78-0441-80

antibody from Invitrogen Antibodies

Targeting: CD44 CD44R, CSPG8, HCELL, IN, MC56, MDU2, MDU3, MIC4, Pgp1

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Antibody Data
Antigen structure
References [81]
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Flow cytometry [1]
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Product number: 78-0441-80 - Provider product page
Provider: Invitrogen Antibodies
Product name: CD44 Monoclonal Antibody (IM7), Super Bright™ 780, eBioscience™
Antibody type: Monoclonal
Antigen: Other
Description: Description: The IM7 monoclonal antibody reacts with all isoforms of mouse CD44 (Pgp-1). CD44 is expressed by hematopoietic and non-hematopoietic cells. Bone marrow myeloid cells and memory T cells highly express this antigen and peripheral B and T cells can upregulate the expression of CD44. CD44 functions as an adhesion molecule through its binding to hyaluronate, an extracellular matrix component.
Antibody clone number: IM7
Concentration: 0.2 mg/mL

CD44 protein structure - 78-0441-80 shown in red.

Supportive validation

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Experimental details: Figure 3 SIM plus HAM enhances the mRNA expression of transcription factors for ADSC chondrogenesis and osteogenesis. ADSCs were pretreated with IM7 (+IM7) or without IM7 (-IM7) prior to SIM treatment and cultivated in wells with/without an HA coating, and the mRNA expression levels of ( A ) BMP-2, SOX-9 and RUNX-2 in the control, SIM, HAM and SIM+HAM groups on day 3 were analyzed. The mRNA levels are expressed relative to those in the control group, which are defined as 1. The values presented are the means +- SEMs ( n = 6). (*) and (**) indicate p < 0.05 and p < 0.01, respectively, compared with the control group. (#) and (##) indicate p < 0.05 and p < 0.01, respectively, and represent the comparison between +IM7 and -IM7 in each group. ( B ) p38 and JNK signaling were analyzed by Western blot. Representative Western blot photographs were shown. ( C ) The p-JNK/beta-actin, JNK/beta-actin and p-JNK/JNK ratios and ( D ) p-p38/beta-actin, p38/beta-actin and p-p38/p38 ratios are expressed relative to that in the control group on day 3, which is defined as 1. The values presented are the means +- SEMs ( n = 6). (*) and (**) indicate p < 0.05 and p < 0.01, respectively, compared with the control group. (#) and (##) indicate p < 0.05 and p < 0.01, respectively, compared with the SIM group.

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Supportive validation

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Supportive validation

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Supportive validation

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Experimental details: Fig. 2 CD25 expression on tumor-infiltrating lymphocytes. (a) Tumor-infiltrating lymphocytes were analyzed with flow cytometry. Tregs accounted for 49.8% of CD4 + T cells. (b) 71.5% of CD25 positive cells were CD3 + CD4 + Foxp3 + Tregs (c) Upper: Surface expression of CD25 was evaluated for NK cells, CD8 + T cells, CD4 + Foxp3 - T cells, and CD4 + Foxp3 + Tregs. Lower: CD4 + Foxp3 + Tregs showed significantly higher mean fluorescence intensity (MFI) of CD25 (left) and CD25 positive percentage (right) ( n = 4; one-way ANOVA followed by Tukey''s test; ****, p < 0.0001). Fig 2

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Experimental details: Figure 4 obASCs promote a cancer stem-like phenotype through leptin. ( A ) Transwell co-culture with shCtrl obASCs upregulates NOTCH1, NOTCH3, DELTA1, and JAGGED2 in ER + BCCs. ( B ) BCCs have increased ability to form mammospheres after co-culture with shCtrl obASCs followed by 2 Gy radiation compared to non-co-cultured cells or cells co-cultured with shLep obASCs. ( C ) Flow cytometric analysis of the breast cancer stem cell markers CD44 + CD24 - was evaluated for BCCs after transwell co-culture with shCtrl obASCs or shLep obASCs. Values reported are the mean of three independent experiments each performed in triplicate. Bars, +- SEM. * p < 0.05, ** p < 0.01, *** p < 0.001.

Supportive validation

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Experimental details: FIGURE 1 Characterization of young and aged MSCs and exosomes. (A) Surface marker profiling of young-MSCs and aged-MSCs. (B) SA-beta-Gal staining showed that senescence increased significantly in aged MSCs. (C) Representative immunoblot images and quantitative analysis of p21, p53, and p16 protein level in young and aged-MSCs. ( n = 3). (D) Quantitation of cell cycle phases by propidium iodide staining. ( n = 3). (E) The CCK-8 assay showed that aged MSCs grew more slowly than young MSCs. ( n = 6). (F) Young and aged exosomes were observed using TEM. (G) The exosome surface markers were analyzed by Western blot. (H) Nanoparticle tracking analysis was used to analyze the particle size and concentration of Young-Exo and Aged-Exo. * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001; NS, not significant.

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Experimental details: Figure 2 CM measurements of the tumor-retrieved cells with different recurrence status before and after flow-cytometry sorting. All cells were assessed with the microplate mechanical measurement system (MMS). The (A) compressive stiffness (CS), (B) tensile stiffness (TS) and (C) adhesion force (AF) of the non-recurrence (Non-Rec) and recurrence (Rec) group were measured and graphed as the mean (dotted line) +- SD (upper and lower index) in the scatter plots. *, p < 0.05; **, p < 0.01. (D, E and F) The red and blue bars represent the Rec and Non-Rec groups, respectively. After sorting, each subgroup of cells was maintained separately for CM measurements. Based on the data, the double positive subgroup had higher CMs than the single positive subgroups, and a greater variation was observed in the double negative subgroup. (G, H and I) The distributions of the CM properties after Gaussian curve fit. Red dotted lines indicate the Rec group, and blue dashed lines indicate the Non-Rec group. The gray areas contain the suspected mesenchymal stem cells (MSCs), which are Sca-1 + -CD44 + . The number of peaks were counted after all CM data were fitted, and noticeably only one peak is present in each of the gray areas from the Rec population.

Supportive validation

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Experimental details: Figure 3 Expression of ST6GALNAC1 in CR-CSCs/CICs and clinical samples ( A ) RT-PCR and qRT-PCR analyses of ST6GALNAC1 in CR-CSCs/CICs, non-CSCs/CICs and normal colon mucosa. Expression of ST6GALNAC1 was analyzed by RT-PCR using cDNAs derived from adherent-cultured cells, sphere-cultured cells, ALDH high cells, ALDH low cells and normal colon tissue (left). GAPDH was used as an internal control. Expression of ST6GALNAC1 was analyzed by qRT-PCR using cDNAs of adherent-cultured cells, sphere-cultured cells, ALDH high cells and ALDH low cells. Data are shown as means +- SD. An asterisk indicates statistical difference. ( B ) Overall survival (OS) for patients with ST6GALNAC1-positive cancer and those with ST6GALNAC1-negative cancer after primary surgery. ST6GALNAC1 protein was detected by immunohistochemical (IHC) staining using an ST6GALNAC1-specific antibody in colorectal cancer cases. The positive rates of ST6GALNAC1 were 0%-80%. ST6GALNAC1-positive patients in Stage III and IV showed a significantly shorter survival time than that of ST6GALNAC1-negative patients in Stage III and IV after surgery (upper panel). Representative images are shown (lower panel). ST6GALNAC1-negative case (0%) and ST6GALNAC1-positive cases (10% and 30%). Magnification, x100 and x400.

Supportive validation

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Experimental details: Figure 3 Knocking down of PIK3CA failed to reverse EMT and reduce CSC population. (A) Western blotting of p110alpha, E-cadherin and vimentin in CU110-2 cells stably transfected with lentiviral-mediated shRNA ( shPIK3CA ) or a scrambled control ( SCR ). GAPDH was used as a loading control. Quantitation of western blots is shown in right. (B) HNSCC Sphe-forming assay of CU110 cells stably transfected either shPIK3CA or SCR lentivirus. Sphes with diameter >= 30 mum were counted; quantification of Sphe is shown on the right, n = 3; error bars indicate SD. * P < 0.05 (two-tailed Student t- test). Scale bar: 100 u m . (C) FACS analysis of CD44 in CU110 cells stably transfected either shPIK3CA or SCR lentivirus. Quantification of CD44 population is shown on top. n = 3; error bars indicate SD. (D) FACS analysis of CD24 in CU110 cells stably transfected either shPIK3CA or SCR lentivirus. Quantification of CD24 population is shown on top. n = 3; error bars indicate SD. (E) SP fraction using Hoechst dye-effluxing analysis in CU110 cells stably transfected either shPIK3CA or SCR lentivirus. Quantification of SP fraction is shown on top. n = 3; error bars indicate SD. * P < 0.05 (two-tailed Student t- test). (F) HNSCC Sphe-forming assay of Fadu or UMSCC47 cell lines stably transfected with either shPIK3CA or SCR . The quantification is shown on the left. Error bars indicate SD. Scale bar: 100 u m.

Supportive validation

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Experimental details: Figure 6 Targeting multiple RTK pathways effectively eliminates CSC populations with inhibiting Ephs, TRKs, and c-Kit the most prominent. (A) FACS analysis of CD44 (left) or ALDH (right) in CU110 cells treated with LDN211904. Error bars indicate SD. n = 3. * P < 0.05 (two-tailed Student t- test). (B) FACS analysis of ALDH in CU110 cells treated with GNF5837. Error bars indicate SD. n = 3. * P < 0.05 (two-tailed Student t- test). (C) FACS analysis of CD44 (left) or SP fraction (right) in CU110 cells treated with imatinib. Error bars indicate SD. n = 3. * P < 0.05 (two-tailed Student t- test). (D) Effect of pharmaceutical inhibitors (as indicated in the figure) on reducing CSC population in human HNSCC cell lines: Fadu and UMSCC47, using Sphe-forming assay. The quantification is shown on right. n = 3; error bars indicate SD. * P < 0.05 (two-tailed Student t- test). Scale bar: 100 u m.

Supportive validation

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Experimental details: Fig. 2 CCL5 promotes the invasion and the PCSCs subpopulation of prostate cancer cells in vitro. a , b CCL5 (2.5-40 ng/ml) had no obvious influences on the proliferation and colony formation capacities of the prostate cancer cell lines DU145 and PC3. c CCL5 addition (20-40 ng/ml) significantly promoted the migration and invasion of DU145 and PC3 cells. Scale bars represent 200 mum for wound healing assay images and 50 mum for transwell assay images. d Western blotting assay revealed that CCL5 (5-40 ng/ml) could promote EMT and metastasis of both DU145 and PC3 cells. e CCL5 treatment (20-40 ng/ml) significantly increased not only the number but also the size of mammospheres formed by prostate cancer cells. Scale bar, 100 mum. f , g CCL5 treatment (20-40 ng/ml) significantly elevated the CD44 + /CD133 + subpopulation and the ALDH + subpopulation in DU145 and PC3 cells, indicating that CCL5 could promote the self-renewal of PCSCs. All values are presented as the mean +- SD. n = 3, * p < 0.05, ** p < 0.01.

Supportive validation

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Experimental details: FIGURE 4 Changes in cellular sub-populations in differentiating MPIEs. (A) CD326 (Epcam) versus CD44 expression in cells harvested at different time points. (B) Transcriptional changes of the major cell marker genes in 3 days of differentiation detected by RT-qPCR. The transcription levels were normalized to that of GAPDH and the relative fold changes were calculated using the 2 -DeltaDeltaCT . Each bar indicated means +- standard deviations for three independent trials. The abbreviations on the map are leucine-rich-repeat-containing G-protein-coupled receptor 5 ( Lgr5 ), B cell-specific moloney murine leukemia virus integration site 1 ( Bmi1 ), Ki-67 ( Ki67 ), chromogranin A ( ChgA ), trefoil factor 3 ( TFF3 ), lysozyme ( Lyz ) and fatty acid-binding protein 1 ( L-Fabp ).

Supportive validation

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Experimental details: Fig. 3 Exposure to disrupted myelin drives GBM progression down the oligodendrocyte lineage. a SOX10 (grey), fluoromyelin (FM, red), DAPI (blue) immunofluorescence of GFP + G144 xenografts (PDX144). Arrowheads denote disrupted areas. Scale = 500 um b , % SOX10 + tumour cells in areas of high (blue)/low (grey) disruption in indicated xenografts. >=120 cells across >=6 ROIs per region. n = 4 xenografts. p = 0.03, Mean, paired one-tailed Student''s t test c , Electron micrographs of myelin bundles in the ipsilateral (infiltrated) and contralateral (intact) striatum of PDX144. Scale=1 um. d - i , quantification of indicated axonal and myelin phenotypes in EM data from b . n = 3-4 xenografts. d p = 0.03, f, p = 0.03, g p < 0.0001, h p = 0.01, i p = 0.01, ** p < 0.01, * p < 0.05, Mean +- SEM, paired one-tailed Student''s t test, 2-way ANOVA or linear regression. j % GFP + tumour cells in contact with axons. >=300 SOX10 + /SOX10 - cells across 3 ROIs. Mean +- SEM, n = 3 tumours, p < 0.0001. Unpaired two-tailed Student''s t test. k i Correlative light and electron micrograph (CLEM) of tumour cell directly interacting with multiple white matter axons. ii-iv magnifications of i highlighting interactions with decompacted myelin (A, B), naked (C), and intact myelinated axon (D) Scale = 10 um (i), 5 um (ii), 1 um (iii, iv). l - s time-course analysis of tumour cell differentiation and glial response during corpus callosum (CC) infiltration in PDX144. l quantification of FM intensity relat

Supportive validation

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Experimental details: Figure 9 Representative gating strategies used to analyze cell types by flow cytometry. Shown are representative dot plots with gating for CD4+/CD62L+ and CD8+/CD62L+ T-cells ( a ), T-regulatory Cells (CD4+/CD25+/FOXP3+) ( b ), CD4+ Memory T-cells (CD4+/CD44+/CD62L+) and CD8+ Memory T-cells (CD8+/CD44+/CD62L+) ( c ), and CCR7+/CD4+ Memory T-cells and CCR7+/CD8+ Memory T-cells ( d ).

Supportive validation

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Experimental details: Fig. 5 HGF induced an effective therapeutic effect against B16F10 tumor. a Schematic illustration of the experiment design to assess the tumor inhibition and the immune responses as triggered by PBS, HACA-Fe, HACA-GW, or HGF NPs on subcutaneous B16F10 tumor model. G1, PBS; G2, HACA-Fe; G3, HACA-GW; G4, HGF. b and c Tumor growth curves during treatment. d Survival rates of different groups over time. e and f Representative flow cytometry plots and quantification of e CD8 + f and CD4 + T cells after gating on CD45 + CD3 + T cells in tumor tissue. g and h Representative flow cytometric analysis of memory T cells (CD3 + CD8 + CD44 + CD62L - , gated on CD3 + CD8 + T cells) in the spleen. Data were presented as mean +- SD. n = 5 biologically independent animals per group. Statistically significant differences between groups were identified by one-way ANOVA with Tukey's post hoc test. * P < 0.05, ** P < 0.01, *** P < 0.001 and **** P < 0.0001.

Supportive validation

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Experimental details: Figure 2. Ectopic expression of NIK prevents T cell exhaustion and promotes antitumor immunity. a-c , Tumor growth curve ( a ), image of day 32 tumors ( b ), and survival curve ( c ) of the MC38-bearing NIK iTg and wildtype control mice. d , e , Tumor growth ( d ) and survival ( e ) curves of NIK iTg and wildtype control mice injected s.c. with 5 x 10 5 B16F10 melanoma cells. f , g , Flow cytometric analysis of the frequency and absolute cell number of CD4 + and CD8 + T cells ( f ) and IFN-gamma-producing CD8 + effector T cells ( g ) in day-32 tumor of MC38-bearing NIK iTg and wildtype control mice ( f , g , n=6 per genotype). h-j , Flow cytometric analysis of the frequency and absolute cell number of CD4 + and CD8 + T cells in the draining lymph node ( h ) and CD44 + CXCR3 + CD8 + effector T cells in the draining lymph node ( i ) or tumor ( j ) of day-32 MC38-implanted NIK iTg and wildtype control mice ( h , n=6 per group; i , n=4 per group; j , n=3 per group). k , l , Flow cytometric analysis of the frequency and absolute cell number of PD1 + Tim3 + and PD1 + Tim3 - CD8 + T cells ( k ) and IFN-gamma-producing gated PD1 + Tim3 + CD8 + T cells ( l ) in day-32 tumor of the MC38-bearing wildtype or iTg mice ( k , l , n=6 per genotype). m , n , Flow cytometry ( m ) and qRT-PCR ( n ) analyses of PD1 and Tim3 expression level in tumor-infiltrating PD1 + Tim3 + CD8 + T cells of MC38-bearing (day 32) wildtype or iTg mice ( n , WT: n=2; NIK iTg : n=3) . o , Schematic of experimental

Supportive validation

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Experimental details: Figure 6. HK2 deletion blocks the autoimmune phenotype of NIK tTg mice. a, Body weight of 36-day old wildtype (WT), NIK tTg (tTg), and NIK tTg Hk tKO (tTg-tKO) littermate mice (WT: n=5, tTg: n=8, tTg-tKO: n=7) . b , Image of inguinal lymph nodes and thymi of four pairs of mice with the indicated genotypes. c , H&E staining of colon and lung sections from moribund NIK tTg , NIK tTg Hk tKO and age-matched littermate wildtype control mice were assessed for leukocyte infiltrates by hematoxylin-eosin stain. Scale bars: 100 mum. (n=3 in each group). d-g , Flow cytometric analysis of the frequency and absolute cell number of double-negative (DN), double-positive (DP), CD8 + single-positive (SP), and CD4 + SP thymocytes ( d ), thymic CD25 + foxp3 + T reg cells ( e ), lymph node CD25 + foxp3 + T reg cells ( f ), and lymph node CD44 - foxp3 + T reg cells ( g ) in NIK tTg , NIK tTg Hk tKO or wildtype mice ( e-f , NIK iTg : n=6, NIK tTg Hk tKO : n=4, wildtype: n=5). Data are representative of two ( a-c , e-g ) or three ( d ) independent experiments. Summary data are shown as mean +- s.e.m. with P values determined by two-tailed Student's t test ( a , d-g ) .

Supportive validation

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Experimental details: Extended Data Fig. 1 NIK regulates T cell exhaustion and antitumor immunity a, genotyping PCR of R26Stop FL Map3k14 (Map3k14 Tg ), Map3k14 +/+ CreER, and R26Stop FL Map3k14 -CreER ( Map3k14 Tg CreER) mice, showing the PCR products of NIK-GFP in Map3k14 Tg allele and CreER. b, Immunoblot analysis of NIK expression in tamoxifen-treated Map3k14 +/+ CreER (WT) and Map3k14 Tg CreER (iTg) mice. c, Schematic of experimental design for producing B16F10 tumor-bearing NIK iTg and WT control mice. Each mouse was injected s.c. with 5 x 10 5 B16F10 cells (WT=9, iTg=7). d,e, Flow cytometric analysis of the frequency and absolute cell number of CD4 and CD8 T cells in the tumor (d) or draining lymph node (e) of day 18 B16F10 tumor-implanted NIK-iTg and WT mice ( d , WT: n=4; iTg: n=5; e , n=6 per genotype). f,g, Flow cytometric analysis of the frequency and absolute number of CD44 + CXCR3 + CD8 effector T cells in the draining lymph node ( f ) or tumor ( g ) of day 18 B16F10 tumor-implanted NIK-iTg and wildtype mice ( f , n=6 per genotype; g, n=4 per genotype). h,i, Flow cytometric analysis of the frequency and absolute number of PD1 + Tim3 + CD8 + T cells ( h ) or IFNgamma-producing PD1 + Tim3 + CD8 T cells ( i ) in the tumor of day 18 B16F10-implanted NIK iTg and wildtype control mice (h,i, n=4 per genotype). Data are representative of three independent experiments. Summary data are shown as mean +- s.e.m. with P values determined by two-tailed Student's t test.

Supportive validation

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Experimental details: Figure 2 NK Cells Contribute to Both Innate and Adaptive Immune Control of Ptgs -/- Tumors (A) Growth profile of Ptgs +/+ and Ptgs -/- melanoma cells implanted into Rag1 -/- or wild-type mice untreated or depleted of NK, CD4 + , and/or CD8 + cells. (B and C) Frequency of CD8 + T cells (B); representative plots and frequency of CD8 + CD44 + , CD8 + IFNgamma + , and CD4 + IFNgamma + T cells (C) gated on live, CD45 + , CD3epsilon + cells in Ptgs +/+ and Ptgs -/- untreated or NK cell-depleted wild-type mice analyzed 7 days post-implantation. (D) Individual growth profiles of Ptgs -/- melanoma cells in wild-type mice depleted of NK cells from the day before or a week after cancer cell implantation. (E) Growth profile of Ptgs +/+ and Ptgs -/- cells in wild-type mice or Ptgs +/+ cells in GPP mice. (F) Tumor weight, NK cell frequency, and number per g of tumor analyzed 4 days after implantation of Ptgs +/+ and Ptgs -/- cells in wild-type or Ptgs +/+ cells in GPP mice. (G) Growth profile of Ptgs +/+ and Ptgs -/- melanoma cells in wild-type or Ptgs +/+ melanoma cells in Ptger2 -/- or Gzmb-Cre Ptger4 floxed/floxed mice. Data are expressed as mean +- SEM, one-way (B-C and F) or two-way ANOVA (A).

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Experimental details: Figure 6 Assessments of organ damage and mouse metabolites during HLSA or recovery from HLSA. A , upper left panel , MMP-1, IL-1beta, and CRP levels in plasma had no significant change between the control group, HLSA group, and R-HLSA group. Upper right panel , CK-MB as a marker of heart injury in the plasma had no significant change between the control group, HLSA group, and R-HLSA group. Lower left panel , creatinine and BUN as markers of kidney injury in the plasma slightly increased in the HLSA group and returned to normal level after recovery from HLSA. Lower right panel , AST and ALT as markers of liver injury in the plasma showed no change between the control group, HLSA group, and R-HLSA group. Data were presented as mean +- SD (N = 6; ANOVA: ** p < 0.01). B , upper panel , food consumption and water consumption 3 days before and 3 days after a single ATP-induced HLSA depicted no change. Data were presented as mean +- SD (N = 6; ANOVA: p > 0.05). Lower panel , metabolomics analysis of scores plot from PCA analysis based on 1 H NMR data from the plasma, brain, liver, and kidney of the control group, HLSA group, and R-HLSA group. The PCA score showcased clusters correspond to metabolic patterns in different groups, with each point representing one sample. Circles represent 95% confidence interval for each score in each group (see also Figs. S5-S8 ). C , draining lymph nodes of mice that underwent HLSA once a day for 10 consecutive days were analyzed with FACS. CD44 and

Supportive validation

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Experimental details: Figure 2 CD10 in CAFs sustains cancer stemness and chemoresistance. A-E) Indicated tumor cell lines were cultured alone (-) or cocultured with CD10 + GPR77 + -depleted CAFs (CD10 + GPR77 + -d) or paired CD10 + GPR77 + CAFs transduced without (-) or with shGFP or shCD10. A) Representative images of mammosphere formation in MCF-7 cells. Scale bar, 100 um. B) Representative images of PKH26 and Numb immunofluorescence staining of MCF-7 cells. Scale bar, 50 um. C,D) Percentage of ALDH1 + cells in C) MCF-7 and D) BT-549 cells detected by flow cytometry. Numerical values are presented as percentage (mean +- SEM, n = 3). E) Percentage of CD44 high CD24 low cells in MCF-7 cells cocultured with indicated CAFs was detected by flow cytometry. Numerical values are presented as percentage (mean +- SEM, n = 3). F,G) Representative flow cytometry plots for F) MCF-7 and G) BT-549 cells treated with docetaxel after being cultured alone (-) or cocultured with the indicated CAFs. The proportion of Annexin V + /Propidium iodide - (early apoptosis) and Annexin V + /Propidium iodide + (late apoptosis) cells is shown. The numerical values indicate Annexin V + percentage. Data are represented as the mean +- SEM of F) n = 4 or G) n = 3 independent experiments. H) Representative immunoblots for cleaved/total caspase-3 and PARP in SK-BR3 cells treated with docetaxel after being cultured alone (-) or cocultured with indicated CAFs ( n = 3). I-L) MCF-7 cells were cocultured with CD10 + GPR77 + CAFs or CD1

Supportive validation

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Experimental details: Fig. 2 Cancer stem cell (CSC)-like cells are enriched in the hypoxic populations freshly isolated from xenografts. Tumor cells are enzymatically dissociated and isolated from either the MDA-MB-231/HRE-EGFP ( a - c ) or MCF7/HRE-EGFP ( d - f ) xenografts. Stem cell characteristics are evaluated by fluorescence-activated cell sorting (FACS) for the expression of CSC-associated surface markers CD24, CD44 and CD49f. Representative FACS plots are shown in a , c , d and f . Quantitative population analyses are shown in b ( n = 4-5; * p < 0.05, *** p < 0.001, Student's t test) and e (n = 4; *** p < 0.001, Student's t test). These results are confirmed by three or more independent experiments. EGFP, enhanced green fluorescent protein; SSC, side scatter

Supportive validation

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Experimental details: Fig. 4 The cancer stem cell (CSC)-like population is further enriched in secondary xenografts derived from the enhanced green fluorescent protein (EGFP) + MDA-MB-231 cells. a Generation of the secondary xenografts. b , c Surface levels of CD24 and CD44 are analyzed by fluorescence-activated cell sorting. b Average CD24 + populations from six individual tumors (*** p < 0.001, Student's t test). c Average CD44 ++ (right-pointing arrow) populations from three individual tumors (* p < 0.05, Student's t test). d Quantitative RT-PCR analysis of expression of CD24 and CD44 genes in the EGFP + and EGFP - cells freshly isolated from either the 2 nd or 1 st xenografts (n = 3; * p < 0.05, ** p < 0.01, Student's t test). e Clonogenic growth of sorted EGFP + and EGFP - cells freshly isolated from the 2 nd xenografts in comparison to the unsorted tumor cells from the 1 st xenografts (n = 3; * p < 0.05, *** p < 0.0001, Student's t test)

Supportive validation

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Experimental details: Figure 2 BRCA1 suppresses CD44 expression in breast cancer cells. The cell surface CD44 levels in HCC1937 +- BRCA1 cells were analyzed by flow cytometry with representative flow cytometry data shown in ( A ) and quantitation in ( B , n = 3). ( C ) Expression levels of the total CD44 (including all isoforms/variants), CD44s, and the CD44v5/6 variant in HCC1937 +- BRCA1 cells measured by qRT-PCR (n = 3). ( D ) CD44 promoter activity in HCC1937 +- BRCA1 cells was measured using luciferase assay (n = 4).

Supportive validation

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Experimental details: Figure 3 Down-regulation of BRCA1 promotes breast cancer stem cell characteristics. ( A ) BRCA1 was down-regulated by RNA inference in the BRCA1-competent SKBR-3 breast cancer cells, which was confirmed by Western blot and qRT-PCR (n = 3). ( B ) Expression of breast cancer stem cell-associated genes in SKBR3 +- siBRCA1 cells were measured by qRT-PCR (n = 3). ( C ) CD44 promoter activity in SKBR3 +- siBRCA1 cells was measured using luciferase assay (n = 3). The cell surface CD44 levels in SKBR3 +- siBRCA1 cells were analyzed by flow cytometry with representative flow cytometry data shown in ( D ) and quantitation in ( E , n = 3). The ALDH activity in SKBR3 +- siBRCA1 cells were analyzed by flow cytometry with representative flow cytometry data shown in ( F ) and quantitation in ( G , n = 3). The DEAB treated cells were used as negative control.

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Experimental details: Figure 4 Down-regulation of BRCA1 promotes cancer cell stemness in neuroblastoma cells. BRCA1 was down-regulated by RNA inference in the SK-N-BE(2)C human neuroblastoma cells (Western blot shown in A ). Effects of BRCA1 on neuroblastoma cell clonogenicity was measured by the clonogenic assay ( B , n = 6). The cell surface levels of CD44 ( C ) and CD24 ( D ) in BE(2)C +- siBRCA1 cells were analyzed by flow cytometry (n = 3). Expression of neuroendocrine cancer stem cell-associated genes in BE(2)C +- siBRCA1 cells were measured by qRT-PCR ( E , n = 3).

Supportive validation

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Experimental details: FIGURE 2 T cell senescence in various adipose tissues of old mice. (A,B) Flow cytometric analysis of CD45 + CD3 + T cells in AT of young and old mice and their quantitation. (C,D) Representative flow cytometric analysis of CD44 subsets in T cells isolated from adipose tissue and their quantification. (E,F) Representative flow cytometry of CD28 + T cells in adipose tissue from young or old mice and their quantification. * P < 0.05; ** P < 0.01; *** P < 0.001 vs. young mice, n = 3~6 per group.

Supportive validation

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Experimental details: Figure 1 Fluorescence-activated cell sorting (FACS) analyses of mesenchymal stem cell MSC)-conjugated control isotype IgG or antibodies against indicated cell-surface proteins. MSCs were negative for CD11b, CD34, and CD45 ( A ) and positive for CD29 and CD44 ( B ).

Supportive validation

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Experimental details: Fig. 1 Isolation and characterization of mesenchymal stem cells. a Schematic showing isolation of mouse bone marrow cells (BMCs) and its properties of self-renewal and differentiation of MSCs. b Representative microscopic images displaying isolated bone marrow cells that show circular and round-shaped morphology of BMCs; whereas, adhered MSCs show fibroblast or eye-shaped morphology. c Immunofluorescence images of MSCs showing the expression of MSC-positive markers (CD29, CD44, and SCA1). d Immunophenotypic characterization of MSCs using flow cytometer showing the absolute counts of MSC positive markers such as CD29, CD44, and SCA1, as well as expression of MSC-negative (CD34, CD45, and CD11b). Isotype controls for each antibody were used as controls and FITC/rhodamine-conjugated secondary antibodies were used for their detection. e Bar graph (quantification from four independent experiments (expressed as mean +- standard error)) showing the percentage of cells expressing the MSC-positive and negative markers respectively. f , g Immunophenotypic characterization of BMCs using flow cytometer showing expression various markers (CD29, CD44, CD45, and CD11b). Bar graph expressed as mean +- standard error shows quantification of respective markers from three independent experiments.

Supportive validation

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Experimental details: Fig. 3 Expression of endothelial cell surface determinants by primary lung MVEC. Lung cells were incubated with primary antibodies directly conjugated to fluorophores and staining intensity analyzed by flow cytometry. Representative dot plots are presented. Human lung FB and MSC were used as known negative controls, and PAEC as a known positive control. DAPI was used to exclude dead cells.

Supportive validation

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Experimental details: Figure 1 Identification of ADSCs. ( A ) ADSCs were isolated from the adipose tissue of breast tumors. After two to three passages, the expressions of ADSCs markers (CD90FITC, CD105PE, and CD44FITC) and the lack of CD34PE and CD45FITC were confirmed by flow cytometry. ( B ) The differentiation ability of ADSCs was tested by adipogenesis, osteogenesis, and chondrogenesis.

Supportive validation

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Experimental details: Figure 3 Paclitaxel dysregulates CD4 + and CD8 + T-cell subpopulations in an eIF4E-dependent manner. (A) Gating strategy used for flow cytometry of lymphocytes from popliteal and inguinal lymph nodes. T-cells were separated from the whole lymphoid cells population using CD3. CD3 + cells were then gated for CD4 + T-cell and CD8 + T-cells. For each of these subsets, cells were further gated for CCR7 or CD25 and CD44. (B) Quantification of CD4 + T-cells from the CD3 population from male mice. (C) CCR7 + T-cells from isolated CD4 + population in males, ** p 0.0063. (D) CD4 + cells gated for CD25 and/or CD44 in males. (E) Quantification of CD4 + T-cells from the CD3 + population from female mice, * p 0.0101. (F) CCR7 + T-cells from isolated CD4 + population in female mice, * p 0.0250. (G) CD4 + cells gated for CD25 and/or CD44 in female mice, ** p 0.0011. (H) Quantification of CD8 + T-cells from the CD3 + population from male mice. (I) CCR7 + T-cells from isolated CD8 + population in males, * p 0.0433. (J) CD8 + cells gated for CD25 and/or CD44 in males, * p 0.0396. (K) Quantification of CD8 + T-cells from the CD3 population from female mice, * p 0.041. (L) CCR7 + T-cells from isolated CD8 + population in female mice, ** p 0.0097. (M) CD8 + cells gated for CD25 and/or CD44 in female mice. All data are presented as mean +- standard error of the mean, n = 3 mice each for male/female WT vehicle-treated and WT paclitaxel groups, n = 4 mice each for male/female eIF4E S209A vehicle-trea

Supportive validation

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Experimental details: Figure 4. SUV420H2 knockdown decreases stemness and anticancer drug resistance of mesenchymal pancreatic cancer cells. (A) CD24 and CD44 RNA expression levels with NTC control or SUV420H2 knockdown determined by RNaseq or qRT-PCR. For graphs, bars indicate mean +- SD. For RNaseq, n = 3 biological replicates and differences assessed by using voom+limma (see Materials and methods). For qRT-PCR, n = 3 biological replicates each averaged from three technical replicates, and differences were assessed by Student's t test compared with siNTC control. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. (B) Cell-surface protein level for CD24 and CD44 analyzed by flow cytometry in PANC-1 cells. B shows one representative panel per condition of a set of triplicates; differences were assessed by Student's t test compared with siNTC control. ***, P < 0.001; ****, P < 0.0001. (C) Tumorsphere formation assay showing representative images from a PANC-1 experiment and quantitation in three pancreatic cancer cell lines. n = 60 fields of view considered for each cell line, composed of 20 across three biological triplicates. Bar graphs depict mean +- SD. Differences were assessed by Student's t test compared with siNTC control in each cell line. *, P < 0.05; ****, P < 0.0001. Bars, 250 um. (D) Cell viability assays demonstrating effects of Gemcitabine and 5-Fluorouracil (5-FU) over 72 h on mesenchymal pancreatic cancer cells with NTC control or SUV420H2 knockdown, with two siRNAs for e

Supportive validation

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Experimental details: Figure 1 Characterization of murine MSCs. (A) Morphology of primary MSCs isolated from mouse bone marrow. MSCs easily form large colonies. (B) Histogram of flow cytometry for cell surface marker of MSCs. (C) Morphology of MSCs under normoxia and hypoxia conditions. Bar equals 200 um in all panels

Supportive validation

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Experimental details: Figure 5 Overexpression of Aiolos upregulates the CSC-like properties in H1299 and A549 cells. ( A ) Representative images (top) and quantification (bottom) of spheroid formation in H1299-Mock and H1299-Aiolos cells and in A549-Mock and A549-Aiolos cells. Scale bars, 100 mum. Asterisk indicates P < 0.05, compared with control cells (Student's t-test). ( B ) Lung cancer stem cell surface markers (CD44 and CD133) in H1299-Aiolos vs H1299-Mock cells and in A549-Aiolos vs A549-Mock cells were analyzed by flow cytometry. ( C ) Real-time PCR analysis of CD44 and CD133 expression in H1299-Aiolos vs H1299-Mock cells (top) and in A549-Aiolos vs A549-Mock cells (bottom). Asterisk indicates P < 0.05, compared with control cells (Student's t-test). ( D ) Survival fraction of H1299-Aiolos cells after irradiation treatment. Asterisks indicate P < 0.05, compared with H1299-Mock cells (Student's t-test). ( E ) Survival fraction of A549-Aiolos cells after irradiation treatment. Asterisks indicate P < 0.05, compared with A549-Mock cells (Student's t-test).

Supportive validation

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Experimental details: Fig. 3 Chop negatively regulates effector CD8 + T cell activity. a Gene set enrichment analysis was performed to determine the specific enrichment in effector CD8 + T cell gene signature in primed wild-type or Ddit3 -/- Pmel CD8 + T cells. b Heatmap showing the expression of selective effector function-related transcripts in primed wild-type vs. Ddit3 -/- Pmel CD8 + T cells, as described in the Methods section. c Carboxyfluorescein succinimidyl ester (CFSE)-labeled wild-type or Ddit3 -/- CD8 + T cells were stimulated with anti-CD3/CD28 and proliferation tested after 72 h by fluorescence-activated cell sorter (FACS). Left: representative histogram of T cell proliferation (n = 6); right: T cell proliferation rates under different concentrations of anti-CD3/CD28 (ug/ml) ( n = 6). d Granzyme B protein (upper panel, long- and short-time exposure) and Gzmb mRNA levels (lower panel) in wild-type or Ddit3 -/- CD8 + T cells primed with anti-CD3/CD28 for 72 h ( n = 5). e Percentage of IFNgamma + cells in wild-type or Ddit3 -/- CD8 + T cells primed as in ( d ). Right: representative FACS findings; left: merged percentage values from n = 4. f Extracellular acidification rate (ECAR) of wild-type or Ddit3 -/- CD8 + T cells primed as in d upon glycolysis stress analysis ( n = 3). g Oxygen consumption rate (OCR) of wild-type or Ddit3 -/- CD8 + T cells activated as in d after mitochondrial stress analysis ( n = 3). h , i Percentage of IFNgamma + cells in CD8 + T cells primed in the presence o

Supportive validation

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Experimental details: Fig. 2 Mutant p53-expressing cells contain larger CD44 Br and Lgr5 Br sub-populations a, b RKO isogenic cell lines were immuno-stained with anti-Lgr5 antibody and the size of Lgr5 Br sub-population was measured by ImageStream X. a Graph presenting an averaged percentage of Lgr5 Br cells obtained from three independent experiments. Error bars represent SE. b Representative photo of Lgr5 Br cedi, c Organoids were produced from intestinal epithelial cells extracted from WTp53, p53 knock-out (p53 KO), or WTp53/mutant p53 R172H heterozygous mice, as previously described [ 15 ]. Lgr5 mRNA expression levels were measured by qRT-FCR using specific primers. Graph represents an average of three independent organoids pools. Error bars represent SE. d RKO isogenic cell lines were immuno-stained with either anti-CD44 antibody that recognizes all CD44 isoforms and the size of CD44 Br sub-populations was measured by FACS. Left: Graph presenting an averaged percentage of CD44 Br cells obtained from three experiments. Error bars represent SE. Right panel shows representative dot plots indicating on percentage of CD44 Br sub-populations, e-g The established shCon and shp53 SW480 cells were immuno-stained with either anti-CD44 antibody that recognizes all CD44 isoforms and the size of CD44 Br sub-populations was measured by ImageStream X. e Graph presenting an averaged percentage of cells obtained from four experiments, f Representative plot of the mean pixel intensity

Supportive validation

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Experimental details: Fig. 2 BMX-ARHGAP upregulation induces SGC7901 stem cell formation, proliferation and invasion. a Protein expression of CD133, CD44, SOX2 and Nanog in transfected SGC7901 cells determined by western blot assay; b CD133 + CD44 + cells sorted by flow cytometry; c the number of formed cell spheres after transfection shown by cell sphere formation assay ( x200); d the number of formed cell colonies after transfection shown by cell colony formation assay; e , the invasion ability of CD133 + and CD44 + evaluated by Transwell assay (x200); f proliferation ability of CD133 + and CD44 + evaluated by EdU labeling assay (x100). * p < 0.05 vs. the pcDNA3.1-transfected cells. Measurement data were expressed as mean +- standard deviation and analyzed by independent t -test; each experiment was repeated three times. BMX bone marrow kinase on chromosome X, ARHGAP RhoA GTPase activating protein

Supportive validation

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Experimental details: Fig. 1 SHP1 deficiency had no effect on the cell morphology, proliferation rate or surface markers. a Phase-contrast images of MSCs derived from bone marrow of WT and me v /me v mice. Scale bar: 50 mum. b The same number of WT and me v /me v MSCs were coated into the 6 well plates, the number were calculated every day until the sixth day and the proliferation rate was monitored. c After isolation from bone marrow and culture for an equal number of passages, me v /me v and WT MSCs were harvested and analyzed for the indicated markers by immunofluorescence staining and flow cytometry. The experiments were repeated at least three times. Error bars represent +- SEM (n = 3), ns, not significant

Supportive validation

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Experimental details: FIGURE 1 Characterization of colorectal CSCs isolated from LoVo and HT29 cells. A, Flow cytometric sorting of CSCs using CD44 and EpCAM as markers. The percentage of parental LoVo and HT29 cells expressing both CD44 and EpCAM was approximately 15%, representing the proportion of CSCs. CSCs isolated from parental LoVo and HT29 cells (denoted as LoVo-CSCs and HT29-CSCs, respectively) exhibited high expression of both markers (>90%). Relative proliferation of (B) LoVo-CSCs and (C) HT29-CSCs was inhibited by ATL-1 at 200 muM for up to 72 h, compared to that of control (+PBS) CSCs. The protein expression of stemness markers OCT-4, SOX-9, and Nanog, relative to GAPDH, in (D) LoVo-CSCs and (E) HT29-CSCs was downregulated by ATL-1 at 200 muM after 48 h of culture, compared to that of control (+PBS) CSCs. Transwell assay of the (F) migration and (G) invasion of LoVo-CSCs demonstrated decreased cell counts in both cases when ATL-1 was administered at 200 muM, compared to those of control (+PBS) CSCs. H, The percentage of apoptotic LoVo-CSCs and HT29-CSCs was elevated in the presence of ATL-1 at 200 muM, compared to that of control (+PBS) CSCs. The data represent the mean +- SD of three independent technical replicates ( t -test); * P < .05; % P < .05 at 72 h

Supportive validation

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Experimental details: Figure 1. Essential role for WNK1 in thymocyte development. ( A ) Flow cytometric analysis of thymocytes from Wnk1 fl/+ CD2-Cre and Wnk1 fl/fl CD2-Cre mice showing double negative (DN, Thy1.2 + Lineage - ) thymocytes subdivided into DN1 (CD44 + CD25 - ), DN2+DN3 (CD25 + ), and DN4 (CD44 - CD25 - ) subsets, immature single positive (ISP, CD4 - CD8 + TCRbeta - ), double positive (DP, CD4 + CD8 + ), CD4 + single positive (4SP, CD4 + CD8 - ), and CD8 + single positive (8SP, CD4 - CD8 + TCRbeta + ) thymocytes. Numbers show % of cells falling into each gate. ( B ) Mean +- SEM number of total thymocytes and of thymocytes at each developmental stage defined using the gates in A, as well as gammadelta thymocytes (CD4 - TCRgamma + ). ( C ) Mean +- SEM number of cells in each thymocyte population in Wnk1 fl/fl CD2-Cre animals normalized to Wnk1 fl/+ CD2-Cre controls (set to 100%). ( D ) Mean +- SEM Wnk1 mRNA levels in thymic subsets from Wnk1 fl/+ CD2-Cre and Wnk1 fl/fl CD2-Cre mice, normalized to Wnk1 fl/+ CD2-Cre controls (set to 100%) measured by Q-PCR from exon 1 to exon 2. CD44 levels were used to separate DN2 (CD44 + ) and DN3 (CD44 - ) thymocytes. ( E ) Flow cytometric analysis of Rag1 -/- radiation chimeras reconstituted with bone marrow from Wnk1 fl/+ RCE and Wnk1 fl/D368A RCE mice, treated with tamoxifen and analyzed 7 d later showing gating for thymocyte subsets as in A, with DN (Thy1.2 + Lineage - ) thymocytes pre-gated on CD4 - CD8 - cells. ( F ) Mean +- SEM number of cells

Supportive validation

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Experimental details: Figure 2. WNK1 is required for thymocytes to develop past the pre-TCR checkpoint. ( A ) Left: flow cytometric analysis of Thy1.2 + Lineage - thymocytes separated by expression of CD44 and CD25, and then DN3 (CD44 - CD25 + ) cells separated into DN3a (small, FSC low CD28 - ) and DN3b (large, FSC high CD28 + ) cells. Right: Mean +- SEM cell numbers in DN subsets. ( B ) Left: Flow cytometric analysis of thymocytes from Wnk1 fl/+ CD2-Cre and Wnk1 fl/fl CD2-Cre mice showing intracellular TCRbeta levels in DN2+DN3 and DN4 subsets. Numbers indicate the percentage of TCRbeta + cells. Right: Mean +- SEM percentage of DN2+DN3 and DN4 cells that are intracellular TCRbeta + . ( C ) Mean +- SEM of CD3epsilon or pre-Talpha surface levels measured as mean fluorescence intensity (MFI) in flow cytometry of DN2+DN3 and DN4 thymocytes from Wnk1 fl/+ CD2-Cre and Wnk1 fl/fl CD2-Cre mice. ( D ) Left: flow cytometric analysis of CD4 and CD8 levels on thymocytes from Wnk1 fl/+ Rag1 -/- CD2-Cre and Wnk1 fl/fl Rag1 -/- CD2-Cre mice harvested 4 d after intraperitoneal injection with PBS or anti-CD3epsilon antibody. Gate indicates DP thymocytes and number shows percentage of cells in the gate. Right: mean +- SEM number of DP thymocytes defined using the gates on the left. *0.01

Supportive validation

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Experimental details: Figure 3. RNAseq of WNK1-deficient thymocytes reveals significant changes in five distinct processes. ( A ) Thymi were harvested from Wnk1 fl/+ Rag1 -/- CD2-Cre and Wnk1 fl/fl Rag1 -/- CD2-Cre mice that were either untreated (0 hr) or had been injected with anti-CD3epsilon antibody 3, 24 or 48 hr earlier. DN3+DN4 thymocytes were sorted, RNA purified and analyzed by RNAseq, results of which are shown in C-E. ( B ) Flow cytometric analysis of DN thymocytes from the experiment described in A. Gates indicate cells (Thy1.2 + , CD44 - ) that were sorted for further RNAseq analysis. ( C ) Principal component analysis using expression of all normalized genes for all samples from the experiment described in A. ( D ) Log 2 fold changes and total number of statistically significant differentially expressed genes (DEGs) in samples from Wnk1 fl/fl Rag1 -/- CD2-Cre (KO) mice compared to Wnk1 fl/+ Rag1 -/- CD2-Cre (HET) mice at each time point ( Supplementary files 2 , 3 ). ( E ) Metacore process analysis of DEGs. Selected processes and their P -values are shown at each time point; graph on left shows the lowest P -value for each process from any of the four time points. Red bars indicate time point with the lowest P -values for each process (Minimal). Ratios indicate the number of DEGs at each time point over the number of all genes in the indicated processes. Significance calculated by Wald's test ( D ) and Hypergeometric test ( E ). Sample sizes: three Wnk1 fl/+ Rag1 -/- CD2-Cre and four

Supportive validation

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Experimental details: Fig. 1 Cell type-dependent levels of 5-methylcytosine and 5-hydroxymethylcytosine. a Representative fluorescent micrographs for canine fetal fibroblasts (cFFs) stained with phycoerythin (PE)-conjugated antibodies against CD44 and CD90/THY1. Scale bar unit length is 50 mum. b Overlay histograms showing cFFs stained with PE-conjugated antibodies (red) or isotype control antibodies (black). Fold difference in c 5-methylcytosine and d 5-hydroxymethylcyctosine levels in canine adult fibroblast (cAF), canine fetal fibroblast (cFF), canine partially reprogrammed (cPR), and canine embryonic stem cells (cESCs). Data are presented as mean +- standard error, n = 4. Relative transcript abundance for e TET1, f TET2, and g TET3 in steady-state cultures of cAF and cFF. Data are presented as mean +- standard error, n = 3. Means annotated with different letters are considered significantly different by one-way analysis of variance and Tukey's honestly squared difference test, P < 0.05

Supportive validation

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Experimental details: Fig. 3 Expression levels of CD44 and EpCAM on KatoIII cells surface and the effect of transient transfection of miR-34a-5p mimic on these markers expression. a The flow cytometry analysis indicated that EpCAM and CD44 are expressed in almost all and ~ 97% of KatoIII cells, respectively. The expression of CD44 on KatoIII cells showed lower intensity than EpCAM expression. In addition, two sub-populations of EpCAM positive cells with different fluorescence intensity were observed in KatoIII cell line. b The frequency and MFI of EpCAM marker were compared between adhesive KatoIII cells dissociated from the flask using trypsin enzyme and non-adhesive KatoIII cells. Data showed that the use of trypsin enzyme for detachment of the adherent cells from the flask reduced the fluorescence intensity of EpCAM (116.5 +- 0.7), in comparison to the suspended cells (180 +- 5.65). But, the use of trypsin enzyme for detachment of the adherent cells had no effect on the frequency of EpCAM positive cells. c According to the flow cytometry analysis, transient transfection of the miR-34a-5p mimic at 25 nM had no effect on percentage of CD44 and EpCAM positive cells in KatoIII cells. MFI: Median Fluorescence Intensity

Supportive validation

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Experimental details: Fig. 5 The effect of stable transfection of pre-mir-34a on the expression levels of CD44 and EpCAM markers. The flow cytometric detection illustrated that the percentage of CD44 + cells and the MFI of CD44 marker were significantly decreased in the KatoIII-pGFPC1-34a cells compared to the KatoIII-pGFPC1- empty cells. No difference was found in percentage of EpCAM + cells between these two stable cells. *p < 0.05; **p < 0.01. MFI: Median Fluorescence Intensity

Supportive validation

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Experimental details: Figure EV3 Sporozoite surface antigen induces a greater effector CD8 + T-cell phenotype than EEF vacuolar membrane antigen C57BL/6 mice received 2 x 10 6 OT-I cells alone ( n = 2) or were additionally immunised with 10,000 gamma-radiation attenuated WT ( n = 3), CSP SIINFEKL ( n = 4) or UIS4 SIINFEKL ( n = 4) sporozoites intravenously. Spleens and livers were harvested either 14 or 42 days later, and proportions of CD8 + T cells expressing effector surface markers were quantified. Flow cytometry plots show representative percentages of CD8 + T cells co-staining K b -SIINFEKL and markers of effector phenotype (CD11a hi , CD49d hi , CD62L lo , CD44 hi ).

Supportive validation

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Experimental details: Figure 1 AD-MSCs characterization; (A) Flow cytometry assay to assess the CD markers in the surface of extracted AD-MSCs. Target cells were positive for CD73 (95.1%), and CD90 (90.6%) surface markers and were negative for CD44 and CD34 markers. (B) Morphology of AD-MSCs at passage 3. (C) Oil red staining to prove the adipogenic potential differentiation of AD-MSCs. (D) Alizarin-red staining to confirm the osteogenic potential differentiation of AD-MSCs. Scale bar = 100 mum. Abbreviations: AD-MSCs: adipose-derived mesenchymal stem cells.

Supportive validation

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Experimental details: Figure 5 Impact of Mito-MGN on T cell activation and effector functions (A) Schematic for analyzing Mito-MGN effects on splenic T cells. (B-D) Changes in T cell activation. Representative flow cytometry plots of CD44 hi CD62L lo levels in T cells (B). Enumeration of activated T cells of CD4 + (C) and CD8 + (D) T cell subsets in Mito-MGN treated and vehicle control cells. Values are mean +- SD, n = 6 independent experiments. Statistical significance determined using a Student's t-test (**, p< 0.01; ***, p< 0.001). Effects of Mito-MGN on T cell proliferation and early activation markers are shown in Figure S8 . (E) Realtime measurement of extracellular acidification rate (ECAR) (left panel) and oxygen consumption rate (OCR) in treated T cells Values are mean +- SD of n = 3 biological replicates completed in technical quadruplicate. Statistical differences at individual time points were analyzed using Student's t-test (****, p< 0.0001). (F and G) IsoPlexis IsoLight assay measured Polyfunctionality Strength Index (PSI) scores (F) and effector or inflammatory cytokine levels (G) in Mito-MGN treated compared to vehicle control T cells. Values are mean +- SD from 2 biological replicates.

Supportive validation

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Experimental details: Fig. 1 Mesodermal progenitors can be derived trough a chemically defined monolayer approach. A Schematic overview of the protocol to differentiate induced pluripotent stem cells towards mesodermal progenitors. B - D Gene expression of markers for pluripotency, early and late mesoderm, ectoderm, and endoderm during mesoderm differentiation. E FACS analysis of Mesogenin1 (MSGN1) during differentiation using a MSGN1-2A-Venus reporter line. F Percentage of MSGN1, CD44, and CD140A/B positive cells during differentiation, based on FACS analysis. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001. n = 3-4.

Supportive validation

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Experimental details: Fig. 1 Tumor stemness is increased in sorafenib-resistant hepatocellular carcinoma cells. A SMMC-7721 and PLC8024 cells were more resistant to sorafenib than HepG2 and Hep3B cells. HCC cells were treated with 0-40 muM sorafenib and the cell viability was analyzed by the CCK8 assay. Data were presented as mean +- SD ( n = 3). B The KEGG analysis on the upregulated/downregulated genes. The genes expression changed more than 2 folds were analyzed between sorafenib-resistant vs. sorafenib-sensitive HCC cells. C Heatmap of gene expression participated in cell cycle pathway, Wnt signaling, and PI3K-AKT pathway. The levels of the gene expression were reflected by different colors, colors from blue to red stood for expression levels from low expression to high expression. D The expression of stem cell markers was enhanced in sorafenib-resistant HCC cells. The expression of ALDH, SOX2, and OCT4 was analyzed. E The CD44 + CD133 + subpopulations were increased in sorafenib-resistant HCC cells. The CD44 + CD133 + subpopulation was analyzed by flow cytometry using anti-CD44 and anti-CD133 antibodies. * P < 0.05, ** P < 0.01. F Stemness was increased in sorafenib-resistant HCC tumors. OCT4 and NANOG expression were detected by IHC. Bar = 100 mum.

Supportive validation

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Experimental details: Fig. 3 3-hydroxyanthranic acid inhibits tumor stemness of sorafenib-resistant HCC cells. A 3-HAA inhibited cell growth of sorafenib-resistant HCC cells. Cell numbers of HCC cells were counted by cytometry. Data were presented as mean +- SD ( n = 3). * P < 0.05, ** P < 0.01. B 3-HAA reduced colony formation in sorafenib-resistant SMMC-7721 and PLC8024 cells. Cells were treated with 3-HAA at the indicated dose. * P < 0.05, ** P < 0.01. C The ratio of CD44 + CD133 + subpopulation was decreased in 3-HAA-treated SMMC-7721 and PLC8024 cells. Cells were treated with 3-HAA at the dose of 100 muM for 48 h. * P < 0.05. D 3-HAA inhibited the expression of stem cell markers in HCC cells. The treating time was 48 h for the dose-response experiment and the dose of 3-HAA was 100 muM for the time-course analysis. E 3-HAA suppressed tumor growth of SMMC-7721 xenografts. The 3-HAA was administrated 100 mg/kg day by intraperitoneal injection for 16 days, five mice were recruited in the control and 3-HAA-treated group. The tumor volumes were presented as mean +- SD. * P < 0.05. F 3-HAA decreased the proportion of CD44 + CD133 + subpopulation in SMMC-7721 xenografts. Tumor cells were analyzed by flow cytometry using anti-CD133-PE and anti-CD44-APC. * P < 0.05. G 3-HAA inhibited the expression of stem cell markers in SMMC-7721 xenografts. Bar = 100 mum.

Supportive validation

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Experimental details: Fig. 5 The 3-HAA increases the sensitivity of HCC cells to sorafenib by suppressing stemness. A The cell viability of 3-HAA-treated SMMC-7721 and PLC8024 cells was analyzed by CCK8 assay. Cells were treated with sorafenib at the indicated dose with or without 100 muM 3-HAA for 4 days. * P < 0.05. B The combination of 3-HAA and sorafenib dramatically inhibited ALDH, SOX2, and OCT4 expression in SMMC-7721 and PLC8024 cells. Cells were treated with 100 muM of 3-HAA and sorafenib at the indicated dose for 24 h. C The combination of sorafenib and 3-HAA significantly reduced the proportion of CD133 + CD44 + tumor cells than either 3-HAA alone or sorafenib alone in SMMC-7721 and PLC8024 cells. Cells were treated with 100 muM 3-HAA and 5 muM sorafenib for 24 h. * P < 0.05, ** P < 0.01. D CHIR99021 recovered the AKT/GSK3beta/beta-catenin signaling and the expression of stemness markers, inhibited by the combination treatment. Cells were treated with 100 muM 3-HAA, 5 muM sorafenib, and/or 5 muM CHIR99021 for 24 h. E CHIR99021 recovered the combination-suppressed tumor growth of SMMC-7721 xenografts. 3-HAA and sorafenib were separately administrated by intraperitoneal injection for 16 days at the dose of 100 and 10 mg/kg day, respectively. CHIR99021 was administered orally at 40 mg/kg day, five mice were recruited in each group. The tumor volumes are presented as mean +- SD. ** P < 0.01. F CHIR99021 increased the ratio of CD44 + CD133 + subpopulation in SMMC-7721 xenografts. Tumor cells

Supportive validation

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Experimental details: FIGURE 7 r Ts Pmy maintains majority of Tregs in an effective suppressor status (CD62L lo CD44 hi eTregs) with greater expression of functional phenotypes of TIGIT and CTLA4 in cLP with DSS-induced colitis. Flow cytometry results showed the frequencies of CD44 hi CD62L lo cells (A) and TIGIT + cells (B) in CD4 + Foxp3 + T cells of cLP from r Ts Pmy or PBS-treated mice with or without DSS colitis. The blank control of antibodies of CD62L and CD44 (A) was shown, and the antibody of TIGIT (B) were cut in FMO control samples. The corresponding percentages are shown on the right ( n = 5). (C) The frequency of Foxp3 + CTLA4 + cells in CD3 + CD4 + T cells. The antibody of CTLA4 was cut in FMO control samples. The corresponding percentage is shown on the right ( n = 3-5). The bars represent the mean +- SEM. * p < 0.05. cLP, colonic lamina propria.

Supportive validation

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Experimental details: Figure 3 CD44 deletion in breast cancer cell lines decreases expression of genes involved in cellular adhesion and cytokine activity. ( A ) CD44 KO was confirmed via Western blot and compared to the loading control beta-tubulin via densitometry. CD44 KO indicates that cells received gRNA targeting exons 1 and 5 of CD44. CD44 WT (CD29+/CD44+) and CD44 KO (CD29+/CD44-) cells were sorted and expanded in culture. ( B ) Venn diagram illustrating RNA sequencing results (submitted in triplicate). A total of 1530 and 320 genes were impacted by CD44 KO in the Hs578T cells and MDA-MB-231 cells, respectively. When comparing each of these data sets, 40 genes were differentially expressed in both Hs578T and MDA-MB-231 cells upon deletion of CD44. ( C ) Heat map demonstrating log fold change of differential gene expression in CD44 WT relative to CD44 KO Hs578T and MDA-MB-231 cells. ( D ) Gene ontology analysis identifying gene sets enriched in CD44 WT relative to CD44 KO Hs578T and MDA-MB-231 cells. Dot size represents the number of genes enriched within that pathway, while color represents an adjusted p -value.

Supportive validation

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Experimental details: Figure 6 Enhanced chromosomal instability induced by MSL disruption exhausts cancer cell proliferative capacity. a . Clonogenic assays comparing MSL LOF ( MSL3 -KO) and control TDF cells visualized by crystal violet staining. Scale bar: 1 mm. b . DNA FISH detecting the pericentromeric region of chromosome 12 in clonal populations grown for 14 d. Cells from distinct locations within the clones are juxtaposed. Scale bar: 10 mum. c-d . Quantification of CIN score ( c ) and relationship with clone size ( d ). N = 105, 96, 121 biologically independent clones collected from two experiments. Horizontal lines: median values. P-value from one-way ANOVA followed by Tukey's test ( c ) and two-sided Spearman correlation test (MSL LOF cells in d ). N.s. : non-significant (p-value > 0.99). R s : correlation coefficient for MSL LOF cells. e-h. Immunodetection of Ki67 ( e , g ) and quantification of non-proliferative Ki67-negative cells ( f , h ). N = 100, 102, 130, 1375, 1300 independent cells for DMSO, 4d and 6d reversine, cntr-KO and MSL LOF ( MSL3 -KO) cells collected from two experiments. MEXF-2090 cells are shown in g - h ; TDF and other PDX-derived cells showed similar results. P-value from two-tailed Fisher's exact test. Scale bar: 10 mum. i-j . Limiting dilution clonogenic assays. Phase contrast images of DMSO- and reversine-treated TDF cells 12 d after plating ( i ) and quantification of populated wells ( j ). The percentage of wells containing at least one clone larger than 20 cel

Supportive validation

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Experimental details: Figure 2 Stemness markers of monolayers and spheroids from RT112 and 5637 cells. ( a - c ) Median fluorescence intensity of Aldefluor TM ( a ), CD44 ( b ) and CD133 ( c ) by flow cytometry analysis on RT112 and 5637 cells grown as monolayers. Results are the mean of two ( a ) and three ( b , c ) experimental replicates. Statistical test: t -test, * for p < 0.05. ( d ) Representative images from confocal immunofluorescence (IF) microscopy of RT112 and 5637 cells using SOX2 Antibody (red) and Hoechst 33342 (blue) for nuclei. Cells were grown as monolayer or spheroids on different (Tissue culture-treated, Not-treated or Cell repellent) supports, before being seeded in adherent condition on chamber slides for IF.

Supportive validation

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Experimental details: Figure 2 The proportion of CD8 + effector memory T (Tem) cells and levels of IFN-gamma, mTOR and S6K in CD8 + Tem cells were significantly increased by IL-12 stimulation but significantly decreased by rapamycin treatment. The peripheral blood mononuclear cells obtained from the cyclophosphamide plus invasive pulmonary aspergillosis (CTX + IPA) mice, CTX + IPA mice treated with IL-12 (CTX + IPA+IL-12) or rapamycin (CTX + IPA+RAPA), and control animals were assessed using flow cytometry seven days after A . fumigatus infection. The side scatter (SSC) and CD8a were applied to gate on CD8 + T lymphocytes, CD44 + CD45 + CD62 +/- were considered to represent the Tem cells. Representative dot plots are shown, and the percentages of Tem cells and of Tem cells expressing IFNgamma, mTOR, and S6K are expressed as the mean +- S.D. * p < 0.05; ** p < 0.01; *** p < 0.001.

Supportive validation

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Experimental details: Figure 3 IL-12 significantly increased the expression of T-bet but significantly decreased the expression of Eomesodermin in CD8 + effector memory T (Tem) cells, which was blocked by rapamycin treatment. The peripheral blood mononuclear cells obtained from the cyclophosphamide plus invasive pulmonary aspergillosis (CTX + IPA) mice, CTX + IPA mice treated with IL-12(CTX + IPA+IL-12) or rapamycin (CTX + IPA+RAPA), and control animals were assessed using flow cytometry seven days after A . fumigatus infection. The side scatter (SSC) and CD8a were applied to gate on CD8 + T lymphocytes, CD44 + CD45 + CD62 +/- were considered to represent the Tem cells. Representative dot plots are shown, and the percentages of Tem cells and of Tem cells expressing T-bet and Eomesodermin are expressed as the mean +- S.D. * p < 0.05; ** p < 0.01; *** p < 0.001.

Supportive validation

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Experimental details: 10.1371/journal.pone.0247990.g003 Fig 3 Enhanced protection against Mtb HN878 in CB6F1 mice with liposomal formulations. (A) Increased polyfunctional ID93-specific CD4+CD44+ T cells from the spleens of immunized CB6F1 mice four weeks after the final immunization. The data are represented as the percentage of CD4+CD44+CD154+ T cells producing one or more cytokines following ex-vivo stimulation with ID93; cytokine producing subsets are shown as stacked bars, with mean + SD of each subset. Comparisons of total cytokine producing cells between groups were performed using one-way ANOVA with Bonferroni's multiple comparison test. Down-inflected lines indicate * p

Supportive validation

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Experimental details: 10.1371/journal.pone.0247990.g004 Fig 4 Immunogenicity of C57BL/6 mice four weeks after the final immunization with ID93+GLA-LSQ. Mice were immunized with ID93 combined with GLA-LS containing different QS-21 doses (10, 2 or 0.4 mug). (A) The percent frequency of single-cytokine producing ID93-specific CD4+ T cells. Bars represent the mean of the group, with vertical lines indicating SD. Groups were compared for each cytokine using one-way ANOVA with Bonferroni's multiple comparison test, with * p

Supportive validation

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Experimental details: 10.1371/journal.pone.0247990.g006 Fig 6 Prophylactic protection with ID93+GLA-SE and ID93+GLA-LSQ in C57BL/6 mice. Mice were immunized with ID93 combined with different adjuvant formulations including SE, LS (liposomes), LSQ (liposomes+QS21), GLA-LS, GLA-LSQ, or GLA-SE. (A) The percent frequency of single-cytokine producing ID93-specific CD4+CD44+ T cells. Bars represent the mean of the group, with vertical line indicating SD. Groups were compared for each cytokine using one-way ANOVA with Bonferroni's multiple comparison test, with * p

Supportive validation

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Experimental details: 10.1371/journal.pone.0247990.g007 Fig 7 Enhanced TH1 immune responses following infection with Mtb H37Rv within the lungs of C57BL/6 mice immunized with ID93+GLA-SE and ID93+GLA-LSQ. Mice were immunized with ID93 combined with different adjuvant formulations including SE, LS (liposomes), LSQ (liposomes+QS21), GLA-LS, GLA-LSQ, or GLA-SE. Four weeks after the last immunization mice were challenged with a low dose aerosol of Mtb H37Rv. Three weeks after challenge mice were euthanized and lungs collected to assess the immune response. (A) The percent frequency of single-cytokine producing ID93-specific CD4+CD44+ T cells within the lung. Bars represent the mean of the group, with vertical line indicating SD. Groups were compared using one-way ANOVA with Bonferroni's multiple comparison test, * p

Supportive validation

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Experimental details: Figure 1 Morphology and antigenicity of the cell surface in THP-1 cells after formalin fixation. ( A , B ) CSLM images showing immunofluorescence single labeling for GCX markers: ( A ) CD44 (green pseudocolor) and ( B ) CS (green pseudocolor) with ( C ) the corresponding negative control with omitted primary antibody. Note the CD44-labeling and scattered clusters of CS close to the plasma membrane (arrows). ( D ) WGA staining (red pseudocolor). ( A - D ) DAPI fluorescence stains for nuclear DNA (blue pseudocolor) Scale bar: ( A - D ) 5 um.

Supportive validation

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Experimental details: Figure 2 Flowchart showing the workflow of the combined HPF/FS/rehydration and pre-embedding immunogold labeling method for TEM. Insert on the left side shows well-preserved intra- and pericellular ultrastructure of THP-1 cells after processing for immuno-TEM. Note the dimension of the GCX. The dashed lines mark the border of the nucleus to cytoplasm and cytoplasm to GCX. Insert on the right shows a higher magnification of the GCX structures with immunogold labeling for CD44 (arrowheads). N, nucleus; C, cytoplasm; GCX, glycocalyx. Scale bar: 1000 nm.

Supportive validation

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Experimental details: Figure S2. Mechanism of action of IRS661. (A) Schematic representation of the experimental setup. Mice were infected intranasally with 1,000 TCID 50 of influenza virus X31 and treated with IRS661 or PBS intranasally (15 nmol in 30 ul) on day 4 after infection. Usually, BALF was isolated on day 6 after infection. Colored dots mark days when mice were treated with alphaPDCA-1 (200-500 ug), 1A8 (150-300 ug), alphaSiglec-H (200-500 ug), or alphaCCR2 (20 ug) depletion antibody i.p. (B) WT 129S7 mice were infected with X31 and treated with IRS661 or PBS intranasally (15 nmol in 30 ul), i.p. (50 nmol in 100 ul), or intravenously (50 nmol in 100 ul) 4 d later. IFN-alpha concentrations were quantified by ELISA in BALF taken on day 5 after infection. n = 3-11 mice per group. (C) Flow cytometry plots representing the gating strategy for cell analysis in Fig. 2 B . Lineage channel includes CD3, CD19, and NKp46. FSC, forward scatter; SSC, side scatter. (D) WT 129S7 mice were infected with 1,000 TCID 50 X31 and treated with IRS661, control ODN 2, or PBS intranasally. Survival was monitored for 14 d. n = 17-18 mice per group. (E and F) Viral loads in lungs of X31-infected mice treated with IRS661 or PBS (E; n = 3-7 mice per group) and/or aPDCA-1 antibody (F; n = 6-7 mice per group) were determined by RT-qPCR or TCID 50 assay at days 2, 3, 5, and 7 (E) or day 6 (F) after infection. (G) WT C57BL/6 mice were infected with 10,000 TCID 50 X31 and treated with IRS661 or PBS intranasally. Survival

Supportive validation

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Experimental details: Figure 2. Modulation of epithelial TGF-beta and/or Ras/MAPK signaling in BCC-RM pos clones drive BST (A) scRNA-seq projection plots of tumor cells obtained from a nBCC analyzed for SCC (red) versus BCC (blue) enrichment score (left panel) and corresponding BCC-RM TACSTD2 , LYPD3 , and LY6D expression (right panels). scRNA-seq projection plots of tumor cells obtained from an additional nBCC sample are shown in Figure S2A . (B) RNA velocity analysis on tumor cells obtained from the nBCC shown in (A). Note the bidirectional nature of the BCC cluster C3 and SCC clusters C4 and C7. Main directionalities are emphasized using magnified red arrows. (C) Relative enrichment of the top-enriched gene lists obtained from clusters 3, 4, and 7 in human BCC (blue, n = 6), BSC (green, n = 3) and well-differentiated SCC (orange, n = 3) bulk RNA-seq. Left panel shows, at higher magnification, the scRNA-seq projection plot of clusters 3, 7, and 4 obtained from the nBCC shown in (A) and (B). Boxes represent the mean and the distribution of values from minimum to maximum. Markers associated with the indicated clusters are listed in Table S2 . (D) GSEA for cancer-related canonical pathways in clusters 4 and 7 compared to cluster 3 (full bars) and human well-differentiated SCCs compared to BCCs (empty bars). Blue and red bars indicate consistently reduced or enriched pathways, respectively. (E) TACSTD2, LYPD3, LY6D, GLI1, CD44, and MUC1 protein expression indicated by immunofluorescence staining on

Supportive validation

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Experimental details: Figure 4. The AP-1 family member c-FOS drives BST (A) H&E, GLI1, ARL13B (for primary cilia), CD44, and MUC1 staining of ASZ xenografted tumors upon c-FOS induction. (B) Quantification of GLI1, CD44, and MUC1 protein expression in (A) by pixel intensity measurements (n >= 40 cells, measured in n >= 3 fields, across n >= 3 tumors for each condition). Quantification of primary cilia (ARL13B) in (A) by the percentage of ciliated tumor cells (measured in n >= 6 fields, across n >= 3 tumors for each condition). (C) Schematic representation of in vivo intratumoral adenoviral-based induction of c-FOS using Ptch +/- ;K14-Cre-ER;p53 fl/fl ;RFP fl/STOP/fl mice. Lower panels show H&E, GFP, GLI1, and CD44 staining of BCC tumors upon vehicle, AAV6_GFP, or AAV6_GFP_cFos injection. Infection rate was determined as shown in Figures S4F , S4G , and S4I . (D) Quantification of SCC-like foci density shown in (C) (number of fields measured - n >= 10, across n = 2 tumors for each condition). (E) Quantification of GLI1 and CD44 protein expression shown in (C) by pixel intensity measurements (n >= 40 cells, measured in n >= 3 fields, across n = 2 tumors for each condition). (F) Relative enrichment for BCC signature (blue) and SCC signature (red) in RNA-seq data obtained from ASZ upon c-FOS induction (n = 2 biological replicates). RNA-seq profile and GSEA plots are shown in Figures S4K and S4L . (G) Enrichment of TF motifs in the regions with decreased (left) or increased (right) chromatin accessibil

Supportive validation

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Experimental details: Figure 5. EGFR/Ras/MAPK inhibitors partially reverse the transcriptional reprogramming of c-FOS-mediated BST (A) DAPI, GLI1, ARL13B (for primary cilia), and CD44 staining of ASZ cells upon 6 days of c-FOS induction (Dox ON), followed by 6 days of c-FOS removal (Dox ON/OFF). The right panels show the quantification of GLI1 and CD44 protein expression by pixel intensity measurements (n >= 40 cells, measured in n >= 3 fields for each condition) and primary cilia (ARL13B) by the percentage of ciliated tumor cells (measured in n >= 6 fields for each condition). (B) Toplist of cancer-related pathways or biological processes identified using GSEA in expBST UP signature. The x axis is -log 10 (p value) of the enrichment score. (C) Proportion (%) of genes having at least one ATAC peak enriched for the AP-1 or ETS motif, with decreased or increased accessibility in the proximity. p values calculated using proportional Z test. **p < 0.01. (D) Schematic depicting the c-FOS-driven BST model. (E) Dose-response curves of Gli1 and Cd44 expression in c-FOS-induced BST upon afatinib or UO126 treatment (n >= 4 biological replicates). EC 50 (half maximal effective concentrations) are indicated in red dotted lines. The upper panel depicts the experimental design. (F) Scatterplot of genes with differential expression upon c-FOS induction and afatinib or UO126 treatment (n = 2 biological replicates). Genes with expression fold change >= 1.5 and p < 0.05 are marked in red, while genes with expressio

Supportive validation

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Experimental details: Figure 6. Targeting EGFR/Ras/MAPK signaling pathway blocks BST (A) H&E, GLI1, ARL13B (for primary cilia), CD44, and MUC1 staining of ASZ xenografted tumors upon c-FOS induction and treatment with afatinib. (B) Quantification of GLI1, CD44, and MUC1 protein expression shown in (A) by pixel intensity measurements (n >= 40 cells, measured in n >= 3 fields, across n >= 3 tumors for each condition). Quantification of primary cilia (ARL13B) shown in (A) by the percentage of ciliated tumor cells (number of fields measured: n >= 6, across n >= 3 tumors for each condition). Horizontal bars and error bars represent the mean +- SD. p values calculated using one-way ANOVA with Tukey's post-test. ns, non-significant. *p < 0.05, ***p < 0.001. (C) GLI1 and CD44 expression fold change upon afatinib compared to DMSO treatment in human tumor explant (lower panels) and related to histopathological diagnosis (BCCs in blue, n = 6; BSCs in green, n = 6; and well-differentiated SCCs in orange, n = 4) and nuclear c-FOS expression (number of fields measured: n >= 2 per tumor). Upper panels show representative H&E, DAPI, and c-FOS staining of the human tumor explants used for the experiment. qRT-PCR error bars represent the SD from two technical replicates per sample. Immunofluorescence error bars represent the SD from individual measurements across one tumor sample. p values calculated using unpaired two-sided Student's t test. ns, non-significant. *p < 0.05. Scale bars in (A) and (C): 100 mum.

Supportive validation

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Experimental details: Fig. 5 QD-Cat-RGD-based RT for promoting DC maturation and antigen presentation in TDLNs and consequently inducing T cell-driven antitumor immunity. a Representative flow cytometric analysis images and relative quantification of co-stimulatory molecules CD80 + CD86 + gating on CD45 + CD11c + cells in TDLNs. b Representative flow cytometric analysis images and relative quantification of MHC-II expression on CD11c + CD45 + cells in the TDLNs. c Representative flow cytometric analysis images and relative quantification of CD3 + T cells gating on CD45 + in tumors. d Representative immunofluorescence images of tumors showing CD8 + T cells and relative quantification of CD8 + CD3 + T cells gating on CD45 + cells in tumors by flow cytometry. Scale bars = 50 mum. The immunofluorescent images were representative of those generated from three mice each group. e Representative flow cytometric analysis images and relative quantification of CD44 + CD62L + Tcm cells gating on CD8 + CD3 + CD45 + cells in the TDLNs. All data are presented as the mean +- s.e.m. ( n = 5 per group) and n represents the number of independent animals. Statistical significance was calculated via one-way ANOVA with Tukey's multiple comparisons test. FMO fluorescence-minus-one. TDLN tumor-draining lymph node. Source data are provided as a Source Data file.

Supportive validation

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Experimental details: Figure 3. Pik3cd E1020K/+ mice fail to develop a robust T CM population (A-F) Viable CD8 + splenocytes from mice infected with LCMV Armstrong (n = 2, 4-5/group/time point). (A-C) NP396-specific CD8 + cells day 15 p.i. (A) CD127 and KLRG1 expression (left: representative staining; right: %KLRG1 + CD127 - ). (B) Representative histogram of CD27 (top) and CD127 (bottom). (C) GzmB and TCF1 staining. Middle: TCF1 MFI; right: GzmB MFI. (D-F) NP396-specific CD8 + cells day 58 p.i. (D) CD44 and CD62L staining. Representative flow (left), % CD44 hi CD62L lo cells (right). (E) CD127 histograms: CD44 hi CD62L lo (top) and CD44 hi CD62L + (bottom). (F) TCF1 MFI. (G) TCF1 staining of allo-reactive CD8 + cells from healthy controls and patients with APDS (n = 2, representative histogram). (H-L) Mice were infected with X31 and challenged with PR8 (n = 2, 3-5 mice/genotype/time point). (H) Infection outline. (I) PA224-specific CD8 + cell numbers. (J) IFN-gamma and TNF-alpha from day 8 cells stimulated with either PA 224-233 (left) or anti-CD3 plus anti-CD28 (right). (K) NP366-specific CD8 + T cell numbers. (L) IFN-gamma and TNF-alpha from day 35 cells stimulated with either NP 366-374 (left) or anti-CD3 plus anti-CD28 (right). (M-O) OT-1 cells were transferred into congenic hosts, infected with influenza X31-OVA and challenged with PR8-OVA (n = 2, 3 mice/genotype/time point). (M) Outline. (N) Viable OT-1 cell numbers. (O) TCF1 and GzmB expression in OT-1 cells on day 35. Representative exper

Supportive validation

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Experimental details: Figure 1. Identification and characteristics of hPDLSCs. Morphological characterization of hPDLSCs in (A) primary culture and (B) culture at passage 3. A periodontal membrane fragment is present and shown in A. Flow cytometry analysis of surface markers expressed on hPDLSCs, showing that they were positive for (D) 0CD44, (F) CD90 and (G) CD105, and negative for (C) CD34 and (E) CD45. (H) Following 3 weeks of culture in osteogenic induction medium, the cells were stained with alizarin red. Mineralized nodules are shown. (I) Following 3 weeks of culture in adipogenic induction medium, the cells were stained with Oil Red O. Lipid globules are shown (black arrow). hPDLSCs, human periodontal ligament stem cells; PE, phycoerythrin.

Supportive validation

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Experimental details: Fig. 6 PSMD14 depletion reduces BMP6-mediated colorectal cancer stemness. (a, b) FACS analysis of CD133 + /CD44 + cells in PSMD14 - or ALK2 -depleted HCT116 cells, which were treated with 100 ng/ml BMP6 for 48 h. The proportion of the CD133 + /CD44 + fraction was described with the density plots (a) and a bar graph (b) . shGFP-expressing HCT116 cells were used as a control. (c) Sphere forming assay of PSMD14 - or ALK2 - depleted HCT116 cells. Spheres with a diameter above 50 mum were counted and described in a bar graph. Scale bars, 50 mum. (d) PSMD14 - or ALK2 -depleted HCT116 cells were treated with BMP6. Expression of pluripotent transcription factors were analyzed by immunoblotting with the indicated antibodies. siCON-expressing HCT116 cells were used as a control. (e, h) 2 x 10 4 cells of PSMD14 -, ALK2 -, ABCA7 - or ABCC4 -depleted HCT116 were respectively treated with 20 muM oxaliplatin and 30 muM DAPT and their viabilities were measured at 6 h. shGFP-expressing HCT116 cells were used as a control. (f, g) PSMD14 - or ALK2 -depleted HCT116 cells were treated with BMP6 for 6 h. Expressions of ABCA7 and ABCC4 were measured by quantitative RT-PCR. The data were statistically analyzed by two-way ANOVA followed by Bonferroni's multiple comparison test ( n = 3, *** P < 0.001 compared to the indicated controls. ns; not significant). The bars represent the mean +- s .d. The images in this figure are representative of three independent experiments. In (b), (c), (e) and (h) were

Supportive validation

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Experimental details: Figure 1. Immunophenotyping results of isolated and cultured bone marrow-derived mesenchymal stem cells. Surface markers by flow cytometry for (A) CD44, (B) CD71 and (C) CD34. CD, cluster of differentiation.

Supportive validation

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Experimental details: 10.1371/journal.pone.0232670.g005 Fig 5 Immunofluorescence staining of adhesion protein CD44 (red) and fibroblast marker TE-7 (green) of BJ cells on HOG film compared to no graphene (no matrix control). Cell nuclei were stained with Hoechst dye (blue). A positive staining for CD44 is an indication of cellular adherence to and movement on the HOG. Positive stain for TE-7 indicates fibroblast cells. HFF-1 fibroblasts were used as positive control for both CD44 and TE-7; MDA cancer cells was used as negative control for TE-7 on HOG. A more intense expression of CD44 was observed on HOG than on the control (with no graphene).

Supportive validation

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Experimental details: Figure 3. Expression of ALDH1, CD133 and CD44 prior to and following induction of differentiation in SP cells. SP or non-SP cells were incubated with anti-ALDH1, anti-CD133 and anti-CD44 antibodies together, and subjected to flow cytometry analysis. (A) Percentage of ALDH1 + , CD133 + or CD44 + cells in non-SP and SP cells prior to (day 0) and following differentiation (day 14). During flow cytometry analysis, Left, cells were analyzed for the expression of ALDH1 and CD133; Middle, cells were analyzed for the expression of ALDH1 and CD44; Right, cells were analyzed for the expression of CD133 and CD44. All these were conducted in the same population of SP or non-SP cells. (B) Percentage of only ALDH1 + cells in the same population of non-SP and SP cells in A prior to (day 0) and following differentiation (day 14). (C) Percentage of ALDH1 + cells in non-SP and SP cells prior to (day 0) and following differentiation (day 14) after three independent experiments. **P

Supportive validation

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Experimental details: Fig. 4 p16 expression activates Wnt-pathway-associated genes. a Diagram of transgenic mouse lines crossed for co-induction of GFP and p16. b FACS plots showing GFP levels and gates used for isolation of GFP + epidermal cells from K5-rtTA/tet-GFP/tet-p16 (right) and control K5-rtTA/tet-GFP (left) mice, after 6 months of induction. Plots show the CD31 - /CD140a - /CD45 - cell fraction only. c Gene sets whose expression was preferentially upregulated (blue) or downregulated (grey) in GFP + cells from p16-expressing mice relative to GFP + cells from control mice. Values indicate -log 10 (adjusted P value) by hypergeometric test. d mRNA levels of genes encoding cytokines and genes associated with the TGFbeta pathway upregulated in p16-expressing GFP + cells, measured by mRNA-seq. Values were normalized to the mean expression levels in GFP + cells from control mice, defined as 1. P < 0.05 for all genes, n = 4 samples per group, each pooled from 3 mice. e Relative mRNA levels of genes associated with the Wnt pathway in the same samples. P < 0.05 for all genes, n = 4 samples per group, each pooled from 3 mice. f Skin sections from K5-rtTA/tet-p16 and control tet-p16 mice treated with dox for 6 months stained for beta-Catenin, Tcf1, Cyclin D1 or CD44. Arrowheads indicate representative positively stained cells. g Percentages of nuclear beta-catenin + , Tcf1 + , and CyclinD1 + IFE cells in control and p16-expressing mice after 6 months of induction, as scored visually from images. P va

Supportive validation

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Experimental details: Figure 4 Protein expression of stem markers. The protein expression of five different stem markers was assessed in the FaDu adherent cell line and 7-day-old SCESM spheroids by Western blot and flow cytometry. ( a - d ) Protein expression analyzed by flow cytometry. Normalized fluorescence intensities of selected proteins are presented, and corresponding flow cytometry visible light and fluorescent photos are attached. Normalized mean values +- SE ( n >= 5, N >= 2000) are presented (**** p < 0.0001 vs. control (adh)); ( a ) CD44 protein expression; ( b ) CD73 protein expression; ( c ) CD90 protein expression; ( d ) CD133 protein expression; ( e ) OCT4 and tubulin protein expression analyzed by Western blot. Western blot membrane photos showing OCT4 and tubulin and a graph depicting normalized OCT4 protein expression analysis from Western blots are presented. Bars represent normalized mean values +- SE ( n >= 3). B: blank; adh: adherent cell line; S: SCESM.

Supportive validation

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Experimental details: Figure 5 Comparative analysis of SCESM spheroids and multi-cellular tumor spheroids (MCTSs). ( a ) Graph representing SCESM spheroid and MCTS mean diameter increase. Spheroids were photographed on days 2, 4, and 7 and representative phase-contrast microscope images of SCESM spheroids and MCTSs on days 2, 4, and 7 are displayed under the graph. Mean values +- SE ( n >= 8) are presented. Scale bars correspond to 400 um; ( b - e ) Protein expression of four different stem markers was assessed in SCESM spheroids and MCTSs by flow cytometry. Normalized fluorescence intensities of selected proteins are presented and corresponding flow cytometry visible light and fluorescent photos are attached ( n >= 5, N >= 2000); (b) CD44 protein expression; ( c ) CD73 protein expression; ( d ) CD90 protein expression; ( e ) CD133 protein expression; ( f ) OCT4 and tubulin protein expressions were assessed in SCESM spheroids and MCTSs by Western blot analysis. Western blot membrane photo showing OCT4 and tubulin and graph depicting normalized OCT4 protein expression analysis from Western blots (using Image Lab software) are presented ( n >= 3); ( g - i ) Relative gene expression of three additional stem markers assessed in 7-day-old MCTSs and SCESM spheroids; Normalized mean values +- SE ( n >= 5) are presented; ( g ) Relative gene expression of ALDH1A1 ; ( h ) Relative gene expression of NANOG ; ( i ) Relative gene expression of SOX2 . (* p < 0.05, **** p < 0.0001 vs. control (MCTS)). B: blank;

Supportive validation

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Experimental details: Figure 4 Diacerein effects on cancer stem cells. A: Quantification of CD44 and representative microphotographs of stained colon sections (magnification 40 x), scale bar: 50 um; B: Representative images of cancer stem cells (CSCs) cultured in serum or stem-selective conditions with or without diacerein (DAR) 100 mM in HT-29 and CACO-2 cells; C: Quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis of CSC markers CD133 and CD44 in parental cells and CSCs ( n = 3) in HT-29 and CACO-2 cells; D: Number of spheres in HT-29 and CACO-2 cells after treatment with interleukin (IL)-1beta (10 ng/mL) for 24 h ( n = 8); E: Quantitative RT-PCR analysis of CD44 and CD133 in parental cells and CSCs; Parental: cells cultivated with Dulbecco's modified Eagle's medium (DMEM) + IL-1beta (10 ng/mL); CSCs: cells cultivated with DMEM + IL-1beta (10 ng/mL, n = 3); F: Cell viability evaluated through MTT assay. Control: Cells cultivated with DMEM; DAR 50 mM, 100 mM, 200 mM and 300 mM: Cells cultivated with DMEM + DAR in different concentrations ( n = 3); G: Quantitative RT-PCR analysis of CD44, CD133 and IL-1beta in parental cells. Control: Cells cultivated with DMEM; DAR 100 mM: Cells cultivated with DMEM + DAR 100 mM ( n = 3); H: Quantitative RT-PCR analysis of CD44, CD133 and IL-1beta in CSCs. Control: Cells cultivated with DMEM; DAR 100 mM: Cells cultivated with DMEM + DAR 100 mM ( n = 3); I: Number of spheres in HT-29 and CACO-2 cells after treatment with DAR 100 mM or ve

Supportive validation

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Experimental details: Fig. 3 EZH2 deficiency in DCs inhibited the CD4 + T-cell response during bacteria-induced liver injury. Ezh2 D-/- mice and WT mice were injected intravenously with P.ac suspended in PBS. The peripheral blood, liver, or spleen were isolated from naive, Ezh2 D-/- mice and WT mice on day 7. Statistical analyses of the numbers of A MNCs isolated from livers and spleens and B the CD4 + T-cell percentage of MNCs are shown. C The levels of CXCR3 and CCR7 expressed on CD4 + T cells were analyzed by flow cytometry. D The levels of CD44 and CD62L on CD4 + T cells were analyzed by flow cytometry. E The levels of serum IFN-gamma, IL-5, and IL-17 were measured by enzyme-linked immunosorbent assay ( n = 8 mice per group). F The production of the inflammatory cytokine IFN-gamma by CD4 + T cells was assessed by intracellular staining and analyzed by flow cytometry. Representative dot plots are shown. G MNCs isolated from livers and spleens were stained for CD4 and Foxp3 and analyzed by flow cytometry. Data are shown as the mean +- SEM of three independent experiments. * P < 0.05.

Supportive validation

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Experimental details: Fig. 4 SRGN functions through its receptor CD44. A Co-immunoprecipitation of SRGN and CD44. RAW264.7 and GCTB-19 cells were cocultured in a ratio of 5:1 for 48 h. Cell lysates were immunoprecipitated with an anti-SRGN antibody followed by immunoblotting with anti-CD44 and anti-SRGN antibodies. B , C Osteoclast quantification ( B ) and representative images ( C ) of mouse primary bone marrow with the treatment of hFOB1.19 CM and the CD44 neutralizing antibody (10 ng/mL) in the osteoclastogenesis assay. D , E Osteoclast quantification ( D ) and representative images ( E ) of mouse primary bone marrow with the treatment of human recombinant SRGN protein (rhSRGN) and the CD44 neutralizing antibody (10 ng/mL). F Validation of CD44 knockout (KO) in RAW264.7 cells. G - J Osteoclastogenesis assay of RAW264.7 CD44 -knockout cells with treatment of hFOB1.19 CM ( G , H ) or human recombinant SRGN protein ( I , J ). Shown are the numbers of giant mature osteoclasts ( G , I ) and representative images ( H , J ). Scale bar, 100 mum. P values were obtained by two-tailed unpaired t test ( B , D , G , I ). Bar graphs are shown as mean +- s.d.

Supportive validation

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Experimental details: Fig. 5 SRGN activates focal adhesion kinase through CD44. A - D Western blot analysis of phosphorylated FAK protein level in RAW264.7 cells after treatment with CM from GCTB-1 ( A ) or GCTB-19 ( B ) with SRGN knockdown, CM from hFOB1.19 with SRGN overexpression ( C ), or human recombinant SRGN protein ( D ). E Western blotting analysis of phosphorylated FAK protein level in RAW264.7 cells after treatment with CM from hFOB1.19 with SRGN overexpression and the CD44 neutralizing antibody. F Western blotting analysis of phosphorylated FAK in RAW264.7 cells after treatment with human recombinant SRGN protein and the CD44 neutralizing antibody. G , H Western blotting analysis of phosphorylated FAK in RAW264.7 CD44 -knockout cells after treatment with CM from hFOB1.19 with SRGN overexpression ( G ) and human recombinant SRGN protein ( H ). I FAK phosphorylation levels in human GCTB samples with different levels of SRGN expression. Protein expression was scored as 0 (negative), 1 (weak), 2 (moderate) and 3 (strong) by immunohistochemistry staining ( n = 71 patients). Scale bar, 100 mum. P values were obtained by chi-squared test ( I ).

Supportive validation

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Experimental details: Figure 5 Forced expression of miR-125b-5p or knockdown of ATXN1 gene increases migration, invasion capability, and cancer stemness of HCC cell lines. ( a ) Representative image of the wound-healing assay in PLC/PRF5-miNC, PLC/PRF5-miR125b, and PLC/PRF5-R2-miNC cells (upper panel). The average migration distance was calculated from the wound healing area, and the time-dependent distance of migration is depicted in the lower panel (mean +- SD; n = 3). ( b ) Similarly, representative images of the wound-healing assay and time-dependent distance of migration in PLC/PRF5-siNC, PLC/PRF5-siATXN1, and PLC/PRF5-R2-siNC cells are shown in the lower panel (mean +- SD; n = 3). ( c ) Representative images of the invasion assay in PLC/PRF5-miNC, PLC/PRF5-miR125b, and PLC/PRF5-R2-miNC cells (left panel). The number of invading cells was counted, and the average numbers of invading cells are shown (right panel). ( d ) Similarly, representative invasion assay images and quantified invading cells in PLC/PRF5-siNC, PLC/PRF5-siATXN1, and PLC/PRF5-R2-siNC cells are shown. ( e ) Expression of CD44 and CD133 in PLC/PRF5-miNC and PLC/PRF5-miR125b cells was evaluated by two-color flow cytometry using mouse anti-human CD44 monoclonal antibody (APC) and mouse anti-human CD133 monoclonal antibody (PE). The percentage of CD44 + CD133 + cells based on the analysis of 10,000 cells is indicated. ( f ) Expression of CD44 and CD133 in PLC/PRF5-siNC and PLC/PRF5-siATXN1 cells was analyzed by flow cytometry and

Supportive validation

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Experimental details: Figure 1 Homozygous RhoA deletion in Treg cells leads to early, fatal spontaneous inflammatory disorders. (A) Survival outcome of RhoA +/+ Foxp3 YFP-Cre and RhoA Flox/Flox Foxp3 YFP-Cre mice. Results were analyzed with a log-rank (Mantel-Cox) test and expressed as Kaplan-Meier survival curves. (B) Image of lymphadenopathy in RhoA Flox/Flox Foxp3 YFP-Cre mice. Inguinal lymph nodes are shown. (C) Images of H&E staining of the indicated organs from RhoA +/+ Foxp3 YFP-Cre and RhoA Flox/Flox Foxp3 YFP-Cre mice (original magnification X 400). (D) Left, representative flow cytogram of CD44 and CD62L staining in CD4 + and CD8 + cells from the spleen of RhoA +/+ Foxp3 YFP-Cre and RhoA Flox/Flox Foxp3 YFP-Cre mice. The numbers indicate percentages of CD44 + , CD44 + CD62L + , and CD62L + cells. Right, average percentages of CD44 + , CD44 + CD62L + , and CD62L + cells. (E) Left, representative flow cytogram of IL-17, IFN-gamma, and IL-4 staining in CD4 + Foxp3 - cells from the spleen of RhoA +/+ Foxp3 YFP-Cre and RhoA Flox/Flox Foxp3 YFP-Cre mice. The numbers indicate percentages of IL-17 + , IFN-gamma + , and IL-4 + cells. Right, average percentages of IL-17 + , IFN-gamma + , and IL-4 + cells. (F) Left, representative flow cytogram of RORgammaT, T-bet and GATA3 staining in CD4 + Foxp3 - cells from the spleen of RhoA +/+ Foxp3 YFP-Cre and RhoA Flox/Flox Foxp3 YFP-Cre mice. The numbers indicate percentages of RORgammaT + , T-bet + , and GATA3 + cells. Right, average percentages of RORgam

Supportive validation

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Experimental details: Figure 1 Deletion of CD95 in 4T1 cells inhibits tumor growth and cancer stemness in BALB/c mice but not in NSG mice (A) Wild-type (vCas9) or CD95 k.o. 4T1 (mixture of clones #54 and #69) cells (10 5 ) were injected into the fat pad of NSG mice. Bioluminescence of tumors was quantified at the indicated times after injection of cells. (B and C) Equal numbers of WT (Parental or vCas9) or CD95 k.o. (#54 or #69) 4T1 cells were transplanted into the mammary fat pad of NSG mice, and tumor weight (B) and tumor volume (C) were measured after two weeks. (D) Wild-type (mixture of clones #3 and #4) or CD95 k.o. 4T1 (mixture of clones #10 and #12) cells (10 5 ) were injected into the mammary fat pad of NSG mice, and tumor volume was measured using a caliper. (E) ALDH1 activity and CD44 surface staining of single-cell suspensions of tumors isolated from NSG mice. n = 3 for each group. (F) IHC quantification of Ly6G positive cells in the WT and CD95 k.o. tumors monitored in (B). n = 3 biological replicates. (G) Equal numbers of WT (Parental or vCas9) or CD95 k.o. (1:1 mixture of #54 or #69) 4T1 cells were transplanted into the mammary fat pad of NSG mice, and tumor nodules of the primary tumor on the surface of the lungs were counted two weeks after transplantation. (H) The appearance of representative lungs analyzed in (G). Scale bar, 5 mm. (I) Luciferase expressing wild-type (cCas9) or CD95 k.o. 4T1 (mixture of two k.o. clones) cells (10 5 ) were injected into the mammary fat pad of BALB/

Supportive validation

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Experimental details: Figure 5. Rac1 inhibition enhances thymus regeneration and peripheral CD4 + naive T cell recovery after acute damage 6- to 8-week C57BL/6 WT or Nod2 -/- mice were treated with the Rac1 inhibitor EHT1864 (40 mg/kg i.p. injection) at days 3, 5, and 7 following a sublethal dose of TBI (550 cGy), and the thymus was analyzed on day 14. (A) Total thymic cellularity at day 14 after SL-TBI (WT, n = 20/treatment across 4 independent experiments; KO, n = 9-12 across three independent experiments). (B) Flow plots showing CD4 and CD8 expression at day 14 after SL-TBI (gated on CD45 + cells; plots were concatenated of all samples in each treatment group from one experiment). (C) Total number of DP, SP4, or SP8 thymocytes (n = 20/treatment across 4 independent experiments). (D) Expression of miR29c analyzed by qPCR on whole thymic tissue (n = 5/group). (E) Total thymic amounts of BMP4 and IL-23 assessed by ELISA at day 7 (n = 4-5/group, representative of two independent experiments). (F) Total number of cTECs and mTECs (n = 15/group across three independent experiments). (G) Flow plots showing CD4 and CD8 expression in the spleen at day 56 after SL-TBI (gated on CD45 + CD3 + cells). (H) Total number of CD4 + and CD8 + T cells in the spleen at d56 (n = 5/group). (I) Plots of CD62L and CD44 on CD4 + and CD8 + T cells (gated on either CD45 + CD3 + CD4 + CD8 - or CD45 + CD3 + CD4 - CD8 + ) cells; plots concatenated of all samples in a given experiment). (J) Ratio of number of naive (CD62L hi C

Supportive validation

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Experimental details: Fig. 2 GPR120 reduced CD4 + T cell responses in mice with liver injury. Wild-type (WT) and GPR120 -/- (GPR120 KO) mice were injected with P. acnes (P.ac). Vehicle or TUG891 (10 mg/kg) was administered i.p. to WT mice on days 0, 2, 4, and 6 after P. acnes injection. Livers and spleens were isolated on day 7 ( n = 7 mice per group). a Absolute numbers of total MNCs in livers and spleens were analyzed by flow cytometry. b Percentages of CD4 + T cells in total MNCs in livers and spleens were analyzed by flow cytometry. c The expression levels of CD44 and CD62L in CD4 + T cells in the livers and spleens were analyzed by flow cytometry. d On day 6 after priming, BrdU was injected i.p. into the mice. MNCs were isolated from livers and spleens the next day. Cells were stained for CD4 and BrdU. The frequencies of CD4 + BrdU + T cells in the livers and spleens were determined by flow cytometry. e The percentages of TNF-alpha + , IFN-gamma + , and Foxp3 + cells in CD4 + T cells were assessed by intracellular staining and flow cytometry. f The levels of serum TNF-alpha, IFN-gamma, IL-4 and IL-10 were measured by enzyme-linked immunosorbent assay. The results are representative of three to six independent experiments and presented as the mean +- SEM. Significant differences were analyzed by One-way ANOVA. * p < 0.05, ** p < 0.01, *** p < 0.001, ns no significance.

Supportive validation

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Experimental details: Fig. 3 GPR120 had no effects on the activation, proliferation, and differentiation of CD4 + T cells in vitro. T cells were isolated from the spleens of wild-type (WT) mice and GPR120 -/- (GPR120 KO) mice. T cells were cultured (2 x 10 5 cells/well) in the presence of anti-CD3 and anti-CD28 antibodies. T cells from WT mice were treated with DMSO, TUG891 (20 muM) with or without AH7614 (20 muM). a , b The expression levels of CD25, CD44, CD62L, and CD69 on CD4 + T cells were analyzed by flow cytometry. c , d Frequencies of the proliferating (CFSE low ) CD4 + T cell proliferation in response to the indicated treatments were measured by flow cytometry. e , f CD4 + T cells were stained for the surface marker CD4 and intracellular expression of TNF-alpha and IFN-gamma on day 5 and analyzed by flow cytometry. g , h CD4 + T cells were stained for the surface marker CD4 and intracellular expression of Foxp3 on day 5 and analyzed by flow cytometry. The results are representative of three independent experiments and presented as the mean +- SEM. Significant differences were analyzed by One-way ANOVA. ns no significance.

Supportive validation

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Experimental details: Figure 5 TNF superfamily members CD153 and CD30 are specifically expressed in SAT cells and ABCs, respectively, inside of TLTs in aged injured kidneys. ( A ) Dot plot of ligand-receptor interactions related to TNF superfamily members between 6 CD4 + T cell subpopulations and 3 B cell subpopulations identified by scRNA-Seq (see Figure 3 ). ( B ) Violin plots showing the expression of Tnfsf8 and Tnfrsf8 in all CD45 + cells. The putative identities of each cluster are specified in the box. DN, double-negative. ( C ) UMAP plot of Tnfsf8 and Tnfrsf8 in CD45 + cells in Figure 2B and enlargement of those of Cd4 , Tnfsf8 , Spp1 , Sostdc1 , Il21 , and Il10 , and those of Cd19 , Cr2 , Tbx21 , and Tnfrsf8 . ( D ) Representative FACS plots of CD153 expression on T cells, B cells, macrophages, dendritic cells, CD4 + T cells, CD8 + T cells, CD44 hi CD4 + T cells, and PD-1 + CD4 + T cells ( n = 3/group). ( E ) Representative FACS plots of CD30 expression on T cells, B cells, macrophages, and dendritic cells ( n = 2/group). ( F ) Plasma soluble CD30 (sCD30) levels of young and aged mice with or without (not treated, NT) ischemic reperfusion injury (IRI) induction ( n = 3/group, samples were collected 45 days after IRI). Data are presented as mean +- SD. Statistical significance was determined by 1-way ANOVA with Bonferroni's post hoc analysis. *** P < 0.001. ( G ) Violin plots showing the expression of Adam10 and Adam17 among 3 B cell subsets identified by scRNA-Seq. ( H ) Representative ISH

Supportive validation

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Experimental details: Figure 7 SLC27A6 expression positively correlates with CD24 and CD44 expression level in NPC cells. (A) Positive correlation between the mRNA expression of SLC27A6 and CD24 in NPC cells (HONE1, R=0.95; 5-8F, R=0.99) by qRT-PCR. (B) No significant difference was shown between the SLC27A6 and CD34 mRNA expression in HONE1 (left panel), while a negative correlation was seen in 5-8F (right panel). (C) Positive correlation between the mRNA expression of SLC27A6 and CD44 in NPC cells (HONE1, R=0.98; 5-8F, R=0.97) by qRT-PCR. (D) The CD44 expression levels in HONE1 (left panel) and 5-8F (right panel) stably transfected cells were measured by flow cytometry. NS, no significance > 0.05; * P < 0.05; ** P < 0.01; *** P < 0.001.

Supportive validation

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Experimental details: Figure 5 CD44 protein expression analyzed by flow cytometry. (A) CD44 regulation by ruxolitinib treatment. The CD44 expression profiles of ruxolitinib-treated myxoid liposarcoma (MLS) 402-91 cells compared with control cells treated with DMSO are shown as an example (left panel). Mean CD44 expressions in ruxolitinib-treated MLS (402-91, 2645-94, and 1765-92) and fibrosarcoma [HT1080 wild-type (WT), HT1080 EGFP, and HT1080 FUS-DDIT3-EGFP] cells are shown (right panel). **** p < 0.0001, paired Student's t -test. (B) CD44 regulation by anoikis resistance. The CD44 expression profiles of anoikis-resistant MLS 402-91 cells in comparison to control cell cultures in monolayer are shown as example (left panel). Mean CD44 expressions in anoikis-resistant cells compared with control cells for MLS (402-91, 2645-94, and 1765-92) cells are shown (right panel). * p < 0.05, paired Student's t -test.

Supportive validation

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Experimental details: Stemness properties of LGR5 + U251 cells in vivo. a Xenografts produced by LGR5 + and LGR5 - U251 cells. b The subcutaneous xenografts growth curve generated by LGR5 + and LGR5 - U251 cells in BALB/c-nu mice (two-way ANOVA, P < 0.001). Data are shown as the mean +- SD (LGR5 + U251: n = 5, LGR5 - U251: n = 5). c IHC staining of LGR5, Ki67, N-cadherin, CD44 and SOX2 expression in LGR5 + xenografts and LGR5 - xenografts (magnification x 200). d The percentage of positive expression of LGR5, Ki67, N-cadherin, CD44 and SOX2 in LGR5 + xenografts and LGR5 - xenografts ( n = 5, Student t test). Error bars represent the mean +- SD. e The correlation between the levels of LGR5 and Ki67 by Spearman correlation analysis ( P < 0.01, r = 0.7794, n = 10). f The correlation between the levels of LGR5 and N-cadherin by Spearman correlation analysis ( P < 0.01, r = 0.8424, n = 10). g The correlation between the levels of LGR5 and SOX2 by Spearman correlation analysis ( P < 0.001, r = 0.8788, n = 10). h The correlation between the levels of LGR5 and CD44 by Spearman correlation analysis ( P < 0.05, r = 0.6970, n = 10). i Double-staining of LGR5 and N-cadherin in U251 subcutaneous xenografts. The xenografts edge (3 and 4) showed many positive cells expressed both LGR5 and N-cadherin, while there was few positive cells in inside xenografts (section "" Methods ""). Scale bar = 100 mum. *, P < 0.05; **, P < 0.01; ***, P < 0.001

Supportive validation

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Experimental details: Effect of LGR5 on intracranial tumor growth and overall survival time of xenograft mice. a T2W images of intracranial tumor in coronal views scanned using 7.0 T MRI on days 12, 25 and 39 after U251-GSCs injection. b The intracranial tumor growth curve of the shLGR5 ( n = 5), Wnt-C59 ( n = 5) and shCtrl ( n = 5) U251-GSCs. Error bars represent the mean +- SD ( n = 5, two-way ANOVA). c Overall survival time (OS) of xenograft mice in the shLGR5 ( n = 5), Wnt-C59 ( n = 5) and shCtrl ( n = 5) U251-GSCs analyzed by Log-rank test. d IHC staining and quantitative analyses of LGR5, Ki67, Active-beta-catenin, SOX2 and CD44 (magnification x 200). e Spearman correlation analysis of LGR5 and Active-beta-catenin between shLGR5 and shCtrl U251-GSCs ( P < 0.001, r = 0.8940, n = 10). f Spearman correlation analysis of LGR5 and Ki67 between shLGR5 and shCtrl U251-GSCs ( P < 0.01, r = 0.7803, n = 10). g Spearman correlation analysis of LGR5 and SOX2 between shLGR5 and shCtrl U251-GSCs ( P < 0.01, r = 0.8182, n = 10). h Spearman correlation analysis of LGR5 and CD44 between shLGR5 and shCtrl U251-GSCs ( P < 0.01, r = 0.8788, n = 10). i T2W images of intracranial tumor in coronal views scanned using 7.0 T MRI on days 10, 20 and 36 after 8591-GSCs injection. j The intracranial tumor growth curve of the shLGR5 ( n = 5), Wnt-C59 ( n = 5) and shCtrl ( n = 5) 8591-GSCs. Error bars represent the mean +- SD ( n = 5, two-way ANOVA). k Overall survival time (OS) of xenograft mice in the shLGR5 ( n = 5), W

Supportive validation

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Experimental details: 5 FIGURE (A) FACS analysis for CD44 or Sca-1-positive subpopulations in primary #1 cells after Wnt small-molecule inhibitors for 24 h. CWP291, 1 uM CWP232291; BC21, 10 uM BC21; CCT, 20 uM CCT031374; PKF, 2 uM PKF 118-774; Cisplatin, 1 uM cisplatin. Right, representative FACS images showing reduced CD44 or Sca-1-positive cells in primary #1 cells after CWP232291 treatment. (B) Sphere-forming assay showing reduced tumorsphere formation from primary #1 cells after the treatment for 7 days with Wnt inhibitors. The spheres greater than 100 mm of diameter were enumerated. Right, representative images of tumor spheres after the treatment with Wnt inhibitors. (C) CWP232291 inhibited primary (with CWP232291) and second sphere formation (without CWP232291) in primary #1 and SW620. (D) Representative images of tumorspheres from primary #1 cells of (C). (E) Representative IF images for CD133, Lgr-5, and Sca-1, putative mouse intestinal cancer stem cell markers, in vehicle- or CWP232291-treated allografts of SCID mice. SCID mice injected with primary #1 cell were treated with 100 mg/kg CWP232291 twice a week for 8 weeks. Bottom, IF scoring for CD133, Lgr-5, and Sca-1-positive tumor cells in vehicle- ( n = 3) or CWP232291-treated ( n = 3) allografts. Bar = 100 um. (F) FACS analysis for CD133 in CWP232291- or vehicle-treated allografts. Single cell suspensions were obtained from allografts after dispase digestion. FACS, fluorescence-activated cell sorting; IF, immunofluorescence. * p < 0.05

Supportive validation

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Experimental details: Figure 2. Characterization of HT29 3D cell culture. A: Aggregation and spheroid growth process on stirred culture system and live/dead assessment (FDA - green; PI - red, respectively) at days 3, 5, and 7 of culture. Diameter distribution of colon cancer spheroids along the culture time; data are mean +- SD of four independent experiments. Scale bar = 300 mm. B: Phenotypic characterization of HT29 spheroids and 2D culture, namely, detection of hypoxic regions (pimonidazole - Hypoxyprobe), apoptosis (NuncView), CD44 and cytokeratin 18 (CK18) along culture time (days 3 and 7 of culture, corresponding to average aggregate diameter of 300 and 500 um, respectively). Cell nuclei were stained with DAPI. Analyses were performed on cryosections (10 mm thickness). Scale bar = 100 mm. C: Flow cytometry analysis of HT29 cells: percentage of ALDH + cells of 2D cell culture and HT29 spheroids collected at days 3 and 7. The left side shows the dot-blot of Aldefluor assay with inhibitor (DEAB) and the right side shows the dot-blot without inhibitor. The ALDH + cell population is identified in green. D: Percentage of ALDH + cells determined on 2D and 3D cell culture. Data are mean +- SD of at least 5 independent experiments performed in triplicates: Asterisks indicate significant differences relative to 2D culture (*** P < 0.001, **** P < 0.0001) by one-way ANOVA analysis with Tukey's post multiple comparison tests.

Supportive validation

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Experimental details: Fig. 4 N2-converted neutrophils inhibit T cell proliferation, activation and Th1 differentiation. a Representative flow cytometry plots and percentage of the indicated T cell subsets in the pre-metastatic lung ( n = 6 mice in each group). b CFSE-labeled CD4 + or CD8 + splenocytes were stimulated with anti-CD3/CD28 antibodies and mixed without (BLANK) or with neutrophils purified from lungs of tumor-bearing mice. The percentage of proliferating T cells is shown ( n = 6 culturing experiments). c CFSE-labeled OT-1 splenocytes (CD8 + ) were mixed with OVA 257-264 -pulsed bone marrow-derived DCs and neutrophils as in panel b. The percentage of proliferating T cells is shown ( n = 6 culturing experiments). d CD4 + and CD8 + T cells in the pre-metastatic lung were subjected to CD44 and CD62L staining. Representative contour plots and summary data were shown ( n = 6 mice in each group). e The expression of IFN-gamma and TNF-alpha were analyzed in CD4 + and CD8 + T cells in the pre-metastatic lung ( n = 6 mice in each group). f CD4 + and CD8 + T cells were purified from naive mice's spleen stimulated with anti-CD3/CD28 antibodies and mixed with the indicated neutrophils. Twenty-four hours later, the cell fraction adopting a CD44 + CD62L - phenotype was determined by flow cytometry ( n = 6 culturing experiments). g Naive CD4 + T cells were stimulated under Th1-stimulating conditions in the presence of the indicated lung neutrophils. Four days later, the cells were re-stimulated with PM

Supportive validation

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Experimental details: Figure 3 Isolation and characterization of interstitial stem cells from murine skeletal muscle. Gating strategy for FACS (fluorescent activated cell sorting) isolation of murine MABs (mesoangioblasts) and FAPs (fibro/adipogenic progenitors) ( A ) and control gates ( B ). ( C ) qPCR analysis of characteristic genes; values shown as relative expression to Rpl13a . n = 4-6. ( D , E ) Flow cytometry analysis of characteristic markers. MAB in orange ( D ), FAP in blue ( E ) and unstained control samples in grey. ( F ) Microscopy images of adipogenic differentiation; nuclei are stained with Hoechst (blue), lipids are stained with Oil Red O (red) and adipocytes are stained with Perilipin (green). ( G ) Microscopy images of myogenic differentiation from the co-culture of mouse MAB or FAP and satellite cells; Myotubes are stained with MyHC (red), MAB or FAP are stained with GFP (green) and nuclei are stained with Hoechst (blue). In ( E , F ), scale bar, 50 um. * p

Supportive validation

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Experimental details: Figure 1 Characterization of bone marrow-derived mesenchymal stem cells (MSC) isolated from mTmG mice. ( A ) Plastic adherent cells were ex vivo expanded until passage 10, maintaining red fluorescent (RFP) expression throughout. ( B ) MSCs differentiated into osteogenic (alizarin red staining), adipogenic (oil red staining), and chondrogenic (alcian blue staining) lineages. Scale bars represent 200 um. ( C ) Flow cytometry analysis for immunophenotyping showed that MSCs, in passages 7-8, were positive for CD 29 (98.8%), SCA-1 (98.2%), CD 44 (6.02%), CD 90 (4.18%), and CD 105 (4.97%), and negative for CD34 (0.49%), CD 45 (1.37%), and CD 31 (0.05%).

Supportive validation

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Experimental details: 7 Figure Fracture callus TSP2 positive cells express a MSC immunophenotype. Transverse femoral fractures were induced in TSP2-GFP reporter mice. Calluses from six mice were harvested 7 days post-fracture, pooled, and digested in trypsin, collagenase A, and hyaluronidase. Cells were labeled with anti-mouse directly conjugated MSC antibodies (CD44, CD105, CD45, and Sca-1) and DAPI before flow cytometry. A, Cells were gated by size and granularity using an SSC-A/FSC-A color density plot. Single cells were sub-gated by FSC-W/FSC-A and dead (DAPI+) cells were discriminated by sub-gating on a DAPI-A/SSC-A. B, Included cells were gated by GFP-A as either T2GFP-neg (red) or T2GFP-pos (green). C, Representative histograms of cell surface markers in T2GFP-pos cells. D, Representative histograms of cell surface markers in T2GFP-neg cells. Histograms were gated for positive selection of CD44, CD105, and Sca-1 and negative selection of CD45 to match the known MSC immunophenotype of CD44+/CD105+/CD45-/Sca-1+. Flow cytometry was repeated two times with an n = 2 per experiment. MSC, mesenchymal progenitor cells; TSP2, thrombospondin-2 [Color figure can be viewed at wileyonlinelibrary.com ]