Fig 2: SEMA7A and ITGB1/ITGA6 promote features of transformation and chemoresistance.a %Celltrace violet bright of singlets in MCF10A EV and OE cells. b, c Number of mammospheres formed by MCF12A cells ± S7a and GoH3 or 9eg7. d Number of colonies formed in soft agar assay. e–g 10ADCIS KD or OE mammospheres cultured in paclitaxel ± 9eg7 or GoH3. e Number of mammospheres. f %CD44 + CD24- of singlets by flow cytometry. g Representative images, ×20 magnification.

Fig 3: SEMA7A is upregulated in multiple breast cancers and predicts for decreased relapse-free survival when expressed with a6-integrin.a–d TCGA data for SEMA7A in a normal (n = 114) vs primary tumor (1097) b normal versus stages I–IV (I: n = 183, II: n = 615, III: n = 247, IV: n = 20) c normal versus cancer stratified by age (21–40: n = 97, 41–60: n = 505, 61–80: n = 431, 81–100: n = 54), d normal versus breast cancer subclass (luminal: n = 566, HER2+: n = 37, TNBC-BL1: n = 13, TNBC-BL2: n = 11, TNBC-IM: n = 20, TNBC-LAR: n = 8, TNBC-MSL: n = 8, TNBC-M: n = 29, TNBC-UNS: n = 27) Error bars indicate mean ± standard error of the mean. Significance denoted as: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. e Kaplan–Meier 5-year relapse-free survival analysis for SEMA7A in ITGA6 low (n = 2032) or high (n = 2032) expressing patients.

Fig 4: High-fat diet induces heightened ERVs expression and T cells responses following S. epidermidis colonization, related to Figure 5WT mice were fed either a control (Ctrl) or a high-fat (HF) diet for 6 weeks and then topically associated with S. epidermidis (S. epi) or left unassociated. (A) Body weight measurement (g ± SEM) in mice after 6 weeks of diet regimen. (B) Representative image of hematoxylin-and-eosin staining of the ear pinnae from mice after 8 weeks of diet regimen. Scale bars = 300 µm or 50 µm (zoom in). (C) Frequency and absolute number of CD49f+Ki-67+ keratinocytes in the ear pinnae of unassociated (Unassoc.) and S. epidermidis (S. epi)-associated mice fed a control (Ctrl) or high-fat (HF) diet at day 14 post association. (D) Flow cytometry analysis of MHC-II expression and absolute number of CD49f+MHC-II+ and CD49f+MHC-II+Ki-67+ keratinocytes from unassociated (Unassoc.) or S. epidermidis (S. epi)-associated mice fed a control (Ctrl) or high-fat (HF) diet at 14 days post association. Plots in (C) and (D) were gated on live CD45–CD31–CD34–Sca-1+ cells. * in the flow plot indicates significant difference between unassociated and S. epi group. (E) Frequency of IL-17A+ or IFN-?+ CD8+ or CD4+ T cells and IL-17A+ ?dTCRlow or MAIT cells in the ear pinnae from unassociated and S. epidermidis-associated mice fed a control (Ctrl) or a high-fat (HD) diet. All cells were stimulated with PMA and ionomycin. (F) Gene ontology assignments of top 3 or top 2 GO terms that were enriched in Sca-1+CD49f+ keratinocytes from WT mice fed a high-fat diet versus control diet and from S. epidermidis-associated (day 7) WT fed a high-fat diet versus control diet, respectively. (G) Heatmap showing transcript levels of the indicated ERVs measured by qRT-PCR of mRNA isolated from ear pinnae from unassociated or S. epidermidis-associated mice fed a high-fat (HF) diet at day 7 post association. Values were normalized to Gapdh expression in the same sample. (H) MLV SU expression detected by flow cytometry on the surface of Sca-1+CD49f+ keratinocytes from unassociated (Unassoc.) or S. epidermidis-associated mice fed a high-fat diet at day 7 post association. (I and J) WT mice were treated with imiquimod (IMQ) cream for 5 consecutive days or not (control). (I) Differential ERV levels analyzed by RNaseq in the ear pinnae 5 days after the beginning of IMQ treatment. Data was reanalyzed from our published study (Hurabielle et al., 2020). **** FDR ? 0.0001. (J) MLV SU expression detected by flow cytometry on the surface of Sca-1+CD49f+ keratinocytes from the ear pinnae 5 days after the beginning of IMQ treatment. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 as calculated with Student’s t test (A), (H) and (J) or two-way ANOVA with Holm-Šidák multiple comparison test (C), (D) and (E). Data are represented as mean ± SEM. Each dot (A), C-E, H-J) represents an individual mouse. Data are representative of two (B), (F), (G), (H), (I) and (J) or three (A), (C), (D) and (E) independent experiments using 4-5 mice per group.

Fig 5: Semaphorin-7a promotes survival via integrins and enriches for pAKT+ cells.a–e Flow cytometry analysis of mammary glands from WT (left, I1: n = 4, I2: n = 6, I3: n = 5, I6: n = 4 glands/group) and SEMA7Atm1Alk/J (right, I1-I6: n = 6 glands/group) mice. a Stratification of MEC subtypes by EpCAM/CD49f staining. b %EpCAMhiCD49f + LPCs of EpCAM+ cells. c %SEMA7A+ of live (Aquazombie-) EpCAMhiCD49f + LPCs. d %ITGB1 + ITGA6+ of EpCAM cells. e %SEMA7A of ITGB1 + ITGA6+ cells. f CC3/7 expression in MCF12A cells ± S7a and/or GoH3. g %pAKT in MCF12A cells ± S7a and/or 9eg7/GoH3, n = 3. Error bars indicate mean ± standard error of the mean. Significance denoted as: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.