(a) The experimental setup for ODT is based on a digital micro-mirror device (DMD) for high-speed illumination scanning. (b) Forty-nine holograms of 1:1 conjugate between a CART19 and a K562-CD19 …
(a) Dataset preparation; raw RI tomograms were annotated with manual parameter selections and curated by three experts. (b) Training stage; the prepared dataset was employed to iteratively train the …
(a) A distance-transform map of a binary mask caused ill segmentation. Red arrow indicates the ill-segmented boundary. (b) Our annotation method was based on iterative parameter adjustment based on …
(a) Representative results of RI maps (first column), annotation masks, (second column), and STAPLE truth estimates from the manually delineated masks of three experts (third column). Top row: …
(a) Overall U-shaped feature flowline of the DCNN architecture. The architecture has the contracting path consisting of ResNet blocks and down-pooling layers and the expanding path consisting of …
Cell surface was obtained by finding the edge of each cell mask. The remaining mask was defined as the cell interior. The synapse was defined as an overlapped region of the dilated masks of CART19 …
(Top row) Masks annotated by manual parameter selections. (Bottom row) Segmentation results using DeepIS. Blue shade indicates the curated data in the training stage. Red shade indicates the data …
(a) RI tomogram over 0.98 × 1.05 × 0.04 mm3 obtained by stitching method. (b) Segmentation using DeepIS. (c) Representative CART19, K562-CD19, and CART19/K562-CD19 cell conjugates are magnified.
(a) Representative 3d rendering images, the xy- and the xz- cross-sections of RI (first column), fluorescence (second column), and their overlapped images (third column). CART19 and K562-CD19 labels …
(a) Representative 3D rendering maps of RI (first column), fluorescence (second column), and their overlapped images (third column). CART19 and K562-CD19 labels were manually delineated based on the …
(a) A 2D wide-field image. (b) Four-channel zoom-in images of CART19/K562-CD19 pair. (c) Merged cross-section images. (d) A 3D Rendering image.
(a) The XY- and XZ-slice images of fluorescein-labeled dextran. White dashed lines: slice regions. (b) Corresponding XY- and XZ- images of SIM and ODT. (c) Comparison of dextran fluorescence, CAR …
(a) Experimental setup. (b) Raw image (left) and corresponding widefield and SIM images (right) of 100-nm-diameter Tetraspeck beads excited by structured illumination beams. (c) Slice images of …
(a) The XY- and XZ-slice images of fluorescein-labeled dextran (top) and merged fluorescence of dextran and CAR (bottom). The 3D-SIM images showed that the synaptic cleft in the vicinity of the CAR …
(a) XY- and XZ-slice images of representative CART19/K562-CD19 conjugates. White-dashed lines: slice regions. White bold lines in SIM + ODT: 3D IS areas defined by DeepIS. (b) En face projected …
(a) Representative XY- and XZ- cross section of background, cell volume (gray), obtained IS (green), and lytic granules (red, defined by the overlapping region between a RI cell volume and a …
(a) Representative snapshots of a video of CART19 cells responding to K562 (top row) and K562-CD19 (bottom row) cells. Purple: K562, Blue: CART19. 0 s: the initial contact point of the effector cell …
Red circles indicate spikes due to ill segmentation (5 spikes out of 1329 points; 0.38%).
(a) Representative images for maximum z-axis projection of intracellular protein density distributions (top row) and en face projection of surface protein density distributions of IS (bottom row). …
(a) LNGFR and CAR expressions at four days after transduction. (b) hCD19 expression of K562-CD19 and K562 cells. (c) hCD19-G4S-Zgreen expression of K562 cells.
In both cases, IS was formed and stabilized within five minutes.
Data | Experiment | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | Total |
---|---|---|---|---|---|---|---|---|---|---|---|---|
# of data | Statistics (Figure 5) | 7 | 10 | - | - | - | - | - | - | - | - | 17 |
dynamics (Figure 7) | 9 | 3 | 3 | 1 | 3 | 3 | 1 | 1 | 2 | 1 | 27 | |
4-1BB (Figure 8) | 20 | 19 | 25 | - | - | - | - | - | - | - | 64 | |
CD28 (Figure 8) | 1 | 11 | 10 | 9 | 23 | - | - | - | - | - | 54 | |
Statistics (Figure 5—figure supplement 1) | 8 | 22 | - | - | - | - | - | - | - | - | 30 | |
10 kDa (Figure 6—figure supplement 2) | 3 | 7 | - | - | - | - | - | - | - | - | 10 | |
2000 kDa (Figure 6—figure supplement 2) | 6 | 3 | - | - | - | - | - | - | - | - | 9 | |
4-1BB (Figure 8—figure supplement 1) | 1 | 1 | 2 | 1 | - | - | - | - | - | - | 5 | |
CD28 (Figure 8—figure supplement 1) | 2 | 1 | - | - | - | - | - | - | - | - | 3 |
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Cell line (Homo sapiens) | K562 | Other | RRID:CVCL_0004 | Obtained from Dr. Travis S. Young at California Institute for Biomedical research. The original stock was purchased from ATCC |
Cell line (Homo sapiens) | K562-CD19 | Other | Obtained from Dr. Travis S. Young at California Institute for Biomedical research. CD19-negative K562 cells were transduced wtih lentiviral vector encoding human CD19. | |
Cell line (Homo sapiens) | Lenti-X 293T | Takara | Cat. #: 632180 | Lentivirus production |
Recombinant DNA reagent | pLV-ΔLNGFR-P2A-CD19-BBz CAR | This paper | Signal peptide: aa 1–28 hLNGFR (Uniprot TNR16_Human) Extracellular domain: aa 29–250 hLNGFR (Uniprot TNR16_Human) Transmembrane domain: aa 251–272 hLNGFR (Uniprot TNR16_Human) Cytosolic sequence: aa 273–275 (Uniprot TNR16_Human) ΔLNGFR was fused with P2A sequence (GGAAGCGGAGCTACTAACTTCAGCCTGCTGAAGCAGGCTGGCGACGTGGAGGAGAACCCTGGACCT) and followed by CAR sequence Signal peptide: aa 2–21 hCD8 (Uniprot CD8A_Human) Extracellular domain: anti-CD19 scFv (Clone: FMC 63); VL –G4S linker VH Hinge/Transmembrane domain aa 138–206 hCD8 (Uniprot CD8A_Human) Co-stimulatory domain sequence: aa 214–255 (Uniprot TNR9_Human) Signaling domain: aa 52–164 (Uniprot CD3Z_Human) | |
Recombinant DNA reagent | pLV- ΔLNGFR -P2A-CD19-28z CAR | This paper | Signal peptide: aa 1–28 (Uniprot TNR16_Human) Extracellular domain: aa 29–250 (Uniprot TNR16_Human) Transmembrane domain: aa 251–272 (Uniprot TNR16_Human) Cytosolic sequence: aa 273–275 (Uniprot TNR16_Human) ΔLNGFR was fused with P2A sequence (GGAAGCGGAGCTACTAACTTCAGCCTGCTGAAGCAGGCTGGCGACGTGGAGGAGAACCCTGGACCT) and followed by CAR sequence Signal peptide: aa 2–21 hCD8 (Uniprot CD8A_Human) Extracellular domain: anti-CD19 scFv (Clone: FMC 63); VL-G4S linker-VH Hinge/Transmembrane domain: aa 138–206 (Uniprot CD8A_Human) Co-stimulatory domain sequence: aa 180–220 (Uniprot CD28_Human) Signaling domain: aa 52–164 (Uniprot CD3Z_Human) | |
Recombinant DNA reagent | pLV-CD19-BBz CAR-G4S-mcherry | This paper | Signal peptide: aa 1–21 (Uniprot CD8A_Human) Extracellular domain: anti-CD19 scFv (Clone: FMC 63) VL –G4S linker VH Hinge/Transmembrane domain: aa 138–206 (Uniprot CD8A_Human) Co-stimulatory domain sequence: aa 214–255 (Uniprot TNR9_Human) Signaling domain: aa 52–164 (Uniprot CD3Z_Human) CAR and mcherry was fused with G4S linker mCherry: aa 2–236 (Uniprot X5DSL3_ANAMA) | |
Recombinant DNA reagent | pLV-hCD19-G4S-Zsgreen | This paper | Signal peptide: aa 1–19 (Uniprot CD19_Human) Extracellular domain: aa 20–291 (Uniprot CD19_Human) Cytoplasmic domain: aa314-556 (Uniprot CD19_Human) CD19 and Zsgreen was fused with G4S linker Zsgreen: aa 2–231 (Uniprot GFPL1_ZOASP) | |
Recombinant DNA reagent | pMDLg/pRRE | other | RRID:Addgene12251 | 3rd Lentivirus packaging vector |
Recombinant DNA reagent | pRSV-Rev | other | RRID:Addgene12253 | 3rd Lentivirus packaging vector |
Recombinant DNA reagent | pMD2.G | other | RRID:Addgene12259 | Lentivirus envelop vector |
Recombinant DNA reagent | pMACS LNGFR | Miltenyi Biotec | Cat. #:130-091-890 | |
Peptide,recombinant protein | rhIL-2 | BMI KOREA | 300IU/mL | |
Peptide,recombinant protein | rhCD19-Fc | ACRO Biosystems | Cat. #: CD9-H5259 | FACS |
Peptide,recombinant protein | AF647-conjugated streptavidin | Biolegend | Cat. #: 405237 | FACS |
Antibody | InVivoMab anti-human CD3 | Bio X cell | Cat. #: BE0001-2-5MG | OKT3 clone 4 μg/mL coated |
Antibody | InVivoMab anti-human CD28 | Bio X cell | Cat. #: BE0291-5MG | CD28.2 clone 2 μg/mL soluble |
Antibody | hLNGFR-APC antibody | Miltenyi Biotec | Cat. #: 130-113-418 | FACS |
Antibody | hCD19-APC antibody | Biolegend | Cat. #: 302212 | FACS |
Other | DPBS | Welgene | Cat. #: LB001-02 | |
Other | Fetal Bovine Serum (FBS) | Gibco | Cat. #: 26140–079 | |
Other | DMEM | Gibco | Cat. #: 11965–118 | |
Other | RPMI | Gibco | Cat. #: 21870–092 | |
Other | HBSS with Ca2+ and Mg2+ | Gibco | Cat #: 14-025-092 | |
Other | HEPES | Gibco | Cat. #: 1530080 | |
Other | 2-Mercaptoethanol | Sigma | Cat. #: M6250-100mL | |
Other | Lipofectamine 2000 | ThermoFisher | Cat. #: 11668019 | |
Other | Glutamax | Gibco | Cat. #: 35050–061 | |
Other | Protamine Sulfate | Sigma | Cat. #: P3369 | |
Other | MEM Non-essential amino acid | Gibco | Cat. #: 111400500 | |
Other | Sodium pyruvate | ThermoFisher | Cat. #: 11360070 | |
Other | penicillin/streptomycin | Gibco | Cat. #: 15140–122 | |
Other | Tomodish | Tomocube | ||
Other | Paraformaldehyde Solution, 4% in PBS | ThermoFisher | Cat. #: AAJ19943K2 | Fixation |
Other | CellBrite Fix 640 Membrane Dye | Biotium | Cat. #: 30089 | Plasma membrane staining |
Other | VECTASHIELD Hardset w/DAPI | VECTOR Laboratory | Cat. #: H-1400 | Mounting Medium |
Other | LysoTracker Deep Red | ThermoFisher | Cat #: L12492 | Dye for labeling and tracking lytic granules |
Other | TetraSpeck Microspheres,0.1 µm, fluorescent blue/green/orange/dark red | ThermoFisher | Cat #: T7279 | Fiducial markers |
Other | FITC-dextran 10 kDa | TdB Labs | Cat #: 20682 | Fluorescein-labeled dextran, 10 kDa |
Other | FITC-dextran 2000 kDa | TdB Labs | Cat #: 20584 | Fluorescein-labeled dextran, 2000 kDa |
Commercial assay or kit | CD271 Microbeads kits, Human | Miltenyi Biotec | Cat. #: 130-099-023 | Isolation of CAR+ T cells |
Commercial assay or kit | SepMate PBMC Isolation tube | STEMCELL | 86460 | PBMC Isolation |
Software, algorithm | Flowjo | Flowjo | Version 10 | |
Software, algorithm | Prism | GraphPad | Version 7 | |
Software, algorithm | ImageJ | NIH |
Documents for cell line authentication.