Additional file 1: of Combined deletion of Xrcc4 and Trp53 in mouse germinal center B cells leads to novel B cell lymphomas with clonal heterogeneity
Creators: name: Zhangguo Chen
name: Elos, Mihret
name: Sawanee Viboolsittiseri
name: Gowan, Katherine
name: Leach, Sonia
name: Rice, Michael
name: Eder, Maxwell
name: Jones, Kenneth
name: Wang, Jing
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. Establishment of G1XP lymphoma model. (A) Specific Xrcc4 deletion via Cγ1Cre in GC B cells. PCR analysis of genomic DNA isolated from bone marrow (BM), thymus, sorted naïve B cells (B220+PNAlow), and GC B cells (B220+PNAhigh) of immunized Cγ1Cre KI or Cγ1CreXc/+ mice. The middle band is non-specific amplification of PCR reaction for BM, thymus and B220+PNAlow B cells. GC B cells (B220+PNAhigh) show the complete deletion of Xrcc4 floxed allele. Splenocytes were stained using anti-B220 and anti-PNA antibodies. (B) Kaplan Meier survival curve of the first cohort of mice including Cγ1CreXcPc/+mice (n=19, blue line), Cγ1CreXc/+Pc mice (n=20, green line) and Cγ1CreXcPc mice (n=47, red line). (C) Southern Blot analysis of 1st cohort of Cγ1CreXcPc mice. G1XP lymphomas harbor clonal JH rearrangements. Southern blot analyses for JH rearrangements in G1XP lymphoma genomic DNA employing EcoRI digestion and the JH4 probe. Germline (GL) bands are indicated (arrow heads). Asterisks (*) indicate rearranged JH locus in lymphoma DNA. MLN stands for mesenteric lymph node. Figure S2. G1XP lymphomas harbor somatic hypermutations. Germline sequences from either the JH1-4 or JH3-4 region were aligned with G1XP lymphoma sequences. The mismatched sequences (in red font) at the beginning of the sequences are derived from rearranged VD or D regions. To exclude the effects of V(D)J recombination in sequence diversity, we only identified the mutations in JH exon or intron regions that could be unequivocally aligned to the germline sequences. The rearranged JH exon regions are underlined for each individual G1XP lymphoma samples, and the mutations are marked with “*”. Figure S3. G1XP lymphomas harbor normal or aberrant V(D)J recombination junctions. NGS data showed the presence of normal D-J (junction 1) and V-D-J (junction 2) junctions at the Igh locus or aberrant V-J junction (junction 3) at Igλ locus.V, D, and J exons were labeled and depicted as orange bars.MH: micro-homology. Figure S4.Clonal Igλtranslocations in G1XP lymphoma. Top: schematics of Igλ locus on chromosome 16. Bottom: Metaphases from G1XP lymphoma samples were analyzed by FISH for hybridization to Igλ probes as indicated in the schematics. Representative Igλ translocations in G1XP lymphomas are shown. Table S1. Phenotypic characterization of G1XP lymphoma via flow cytometry. Table S2. Summary of translocation involved Igh and Igl genes. Table S3.Validation of Translocations by PCR, Sanger Sequencing or FISH.(PDF 1221 kb)