For CDR3 size polymorphism analysis we used the Immunoscope software package.
23 Immunoscope analysis couples fluorescence PCR and software analysis and allows the direct and accurate sizing of a clonal population of T or B cells within a polyclonal milieu. Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation on single-density gradient (Ficoll Hypaque; Pharmacia, Upsala, Sweden) and processed for Immunoscope analysis, as previously described.
25 An Epstein-Barr virus (EBV)–transformed human B lymphoblastoid cell line (BLCL) was established in the laboratory and maintained as previously described.
26 The vitreous humor was obtained after vitrectomy. Approximately 200 μL of vitreous humor was diluted in a saline solution to a final volume of 1 mL, and the samples were centrifuged immediately (910
g for 10 minutes at 4°C). Previous morphologic studies revealed that such amounts of vitreous humor obtained from PIOL patients contain, on average, 1000 cells (Merle-Beral H, unpublished results, 2003). The total RNA from the cells obtained by ocular sampling was immediately reverse-transcribed for RT-PCR analysis. Briefly, total RNA was purified from the cell pellet according to the method of Chomczynki and Sacchi,
27 and RNA was reverse transcribed in a 50-μL reaction volume, using the reagents provided in an RT-PCR kit (ProSTAR First Strand; Stratagene, La Jolla, CA), according to the manufacturer’s instructions. We designed three oligonucleotides that allowed us to perform a nested amplification of all the transcripts coding for a VH repertoire. The upstream degenerated primers hybridize with a conserved sequence coding for a part of the framework regions (FR2 or FR3) of the VH domains. The downstream primer hybridizes with a sequence shared by the various human JH segments. Two microliters of the RT reaction were used as a template in a first round of PCR using the primers FR2 5′-TGGRTCCGMCAGSCYYCNGG-3′ and IgHJ 5′-TGARGAGACGGTGACCRK-3′ for 30 cycles of amplification. One microliter of the previous reaction was used as a template in a second, semi-nested PCR, using the primers FR3 5′-ACACGGCYSTGTATTACTGT-3′ and IgHJ for 25 cycles of amplification. Each cycle consisted of 95°C for 5 minutes, 94°C for 40 seconds, 48°C for 40 seconds, and 72°C for 50 seconds, with an additional extension interval of 5 minutes at 72°C after the last cycle. The PCR products were then fluorescently labeled using a run-off procedure: Two microliters of PCR product was added to an 8-μL mixture containing 10 mM Tris-HCl, 1.5 mM MgCl
2, 50 mM KCl (pH 8.3), 0.2 mM of each dNTP, 0.2 U of
Taq polymerase, and 0.1 μM of fluorescently labeled IgH ROX 5′-GAGACGGTGACCRKKGTYCC-3′ oligonucleotide. Run-off products were then loaded on a 4% acrylamide, 4 M urea sequencing gel and run on a DNA sequencer (model 377; Applied Biosystems, Foster City, CA). A mixture of dye-labeled size standards was also loaded on the sequencing gel to allow the precise determination of the sizes of the VH-JH run-off reaction products. The size and area of the peaks corresponding to the DNA products were determined using the Immunoscope software.
23 The percentage of representation of each peak size among all VH-JH segments was subsequently calculated. The observed peaks are usually separated by 3 bases, and correspond to in-frame transcripts coding for antibody heavy chains. Windows of analysis were centered on expected sizes corresponding to VH transcripts encoding a 15-residue CDR3 region, defined according to Kabat et al.
28 Reference Immunoscope VH profiles were established from the PBMCs of 16 healthy subjects. This study showed that the VH CDR3 size distribution profile is made up of an average of 25 peaks. The size of the CDR3 loops ranged, according to this analysis, anywhere from 3 to 27 amino acids. The most common length for a human CDR3 VH loop is 13 amino acids (data not shown; Gorochov G, manuscript in preparation).