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Molecular Biology and Genetics |
Departments of Molecular Oncology [J. B. B. R., E. N., P. C.], Molecular Biology [J. L., J. B., A. G.], and Protein Chemistry [J. A. K.], Genentech Inc., South San Francisco, California 94080
| ABSTRACT |
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| INTRODUCTION |
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The traditional approach to obtaining tumor-specific antibodies has been to immunize mice with tumor cells and to screen the resultant monoclonal antibodies for their binding specificity. Unfortunately, tumor-binding antibodies obtained in this way often cross-react with many normal cells, which may interfere with their clinical use. Ideally, one would like to select rather than screen for antibodies that bind selectively to tumor. The advent of antibody fragment display on phage (12) and the development of large (>6 x 109 clones) phage display libraries (13, 14, 15) offer a potential way of doing this by panning using tumor cells and counter-selecting using nontumor cells. An additional advantage of antibody phage is that, unlike hybridoma technology, it is readily possible to obtain antibodies binding antigens that are highly conserved between mouse and man (16) .
Naïve antibody phage libraries have proved to be a rapid and general method for identifying antibodies binding to purified antigens (13, 14, 15, 16) . In contrast, panning cellular targets with antibody phage has proved much more difficult because of the much lower effective antigen concentration, greater antigen complexity, and the tendency of phage to bind nonspecifically to cells. Nevertheless, significant progress has been made, allowing the identification of antibodies against cell surface antigens (17, 18, 19, 20, 21, 22, 23) . Indeed, melanoma-specific antibodies have been identified by selecting for antibody phage that bind to melanoma cells, but not melanocytes, using antibody phage libraries constructed from human donors immunized with their own tumor cells (21, 22, 23) .
We have extended the use of antibody phage libraries for panning on live tumor cells by using a large naïve library (14) . This obviates the need for creating custom libraries from immunized donors (21 , 23) . In addition, live rather than fixed cells (21, 22, 23) were used for screening to facilitate the identification of antibodies that bind to native rather than denatured antigens. This was done to facilitate subsequent expression cloning of corresponding antigen, as well as enhance the therapeutic potential of antibodies obtained. Indeed, we cloned the antigen corresponding to a scFv4 fragment identified with significant tumor selectivity.
| MATERIALS AND METHODS |
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Live Cell Panning with scFv Phage.
An aliquot containing 2.5 x 1012 cfu phage, from a large human scFv phage library (14)
was blocked with 500 µl of RPMI containing 10% (v/v) FBS, 1 mM phenylmethylsulfonyl fluoride, and 2.5 mM EDTA to reduce nonspecific binding to cell surfaces. The blocked phage were added to 1 x 106 BEAS-2B cells in 500 µl of RPMI/DMEM/FBS and mixed gently for 30 min at
20°C. Cells were then pelleted, at this and subsequent panning steps, by centrifugation at 500 x g for 5 min at 4°C. The phage-containing supernatant was used to resuspend a fresh pellet of 1 x 106 BEAS-2B cells and was incubated for 30 min at
20°C, followed by pelleting the cells. After repeating this counter-selection step, the resultant "subtracted" phage supernatant was incubated with 5 x 106 1264 cells for 1 h at
20°C with gentle mixing. The cells were pelleted and washed three times with PBS. The cell-bound phage were eluted with 0.5 ml of PBS containing 100 mM citric acid (pH 2.2) for 10 min and then neutralized with 0.5 ml of 1.0 M Tris-HCl (pH 7.5).
Escherichia coli strain TG1 (New England Biolabs, Beverly, MA) in mid-logarithmic growth phase (A550 = 0.40.8) was infected with the eluted phage and plated on 2YT agar containing 2% (w/v) glucose and 50 µg/ml carbenicillin (2YTGC). The resultant colonies were propagated and used to prepare phage (24)
. An aliquot containing
1 x 1012 cfu phage was used for a second round of panning, consisting of five counter-selections using 1 x 106 BEAS-2B cells, followed by selection using 1 x 107 1264 cells for
15 h at
20°C. After 10 washes with PBS, the cell-bound phage were eluted and then neutralized as in the first round of panning. The eluted phage were propagated, and a third round of panning was performed using 1.0 x 1012 cfu phage and the second round protocol.
Cell ELISA with Phage.
The scFv-phage were compared in their binding to live tumor and nontumor cells by ELISA as a primary screen of their binding specificity. After the third round of panning, a culture of TG1 was infected with the eluted phage and plated on 2YTGC. Clones for analysis were transferred into 96-well plates with 100 µl of 2YT media containing 2% (w/v) glucose and carbenicillin (100 µg/ml) and grown for
18 h with agitation at 30°C. Glycerol (50 µl 50%, v/v) was added to each well of these master plates before storage at -70°C.
Replicas of the master plates were prepared, and scFv-phage were induced by superinfection with M13KO7 helper phage and overnight incubation at 30°C (24)
. The plates were centrifuged (300 x g, 5 min, 4°C) at this and subsequent cell ELISA steps to pellet the bacteria, and 100 µl of scFv-phage-containing supernatants were transferred to 96-well plates containing 100 µl of 6% (w/v) BSA in PBS/well. Blocked scFv-phage supernatants (100 µl) were added to parallel plates containing either 1 x 105 1264 or BEAS-2B cells/well (1 h, 4°C, gentle agitation). The plates were centrifuged, and supernatants were aspirated without disturbing the pellets. The cells were washed twice by resuspension in 200 µl of 4% (v/v) FBS in PBS (ELISA buffer) at 4°C, followed by centrifugation. Pellets were then resuspended in 100 µl of ELISA buffer containing a 1:5,000 dilution of horseradish peroxidase conjugated to a sheep anti-M13 polyclonal (Amersham Pharmacia Biotech, Piscataway, NJ) and incubated for 20 min at 4°C. Cells were centrifuged and washed three times in ELISA buffer. Cell pellets were resuspended in 100 µl of TMB reagents (Kirkegaard and Perry Laboratories, Inc., Gaithersburg, MD) and developed for
10 min before quenching with 100 µl of 1 M phosphoric acid. The ELISA plates were read (A450-A650) using a Spectramax 340 microtiter plate reader (Molecular Devices, Sunnyvale, CA), and data were analyzed using a spreadsheet program (Microsoft Excel 5.0a).
Flow Cytometry with Phage and scFv.
Culture supernatants containing scFv phage were incubated with cells and washed, as described above, for the cell ELISA with the following modifications. The anti-M13 polyclonal antibody was used in unconjugated form. After washing, the cells were incubated for 20 min at 4°C with an R-phycoerythin-conjugated F(ab')2 fragment from a donkey antisheep IgG (Jackson Immunoresearch Laboratories, West Grove, PA) diluted 1:200 in ELISA buffer, followed by three washes and resuspension in 0.5 ml of ELISA buffer. Cells were analyzed using a FACScan flow cytometer (Beckton and Dickinson, Mountain View, CA).
For cytometric analysis with scFv fragments, 1 x 105 cells in ELISA buffer were incubated for 1 h at 4°C with 3 µg/ml scFv fragment. The cells were washed twice by centrifugation and resuspension in ELISA buffer. Cell pellets were then resuspended in 100 µl of ELISA buffer containing 1 µg/ml BMG-His1 (Boehringer Mannheim, Indianapolis, IN), the antihexahistidine monoclonal antibody. Cells were washed three times in ELISA buffer before resuspension in 100 µl of ELISA buffer containing a 1:200 dilution of a F(ab')2 fragment of a goat antimouse IgG conjugated with FITC (Jackson Immunoresearch Laboratories). After three additional washes, the cells were analyzed by flow cytometry.
Quantitation of Cell Surface DAF.
The mean number of DAF molecules/cell was estimated by flow cytometry using a FITC-labeled antibody in comparison with FITC-conjugated beads, using the method of Christensen and Leslie (25)
, with the following modifications. Murine anti-DAF monoclonal antibody 1A10 (250 µg; Genentech Inc.) in 50 mM sodium carbonate (pH 8.5) was incubated with 12 µg of N-hydroxysuccinimidyl-fluorescein (Pierce Chemical Co., Rockford, IL) for 2 h at 20°C, followed by extensive dialysis against PBS. The molar ratio of FITC to protein was determined from the absorbance at 280 nm and 492 nm (25)
. Cells were incubated with varying levels of the FITC-labeled anti-DAF antibody to achieve saturation and then prepared for flow cytometry, as above.
Clone Diversity Analysis.
The diversity of antigen-positive clones was analyzed by PCR-amplification of the scFv insert using the primers fdtetseq and PUC19 reverse (16)
, digestion with BstNI (24)
, and analysis by PAGE. Comparison of BstNI fingerprints was facilitated by digitization of the gel data using an AlphaImager (Alpha Innotech Corp., San Leandro, CA) and analysis using ProRFLP version 2.34 (DNA ProScan, Nashville, TN). Up to 10 clones/BstNI fingerprint were then cycle-sequenced using rhodamine-labeled dideoxy chain terminators (Applied Biosystems, Foster City, CA), using M13 reverse (New England Biolabs) and mycseq10 primers (16)
. Samples were analyzed using Applied Biosystems Automated DNA Sequencers (models 373 and 377), and sequence data were analyzed using the program Sequencher version 3.1 (Gene Codes Corp., Ann Arbor, MI).
scFv Production.
Selected scFv clones were transformed into E. coli strain 33D3 (W3110 tonA ptr3 phoA
E15 lacIqlacL8 degP kanR; Ref. 26
) and cultured for 18 h at 30°C in 2YT media containing 0.2 mM isopropyl-ß-D-galactopyranoside to induce scFv expression. Periplasmic extracts were prepared by resuspending a bacterial pellet from a 500-ml culture in 10 ml of 50 mM sodium phosphate buffer (pH 8.0) containing 0.5 M NaCl, 25 mM imidazole, 0.2 mg/ml hen egg white lysozyme, and 1 mM phenylmethylsulfonyl fluoride. After incubation for 1 h at 4°C, the debris was removed by centrifugation. Supernatants were filtered (0.2 µm) and, the His-tagged scFv fragments were purified by immobilized metal affinity chromatography using Ni2+-nitrilotriacetic acid agarose (Qiagen, Valencia, CA). The scFv fragments were eluted with 250 mM imidazole in PBS, then dialyzed into PBS, flash frozen, and stored at -70°C. Clones LU1, LU4, LU13, LU20, and LU30 were grown to high cell density in the fermenter, as described previously (27)
. scFv fragments were purified from 2 g of fermentation pastes, as for cell pellets from shake flasks.
cDNA Library Construction.
Total cellular RNA was purified from guanidine thiocyanate homogenates from 6 g of cultured 1264 cells (28)
. mRNA was isolated from the total RNA using oligo-d(T) cellulose (Collaborative Research, Bedford, MA; Ref. 29
). Oriented cDNA transcripts were prepared from 5 µg of poly(A)+ mRNA using the SuperScript Plasmid System (Life Technologies, Inc., Gaithersburg, MD), fractionated by electrophoresis on a 5% polyacrylamide gel, and size selected in the ranges of 0.62.0 kb and >2 kb. Eluted cDNAs were ligated into the XhoI and NotI sites of the mammalian expression vector pRK5 (30)
and then electroporated into DH10B (Life Technologies, Inc.) cells under conditions recommended by the supplier.
Antigen Expression Cloning from cDNA Library.
DNA from 10 pools of 50,000 clones each of the 0.62 kb and
2 kb cDNA libraries was prepared for expression cloning the antigens recognized by tumor-selective scFv fragments. Plasmid DNA (10 µg) from each of the 20 pools was electroporated into 2 x 106 COS7 cells in 180 µl of PBS using 4-mm gap cuvettes with a Gene Pulser electroporator (Bio-Rad, Hercules, CA) with an applied voltage of 300 V and a capacitance of 125 µF. After incubation for 72 h at 37°C, the COS7 cells were detached with 2.5 mM EDTA in PBS. The cells were washed and then incubated in 1 ml of growth media containing one or more purified scFv fragment (10 µg/ml each) for 1 h at 4°C. The cells were washed twice to remove unbound scFv, resuspended in 1 ml of media containing 5 µg of anti-penta-histidine antibody (Qiagen) and incubated for 1 h at 4°C. After two to three washes, the cells were resuspended in 5 ml of media and transferred to a polystyrene dish coated with a polyclonal antimouse IgG (ICN/Cappel, Aurora, OH) and allowed to bind for 1 h at 4°C. Plates were washed gently three to four times with PBS. Remaining attached cells were lysed, plasmid DNA-extracted, and amplified (31)
. This DNA was then electroporated into COS7 cells for additional panning. In one case, an increasing number of cells were captured during the second to fourth rounds of panning. Plasmid DNA extracted from the COS7 cells was transformed into TG1, and single colonies were picked into 96-well plates. DNA was prepared from pools of 1020 clones each, electroporated into COS7 cells, and panned with scFv fragments, as described above. Pools of clones positive for cells binding to the Petri dishes were broken down from the E. coli master plates, and individual clones were tested by panning. An individual positive clone was cycle-sequenced using rhodamine-labeled dideoxy chain terminators.
Affinity Measurements.
Kinetic measurements were made by surface plasmon resonance using a Biacore 1000 Biosensor (Biacore, AB Uppsala, Sweden). CM-5 chips were functionalized with 350 response units of recombinant human DAF in 10 mM sodium acetate (pH 4.6) or 8000 response units of BSA as a negative control. The DAF-derivatized chip was saturated with LU30 scFv (25100 nM) by injecting this fragment at 10 µl/min in PBS containing 0.5% (w/v) BSA and 0.05% (v/v) Tween 20. The resultant sensorgrams were analyzed using BIAevaluation software 3.0.
| RESULTS |
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The number of phage recovered after one, two, and three rounds of panning was 1.5 x 107, 7.0 x 105, and 4.0 x 106 cfu, respectively. The phage populations after each round of panning were analyzed by flow cytometry. The phage from the third round showed a large increase in binding to 1264 cells and a slightly smaller increase with BEAS-2B cells when compared with phage from prior rounds and unselected phage (Fig. 1)
. This apparent differential increase in binding to 1264 over BEAS-2B cells encouraged us to screen individual phage from the third round population for selective binding to the 1264 tumor cells.
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0.3) and much weaker if detectable binding to BEAS-2B cells (
10-fold lower ELISA signal). The diversity of clones satisfying these primary criteria was assessed by BstNI fingerprinting of the PCR-amplified scFv fragments, and nucleotide sequencing of up to 10 clones/fingerprint pattern. A small number of clones that did not satisfy the primary criteria were also fingerprinted (n = 29) and sequenced (n = 11). Secondary criteria were then used to choose unique and apparently tumor-selective clones for further analysis: (a) open reading frame for scFv; and (b) majority of clones that share the same nucleotide sequence also satisfy the primary selection criteria.
As anticipated, the majority of clones assayed show detectable binding to 1264 cells by phage ELISA, many with limited cross-reactivity to BEAS-2B cells (Fig. 2)
. Of 673 clones analyzed, 239 satisfied the primary criteria for selective binding, and 197 clones could be assigned to 15 different BstNI fingerprint patterns (Table 1)
. In the majority of cases (13 of 15), one fingerprint pattern gave rise to a single nucleotide sequence, whereas in 2 of 15 cases, two different sequences were found with indistinguishable BstNI fingerprint patterns. Thus, a total of 17 scFv clones that satisfy the secondary selection criteria were identified. The two most abundant clones, fingerprints types 1 and 2, represented
80% of the clones satisfying the secondary criteria. In contrast, the other 15 clones each represent
5% of the clones identified. Four of the 17 clones (LU1, LU3, LU22, and LU36) are so closely related (
97% amino acid identity for scFv; Fig. 3A
) that they were considered to be four variants of one distinct scFv. Thus, from the 673 clones initially screened, 14 distinct scFv clones were identified that show selective binding to 1264 cells as judged by phage ELISA. These 14 distinct scFv fragments have divergent VH sequences (Fig. 3B)
, whereas their corresponding VL domains are more limited in diversity (Fig. 3C)
. Indeed, many of the scFv clones isolated use identical or very closely related VL sequences as, noted previously (14
, 32)
. This reflects the very limited size of the light chain repertoire in the phage library.
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| DISCUSSION |
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6-fold greater levels on 1264 cells than BEAS cells used for counter-selection. Thus, the counter-selection process is not 100% efficient, permitting identification of a scFv fragment that binds to antigen that is present at much higher levels on target than control cells. This bodes well for the use of this method because cell surface antigens that are overexpressed in tumors compared with normal tissues occur frequently [e.g., HER2/neu (33)
and epidermal growth factor receptor (34)
]. Antigens that are present in tumors but absent from normal tissues have been much sought after, but have, thus far, proved elusive. The LU30 antigen DAF is a glycophosphatidylinositol-anchored protein that acts together with two other glycophosphatidylinositol-anchored proteins, CD46 and CD59, in protecting host cells from complement-mediated cell lysis (35) . DAF is expressed at widely varying levels on tumor cell lines, and its overexpression correlates with enhanced resistance to complement-mediated cell lysis in vitro (36) . DAF overexpression has been observed on a variety of human tumor tissues including six of nine lung adenocarcinomas and two of seven lung squamous cell carcinomas (37) . Nevertheless, DAF seems poorly suited as a target for tumor immunotherapy because it is broadly expressed on the surface of normal cells, particularly those exposed to serum complement (35) . Regarding normal lung tissue, DAF has been detected by immunohistochemistry on the alveolar epithelium, interstitium, and endothelium, as well as the bronchial epithelium, glands and ducts, and also blood vessels (37) .
Antibody phage panning method offers a potential direct and broadly applicable route to the identification of human antibodies suitable for antitumor therapy. This strategy likely favors the identification of antibodies to highly expressed antigens, such as DAF shown here, because high antigen levels are anticipated to facilitate enrichment of cognate-scFv phage during panning. This seems desirable because high-level antigen expression may also facilitate tumor localization of antitumor antibodies in vivo.
Antibody phage panning could potentially identify tumor-associated antigens resulting from posttranslational modifications that differ between tumor and nontumor cells [e.g., the mucin product of the MUC1 gene is underglycosylated in many human tumors (38) exposing new epitopes for antibody targeting]. This has prompted the development of humanized anti-MUC1 antigen (39, 40, 41) . Furthermore, human antibodies recognizing MUC1 on tumor cells have been identified by panning with a MUC1 peptide (42) . In contrast, such posttranslational differences between tumor and nontumor cells will not be detected by powerful high throughput transcriptome and genomic methods, such as differential display (43) cDNA (44 , 45) or oligonucleotide (46) microarray and serial analysis of gene expression (47, 48, 49) . Transcriptome and genomic methods will also fail to detect proteins which are overexpressed in tumors despite unchanged RNA transcript levels and gene copy number, respectively.
Serial analysis of gene expression has identified significant differences in RNA transcript levels between primary human tumors and tumor cells lines (48) . This raises the possibility that antibody phage panning may fail to detect tumor-associated antigens found on primary human tumors, but absent on cell lines. Conversely, antibodies may be identified that are cell line-specific as judged by failure to bind primary human tumor cells. Direct panning on primary human tumor cells is anticipated to avoid these problems, but entails as yet unaddressed technical challenges. Credence to the notion that these obstacles are surmountable is provided by reports of successful panning with peptide phage libraries in vivo (50, 51, 52) .
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Present address: Rush Medical College, Chicago, IL 60612. ![]()
2 Present address: University of Iowa College of Medicine, Department of Internal Medicine, Iowa City, IA 52242. ![]()
3 To whom requests for reprints should be addressed, at Genentech Inc., 1 DNA Way, South San Francisco, CA 94080. Phone: (650) 225-1932; Fax: (650) 225-1716; E-mail: pjc{at}gene.com ![]()
4 The abbreviations used are: scFv, single-chain Fv; DAF, decay-accelerating factor; FBS, fetal bovine serum; cfu, colony-forming unit; NHBE, normal human bronchial epithelial; NHEK, normal human epidermal keratinocyte. ![]()
Received 1/18/99. Accepted 4/ 1/99.
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