Dear Editor,
Polycythemia vera (PV) is a myeloproliferative neoplasm (MPN) marked by hyperproliferation
of all myeloid cell lineages and characterized by activated JAK-STAT signaling due
to an activating mutation in JAK2
1
. Disease-driving pathogenic changes in MPNs are thought to arise in hematopoietic
stem cells (HSCs) that give rise to the diseased clonal progeny
2,3
. We recently developed a new data-independent acquisition (DIA) mass spectrometry
(MS) technology for rare human hematopoietic stem and progenitor cell (HSPC) subpopulations
4
. This DIA-MS proteomic analysis was applied to human hematopoietic stem/multipotent
progenitor cells (HSC/MPPs) and common myeloid/megakaryocyte-erythrocyte progenitors
(CMP/MEPs) isolated from 123 blood samples of 18 PV patients and 21 controls (Supplementary
Table 1). The proteomic dataset was complemented with RNA-sequencing data of the same
patient and control samples.
Comparing the proteomic and transcriptomic datasets in the corresponding patient and
control samples demonstrated mainly positive correlations: 70% of genes had positive
Spearman’s correlation coefficients for protein and RNA expression. In line with our
previous observations in HSC/MPPs of healthy stem cell donors
4
, 30% of genes with altered expression in PV patients and their controls demonstrated
negative correlation coefficients for protein and RNA expression, indicating additional
information gained by proteomic compared to transcriptomic data.
Downregulation of megakaryocyte differentiation and upregulation of cell proliferation
in PV HSPCs and its reversal upon treatment with hydroxyurea (HU)
To further examine the added information provided by protein compared to RNA expression
data, we performed enrichment analyses for gene ontologies in HSPC subpopulations
of PV patients on protein and RNA levels. Megakaryocyte differentiation and regulation
was significantly downregulated in untreated PV patients at the protein level, but
not at the RNA level in all HSPCs analyzed (Fig. 1A with individual gene ontology
protein members shown in Fig. 1B). Similarly, RNAs and proteins implicated in DNA
replication and G1/S transition of the mitotic cell cycle were discordantly regulated
in HSC/MPPs of untreated PV patients (Fig. 1A). In contrast to the discordant protein
and RNA expression in these gene sets, we observed concordant expression on the protein
and RNA level for erythrocyte differentiation, regulation, development and maturation,
receptor signaling via JAK-STAT, interferon-gamma signaling, cholesterol biosynthetic
process, and TGFβ and MAPK signaling and regulation in HSPCs of untreated PV patients
compared to controls (Fig. 1A).
Fig. 1
Comparative unbiased proteomic analysis identifies downregulation of CXCL4/PF4 in
HSC/MPPs of PV patients.
A Gene set enrichment analysis (GSEA) comparing untreated PV patients against controls
(PV.UT.HSC/MPP versus Control.HSC/MPP; PV.UT.CMP/MEP versus Control.CMP/MEP) and assessing
for the effect of treatment with hydroxyurea (PV.HU.HSC/MPP versus PV.UT.HSC/MPP;
PV.HU.CMP/MEP versus PV.UT.CMP/MEP). Shown are normalized enrichment scores (NES)
for individual gene sets. Significantly upregulated gene sets are marked in red color,
significantly downregulated gene sets are marked in blue color. Only RNAs and proteins
expressed in at least half of the replicates in both comparison groups were considered.
UT untreated, HU patient under treatment with hydroxyurea. B Heatmap of proteins enriched
in different patient and control groups for megakaryocyte differentiation and regulation.
C Volcano plot of protein intensity fold changes and p-values comparing HSC/MPPs of
untreated PV patients (PV.UT.HSC/MPP) against controls (Control.HSC/MPP). D Normalized
protein intensities for CXCL4/PF4 in the subgroups of controls, chronic PV patients
without cytoreductive therapy (PVchron.UT), chronic PV patients with hydroxyurea therapy
(PVchron.HU), and progressed PV patients (PVprog). Error bars represent standard deviations.
*adj. P < 0.05; **adj. P < 0.01; ***adj. P < 0.001 Peptide profiles for CXCL4/PF4
are provided in Supplementary Fig. 1. E Graphical summary of intracellular FACS staining
experiments for CXCL4/PF4 in six untreated chronic PV patients and age- and gender-matched
controls. Error bars represent standard deviations. F Normalized CXCL4/PF4 expression
values for protein and RNA in individual patient and control samples. Discrepant high
RNA and low protein levels were seen in progressed PV patients with fibrosis (post-PV
MF) but not in post-PV AML.
Cytoreductive therapy with hydroxyurea reverted downregulation of megakaryocyte differentiation
and regulation on protein level (Fig. 1A, B). It also reversed upregulation of cell
proliferation (DNA replication, G1/S transition of the mitotic cell cycle, DNA repair)
on RNA level and downregulation of TGFβ signaling on protein and RNA level (Fig. 1A).
Erythrocyte differentiation and regulation were reversed by hydroxyurea on the protein
but not RNA level, whereas interferon-gamma signaling was not affected by the treatment
of patients with hydroxyurea (Fig. 1A).
Reduced CXCL4/PF4 expression in HSC/MPPs of untreated PV patients
To better characterize the molecular phenotype underlying PV stem and progenitor cell
biology, we next focused on individual differentially regulated proteins in HSC/MPPs
of untreated PV patients compared to controls. Consistent with the downregulation
of megakaryocyte differentiation and regulation observed in the gene ontology enrichment
analysis (Fig. 1A, B), we observed significant downregulation of the megakaryocytic
lineage protein CXCL4/PF4 (platelet factor 4) (Fig. 1C, D and Supplementary Fig. 1).
Intracellular flow cytometry confirmed the downregulation of CXCL4/PF4 in HSC/MPPs
of untreated chronic phase PV patients in comparison to age- and gender-matched controls
(Fig. 1E). Treatment with hydroxyurea abrogated the downregulation of CXCL4/PF4 protein
expression in PV HSC/MPPs (Fig. 1D).
Since all PV patients analyzed in this study carried the JAK2V617F mutation, we tested
for a potential direct relationship between the JAK2V617F allele burden and CXCL4/PF4
protein expression. No significant correlation was observed (Supplementary Fig. 2),
suggesting that reduced CXCL4/PF4 expression in PV is a JAK2V617F allele burden-independent
disease manifestation.
CXCL4/PF4 did not show equally significant expression changes on the RNA level as
on the protein level. Exploring protein-RNA-correlations in more detail, we observed
that protein and RNA levels became discordant upon disease progression (Fig. 1F).
Upregulated RNA and downregulated protein levels for CXCL4/PF4 were observed in HSC/MPPs
of post-PV myelofibrosis (MF) patients but not in post-PV acute myeloid leukemia (AML)
stem cells. In controls and non-progressed PV patients, protein and RNA levels of
CXCL4/PF4 were better aligned even if not systematically coordinated (Fig. 1F).
Decreased ELF1 and USF2 activity explains reduced CXCL4/PF4 expression, which is linked
to downregulated TGFβ signaling and loss of stem cell quiescence
We next assessed the activities of transcription factors (TFs), which bind the CXCL4/PF4
promoter and may regulate CXCL4/PF4 expression in PV HSC/MPPs (Fig. 2A)
5–8
. We found a significantly decreased activity for ELF1 and to a lesser extent also
for USF2 in HSC/MPPs of untreated PV compared to controls and HU-treated PV (Fig.
2A), suggesting a potential link between diminished ELF1 and USF2 activity and a reduction
of CXCL4/PF4 expression in HSC/MPPs of untreated PV patients
5,8
. Upon progression to post-PV MF, the activities of the TFs USF2 and also NKX2-2 increased,
potentially explaining upregulated RNA levels of CXCL4/PF4 in these patients (Supplementary
Fig. 3)
5
.
Fig. 2
CXCL4/PF4 protein is associated with transcriptional stem cell quiescence in untreated
PV and inhibits the colony-formation capacity of PV HSC/MPPs.
A Activity analysis of transcription factors (TFs) regulating CXCL4/PF4 expression
showed significantly downregulated activity for the TF ELF1 and to a lesser degree
for the TF USF2 in untreated PV patients compared to controls and HU-treated PV patients.
Error bars represent standard errors. *P < 0.05. B Gene set enrichment analysis showed
strong and significant enrichment for genes downregulated in stem cell quiescence
in HSC/MPPs of untreated PV patients (PV.UT) compared to HSC/MPPs of controls, suggesting
cessation of stem cell quiescence in PV stem cells. C Treatment of patients with hydroxyurea
(PV.HU.HSC/MPP versus PV.UT.HSC/MPP) reversed the loss of stem cell quiescence in
the PV HSC/MPP subpopulation. NES normalized enrichment score. D Heatmap of RNAs enriched
in different patient/control groups for genes downregulated in stem cell quiescence.
The corresponding enrichment plots and heatmap for the protein level are shown in
Supplementary Fig. 4A-C. E Functional single-cell CXCL4/PF4 assay: colony growth of
FACS-sorted HSC/MPPs from untreated chronic PV patients (PVchron.UT) singly incubated
in cytokine-enriched serum-free medium was assessed in presence or absence of CXCL4/PF4.
Colony growth as depicted was evaluated in 864 wells after 7 days of incubation. In
individual patients, significance was determined using Fisher’s exact test; significance
overall was calculated using two-tailed and paired Student’s t test (see Supplementary
Methods). A strong growth inhibitory role of CXCL4/PF4 was observed. F Methylcellulose
colony assay: the growth of different myeloid colony subtypes from FACS-sorted HSC/MPPs
of untreated chronic PV patients (PVchron.UT) was evaluated in presence or absence
of CXCL4/PF4. Reductions in colony growth due to CXCL4/PF4 protein were observed for
all colony subtypes with significant inhibitions seen in the CFU-GM and BFU-E colony
subtypes as well as in composite granulocyte/macrophage (CFU-GM and CFU-G and CFU-M)
and erythroid (BFU-E and CFU-E) colonies. Relative numbers of colonies related to
the total cell numbers plated are plotted. Error bars represent standard deviations.
*P < 0.05. CFU-GEMM (mixed colonies), CFU-GM colony-forming unit–granulocyte/macrophage,
CFU-G colony-forming unit–granulocyte, CFU-M colony-forming unit–macrophage, BFU-E
burst-forming unit–erythroid, CFU-E colony-forming unit–erythroid.
Reduced CXCL4/PF4 expression in HSC/MPPs of PV patients was associated with significant
upregulation of genes downregulated in stem cell quiescence both on RNA (Fig. 2B,
D) and protein (Supplementary Fig. 4A and 4C) level
9
. This pattern was reversed by treatment of patients with cytoreductive hydroxyurea
(Fig. 2C, D and Supplementary Fig. 4B, C). Mechanistically, CXCL4/PF4 upregulates
TGFβ
10
, which promotes stem cell quiescence
11
. We observed downregulation of TGFβ signaling in untreated PV patients that also
exhibited downregulated CXCL4/PF4 levels (Fig. 1A). These data suggest that reduced
CXCL4/PF4 expression in PV HSC/MPPs leads to the cessation of stem cell quiescence
via downregulation of TGFβ signaling.
CXCL4/PF4 inhibits colony formation of HSC/MPPs isolated from untreated chronic phase
PV patients
To assess the functional relevance of CXCL4/PF4 downregulation and to examine its
causal link to HSC/MPP proliferation and differentiation in PV, we cultured HSC/MPPs
of untreated chronic phase PV patients in the presence or absence of CXCL4/PF4 using
two independent colony formation assays. Supplementation with CXCL4/PF4 inhibited
colony formation of singly sorted PV HSC/MPPs after 7 days in the cytokine-enriched
serum-free medium by 63–71% (Fig. 2E). In methylcellulose assays, a 54–61% inhibition
of total colony formation was observed upon reconstitution/treatment with CXCL4/PF4
for FACS-sorted HSC/MPPs from PV patients (Fig. 2F). Detailed analyses for colony
subtypes as defined by Manz et al.
12
showed significant reductions in colony growth from PV HSC/MPPs upon exposure to supplemental
CXCL4/PF4 for CFU-GM (colony-forming unit–granulocyte/macrophage) and BFU-E (burst-forming
unit–erythroid) (Fig. 2F). These results demonstrate that CXCL4/PF4 is linked to HSC/MPP
proliferation and differentiation in PV, and reduced CXCL4/PF4 expression in HSC/MPPs
may contribute to the proliferative state of PV.
Discussion
This study identifies reduced CXCL4/PF4 protein expression in HSC/MPPs of untreated
PV patients compared to controls. Treatment of patients with cytoreductive hydroxyurea
abrogated this effect. We demonstrated transcriptional cessation of stem cell quiescence
to be associated with reduced CXCL4/PF4 expression in PV HSC/MPPs, and supplementation
with CXCL4/PF4 strongly inhibited the in vitro colony-formation capacity of HSC/MPPs
from PV patients. These findings extend previous reports in healthy hematopoietic
stem cells and non-PV JAK2-mutated erythroblast-like cells
13
. CXCL4/PF4-/- mice were shown to exhibit increased numbers and proliferation of HSCs
and MPPs
14
, and high CXCL4/PF4 levels were found to strongly inhibit hematopoiesis in non-PV
mice
14
. The inhibitory role of CXCL4/PF4 on HSPC proliferation in our PV patients supports
a key role of downregulated CXCL4/PF4 for the proliferative phenotype of PV HSC/MPPs.
Mechanistically, we observed downregulation of TGFβ signaling in untreated PV patients
showing reduced CXCL4/PF4 expression. CXCL4/PF4 was previously shown to activate stem
cell quiescence-inducing TGFβ
10,11
. Upstream of CXCL4/PF4, we identified reduced activity of the CXCL4/PF4-regulating
transcription factors ELF1
8
and USF2
5
in HSC/MPPs of untreated PV patients. Our data thus support a model in which decreased
ELF1 and USF2 activity in PV HSC/MPPs leads to reduced CXCL4/PF4 expression, which
leads to decreased TGFβ signaling and concomitant cessation of stem cell quiescence.
Upon progression to post-PV MF, USF2 activity increased, explaining elevated CXCL4/PF4
RNA levels in this patient group.
The PV disease stages and controls were better separated by CXCL4/PF4 protein expression
than by CXCL4/PF4 RNA expression. Whereas transcriptomics reinforced the proteomic
results for CXCL4/PF4 in chronic phase PV, discrepant RNA and protein levels were
observed in HSC/MPPs of post-PV MF patients. Our findings in fibrotic patients are
in line with recent observations of upregulated CXCL4/PF4 RNA levels in co-cultured
HSPCs of a murine PMF model
15
. The congruent CXCL4/PF4 protein and RNA expression in control, chronic PV, and post-PV
AML, but not in post-PV MF suggests post-transcriptional regulation at the base of
discrepant RNA and protein levels in post-PV MF.
In summary, this study identified downregulation of CXCL4/PF4 expression in HSC/MPPs
with the cessation of stem cell quiescence through downregulation of TGFβ signaling
as a potential new driver of the proliferative state of PV.
Supplementary information
Supplemental material