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9 protocols using trucount absolute count tubes

1

Splenic Leukocyte Immunophenotyping

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Fresh spleens were minced and dissolved in PBS, filtered through a 40-μm cell strainer, and centrifuged at 350 ×g for 10 min at 4°C. Cells were washed with PBS and re-suspended in 2 ml PBA (∼1–5 × 107 cells/ml). The suspension (50 μl) was incubated with anti-CD3 (eBioscience, San Diego, CA, United States PE-Cyanine7, 1:100), CD4 (eBioscience, San Diego, CA, United States APC/Cy7, 1:100), CD8 (eBioscience, San Diego, CA, United States APC, 1:100), CD19 (eBioscience, San Diego, CA, United States PE, 1:100) for 20 min at 4°C, and then mixed with 448 μl PBS. The suspension was transferred to BD Trucount Absolute Count Tubes (BD, New Jersey, FL). The standard of the experiment is to collect 4000 beads in every BD Trucount Absolute Count Tubes to stop counting. Cells and beads were analyzed by using a BD FacScanto II flow cytometer.
Non-specific binding of secondary antibodies was quantified, and a fluorescent signal was subtracted from values of experimental groups. Single-stained cells or OneComp eBeads (eBioscience, San Diego, CA, United States) were used for calculations. Unstained cells, GFP-expressing cells with 7-AAD, and fluorescence minus one (FMO) controls were used for cytometry and gating set up.
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2

Isolation and Purification of CD34+ Cells from Cord Blood

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Fresh cord blood (CB) samples were collected after normal vaginal delivery in women without infectious diseases or maternal complications, after informed written consent. Mononuclear cells (MNC) were isolated from 30 ml of CB after density gradient centrifugation using lymphocytes separation media (Histopaque®, Sigma-Aldrich) stratification (2000 rpm, 20 min). After washing with Phosphate-Buffered Saline (PBS) (Gibco), MNC were incubated with immunomagnetic beads (CD34+) (Miltenyi) following manufacturer’s instruction. After CD34+ cell recovery, cell purity was assessed by flow cytometry (FACS Canto II®, BD) using a panel of CD34-PE and CD45-FITC (BD) fluorochrome-conjugated monoclonal antibodies. TruCount® Absolute-Count Tubes (BD) were used for determining the number of CD34+ cells. The strategy of gating is reported in the S1 and S2 Figs. CB samples were processed within 8 hours from collection; cells with at least 90% of purity were used for co-culture experiments.
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3

PBMC Isolation and Viral Load Measurement

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Forty ml of whole blood were collected from study participants, centrifuged to separate plasma, and stored at −80°C. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation (Amersham, Sweden) and cryopreserved for subsequent functional assays. Plasma viral load (VL) was determined by branched-DNA, Versant HIV-1 RNA 3.0 assay (Siemens Healthcare, UK). CD4+ and CD8+ T-cell counts were determined using TruCount absolute-count tubes (BD Bioscences, USA) on a BD FACSCalibur flow cytometer.
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4

Cytotoxicity Assay of CAR T-cells against B-ALL

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For cytotoxicity assays, BM-MSCs were seeded at 1×104 cells/well in flat-bottom 96-well plates containing complete Advanced DMEM medium and incubated at 37°C for 24 hours. The next day, target cells (B-ALL cell lines or primary B-ALL cells, 1×105 target cells/well) were incubated with CD19-CAR T-cells at an Effector:Target (E:T) ratio of 1:1, or alone, for the indicated periods in the absence/presence of BM-MSC. Cell lines were cultured in RPMI complete medium and primary cells were cultured in StemSpan supplemented with 20% heat-inactivated FBS, P/S, ITS, hSCF (100 ng/mL), hFLT3-L (100 ng/mL), hIL-3 (10 ng/mL) and hIL-7 (10 ng/mL). After 2 and 6 days of culture, non-adherent cells were collected, washed and stained with anti-CD3, anti-CD19, anti-CD10, anti-CD22 mAbs and 7-AAD. CAR T-cell-mediated cytotoxicity was determined by analyzing the residual living (CD10+CD22+7-AAD-) target cells at each time point. BD TruCount absolute count tubes (BD Biosciences) were used for absolute cell counting. Quantification of the pro-inflammatory cytokines IL-2, IFN-γ and TNF-α was measured by ELISA using the OptEIA Human ELISA Kit (BD Biosciences) on supernatants harvested after 2 days of coculture at a 1:1 E:T ratio. ELISA determinations were performed in triplicate.
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5

Comprehensive Immune Cell Profiling

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The proportions of neutrophils, lymphocytes, monocytes, CD4+ T, CD8+ T, CD19+ B, NK (CD3-CD56+), and NKT (CD3+CD56+) cell were analyzed by flow cytometry. The absolute counts of immune cells were measured by using BD TruCount Absolute-Count Tubes (BD340334). The following antibodies (CD3-FITC, CD8-APC-Cy7, CD4-PE-Cy7, CD45-Percp-Cy5.5, CD56-PE, and CD19-APC) were used, and all reagents were purchased from BD Biosciences. All samples were detected by a BD FACS Canto II flow cytometry system and analyzed with the BD FACS Diva software.
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6

Evaluating CAR T-cell Cytotoxicity

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Target cells (B-ALL cell lines, primary B-ALL cells, and B-ALL PDXs cells; 1 × 105 target cells/well) were incubated with Mock-, CD19-, or Tan-CAR T cells at different E:T ratios for the indicated time periods. Cell lines were cultured in complete RPMI medium and primary cells/PDXs were cultured in StemSpan SFEM supplemented with 20% heat-inactivated FBS, P/S, ITS, hSCF (100 ng/mL), hFLT3-L (100 ng/mL), hIL-3 (10 ng/mL), and hIL-7 (10 ng/mL). At each time point, cells were collected, washed, and stained with anti-CD3, anti-CD19, anti-CD10, and anti-CD22 mAbs, and 7-AAD. CAR T cell-mediated cytotoxicity was determined by analyzing the residual living (7-AADCD3GFPCD10+) target cells at each time point and E:T ratio (Figure S1A). BD TruCount absolute count tubes (BD Biosciences) were used for absolute cell counting. The quantification of IL-2, IFN-γ, and TNF-α was measured by enzyme-linked immunosorbent assay (ELISA) using the OptEIA Human ELISA Kit (BD Biosciences) on supernatants harvested after 1–2 days of co-culture at a 1:1 E:T ratio. ELISA determinations were performed in triplicate.
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7

Rhesus Macaque T-Cell Enumeration

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Blood samples from rhesus macaques were all collected following standard protocols. BD Trucount Absolute Count Tubes (BD, Cat. No. 340334) were used to quantify the T cells in 100 µL of blood. Antibodies that label different kinds of T cells were adopted in this study. Information on antibodies is listed in Table S3. FACS Lysing solution (BD Cat. No. 349202) was diluted 10 times before being added, and the suspensions were incubated at 4°C for 10 min. All data were collected through BD Accuri C6 Plus. PBMCs were collected to test the phenotypic characteristics of T cells, and the antibodies used are all listed in Table S3. All data were collected by an LSRFortessa (BD Biosciences) instrument and were analyzed using FlowJo software (Tree Star, Inc).
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8

Rhesus Macaque T-Cell Enumeration

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Blood samples from rhesus macaques were all collected following standard protocols. BD Trucount Absolute Count Tubes (BD, Cat. No. 340334) were used to quantify the T cells in 100 µL of blood. Antibodies that label different kinds of T cells were adopted in this study. Information on antibodies is listed in Table S3. FACS Lysing solution (BD Cat. No. 349202) was diluted 10 times before being added, and the suspensions were incubated at 4°C for 10 min. All data were collected through BD Accuri C6 Plus. PBMCs were collected to test the phenotypic characteristics of T cells, and the antibodies used are all listed in Table S3. All data were collected by an LSRFortessa (BD Biosciences) instrument and were analyzed using FlowJo software (Tree Star, Inc).
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9

Quantification of T Cell Subsets

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The numbers of circulating CD4+ T and CD8+ T lymphocytes were determined using BD Trucount absolute count tubes according to the manufacturer’s instructions (BD Biosciences). For detection of central memory CD4+ T (CD3 + CD4 + CD28 + CD95 + cells), effector memory CD4+ T (CD3 + CD4 + CD28-CD95+ cells) and TFH cell (CD3 + CD4 + CXCR5+ PD-1+) cells, PBMCs were stained with the following fluorescein-labeled antibodies: anti-CD3 (BD Bioscience), anti-CD4 (BD Bioscience), anti-CD8 (BD Bioscience), anti-CD28 (BD Bioscience), anti-CD95 (BD Bioscience), anti-CXCR5 (eBioscience), and anti-PD-1 (eBioscience) for 30 min and detected with a BD FACS LSR Fortessa flow cytometer (BD Biosciences, USA). Data were analyzed using FlowJo software (Tree Star, USA).
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