Additional file 2: of Clonal dynamics studied in cultured induced pluripotent stem cells reveal major growth imbalances within a few weeks

Video S1. Video-optical recording of RGB-marked EHT. The EHT displayed unaltered contractility with similar force and frequency of contraction as unmarked controls (MP4 7660 kb

Additional file 1: Figure S1. of Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion

eGFP expression and clonal kinetics in the BcrAbl_bulk culture. Figure S2: Overlap of barcodes from plasmid library and first sample. Figure S3: Clonal kinetics in the eGFP-positive cultures after sorting. Figure S4: Spleens from diseased (and control) animals. Figure S5: Read counts for Klf6 and Sprouty1. Figure S6: Comparison of samples. Figure S7: KEGG enrichment analysis. Table S1: Spleen weights and eGFP expression in the diseased animals. Supplementary Model Description. Table S2: Model Parameters. Table S3: Oligonucleotides. (PDF 7697 kb

T cell reconstitution in patients after cell therapy.

<p>P1, a child with Fanconi anaemia, underwent a second mismatched donor, CD34 selected stem cell graft after in the context of relapsed MDS. Donor HSVTK/CD34 modified T cells were infused in two dose aliquots and were detectable at low level in peripheral blood for over 12 weeks before the patient died of disease relapse. The persistence of non-modified T cells reflects the reduced intensity conditioning and absence of serotherapy. P2, an infant with RAG1 deficient SCID had no pre-existing T cell immunity and was conditioned whist infected with H1N1 influenza. Modified T cells persisted for over 12 months, with eventual recovery of thymic derived donor T cells after one year and normalisation of immunity. P3 suffered Ligase IV deficiency, a form of radiosensitive SCID. Expansion of modified donor T cells was detected within two weeks of first infusion, but the patient died from mucositis related pulmonary and gastrointestinal haemorrhage before dose escalation.</p

Production of donor HSVTK-CD34 T cells.

<p>Production of donor HSVTK-CD34 T cells.</p

Transfer and tracking of T cell mediated virus specific immunity.

<p>Most compelling, and beneficial, was transfer of immunity against pandemic H1N1 infulenza in P2. The haploidentical donor had been electively vaccinated against the strain before leukapheresis harvest of peripheral blood lymphocytes. The transduced and CD34 enriched populations exhibited specific IFNγ responses against HI1N1 compared to non-stimulated control cells. Samples collected 150 days after donor lymphocyte infusion from the patient showed similar H1N1 specific IFNγ responses, which coincided with clearance of persistent H1N1 respiratory infection. These responses were still detectable after 350 days.</p

Mesenchymal Stem Cells Engineering: Microcapsules-Assisted Gene Transfection and Magnetic Cell Separation

Stem cell engineeringthe manipulation and functionalization of stem cells involving genetic modificationcan significantly expand their applicability for cell therapy in humans. Toward this aim, reliable, standardized, and cost-effective methods for cell manipulation are required. Here we explore the potential of magnetic multilayer capsules to serve as a universal platform for nonviral gene transfer, stem cell magnetization, and magnetic cell separation to improve gene transfer efficiency. In particular, the following experiments were performed: (i) a study of the process of internalization of magnetic capsules into stem cells, including capsule co-localization with established markers of endo-lysosomal pathway; (ii) characterization and quantification of capsule uptake with confocal microscopy, electron microscopy, and flow cytometry; (iii) intracellular delivery of messenger RNA and separation of gene-modified cells by magnetic cell sorting (MACS); and (iv) analysis of the influence of capsules on cell proliferation potential. Importantly, based on the internalization of magnetic capsules, transfected cells became susceptible to external magnetic fields, which made it easy to enrich gene-modified cells using MACS (purity ∼95%), and also to influence their migration behavior. In summary, our results underline the high potential of magnetic capsules in stem cell functionalization, namely (i) to increase gene-transfer efficiency and (ii) to facilitate enrichment and targeting of transfected cells. Finally, we did not observe a negative impact of the capsules used on the proliferative capacity of stem cells, proving their high biocompatibility

T cell repertoire diversity before and after modification.

<p>Complementarity determining region-3 (CDR3) T-cell receptor (TCR) spectratyping was performed as previously described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077106#pone.0077106-Qasim3" target="_blank">[18]</a>. Briefly, RNA was extracted and cDNA prepared from pre- and post-transduced cells. Twenty four Vβ-specific primers were used with a fluorescent-labelled constant region (Cβ)-specific primer to RT-PCR amplify the CDR3 region of the TCR β chain. Products were run on an AB3130 Genetic Analyzer and analysed using GeneMapper v4.0 software (Applied Biosystems, Warrington, UK). Representative data for P2 is showing preservation Vβ family distributions is shown.</p

Vector configuration and study schema.

<p>1a. A gamma retroviral platform incorporating long terminal repeals (LTRs) from Myeloproliferative sarcoma virus (MPSV) and leader sequence 71 derived from Murine embryonic stem cell virus (MESV). The splice site corrected herpes simplex virus thymidine kinase suicide gene (scHSVTK) fused to a truncated (splice variant) human CD34 gene is shown. 1b. Subjects undergoing CD34 selected mismatched allografts and receiving grafts carrying <5×10⁴ T cells/kg following conditioning (but not serotherapy) were eligible. Gene modified T cells were scheduled at two cell doses, the first 5×10⁴/kg the day following the stem cell graft, and the second programmed within 28 days at a higher dose of 5×10⁵/kg. In the event of GVHD>Grade I, Ganciclovir therapy was scheduled for seven days to eliminate gene modified T cells.</p

GMP compliant T cell transduction procedure.

<p>GMP compliant T cell transduction procedure.</p

Transduction, enrichment and suicide gene function.

<p>(a) Flow cytometry of peripheral blood lymphocytes after transduction. Cells were activated with anti-CD3/28 beads and underwent two rounds of exposure to vector before removal of activation beads and magnetic bead enrichment using a CliniMacs device. (b) Transduced T cells were enriched (CD34+) to >90% purity for all three products. (c) Upon exposure to the prodrug Ganciclovir (GCV, 10 uM), engineered cells from all three donors had reduced survival compared to non-modified controls (P<0.001). Means of triplicate wells and standard error of means are shown.</p