A novel human pluripotent stem cell gene activation system identifies IGFBP2 as a mediator in the production of haematopoietic progenitors in vitro

  1. Paolo Petazzi
  2. Telma Ventura
  3. Francesca Paola Luongo
  4. Heather McClafferty
  5. Alisha May
  6. Helen Alice Taylor
  7. Michael J Shipston
  8. Nicola Romanò
  9. Lesley M Forrester
  10. Pablo Menendez
  11. Antonella Fidanza  Is a corresponding author
  1. Josep Carreras Leukemia Research Institute, Spain
  2. Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, United Kingdom
  3. Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, United Kingdom
  4. Zhejiang University-University of Edinburgh Joint Institute, Zhejiang University School of Medicine, Zhejiang University, China
  5. CIBER-ONC, ISCIII, Spain
  6. Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
  7. Department of Biomedicine, School of Medicine, University of Barcelona, Spain
  8. Pediatric Cancer Centre Barcelona-Institut de Recerca Sant Joan de Deu (PCCB-SJD), Barcelona, Spain, Spain
  9. Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, United Kingdom
6 figures, 1 table and 2 additional files

Figures

Figure 1 with 1 supplement
Comparison of in vitro induced pluripotent stem cell (iPSC)-derived and in vivo aorta-gonad-mesonephros (AGM)-derived endothelial cells identifies nine differentially expressed transcription factors.

(A) Schematic of the analytic pipeline used to identify the target genes. (B) Integrative analysis of single-cell transcriptome of in vitro-derived endothelial (IVD_Endo) and haematopoietic cells (IVD_HPCs) with in vivo developed endothelial cells (venous, vEC; arterial, aEC; arterial haemogenic, HECs) from human embryos (CS12-CS14) visualised on UMAP dimensions. (C) Target genes expression level showing higher expression in arterial haemogenic endothelium in vivo than in vitro-derived cells.

Figure 1—figure supplement 1
Gene expression profile of the target genes in an additional human AGM dataset.

(A) Single-cell transcriptomic analysis of developing aorta-gonad-mesonephros (AGM) collected from human embryos at Carnegie stages 14 and 15 enriched for CD31+ and CD34+ cells from Calvanese et al., 2022, Nature. Arterial haemogenic endothelium, dashed line, is identified by the colocalisation of DLL4 and RUNX1. (B) Gene expression analysis of the nine selected target genes in the developing human aorta, showing their expression in the haemogenic endothelium.

Figure 2 with 2 supplements
The inducible SAM (iSAM) cassette successfully mediates activation of endogenous gene expression upon doxycycline (DOX) induction.

(A) Schematic of the iSAM cassette containing the TET-on system under the control of EF1α and dCAS9-P2A-MS2-p65-HSF1-T2A-mCherry under the rTTA responsive elements, separated by genetic silencer and flanked by AAVS1 specific homology arms. (B) RUNX1C gene expression activation after transient transfection of the iSAM plasmid and gRNAs in presence or absence of DOX in human induced pluripotent stem cell (iPSC) line (n=3 from independent transfections). (C) RUNX1 protein expression upon iSAM activation after transient transfection of the iSAM plasmid and gRNAs with DOX in human iPSC line detected by immunostaining. (D) Expression of the iSAM cassette reported by mCherry tag during the differentiation protocol, the representative images (bright field - BF, and fluorescence) show embryoid bodies at day 3 of differentiation. (E) Schematic of the gRNA 2.1 containing the capture sequence for detection during the single-cell RNA sequencing (scRNAseq) pipeline. (F) RUNX1C gene activation level obtained using either the gRNA 2.0 or 2.1 backbone (n=3 from independent transfections of the 4 different gRNAs). (G) Statistical analysis of the gRNAs activation level showing no significant variation following addition of the capture sequence (n=3 for each of the 4 different gRNAs).

Figure 2—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 2.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
Functional validation of the iSAM plasmid.

(A) Schematic of the inducible SAM (iSAM)-mediated activation of RUNX1C by transient transfection in HeLa cells with the iSAM vector and the RUNX1C gRNA; fluorescent microscopy demonstrating the expression of the mCherry tag. (B) Linear regression of RUNX1C RNA expression in relation to the concentration of doxycycline (DOX) added to HeLa cells (n=3). (C) Schematic of the iSAM-mediated activation of the human embryonic stem cells (hESCs) RUNX1C-GFP reporter cell line by transient transfection of the iSAM vector and RUNX1C gRNA. (D) Flow cytometry analysis of RUNX1C-GFP expression and mCherry in the hESCs RUNX1C-GFP reporter line after exposure to different DOX concentrations. (E) Linear regression of the mCherry tag expression in relation to the concentration of DOX added (in ng/ml) to the hESCs RUN1C-GFP reporter line (n=3). (F) Percentage of activated cells (GFP+mCherry+) in the presence of different concentrations of DOX (in ng/ml) (n=3). (G) RUNX1C single-cell expression level analysed by flow cytometry in hESCs exposed to different DOX concentrations (n=4).

Figure 2—figure supplement 1—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 2—figure supplement 1.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig2-figsupp1-data1-v1.xlsx
Figure 2—figure supplement 2
Validation of the iSAM hiPSC cell lines.

(A) PCR screening of the clones obtained from the AAVS1 targeting showing specific integration with amplification across the 5’ end, and (B) the wild-type (WT) locus. Clone 3.13 was selected for the study and referred to as inducible SAM (iSAM). (C) Flow cytometry analysis of mCherry+ cells upon DOX addition in human induced pluripotent stem cells (hiPSCs) with iSAM targeted into the AAVS1 locus following maintenance. (D) Flow cytometry analysis of the expression of the mCherry tag, in hiPSCs with iSAM targeted into the AAVS1 locus, following 48 hr sodium butyrate and DOX treatment at different concentrations. (E) Flow cytometry analysis of the expression of the mCherry tag upon DOX addition, in hiPSCs with iSAM targeted into the AAVS1 locus, maintained in the presence of 500 μM sodium butyrate. (F) The cell count of iPSCs maintained in the presence of sodium butyrate shows no significant differences (Mann-Whitney unpaired t-test, p=0.45). (G) Cell viability was comparable when iPSCs were maintained in control conditions or in the presence of sodium butyrate (Mann-Whitney unpaired t-test, p=0.46). (H) PCR screening for the integration of the gRNA into the genome of the iSAM hiPSCs line (from left to right: iSAM line before infection, after infection with non-targeting gRNA, after infection with aorta-gonad-mesonephros [AGM] library and water negative control). (I) Sanger sequencing trace of the amplicons obtained from the iSAM line infected with the non-targeting gRNA (top) or the AGM library (bottom).

Figure 2—figure supplement 2—source data 1

Spreadsheet source file contains the source data used for the plots in Figure 2—figure supplement 2.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig2-figsupp2-data1-v1.xlsx
Figure 2—figure supplement 2—source data 2

Raw uncropped images of the entire gels used in Figure 2—figure supplement 2.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig2-figsupp2-data2-v1.zip
Figure 2—figure supplement 2—source data 3

Raw uncropped images of the entire gels used in Figure 2 figure with labelling of the band highlighted in Figure 2—figure supplement 2.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig2-figsupp2-data3-v1.zip
Figure 3 with 1 supplement
Single-cell RNA sequencing (scRNAseq) in combination with CRISPR activation identifies arterial cell type and functional haematopoietic expansion in association with activation of the nine target genes.

(A) Gene expression profile of target genes following target genes’ activation, heatmap shows the expression level of the target genes in the iSAM_NT and iSAM_AGM treated with doxycycline (DOX) following normalisation on the -DOX control. (B) Dimension reduction and clustering analysis of the scRNAseq data following activation, filtered on cells where the gRNA expression was detected. (C) Arterial (GJA4, DLL4), venous (NRP2, APLNR), and haemogenic marker (CD44, RUNX1) expression distribution in the clusters indicated by the colour. (D) Expression distribution visualised on the UMAP plot showing the location of arterial cells marked by DLL4, and haemogenic endothelium marked by CD44 and RUNX1. (E) Heatmap of the top 15 marker genes for each of the clusters. (F) Contribution of the different libraries to the clusters showing that arterial cell cluster is overrepresented in the iSAM_AGM treated with DOX, compared to the other libraries. (G) Expansion of the arterial population assessed by the membrane marker expression of DLL4+ following targets’ activation, quantified by flow cytometry at day 8 of differentiation. (Data are normalised on the iSAM_NT+DOX sample, n=5 independent differentiations, *p=0.0417 paired t-test.) (H) Colony-forming potential of the suspension progenitor cells derived from the two lines treated with or without DOX following OP9 coculture activation, data show the colony obtained for 104 CD34+ input equivalent (n=3 from independent differentiations *p<0.05, Tukey’s two-way ANOVA).

Figure 3—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 3.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig3-data1-v1.xlsx
Figure 3—figure supplement 1
Experimental design and further characterisation of the activation results.

(A) Schematic of the derivation of the inducible SAM (iSAM) cell line by ZNFs mediated targeting of the AAVS1 locus and the subsequent derivation of the iSAM_NT (containing the non-targeting control gRNA) and iSAM_AGM (containing the gRNAs for the target genes) by viral transduction of the gRNAs. (B) Schematic of the differentiation protocol with activation of the target genes, used for both the control line iSAM_NT and iSAM_AGM. (C) Schematic of the IGFBP2 functional validation experiment. (D) Expansion of the arterial population marker by membrane expression of DLL4+ following targets’ activation, quantified by flow cytometry at day 8 of differentiation (*p=0.0190, **p=0.0011, Sidak’s two-way ANOVA). (E) Flow cytometry analysis of the cell cycle analysis of suspension progenitor cells was obtained following the OP9 coculture of cells treated with IGFBP2 and control at day 13. (F) iSAM expressing cells at day 8 of differentiation upon doxycycline (DOX) treatment. (G) Target genes’ expression profile across the different libraries, the colour legend for the libraries is on the top right. (H) IGFBP2 expression profile across the cell clusters and in the cell lines and conditions indicated in the title (cluster legend same as in I). (I) Contribution of each of the libraries to the cell clusters, grouped by libraries (cluster legend at the bottom).

Figure 3—figure supplement 1—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 3—figure supplement 1.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig3-figsupp1-data1-v1.xlsx
IGFBP2 addition to the in vitro differentiation leads to a higher number of functional haematopoietic progenitor cells.

(A) Violin plot of IGFBP2 expression profile in the arterial cells obtained from the different conditions, in the presence or absence of gRNAs and doxycycline (DOX). (B) Number of haematopoietic colonies obtained after coculture on OP9 in the presence or absence of IGFBP2 (n=3–4 from independent differentiations, **p=0.0080, Sidak’s two-way ANOVA). (C) Percentage of DLL4+ arterial cells differentiation within the CD34+ compartment analysed by flow cytometry in day 8 embryoid bodies (EBs) (n=4 from independent differentiations, two-way ANOVA, ns = p>0.99). (D) Expansion of haematopoietic progenitors analysed using markers’ expression on suspension progenitors derived after coculture of CD34+ cells onto OP9 support (data are expressed as fold over the CTR in the absence of IGFBP2; n=4 from independent differentiations, *p<0.02, Sidak’s two-way ANOVA). (E) Single-cell transcriptomic analysis of developing aorta-gonad-mesonephros (AGM) collected from human embryos at Carnegie stages14 and 15 enriched for CD31+ and CD34+ showing the IGFBP2 expression profile in vivo in the AGM.

Figure 4—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 4.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig4-data1-v1.xlsx
Figure 5 with 1 supplement
IGFBP2 alters cell metabolism by inducing a reduction in glycolytic ATP production.

(A) Clustering analysis of the single-cell transcriptomic time course analysis of differentiating cells at day 10 and day 13 in the absence (CTR) or presence of IGFBP2. Arrows indicate the difference in the clustering due to the addition of IGFBP2 compared to control. (B) Expression profile of arterial markers, GJA4 and DLL4, and haemogenic marker RUNX1 (top - the dashed line shows the location of the shift in gene expression of cells treated with IGFBP2) and their expression profile in the endothelial cells cluster marked by growth factor binding in the absence (CTR) and in the presence of IGFBP2 (GJA4 p=1E–54, DLL4 p=1.2E–119, RUNX1 p=8.2E–163). (C) KEGG enrichment analysis of the genes upregulated at day 13 upon IGFBP2 treatment. The arrow shows the ranking of the oxidative phosphorylation pathway. (D) Dot plot showing the expression profile of the genes coding for the enzyme of the oxidative phosphorylation pathway. (E) Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) profile in cells at day 13 of differentiation reporting mitochondrial respiration and glycolysis, respectively. (F) ATP production rate divided by that deriving from glycolysis and from mitochondrial respiration, in cells treated with IGFBP2 and controls at day 13. (G) Ratio of the ATP production between glycolysis and mitochondrial respiration in cells treated with IGFBP2 and controls at day 13.

Figure 5—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 5.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig5-data1-v1.xlsx
Figure 5—figure supplement 1
Additional analyses of the effect of IGFBP2 addition during in vitro differentiation.

(A) Dot plot showing the expression profile of the genes coding for the enzymes mediating glycolysis in CTR and IGFBP2-treated cells at day 10 and 13. (B) Dot plot showing the expression profile of the genes coding for the checkpoints of the glycolysis in CTR and IGFBP2-treated cells at days 10 and 13. (C) Percentage of cells expressing different markers following OP9 coculture of CD34+ cells (ns for all markers, Kruskall-Wallis one-way ANOVA). (D) OP9 cocultures of CD34+ DLL4+ and CD34+DLLL4- (scale bar indicates 50 μm), and in (E) their colony formation capacities following 1 week of OP9 coculture (mixed-effect analysis, Sidak’s post-test, ****p<0.0001, **p<0.01). (F) Cluster composition in cells treated with IGFBP2 data shows the composition at day 10 and day 13.

Figure 5—figure supplement 1—source data 1

Spreadsheet source file containing the source data used for the plots in Figure 5—figure supplement 1.

Each tab is labelled to uniquely refer to a specific panel.

https://cdn.elifesciences.org/articles/94884/elife-94884-fig5-figsupp1-data1-v1.xlsx
Model summarising the results.

During development, some endothelial cells undergo arterialisation, as identified by their arterial genes’ expression profile (e.g. DLL4). Arterial cells, characterised by high dependency on glycolysis, are expanded by our CRISPR activation approach, resulting in more blood production since these cells are the cell-of-origin of the haemogenic endothelium. Once arterial cells commit to haemogenic endothelium fate, they start to express haematopoietic genes (e.g. RUNX1); this process is enhanced by IGFBP2 via induction of both RUNX1 expression and increased dependency on oxidative phosphorylation, known to be important for the progression of the endothelial to haematopoietic transition.

Tables

Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Escherichia coli)StBL3Expanded in the labStBL3Electrocompetent cells for the expansion and cloning
of the plasmid in this paper, use of alternative strains
leads to lower yield
Cell line (Homo sapiens)HeLaLabHeLaEpithelial immortalised cell line from cervical cancer
Cell line (Homo sapiens)hiPSCsLab, reference:
Yang CT, et al. Stem Cells. 2017;35(4):886–897.
SFCi55Dermal fibroblast from O Rh- donor reprogrammed using
episomal OCT4, KLF2, SOX2, and MYC
Cell line (Homo sapiens)hiPSCsThis paperiSAMHuman iPSCs with the DOX-inducible SAM cassette inserted
in the AAVS1 locus
Cell line (Homo sapiens)hiPSCsThis paperiSAM-AGMHuman iPSCs with the DOX-inducible
SAM cassette inserted in the AAVS1 locus+random
integration of the 49 gRNAs
Cell line (Homo sapiens)hiPSCsThis paperiSAM-NTHuman iPSCs with the DOX-inducible SAM
cassette inserted in the AAVS1 locus+random
integration of the non-targeting gRNA
Recombinant DNA reagentAAVS1-iSAM (plasmid)This paperRRID:Addgene_211495AAVS1 targeting vector for the insertion of the
iSAM cassette on chromosome 19
Recombinant DNA reagentgRNA 2.1 backbone
(plasmid)
This paperRRID:Addgene_211496Lentiviral vector for the U6-driven expression of
gRNA compatible with the SAM system containing
the capture sequencing for 10X scRNAseq
Recombinant DNA reagentNon-targeting CTR gRNAThis paper,
Supplementary file 1
NT-gRNACGGAGGCTAAGCGTCGCAAC
Recombinant DNA reagentLibrary of targeting gRNAThis paper, Supplementary file 1AGM-gRNAs
AntibodyAnti-human CD34 Percp-Efluor710
(mouse monoclonal)
eBioscienceClone 4H11Flow cytometry 1:100
AntibodyAnti-human CD34 PE
(mouse monoclonal)
eBioscienceClone 4H11Flow cytometry 1:200
AntibodyAnti-human CD43 APC
(mouse monoclonal)
eBioscienceClone eBio84-3C1Flow cytometry 1:100
AntibodyAnti-human CD45 FITC
(mouse monoclonal)
eBioscienceClone 2D1Flow cytometry 1:100
AntibodyAnti-human DLL4 PE
(mouse monoclonal)
BioLegendClone MHD4-46Flow cytometry 1:200
AntibodyAnti-human CD41 PE (mouse monoclonal)BioLegendClone HIP8Flow cytometry 1:200
AntibodyAnti-human CD144 APC (mouse monoclonal)eBioscienceClone 16B1Flow cytometry 1:100
AntibodyAnti-human CD235a FITC (mouse monoclonal)BD BioscienceClone HIR2Flow cytometry 1:250
Sequence-based reagentFWSynthetised by IDTPCR primer for the amplification of the UniSAM plasmid RRID:Addgene_99866aggggacccggttcgagaaggggctcttcatcactagggccgctagctctagagagcgtcgaatt
Sequence-based reagentRVSynthetised by IDTPCR primer for the amplification of the UniSAM plasmid RRID:Addgene_99866ttcgggtcccaattgccgtcgtgctggcggctcttcccacctttctcttcttcttggggctcatggtggcc
Sequence-based reagentSigma_AAVS1Synthetised by IDTForward PCR primer to test for the specific AAVS1 integration of the iSAM cassette and for the wild type not integrated locusCGG AAC TCT GCC CTC TAA CG
Sequence-based reagentNeoRSynthetised by IDTReverse PCR primer to test for the specific AAVS1 integration of the iSAM cassetteGAT ATT GCT GAA GAG CTT GGC GG
Sequence-based reagentAVVS1_EXT3_RVSynthetised by IDTForward PCR primer to test for the wild type AVVS1 not integrated locusACA CCC AGA CCT GAC CCA AA
Sequence-based reagentgRNA_FWSynthetised by IDTForward primer used for the PCR to insert the capture sequence in the gRNA plasmid RRID:Addgene_73797gagggcctatttcccatgattcct
Sequence-based reagentgRNA_Cap_RVSynthetised by IDTReverse primer used for the PCR to insert the capture sequence in the gRNA plasmid RRID:Addgene_73797aaaaaaggatccaaaaaaCCTTAGCCGCTAATAGGTGAGCgcaccgactcggtgcc.
Peptide, recombinant proteinrhBMP4R&D314-BP-01020 ng/ml
Peptide, recombinant proteinrhEPOR&D287-TC-5003 U/ml
Peptide, recombinant proteinrhIGF1Peprotech100-11-100uG25 ng/ml
Peptide, recombinant proteinrhIL11Peprotech200-11-10uG5 ng/ml
Peptide, recombinant proteinrhIL3Peprotech200-03-10uG30 ng/ml
Peptide, recombinant proteinrhIL6R&D206-IL-01010 ng/ml
Peptide, recombinant proteinrhSCFLife TechnologiesPHC211150 ng/ml
Peptide, recombinant proteinrhTPOR&D288-TPN-02530 ng/ml
Peptide, recombinant proteinrhVEGFR&D293-VE-01015 ng/ml
Peptide, recombinant proteinrhIGFBP2BioLegend793404100 ng/ml
Chemical compound, drugCHIRCayman13122-1mg-CAY3 μM

Additional files

Supplementary file 1

Spreadsheet containing tables of the gRNAs’ sequence used to activate the target genes and the non-targeting gRNA used as control (tab 1), the marker genes identified for the cell clusters identified in Figure 3 (tab 2), the differentially expressed genes identified from the comparison of in vivo aorta-gonad-mesonephros (AGM) cells with those derived in vitro from human induced pluripotent stem cells (iPSCs) (tab 3), the gRNA enrichment analysis in arterial cells iSAM_AGM+DOX versus iSAM_AGM-DOX (tab 4).

https://cdn.elifesciences.org/articles/94884/elife-94884-supp1-v1.xlsx
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https://cdn.elifesciences.org/articles/94884/elife-94884-mdarchecklist1-v1.pdf

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  1. Paolo Petazzi
  2. Telma Ventura
  3. Francesca Paola Luongo
  4. Heather McClafferty
  5. Alisha May
  6. Helen Alice Taylor
  7. Michael J Shipston
  8. Nicola Romanò
  9. Lesley M Forrester
  10. Pablo Menendez
  11. Antonella Fidanza
(2024)
A novel human pluripotent stem cell gene activation system identifies IGFBP2 as a mediator in the production of haematopoietic progenitors in vitro
eLife 13:RP94884.
https://doi.org/10.7554/eLife.94884.3