Article reSeArcH
MF01 MF02 MF03 MF04
HSPC WT
HSPC MUT
MkP WT
MkP MUT
HSPC
MkP
MEP
Log
(Cell cycle module) 2
3
4
5
6
P = 0.66
3
4
5
6
P = 0.047
2
3
4
5
P = 0.39
2
3
4
5
P = 0.23
WT
(n=27)
MUT
(n=23)
WT
(n=102)
MUT
(n=554)
WT
(n=51)
MUT
(n=332)
WT
(n=173)
MUT
(n=339)
3
4
5
6
7
P = 3.2 x 10-8
2
4
6
8
P =1.5 x 10-8
0
2
4
6
8
P = 0.15
0
2
4
6
P = 0.019
WT
(n=11)
MUT
(n=16)
WT
(n=56)
MUT
(n=418)
WT
(n=79)
MUT
(n=737)
WT
(n=184)
MUT
(n=569)
4
5
6
7
8
P = 1.5 x 10-9
3
4
5
6
7
8
P = 2.2 x 10-6
3
4
5
6
7
8
P = 6.8 x 10-6
2
3
4
5
6
P = 0.32
WT
(n=30)
MUT
(n=40)
WT
(n=40)
MUT
(n=375)
WT
(n=43)
MUT
(n=424)
WT
(n=118)
MUT
(n=503)
Log
(Cell cycle module) 2
Log
(Cell cycle module) 2
MEP WT
MEP MUT
4
5
6
7
4
5
6
7
4
5
6
7
3
4
5
P = 0.14 P = 2.7 x 10-4 P = 4.2 x 10-7 P = 5.9 x 10-15
WT
(n=29)
MUT
(n=36)
WT
(n=44)
MUT
(n=273)
WT
(n=128)
MUT
(n=892)
WT
(n=180)
MUT
(n=533)
EP
Log
(Cell cycle module) 2
EP WT
EP MUT
e
HSP90AA1
LIMS1
HMGN2
H2AFZ
CCND3
TYMS
SMC2
TMSB4X
CKS1B
RAN
0
5
10
15
20
-2 02
Log 2 (Fold Change)
-Log
(adjusted 10
Pvalue)
CD74
CYTL1
PRSS57
CRHBP
CPPED1
ACTB
PDLIM1
SLC44A1
HBD
Higher in WT MkPs
with High Cell Cycle
Higher in WT MkPs
with Low Cell Cycle
Cell cycle-related genes
Unfolded protein binding genes
d
0
0.1
0.2
0.3
0.4
MUTWT
Pseudotime
P = 0.08
c
Patient ID
MF01
MF02
MF03
MF04
t-SNE2
t-SNE1
t-SNE2
t-SNE1
Pseudotime
Early
Late
t-SNE2
t-SNE1
a b
0
5
10
15
MUT TGFb module / WT TGFb module
MF-2/3
MF-3/3
Fibrosis Score (MF)
P = 4.7 x 10-4
P = 0.0058
P = 0.0091
P = 0.062
MF02MF04MF01MF03
# cells = 11,093
Extended Data Fig. 8 | CALR-mutated haematopoietic progenitor cells
from myelofibrosis show upregulation of the IRE1-mediated UPR.
a, t-SNE projection of CD34+ progenitor cells from samples MF01–MF04,
after integration and batch correction using the Seurat package (Methods)
(n = 11,093). b, Left, t-SNE projection of CD34+ progenitor cells from
samples MF01–MF04 labelled with pseuodotime^21 (n = 11,093). Right,
pseudotime comparison between wild-type (n = 2,221) and mutant
(n = 7,483) cells. P values from likelihood ratio tests of linear mixed model
with genotype as fixed effect and individual patient samples as random
effect, against the model without the genotype effect (Methods). c, Cell-
cycle module score comparison between wild-type and mutant cells in
patients with myelofibrosis (two-sided Wilcoxon rank-sum test). d, Ratio
of TGFβ-signalling-pathway gene expression of mutant and wild-type
MkPs. One mutant and one wild-type MkP were randomly sampled for
each round of analysis (n = 100 iterations; two-sided Wilcoxon-rank sum
test). e, Differentially expressed genes between wild-type MkPs with high
cell-cycle expression (n = 220) and wild-type MkPs with low cell-cycle
expression (n = 110), common across samples MF02–MF04. P values
were combined using Fisher’s combined test with Benjamini–Hochberg
adjustments. Weighted average of fold change (expressed in log 2 ) based on
cell number across samples is shown (Methods).