EMBO/soda-nel huggingface dataset:
Role of bulge epidermal stem cells and TSLP signaling
in psoriasis (2019)
Figure 1

Figure 1: Scalp psoriasis exhibits reduced expression of c-JUN and JUNB in hair follicle stem cells (HF-SCs)

A-D. Representative composite immune-fluorescent images of whole hair follicle units from non-lesional and lesional scalp psoriasis patients. K15 (green), c-JUN (red A, C) and JUNB (red B, D) and DAPI (blue).

E-H. Confocal images of the bulge region of human psoriatic hair follicles from non-lesional and lesional regions of the scalp. K15 (green), c-JUN (red E, G) and JUNB (red F, H) and DAPI (blue).

I, J. Percentage of HF-SCs (K15+) that express c-JUN (I) and JUNB (J) in the bulge region of human psoriatic hair follicles from non-lesional and lesional scalp in comparison with healthy scalp. n=2-6 hair follicles in anagen per group from five psoriatic patients and two healthy patients. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to controls). See Supplemental Appendix Table 2 for exact p-Value.
Role of bulge epidermal stem cells and TSLP signaling
in psoriasis (2019)
Figure 3

Figure 3: Inactivation of c-Jun and JunB in bulge HF-SCs is sufficient to initiate psoriasis-like development

A. Experimental timeline showing the different time points analyzed after mifespristone induction (day 5, 7, 15 and 30, green) to evaluate GFP expression in ear skin from control (CoK15-mT/mG) and mutant (DKO*K15-mT/mG) mice.

B. Ear pictures of control, DKO*, and DKO*K15 mice after 15 days of induction show clear signs of inflammation and psoriatic-like scales in both models.

C. Representative images of hematoxylin and eosin (H&E) staining of ear sections from control, DKO* and DKO*K15 mice.

D. Ear thickness measurement at different time points during psoriasis-like development in control, DKO* and DKO*K15 mice. n > 5 per group. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to control group). See Supplemental Appendix Table 2 for exact p-Value.

E. FACS quantification of CD45+ cells from ear skin of control, DKO* and DKO*K15 mice at different time points during psoriasis-like development. n > 5 per group. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to controls). See Supplemental Appendix Table 2 for exact p-Value.

F-H. Quantification of IL-17A, IL-6 and LCN2 production in sera of control, DKO* and DKO*K15 mice at day 30 of psoriasis-like disease by ELISA. n > 4 per group. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to controls). See Supplemental Appendix Table 2 for exact p-Value.

I. Quantification of total number of GFP+ epidermal cells by FACS analysis from DKO*-mT/mG and DKO*K15-mT/mG mice at different time points during psoriasis-like progression compared to Co-mT/mG mice. n = 3-6 per group and time point. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to control group). See Supplemental Appendix Table 2 for exact p-Value.

J. Representative immunofluorescence images of ear sections from CoK15-mT/mG and DKO*K15-mT/mG mouse models after 15 days of induction. Red (Tomato), green (GFP) and blue (DAPI). Hyperplasia of Tomato+ keratinocytes in psoriatic-like DKO*K15-mT/mG mouse with clusters of GFP+ keratinocytes are derived from hair follicle K15+ GFP+ stem cells. n=3 per group. Dotted lines separate epidermis and dermis.

K. Quantification analysis of cleaved Caspase-3 (cCas3) and Ki67 in ear skin of DKO*K15-mT/mG mice at different time points during psoriasis-like disease progression. n=3-5 per group. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test). See Supplemental Appendix Table 2 for exact p-Value.
Role of bulge epidermal stem cells and TSLP signaling
in psoriasis (2019)
Figure 5

Figure 5: Different molecular signatures of mutant and non-mutant epidermal stem cells (EpSC)

A. Differentially expressed genes (DEGs) from the four subpopulations (bulge HF-SCGFP; bulge HF-SCTom; b-KCGFP; and b-KCTom) from psoriatic DKO*-mT/mG mice in comparison with their control counterparts (Co). The graphs represent the number of genes differentially up-regulated or down-regulated specifically in each group of interest obtained by Venn diagram analysis (EV 4 B, C).

B. Heat map for specific genes relative to biological process enriched based on Gene Ontology IDs for DEGs that are: i) exclusively up-regulated in HF-SCGFP; ii) exclusively up-regulated in HF-SCTom; iii) commonly up-regulated in HF-SCGFP and HF-SCTom.

C. Prediction of secreted proteins enriched in GFP+ subpopulations by the analysis of DEG commonly up-regulated in HF-SCGFP and b-KCGFP by ProteINSIDE analysis of RNA-seq.

D, E. Gene and protein expression of TSLP in different epidermal cell subpopulations sorted at mid-term (D7) or late-term (D30) of psoriasis-like progression in DKO* mice. n=2-3. Statistical significance *p<0.05, **p<0.01, ***p<0.001 (t-student two tailed-test relative to control groups). See Supplemental Appendix Table 2 for exact p-Value.

F. Quantification of TSLP production in sera of control, DKO* and DKO*K15 mice at day 30 of psoriasis-like disease by ELISA. n = 4 per group. Statistical significance *p<0.05, **p<0.01 (t-student two tailed-test relative to controls). See Supplemental Appendix Table 2 for exact p-Value.
Role of bulge epidermal stem cells and TSLP signaling
in psoriasis (2019)
Figure 6

Figure 6: TSLP secreted by mutantGFP epidermal cells induces hyper-proliferation of non-mutantTom keratinocytes

A. Experimental design for induction of mutantGFP KCs in vitro and neutralization of secreted TSLP by anti-TSLP. Primary keratinocytes were cultured from the skin of Junblox/lox; c-Junlox/lox; RosaKi/+; K5cre-ERT+/+ mice. 50% of mutantGFP KCs were induced by infection with Cre Adenovirus, the non-infected cells were non-mutantTom KCs. Adeno-empty was used as control. EdU was added for 5 hours to label proliferating tomato+ cells in 6-day co-culture. Quantification was performed by Confocal imaging analysis.

B. TSLP production in conditioned media quantified by ELISA three days after infection with Ad-empty or Ad-cre. n=3 independent experiments. Statistical significance ***p<0.001 (t-student two tailed-test relative to control group). See Supplemental Appendix Table 2 for exact p-Value.

C. Percentage of EdU+ Tomato+ keratinocytes after blocking with anti-TSLP. Anti-TSLP neutralizes the hyper-proliferation of non-mutantTom KCs in vitro after infection with Ad-cre. n=3 independent experiments, 6 fields per experiment. Statistical significance *p<0.05 (Two-way ANOVA and Bonferroni post test).

D. Gene expression of Tslpr after TSLP neutralization is reduced. n=3 independent experiments. Statistical significance ***p<0.05 (t-student two tailed-test relative to control group). See Supplemental Appendix Table 2 for exact p-Value.

E. Gene expression of IL-7ra after TSLP neutralization is increased. n=3 independent experiments. Statistical significance ***p<0.05 (t-student two tailed-test relative to control group). See Supplemental Appendix Table 2 for exact p-Value.

F. Gene expression of VEGFα after TSLP neutralization is reduced. n=3 independent experiments. Statistical significance *p<0.05, ***p<0.001 (t-student two tailed-test relative to control groups). See Supplemental Appendix Table 2 for exact p-Value.

G. Experimental design for TSLP neutralization in vivo. TSLP neutralization was performed by triple intra-dermal injections of 20 μg of anti-TSLP or IgG to the right ears of DKO* and DKO*15 mice five days after of psoriasis-like induction. EdU was added into mice by IP injection 2 hour before euthanasia.

H. Representative images of treated ears after 9 days of anti-TSLP or IgG treatment.

I, J. Longitudinal analysis of ear thickness (I) and Trans-epidermal water loss (TEWL) (J) in DKO* mice at different time points during psoriasis-like disease progression (Two-way ANOVA and Bonferroni post test, n=4, *p<0.05).

K. Percentage of EdU+ epidermal cells (CD45-CD49f+) after blocking with anti-TSLP in DKO* and DKO*15 mice (Two-way ANOVA and Bonferroni post test, DKO* n=4 and DKO*15 n=3 per group, *p<0.05).

L. Representative immune-fluorescence images of ear sections from control or DKO* mice treated with IgG or anti-TSLP) stained for Ki67. Ki67 expression was reduced in mice treated with anti-TSLP (n =3).
Role of bulge epidermal stem cells and TSLP signaling
in psoriasis (2019)
Figure 7

Figure 7: Scalp psoriasis patient skin shows increased expression of TSLP in hair follicles and epidermis

A. Representative composite immune-fluorescent images of whole hair follicle units by confocal from non-lesional and lesional scalp psoriasis patients. c-JUN (purple), K-15 (green), TSLP (red) and DAPI (blue).

B, C. TSLP intensity measurement in hair follicle units and epidermis by ImageJ from healthy scalp, non-lesional and lesional scalp psoriasis patients. Representation of fold change relative to control healthy scalp. n= 3 samples. Statistical significance *p<0.05, **p<0.01 (t-student two tailed-test). See Supplemental Appendix Table 2 for exact p-Value.

D, E. Representative composite immune-fluorescent images of whole hair follicle units by confocal from non-lesional and lesional scalp psoriasis patients (D) and magnification images of specific regions from the HFs (E). CD200 (green), c-JUN (white), TSLP (red), DAPI (blue).

EXPANDED VIEW FIGURE LEGENDS
The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation (2019)
Figure 1

Figure 1 - Lack of H3K27me3 and H2AK119ub enrichment over the X chromosome in the absence of Xist repeats B and C

Schematic representation of the novel Xist-TetOP mutants generated by CRISPR/Cas9 genome editing in J1 XY ESCs; the different repeats are highlighted in color boxes; Dif. - differentiation; DOX - doxycycline.

Representative images of combined IF for H3K27me3 or H2AK119ub (green) with RNA FISH for Xist (red) in Xist-TetOP lines (for clone 1 of each mutant type) upon D2 in DOX conditions; Blue - DAPI staining; Scale bar: 10 µm.

Graph represents the mean % + S.E.M. of Xist-coated X chromosomes enriched for H3K27me3 or H2AK119ub in the different Xist-TetOP mutants (for clone 1 of each mutant type) from 2-to-4 independent experiments; A minimum of 50 Xist-coated X chromosomes were counted per experiment; Only p-values corresponding to significant differences from unpaired Student's t-test comparing mutants to Xist FL are indicated as * (p-value < 0.05).
The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation (2019)
Figure 2

Figure 2 - Absence of PCGF3/5-PRC1 proteins from the Xist ΔB+C RNA protein interactome

Scheme of the ChIRP-MS workflow performed on Xist FL (DOX and noDOX conditions) and Xist ΔB+C (DOX) at day 3 of differentiation; RBP - RNA binding protein.

Top 20 protein hits from the ChIRP-MS of Xist FL; The ranking was based on fold-enrichment of Xist FL DOX versus Xist FL noDOX; Weakly annotated protein isoforms with an Annotation score in UniprotKB < 3 (out of 5) were excluded; Fold-enrichment for Xist ΔB+C is also displayed for comparison; Light green boxes correspond to proteins previously described by Chu et al. (2015) as Xist interactors [13]; protein in red (RNF2/RING1B) represents a protein not found in the Xist ΔB+C interactome; Protein in light brown (TRIM71) is less enriched in Xist ΔB+C than in Xist FL.

Scatter plot displaying the differences in peptide counts between Xist FL and Xist ΔB+C for the 74 out of 81 Xist-interactors from Chu et al., 2015 [13] with a minimum of fold-change of 2.5 in Xist FL or Xist ΔB+C; Shown is the log2 fold change of peptide counts of each mutant in DOX conditions compared with the Xist FL in noDOX conditions; proteins retrieved by both Xist FL and Xist ΔB+C ChIRPs with a proposed role in XCI such as SPEN, RBM15, WTAP, YTHDC1 and hnRNPU are indicated; light brown dots mark proteins more represented in Xist FL than in Xist ΔB+C ChIRPs, while red dots display proteins which are only retrieved by Xist FL ChIRP.
The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation (2019)
Figure 3

Figure 3 - nChIP-seq reveals chromosome-wide absence of H3K27me3 and H2AK119ub enrichment, but residual enrichment at initially active genes in the Xist ΔB+C

Plots showing H3K27me3 and H2AK119ub accumulation over the X chromosome in Xist FL and Xist ΔB+C with upon DOX induction at day 2 (D2) of differentiation; Each dot represents a single 10Kb window and its enrichment relative to noDOX condition; Black line is a loess regression on all windows; Xist locus is represented by a blue long line, active genes by green lines.

Violin plots quantifying H3K27me3 and H2AK119ub enrichment over intergenic regions, active promoters and active gene bodies in the X chromosome in Xist FL and Xist ΔB+C cell lines at D2 upon DOX induction; Shown is the log2 fold change of DOX vs noDOX conditions; violin plots represent the distribution of the values, the horizontal band is the median, the lower and upper hinges correspond to the 25th and 75th percentiles; n = indicates the number of regions/genes analyzed; p-values were calculated using paired Wilcoxon test, comparing Xist FL and Xist ΔB+C cell lines.

Average plots showing the mean enrichment of H3K27me3 (top) and H2AK119ub (bottom) over all X-linked initially active transcriptional start sites (TSS); Shown is the mean of normalized log2 enrichment of DOX vs noDOX in both Xist FL and Xist ΔB+C cell lines.

Genome browser plots showing H3K27me3 (top) and H2AK119ub (bottom) enrichments in a region encompassing the inactive Atp1b4 and the initially active Lamp2 genes within the XqA3.3 region and the initially active Rlim/Rnf12 gene at the XqD region; Region around the promoter of Rlim/Rnf12 is highlighted in yellow.
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein (2020)
Figure 1.

hACE2 is a functional receptor for SARS-CoV-2 S.A. Entry of MLV pseudotyped with SARS-CoV-2 S, SARS-CoV-2 Sfur/mut and SARS-CoV S in VeroE6 cells. B. Entry of MLV pseudotyped with SARS-CoV-2 S or SARS-CoV-2 Sfur/mut in BHK cells transiently transfected with hACE2. The experiments were carried out in triplicate with two independent pseudovirus preparations and a representative experiment is shown. C. Sequence alignment of SARS-CoV-2 S with multiple related SARS-CoV and SARSr-CoV S glycoproteins reveals the introduction of an S1/S2 furin cleavage site in this novel coronavirus. Identical and similar positions are respectively shown with white or red font. The four amino acid residue insertion at SARS-CoV-2 S positions 690-693 is indicated with periods. The entire sequence alignment is presented in Fig. S1. D. Western blot analysis of SARS-CoV-2 S-MLV, SARS-CoV-2 Sfur/mut-MLV and SARS-CoV S-MLV pseudovirions using an anti-SARS-CoV S2 antibody.
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein (2020)
Figure 2.

SARS-CoV-2 S recognizes hACE2 with comparable affinity to SARS-CoV S.A-B. Biolayer interferometry binding analysis of the hACE2 ectodomain to immobilized SARS-CoV-2 SB (B) or SARS-CoV SB (C). The experiments were performed in duplicates with different protein preparations and one representative set of curves is shown. Dotted lines correspond to a global fit of the data using a 1:1 binding model. C. Sequence alignment of SARS-CoV-2 SB and SARS-CoV SB Urbani (late phase of the 2002-2003 SARS-CoV epidemic). Identical and similar positions are respectively shown with white or red font. The single amino acid insertion at position 492 of the SARS-CoV-2 SB is indicated with a period at the corresponding SARS-CoV SB position. The 14 residues that are key for binding of SARS-CoV SB to hACE2 are labeled with a star.
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein (2020)
Figure 3.

CryoEM structures of the SARS-CoV-2 S glycoprotein.A-B. Two orthogonal views of the closed SARS-CoV-2 S trimer cryoEM map. C. Atomic model of the closed SARS-CoV-2 S trimer in the same orientation as in panel A. D-E. Two orthogonal views of the partially open SARS-CoV-2 S trimer cryoEM map (one SB domain is open). F. Atomic model of the closed SARS-CoV-2 S trimer in the same orientation as in panel D. The glycans were omitted for clarity.
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein (2020)
Figure 5.

SARS-CoV S elicits antibodies neutralizing SARS-CoV-2 S mediated entry into host cells.A-B. Sequence conservation of sarbecovirus S glycoproteins plotted on the SARS-CoV-2 S structure. C. Entry of SARS-CoV-2 and SARS-CoV S pseudotyped viruses is potently inhibited by four SARS-CoV S mouse polyclonal immune plasma.
TIFA has dual functions in Helicobacter pylori-induced classical and alternative NF-kB pathways (2021)
Figure 1

Figure 1. H. pylori-induced classical and alternative NF‑κB pathways depend on ADP‑heptose

A. AGS cells were infected with H. pylori or treated with 20 ng/ml LTα1β2 for the indicated times. Total cell lysates were analyzed by immunoblotting using the indicated antibodies.

B, C. AGS cells were infected with H. pylori P1 wild‑type or isogenic ∆HP0857 (mutated in the gmhA gene) strains. Total cell lysates were analyzed by immunoblotting using the indicated antibodies.

D. AGS cells were treated with 200 nM synthetic ADP‑heptose for the indicated times. Total cell lysates were analyzed by immunoblotting using the indicated antibodies.

E. AGS cells were pre‑incubated with 100 μM dynamin GTPase inhibitor Dynasore for 60 min followed by H. pylori infection or addition of ADP-heptose (200 nM). Total cell lysates were analyzed by immunoblotting using the indicated antibodies. CagA demonstrated a similar infection rate.

Data information: Data shown are representative for at least two independent experiments. GAPDH served as loading control.
TIFA has dual functions in Helicobacter pylori-induced classical and alternative NF-kB pathways (2021)
Figure 2

Figure 2. ALPK1 and TIFA are required for induction of the classical NF‑κB pathway in H. pylori infection

A. Parental AGS, ALPK1‑KO and TIFA‑KO cells were infected with H. pylori for the times shown. Total cell lysates were analyzed by immunoblotting using the indicated antibodies. CagA demonstrated a similar infection rate of the different cells. Asterisk denotes an unspecific band and the arrow indicates the band corresponding to phosphorylated p100.

B. Total RNA was isolated from ALPK1‑KO cells and analyzed using quantitative RT‑PCR for the ALPK1 transcript. Data shown depict the average of triplicate determinations normalized to the RPL13A housekeeping gene. Error bars denote RQ ± RQmin/RQmax.

C. TIFA-KO cells were transfected with His‑tagged recombinant TIFA protein 24 h prior to H. pylori infection. Co‑IP with an anti‑His antibody was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies. Asterisk denotes an unspecific band and the arrow indicates the TRAF2 band.

D, E. AGS and ALPK1-KO (D) or TIFA-KO (E) cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

F. AGS and TIFA-KO cells were treated with 30 ng/ml IL-1β for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

Data information: Data shown (A, C-F) are representative for at least two independent experiments. GAPDH served as loading control. Data shown in B are from one experiment with three technical repeats.
TIFA has dual functions in Helicobacter pylori-induced classical and alternative NF-kB pathways (2021)
Figure 3

Figure 3. ALPK1‑mediated TIFA oligomerization is required for induction of the alternative NF‑κB pathway in H. pylori infection

A. TIFA-KO cells were transfected with His‑tagged recombinant TIFA protein 24 h prior to H. pylori infection or treatment with 30 ng/ml LTα1β2. Co‑IP with an anti‑His antibody was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

B. AGS cells were pre‑incubated with 100 μM dynamin GTPase inhibitor Dynasore for 60 min followed by addition of ADP-heptose (200 nM). Co‑IP with an anti‑TIFA antibody was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies. Asterisk indicates an unspecific band and the arrow indicates the TRAF3 band.

C. AGS and ALPK1-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TIFA antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

D. AGS and TIFA-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF2 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

E. AGS cells were transfected with siRNA against cIAP1. Co‑IP with an anti‑TIFA antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.

F. TIFA-KO cells were transfected with empty vector plasmid (pCMV6), wild‑type human (phTIFA), phosphorylation‑defective mutant (pT9A) or TRAF6 binding‑defective mutant (pE178A) FLAG‑tagged TIFA plasmids. Total cell lysates were analyzed by immunoblotting using the indicated antibodies.

G. TIFA-KO cells were transfected with empty vector plasmid (pCMV6), wild‑type human (phTIFA), phosphorylation‑defective mutant (pT9A) or TRAF6 binding‑defective mutant (pE178A) FLAG‑tagged TIFA plasmids. Total cell lysates were separated by native gel electrophoresis under non-reducing conditions.

Data information: Data shown are representative for at least two independent experiments. GAPDH served as loading control.
TIFA has dual functions in Helicobacter pylori-induced classical and alternative NF-kB pathways (2021)
Figure 4

Figure 4. Co‑localization of proteins involved in the activation of classical and alternative NF‑κB pathways with the TIFAsomes in H. pylori infection

A-D In TIFA‑KO cells transiently expressing TIFA‑tdTomato, co-localization of TRAF6 (A), TRAF2 (B), cIAP1 (C) and TRAF3 (D) with TIFA-tdTomato, which formed TIFAsomes upon infection with H. pylori P1 wild‑type strain, were detected by immunofluorescence staining. The nuclei were counterstained with DAPI. Scale bar = 10 µm.

E. TIFA‑KO cells transiently expressing TIFA‑tdTomato were infected with H. pylori P1 strain mutated in the gmhA gene (∆HP0857). Scale bar = 10 µm.

Data information: Data shown are representative for at least two independent experiments.

Expanded View Figure Legends