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18 protocols using negative magnetic bead selection

1

Isolation and Co-culture of B Cell Subsets and T Cells

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B6 mice (Ly5.2+) were inoculated with OVA-Ab conjugates. Splenocytes were processed to single cells as above. CD11c+ cells were isolated by magnetic bead positive selection (Miltenyi Biotec) according to manufacturer’s instructions. From the negative fraction, B cells were isolated by magnetic bead negative selection (StemCell Technologies) according to manufacturer’s instructions. B cells were then FACS sorted into T1 (B220+, CD24hi, CD21lo), FO (B220+, CD24mid, CD21mid) and MZ (B220+, CD24hi, CD21hi) subsets (as in Figure 1A, with smaller gates to limit subset spillover, as is a common sorting procedure), using an Aria flow cytometer (BD). Meanwhile, CD4+ T cells (Ly5.1+) were isolated from splenocytes from OT-II mice by magnetic bead negative selection (StemCell Technologies) and labeled with CFSE as above. 1×105 CFSE-labeled CD4+ T cells were combined with 1×105 APC (DC or B cell subset) and incubated in a 96-well plate for three days, following which cells were stained for surface markers and analyzed by flow cytometry as above.
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2

Metabolic Profile of CD8+ T Cells in Viral Pneumonia

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CD8+ T cells were isolated from the single cell suspension of mouse BALF and digested lungs at day 10 post PR8 infection using magnetic bead negative selection (Stemcell, Vancouver, Canada) in Easy-Sep buffer (PBS + 2% FBS + 1 mM EDTA). Isolated cells were counted using the Bio-Rad TC20 with trypan blue exclusion for viability. XFe96 cell culture microplates were treated with Cell-Tak™ (Corning, Corning, NY, USA) in 0.1 M sodium bicarbonate to allow for cell adherence. CD8+ T cells were plated in non-buffered RPMI-1640 with freshly added 10 mM glucose, 2 mM glutamine, and 1 mM pyruvate at 300,000 cells per well. Extracellular acidification (ECAR) and oxygen consumption rates (OCR) were determined using the Seahorse XFe96 Flux analyzer (Agilent, Santa Clara, CA, USA) at 37°C as previously described.35 OCR and ECAR were normalized to cell number.
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3

CFSE-labeled B Cell Transfer

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Splenocytes from B1-8hi mice were processed by mechanical disruption between frosted glass slides. B cells were isolated by magnetic bead negative selection (StemCell Technologies) and were >95% pure as determined by flow cytometry. 50×10^6 B cells/mL were labeled with 20μM CFSE (Invitrogen) at 37°C for 10 min and washed thoroughly. Labeled cells were transferred in 200μL i.v. 16-18 h prior to Ag-Ab inoculation. Male cells were never transferred into female mice.
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4

Isolation of Human NK Cells

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Fresh human NK cells were isolated from buffy coats of healthy volunteer donors (NIH Blood Bank) via magnetic bead negative selection (Stem Cell Technology). >95% purity of CD45+ CD56+ CD3- NK cells was deemed acceptable for further experiments (Supplementary Fig. 1).
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5

Metabolic Profiling of CD8+ T Cells

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CD8 + T cells were isolated from the single cell suspension of mouse lungs at day 10 post PR8 infection using magnetic bead negative selection (Stemcell, Vancoover, Canada) in EasySep buffer (PBS + 2% FBS + 1mM EDTA). Isolated cells were counted using the Bio-Rad TC20 with trypan blue exclusion for viability. XFe96 cell culture microplates were treated with Cell-Tak TM (Corning, Corning, NY, USA) in 0.1M sodium bicarbonate to allow for cell adherence. CD8 + T cells were plated in non-buffered RPMI-1640 with freshly added 10mM glucose, 2mM glutamine, and 1mM pyruvate at 300,000 cells per well. Extracellular acidification (ECAR) and oxygen consumption rates (OCR) were determined using the Seahorse XFe96 Flux analyzer (Agilent, Santa Clara, CA, USA) at 37 o C as previously described (27) . OCR and ECAR were normalized to cell number.
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6

Isolation and Stimulation of CD4+ T Cells

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CD4 T cells were isolated from PBMC by negative magnetic bead selection (StemCell), resulting in an untouched population defined as CD3+CD4+/-CD8-CD14-CD19- (purity routinely over 95%). Cells were stimulated for 36–40 hr in RPMI with PHA-L (10μg/ml, Sigma) and IL-2 (50U/ml), then washed and maintained for 6–7 days in RPMI with IL-2 (100U/ml). In some experiments, ARVs (T20 (7.5μg/ml) + AZT (1μM)) were added. Enfuvirtide (T-20), Zidovudine (AZT), and IL-2 (Lahm and Stein, 1985 (link)) were obtained through NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: human rIL-2 from Dr. Maurice Gately, Hoffmann - La Roche Inc.
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7

Modulation of IL-8 Secretion in M2-like Macrophages

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Example 2

CD14+ monocytes were isolated from human PBMCs using negative magnetic bead selection (Stemcell Technologies) on day 0. Cells were cultured with M-CSF to differentiate monocytes to macrophages. On day 6, cells were treated with L-AP4 (selective group III metabotropic glutamate receptor agonist) (Sigma-Aldrich), at concentrations 1 μM and 10 μM overnight. Supernatant was collected and LEGENDplex™ bead-based immunoassays (Biolegend) were performed to detect for changes in cytokines secreted.

Secretion of the inflammatory cytokine, IL-8, was decreased with the addition of the mGluR8 agonist in M2-like macrophages, consistent across multiple donors, as shown in Table 17 below.

TABLE 17
SECRETION OF IL-8 IN MACROPHAGES
Fold change of IL-8 (Normalized
to M2-like Macs + LPS with
Sampleno compound treatment)
M2-like Macs1.00
M2-like Macs + L-AP4 (1 μM)0.646
M2-like Macs + L-AP4 (10 μM)0.866

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8

Macrophage Polarization and Calcitonin Receptor Expression

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Example 1

CD14+ monocytes were isolated from human PBMCs using negative magnetic bead selection (Stemcell Technologies) on day 0. Cells were cultured two days with M-CSF to differentiate monocytes to macrophages. On day 3, macrophages were polarized to M1-like macrophages with IFNγ and LPS; and M2-like macrophages with IL4, IL10, and TGFβ. Cells were harvested on day 6. The cells were lysed and RNA was extracted using an RNA extraction kit (Qiagen). qPCR was performed using integrated fluidic circuits (IFCs) run on a real-time PCR machine (Fluidigm) with primers specific for CALCR and RAMP1 (Life Technologies). Gene expression was normalized to HPRT1. Expression level was calculated by 2{circumflex over ( )}(−delta CT), where delta CT is (GOI Ct—HPRT Ct).

Gene expression for CALCR in M2-like macrophages and RAMP1 in both M1-like and M2-like macrophages was determined. RAMP1 expression was higher in M2-like macrophages compared to M1-like macrophages, as shown in Table 12 below.

TABLE 12
EXPRESSION OF CALCITONIN RECEPTORS IN MACROPHAGES
Expression Level
Cell TypeGene Name(Relative to HPRT1)
M1-like MacrophagesCALCR (Entrez: 799)Not detected
M2-like MacrophagesCALCR (Entrez: 799)0.0304
M1-like MacrophagesRAMP1 (Entrez: 10267)0.01045
M2-like MacrophagesRAMP1 (Entrez: 10267)5.7757

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9

Modulation of CD8+ T-cell Cytokine Secretion by SERCA Inhibitors

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Example 2

CD8+ T-cells were isolated from human PBMCs using negative magnetic bead selection (Stemcell Technologies). Cells stimulated with anti-CD3/anti-CD28 beads (Life Technologies) and were treated with different SERCA inhibitors: thapsigargin (1.5 μM), cyclopiazonic acid (3 μM), and NS-1619 (30-100 μM). All incubations were done overnight. Subsequent activation was measured by cytokine release using intracellular staining flow cytometry of IFNγ and TNFα, using fluorescently labeled antibodies (Biolegend).

Secretion of the inflammatory cytokine, IFNγ, was increased by CD8+ T cells with the addition of each of the different SERCA inhibitors, as shown in Table 17 below.

TABLE 17
SECRETION OF IFNγ FROM IMMUNE CELLS TREATED WITH
SERCA PUMP INHIBITORS
Fold Change % IFNγ+ Cells
(Normalized to Bead
SampleStimulated Only)
CD8+ T-Cell Bead Stimulated Only1
CD8+ T-Cell Bead Stimulated + 2.08
Thapsigargin 1.5 μM
CD8+ T-Cell Bead Stimulated + 2.38
Cyclopiazonic Acid 3 μM
CD8+ T-Cell Bead Stimulated + 1.1
NS-1619 30 μM
CD8+ T-Cell Bead Stimulated + 2.68
NS-1619 100 μM

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10

Serotonin Receptor Expression in Polarized Macrophages

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Example 1

CD14+ monocytes were isolated from human PBMCs using negative magnetic bead selection (Stemcell Technologies) on day 0. Cells were cultured two days with M-CSF to differentiate monocytes to macrophages. On day 3, macrophages were polarized to M1-like macrophages with IFNγ and LPS; and M2-like macrophages with IL4, IL10, and TGF8. Cells were harvested on day 6. The cells were lysed and RNA was extracted using an RNA extraction kit (Qiagen). qPCR was performed using integrated fluidic circuits (IFCs) run on a real-time PCR machine (Fluidigm) with primers specific for HTR2B, HTR2C, and HTR7 (Life Technologies). Gene expression was normalized to HPRT1. Expression level was calculated by 2{circumflex over ( )}(−delta CT), where delta CT is (GOI Ct-HPRT Ct).

Gene expression for HTR2B and HTR7 in M1-like and M2-like macrophages was determined. Both HTR2B and HTR7 expression levels were higher on M1-like macrophages, as shown in Table 17 below.

TABLE 17
EXPRESSION OF SEROTONIN RECEPTORS
IN M1- AND M2-LIKE MACROPHAGES
Expression Level
Cell Type Gene Name (Relative to HPRT1)
M1-like Macrophages HTR2B (Entrez: 3357) 0.7687
M2-like MacrophagesHTR2B (Entrez: 3357)0.0177
M1-like Macrophages HTR7 (Entrez: 3363) 0.0162
M2-like Macrophages HTR7 (Entrez: 3363)0.0068

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