems), Ig-kappa (F(ab)2; DAKO, G20-193), and Ig-lambda (F(ab)2; JDC12, DAKO).
(26) RT-PCR. We carried out quantitative RT-PCR with a BioRad iCycler and used the 2.sup.(AACT) method to calculate relative mRNA expression levels normalized to ACTIN. Primers for AICDA (encoding AID) are described (Smit, L. A. et al. Cancer Res 63, 3894-8 (2003)).
(27) ELISA. We coated plates with anti-human IgG Fc-fragment (Jackson ImmunoResearch Laboratories) at 5.mu.g ml.sup.1 in PBS for 1 h at 37. C. or o/n at 4. C. and washed them in ELISA wash buffer (PBS, 0.5% Tween-20). 4% milk in PBS was used as blocking agent, before we added serial dilutions of cell culture supernatants and HRP-conjugated detection Abs (dilutions 1:2500 for HRP-conjugated IgG antibody (Jackson). We used TMB substrate solution (Biosource) for development of the ELISAs.
(28) Cloning and sequencing of mutants of D25. We isolated total RNA using the RNeasy mini kit (Qiagen), generated cDNA and performed the VH1-69 PCR to determine the sequence of the D25 subclones. From interesting clones (#29, #59, #77, #189) the heavy chain variable region was cloned into the pCR2.1 TA cloning vector (Invitrogen). To rule out reverse transcriptase or DNA polymerase induced mutations, we performed several independent cloning experiments. To produce recombinant D25 mAb we cloned D25 mutated heavy and original light variable regions in frame with human IgG1 and Kappa constant regions into a pcDNA3.1 (Invitrogen) based vector and transiently transfected 293T cells. VL sequences of D25 subclones were also determined but did not harbor any mutations compared to the original D25 light chain sequence. We purified recombinant D25 from the culture supernatant with Protein A.
(29) Results
(30) Human Peripheral Memory B-Cells Transduced with BCL6 and Bcl-xL Resemble GC-Like B-Cells
(31) We showed that overexpression of BCL6 and Bcl-xL (which are expressed in Germinal center (GC) B-cells and are under control of STATS (Scheeren, F. A. et al. Nat Immunol 6, 303-13 (2005); PCT/NL2008/050333)) synergize to increase the proliferative and survival potential of human memory B-cells in vitro when cultured on irradiated CD40L expressing L cells (CD40L-L cells) in the presence of IL 21. Normal human B-cells rapidly differentiate to antibody-producing plasma cells when cultured on CD40L-L cells in the presence of IL 21 (Ettinger, R. et al. J Immunol 175, 7867-79 (2005)) which is accompanied by a decrease in expression of surface BCR and MHC class II and an increase in expression of CD38 (Liu, Y. J. & Arpin, C. Immunol Rev 156, 111-26 (1997)). In contrast to non-transduced cells or cells expressing Bcl-xL only in the same culture, BCL6-only and BCL6+Bcl-xL cells both retained BCR expression and were HLA-DRhighCD38 intermediate (
(32) BCL6+Bcl-xL positive B-cells expanded with CD40L and IL 21 express CD19, CD20, CD21 and CD22, the activation markers CD25, CD30, CD70, CD80, CD86, CD95, ICOSL, and the cytokine receptors CD132c) and IL-21R. These cells express CD38 and CD20 at levels equivalent to tonsil GC cells. The expression of CD27, CXCR4, CD71, CD10 and HLA-DR on transduced cells is consistently higher compared to freshly isolated tonsil GC cells (
(33) BCL6+Bcl-xL transduced cells expressed AICDA (encoding the enzyme AID) at levels comparable to those expressed by freshly isolated GC B-cells (
(34) Anti-RSV Antibody D25 and D25 Mutants
(35) BCL6+Bcl-xL transduced B-cells secrete relatively high amounts of antibodies. Thereby we could select antigen-specific B-cells on the basis of secretion of specific antibody. We chose the pathogenic Respiratory Syncytial virus (RSV) as the antigenic moiety. RSV is the most common cause of bronchiolitis and pneumonia among infants and children under 1 year of age and is a serious health problem for elderly people (Thompson, W. W. et al. JAMA 289, 179-86 (2003); Hall C. B. et al NEMJ 360, 588-599 (2009)). BCL6+Bcl-xL transduced memory B-cells of a healthy donor were expanded with CD40L-L cells and IL 21 and screened for the presence of RSV-neutralizing antibodies in a microneutralization experiment (Johnson, S. et al. J Infect Dis 180, 35-40 (1999)). One of the antibodies, D25, with highest neutralizing activity was cloned by limiting dilution and further characterized (PCT/NL2008/050333). We observed median half maximum inhibitory concentrations (IC50) against the RSV-A2 virus in the range of 2.1 ng ml.sup.1.
(36) Before we studied the functional activity of AID in the D25 cell line we analyzed the AICDA expression in 23 monoclonal cell lines by real-time PCR. AID expression in these cell lines was variable. Several clones expressed levels similar to GC tonsil B-cells, whereas others were AICDA low (
(37) While the supernatants of the majority of D25 subclones bound to RSV-infected HEp2 cells similar to recombinant D25, some of those clones bound either less or better than D25 (
(38) Regulation of AID Expression in Bcl6+Bcl-xL Transduced B Cells
(39) For some applications it is desirable to inhibit AID to prevent accumulation of mutations in the Ig genes of BCL6+Bcl-xL transduced B-cell clones. To achieve this we took advantage of the fact that AID is regulated by the basic Helix Loop Helix transcription factor E47 (Sayegh, C. E., et al. Nat Immunol 4, 586-93 (2003)). We overexpressed the Helix loop Helix factor inhibitors of DNA binding ID2 and ID3 which are known to form transcriptionally inactive complexes with E47, thereby inhibiting AID expression (Sayegh, C. E., et al. Nat Immunol 4, 586-93 (2003)). As shown in
(40) Function of D25 is Altered by Amino Acid Substitution Due to AID Activity
(41) We wondered if we might find new subclones of D25 that show an altered function. However, since the affinity of D25 for it putative target, the RSV Fusion (F) protein is already high and D25 neutralizes RSV already at low concentration it was difficult to find clones that would be better than D25 itself. Nevertheless we tested the B-cell culture supernatant of the D25 subclones twice for binding to RSV infected HEp2 cells and once for competition with PE-labeled D25. These experiments gave variable results (data not shown) but when all the top 25 antibodies from each data set were compared with the VH sequences some very interesting amino acid position appeared. Several D25 subclones were produced as recombinant protein of which clone #59 still had the same configuration as the original D25 clone, #77 contained a very typical mutation at position 107 (E107K), that seem to cause a reduced binding to RSV infected HEp2 cells since other clones that lost binding to infected HEp2 cells also gathered this mutation. Furthermore clone#29 (S83Y/V111I/V112L) and #189 (G63D/V111I/V112L) share a mutation at position 111 and 112 (V.fwdarw.I and V.fwdarw.L). These two clones replace the original D25 antibody from binding to RSV infected HEp2 cells (
(42) Expression of the Anti-Apoptotic Gene MCL-1 Alone or in Combination with BCL6 and/or Bcl-xL Increases Survival and Proliferation of Human B Cells
(43) Since B cell cultures with BCL6 alone and co-stimulated with CD40L and 11-21 show a block in differentiation toward plasmablasts but lack the signals for enhancing survival and proliferation, we studied besides Bcl-xL also the role of the anti-apoptotic molecule MCL-1 in this process. When activated CD19.sup.+ CD27.sup.+ IgM.sup.IgA.sup.memory cells were transduced with: (i) BCL6-GFP and MCL-1-NGFR, or (ii) BCL6-GFP and Bcl-xL-NGFR or (iii) BCL6-Bcl-xL-GFP and MCL-1-NGFR (
(44) Regulation of AID Expression in Bcl6+Mcl-1 Transduced B Cells
(45) As shown above for the BCL6+Bcl-xL transduced B-cell clones, ID2 and ID3 are also overexpressed in Bcl6+Mcl-1 transduced B cells, thereby inhibiting AID expression (Sayegh, C. E., et al. Nat Immunol 4, 586-93 (2003)).
(46) Subsequently, it is demonstrated, for instance by using quantitative RT-PCR, overexpression of both ID2 and ID3 reduce AICDA levels in these cells. Thus increasing ID2 and/or ID3 levels provides a method to prevent AID
(47) induced mutations in BCL6+Mcl-1 transduced B-cells. The procedures are described in the Methods section above.
REFERENCES
(48) Adams J. M. et al. Current Opinion in Immunology 19, 488-496 (2007) Banchereau J et al. Science 251, 70-72 (1991) Baron, U. and Bujard, H. Methods Enzymol 327, 401-21 (2000) Boise, L. H. et al. Cell 74, 597-608 (1993) Chipuk, J. E. et al. Trends in Cell Biol 18, 157-163 (2007) Christopherson, K. S. et al. PNAS 89, 6314-8 (1992) Close, P. M., et al. J Pathol 162, 209-16 (1990) Diehl, S. A. et al. J Immunol 180, 4805-15 (2008) Ettinger, R. et al. J Immunol 175, 7867-79 (2005) Good, K. L et al. J Immunol 177, 5236-47 (2006) Gossen, M. and Bujard, H. Proc Natl Acad Sci USA 89, 5547-51 (1992) Gossen, M. et al. Science 268, 1766-9 (1995) Guzman, L. M. et al. Bacteriol 177, 4121-4130 (1995) Hall C. B. et al. NEMJ 360, 588-599 (2009) Ichikawa H. T. et al. J Immunol 177, 355-361 (2006) Johnson, S. et al. J Infect Dis 180, 35-40 (1999) Kee B. L. Nat Rev Immunol 9, 175-84 (2009) Kinsella, T. M. et al Hum Gene Ther 7, 1405-1413 (1996) Kuo, T. C. et al. J Exp Med 204, 819-830 (2007) Liu, Y. J. & Arpin, C. Immunol Rev 156, 111-26 (1997) Maurer, U. et al. Mol Cell 21, 749-760 (2006) Muramatsu, M. et al. J Biol Chem 274, 18470-6 (1999) Peled, J. U. et al. Annu Rev Immunol 26, 481-511 (2008) Rousset F et al. PNAS 89, 1890-1893 (1992) Sayegh, C. E., et al. Nat Immunol 4, 586-93 (2003) Scheeren, F. A. et al. Nat Immunol 6, 303-13 (2005) Sidwell, R. W. & Barnard, D. L. Antiviral Res 71, 379-90 (2006) Smit, L. A. et al. Cancer Res 63, 3894-8 (2003) Spits H. et al. J Exp Med 192, 1775-83 (2000) Tan S et al. PNAS 100, 11997-12002 (2003) Thompson, W. W. et al. JAMA 289, 179-86 (2003) Zamore et al. Cell 101, 25-33 (2000)