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Single-cell mass cytometry adapted to measurements of the cell cycle
G0/1
S
G2
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• Method for cell cycle analysis– Markers of cell cycle phases
• S-phase• G0• G1, G2, M
– Validation with cycling T Cells• System-level analysis of cell cycle in normal
and malignant hematopoiesis– SPADE clustering– 35 parameter analysis of normal bone marrow
cell cycle– Application to hematologic malignancies
Cell cycle analysis by mass cytometry
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Mass cytometry DNA staining
G0
G1
G2
S
Hoechst Ir Intercalator
(pentamethylcyclopentadienyl)-Ir(III)-dipyridophenazine
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IdU incorporates rapidly into S-phase cells
56.5% 47.6%
Ir Intercalator
Uri
din
e
FluorescentCytometry
Mass Cytometry
Hoechst
Uri
din
e
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IdU incorporates rapidly into S-phase cells
56.5% 47.6%
Ir Intercalator
Uri
din
e
FluorescentCytometry
Mass Cytometry
Hoechst
Uri
din
e
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Intercalator Ir193IdU
I127
No IdU 5 min 10 min 15 min
30 min 60 min 120 min
0.3% 21.9% 20.6% 24.2%
24.3% 26.6% 28.9%
IdU incorporates rapidly into S-phase cells
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-Andrew Hughes, Gene Ther Mol Biol., 2006; 10:41
p-histone H3
Additional markers allow for complete cell cycle state assignment
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p-histone H3
Additional markers allow for complete cell cycle state assignment
p-R
b (
S807/S
811)
Uridine
G0
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p-histone H3
Additional markers allow for complete cell cycle state assignment
p-histone H3
Uridine
Cyclin
B1
G0/G1
S
G2
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p-histone H3
Additional markers allow for complete cell cycle state assignment
p-histone H3
Uridinep-H
isto
ne H
3 (
S28)
M
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B
A
C
Cyclin B1 Dy164
IdU
I127
p-Rb Ho165
IdU
I127
p-Histone H3 Er168
IdU
I127
human T cells
G0
M
S
G2/MG0/G1
U937 cells HL60 cells NALM6 cells
Cell cycle assessment is robust and consistent across multiple cell types
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U937 cells HL60 cellshuman T cells
B
A
CCyclin B1 Dy164
IdU
I127
p-Rb Ho165
IdU
I127
p-Histone H3 Er168
IdU
I127
G0
M
S
G2/MG0/G1
NALM6 cells
G0 G1 S G2 M0
10
20
30
40
50
60
70
Fluorescence Cytometry
Mass Cytome-try
Cell cycle assessment is robust and consistent across multiple cell types
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Pyro
nin
Y
Hoechst
Hoechst
p-R
b A
lexa 6
47
Pyro
nin
Y
IdU FITC
IdU FITC
p-R
b A
lexa 6
47
p-R
b H
o1
65
IdU I127
p-R
b H
o1
65
Intercalator Ir193
A
B
C
D24.4%
75.6%
23.8%
76.3%
72.3%
27.6%
Phosphorylated Rb (S807/S811) discriminates G0 and G1 phase cells
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The same cell cycle markers can be used for fluorescence cytometry
IdU
Cyclin B1pRb
Mass Cytometry
S
G0/G1 G2/M
G0
Hoechst
Cyclin B1pRb
Fluorescence Cytometry
IdU
Pyro
nin
Y
Hoechst
S
S
G0/G1
G0/G1
G2/M
G2/M
G0
G0
IdU
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0h
28h
48h
Mass cytometry cell cycle analysis is equivalent to fluorescent methodologies
Fluorescent cytometry Mass cytometry
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0h
28h
48h
Mass cytometry cell cycle analysis is equivalent to fluorescent methodologies
Fluorescent cytometry Mass cytometry
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0h
28h
48h
Mass cytometry cell cycle analysis is equivalent to fluorescent methodologies
Fluorescent cytometry Mass cytometry
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0h
28h
48h
G0 G1 S G2 M0
20
40
60
80
100
Fluorescent Cytometry
Mass Cytome-try
G0 G1 S G2 M0
20
40
60
80
100
Fluorescent Cytometry
Mass Cy-tometry
G0 G1 S G2 M0
20
40
60
80
100
Fluorescent Cytometry
Mass cytome-try
Mass cytometry cell cycle analysis is equivalent to fluorescent methodologies
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• Method for cell cycle analysis– Markers of cell cycle phases
• S-phase• G0• G1, G2, M
– Validation with cycling T Cells• System-level analysis of cell cycle in
normal and malignant hematopoiesis– SPADE clustering– 35 parameter analysis of normal bone marrow
cell cycle– Application to hematologic malignancies
Cell cycle analysis by mass cytometry
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Panel for analysis of cell cycle in human marrow
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Biaxial plots are not a scalable solution
Parameters:
481432
Plots: 62891496
Sean Bendall, Erin Simonds. Science, May 2011
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SPADE: Spanning-tree Progression Analysis of Density-normalized Events – Peng Qiu
1. Determine Tree Structure
2. Overlay regions with surface marker expression levels
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SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD45
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Naïve CD4 T
CD4 T
NK
CD8 T
Naïve CD8 T
NKT
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD3
CD45
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Early
Mature Myeloid
Meta-myelocytes
Myelocytes
LatePromyelocytes
Myeloblasts
CMP
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD15
CD45
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Macrophages
Mature Monocytes
EarlyMonocytes
PC-DCs
Pro-monocytes
Monoblasts
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD14
CD45
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Mature B cells
ImmatureB cells
Pre-BII
Plasma
Pre-BI
Pro-B
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD20
CD45
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Erythroblasts
NucleatedRBCs
Pro-erythroblasts
MEP
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD235
CD45
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HSC
Vasc. Progen?MPP
Pre-BI
Pro-B
Pro-erythroblasts
MonoblastsMyeloblasts
CMP
MEP
GMP
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD34
CD45
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HSC
Macrophages
Mature Monocytes
EarlyMonocytes
PC-DCs
Pro-monocytes
Naïve CD4 T
CD4 T
NK
CD8 T
Naïve CD8 T
Vasc. Progen?MPP
Mature B cells
ImmatureB cells
Pre-BII
Plasma
Pre-BI
Pro-B
Erythroblasts
NucleatedRBCs
Early
Mature Myeloid
Meta-myelocytes
Myelocytes
LatePromyelocytes
Pro-erythroblasts
MonoblastsMyeloblasts
CMP
MEP
GMPNKT
SPADE clustering of normal bone marrow mirrors immunophenotypic differentiation.
CD45
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B cell proliferation is concentrated in pre-BII population
CD34
CD10
CD19
CD20
Pro-B
Pre-BI
Pre-BII
Mature B
Normal Human Bone MarrowColored for CD45
G1
S
G2
= 200 Cells
= 67%
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Erythroid cell proliferation is concentrated in erythroblast population
Normal Human Bone MarrowColored for CD45
G1 S G2
CD34 CD71 CD235
MEP
Pro-erythro-blast
Erythro-blast
NucleatedRBC
= 200 Cells
= 67%
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Myelocyte proliferation peaks at early promyelocyte stage
Normal Human Bone MarrowColored for CD45
CD11b
CD15
CD16
EarlyPromyelo-cytes
Metamyelocyte
Mature myelocyte
LatePromyelo-cytes
Myelocyte
= 3500 Cells
= 67%
S
G2
G1
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SPADE analysis allows for identification of distinct AML immunophenotypes
NK Cell
T Cell
Mature Myeloid
Promyelocyte /Myelocyte
HSC /Early Progenitor
B Cell
?Pro-B /Pre-B
Mature Monocytic
Promonocyte
Normal human bone marrowClustered alongside AML samples
Colored for CD45
Myleo/mono-blast
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Cell cycle distribution varies across the immunophenotypic subsets within each AML sample
AML9AML5
CD34
S
= 20%
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Conclusions
• Validated methodology for using mass cytometry to asses cell cycle state in combination with high-parameter immunophenotypic analysis
• System-wide analysis of proliferation across normal human hematopoiesis
• The ability to combine cell cycle state with multiple other variables in the monitoring of cellular responses at the single-cell level
• We intend to use this methodology to characterize the cell cycle within complex human cancer samples
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• Hematology– Bruno Medeiros– Peter Greenberg– Beverly Mitchell
• Aparna Raval
• Cytobank– Nikesh Kotecha
Acknowledgements
• Nolan Lab– Garry Nolan– Wendy Fantl– Sean Bendall– Erin Simmonds– Rachel Fink– Matt Clutter– Angelica Trejo– Matt Hale
• Stanford– Michael Linderman– Sylvia Plevritis
• MD Anderson– Peng Qiu