SUPPLEMENTARY INFORMATION

doi:10.1038/nature22977 Supplementary Data 1 Fig. 4d + CM (no MDK) + CM (MDK) 10 15 30 1h 12h 24h 10 15 30 1h 12h 24h P- P- Fig. 4e CM GoF CM LoF-M5 CM GoF MDK - + + - + + + Vehicle - + + - + + + Rapamycin - - - - - + - Torin 1 - - - - - - + VEGFR3 P- β-actin 2 1 100-75- 15-10- 5-2- VEGFR3 P- β-actin 2 1 100-75- WWW.NATURE.COM/NATURE 1

RESEARCH SUPPLEMENTARY INFORMATION Supplementary Table S1 Line Stage BRAF PTEN N-ras c-kit CDK4 MET V600E WT WT WT WT WM35 RGP V600E Mutant WT WT WT WM902B MET V600E WT WT WT WT WM115 VGP V600D Hem Del WT WT WT 451LU Xenograft MET V600E WT WT WT WT UACC-62 MET V600E Mutant WT WT WT SK-Mel-28 MET V600E MU WT WT R24C SK-Mel-103 MET WT WT Q61R WT WT SK-Mel-147 MET WT WT Q61R WT WT Table S1. Human melanoma cell lines used in this study. Genetic information are as described in Soengas et al. Nature 2001 and http://www.wistar.org/lab/meenhard-herlyn-dvm-dsc/page/melanoma-cell-lines-0. 2 WWW.NATURE.COM/NATURE

RESEARCH Supplementary Table 2 Gene symbols 451LU vs SK-Mel-103 vs SK-Mel-28 vs MDK 5.34 3.91 2.37 PRRT2 4.11 7.36 10.35 PROCR 4.10 5.49 5.32 RPL12 3.75 3.20 3.34 RPL28 3.40 1.93 1.66 AGRN 3.38 2.24 3.45 CD9 3.24 1.70 1.77 SDC1 3.12 5.50 3.83 TMSB10 2.81 3.38 3.19 IGF2BP3 2.61 4.54 3.86 IGF2BP1 2.53 3.26 2.75 CTSZ 2.35 2.30 1.75 RNPEP 2.28 2.91 1.96 CALU 2.19 1.26 2.30 ILF2 2.09 5.76 4.29 HNRNPK 2.05 2.42 2.36 RPS15A 2.05 3.81 1.08 TUBB4A 1.94 1.52 1.67 DBN1 1.86 1.30 1.44 SRP14 1.84 9.13 7.88 CAPNS1 1.74 1.66 1.19 ITGB5 1.72 2.61 2.46 RBM3 1.61 5.83 4.60 PLAUR 1.60 3.98 3.18 RHOB 1.58 1.99 1.62 ALCAM 1.53 5.14 3.89 FLG2 1.52 4.02 5.16 CBR1 1.45 0.82 0.77 RPL31 1.45 1.12 1.05 RPS3A 1.43 1.62 1.44 LGALS1 1.39 1.34 1.67 RPS23 1.37 1.13 0.92 TUBB3 1.29 1.15 0.74 RPLP0 1.14 1.48 0.70 RPS3 1.14 1.33 0.72 RUVBL1 1.11 1.28 1.04 HSD17B12 1.07 1.42 2.31 PSMD14 1.01 0.97 1.14 RPLP2 1.00 1.96 1.57 TUBA1C 0.96 1.60 1.28 TAOK3 0.91 2.01 2.40 MARCKSL1-0.98-1.43-1.12 IGF1R -2.21-2.75-1.12 DAAM2-2.49-2.14-2.12 FXYD3-4.99-2.05-1.56 Table S2. Pro-metastatic factors identified by proteomic analyses of the secretome of the indicated cell lines. Shown are differential ratios of protein expression (Log2 scale) estimated with respect to basal levels in the nonlymphangiogenic cell line. Additional filters were applied to remove factors present in the non-metastatic WM35, which does not activate distal lymphangiogenesis. WWW.NATURE.COM/NATURE 3

RESEARCH SUPPLEMENTARY INFORMATION Supplementary Table 3 MDK/NEG UP & shm1/shc DOWN & shm5/shc DOWN MDK/NEG DOWN & shm1/shc UP & shm5/shc UP MDK/NEG shm1/shc shm5/shc MTOR_UP.N4.V1_UP <0.001 <0.001 <0.001 HINATA_NFKB_IMMU_INF <0.001 <0.001 <0.001 LTE2_UP.V1_DN <0.001 0.001 0.026 STK33_UP <0.001 0.006 <0.001 EGFR_UP.V1_UP <0.001 <0.001 <0.001 CAMP_UP.V1_UP <0.001 0.001 <0.001 BMI1_DN_MEL18_DN.V1_UP <0.001 <0.001 0.002 E2F1_UP.V1_DN <0.001 0.003 <0.001 HOXA9_DN.V1_UP 0.001 0.009 <0.001 ALK_DN.V1_UP 0.002 0.003 0.016 MEL18_DN.V1_UP 0.004 0.001 0.022 RB_P107_DN.V1_DN 0.012 0.200 <0.001 ESC_J1_UP_EARLY.V1_DN 0.012 0.197 0.004 KRAS.300_UP.V1_DN 0.025 0.007 0.034 RPS14_DN.V1_UP 0.028 0.014 0.026 SIRNA_EIF4GI_UP 0.029 0.022 0.002 DCA_UP.V1_UP 0.066 0.199 0.206 P53_DN.V2_UP 0.120 0.022 0.165 IL15_UP.V1_DN 0.123 0.198 0.130 VEGF_A_UP.V1_UP 0.140 <0.001 <0.001 CAHOY_ASTROGLIAL 0.220 0.003 0.093 HINATA_NFKB_MATRIX 0.249 0.001 0.034 RB_P107_DN.V1_UP <0.001 <0.001 <0.001 PRC2_EDD_UP.V1_UP <0.001 <0.001 <0.001 CSR_LATE_UP.V1_UP <0.001 <0.001 <0.001 HOXA9_DN.V1_DN <0.001 0.003 0.002 E2F3_UP.V1_UP <0.001 <0.001 <0.001 E2F1_UP.V1_UP <0.001 <0.001 <0.001 MEK_UP.V1_UP <0.001 0.002 <0.001 LTE2_UP.V1_UP <0.001 0.004 <0.001 RPS14_DN.V1_DN <0.001 <0.001 <0.001 EGFR_UP.V1_DN <0.001 <0.001 <0.001 KRAS.DF.V1_UP <0.001 <0.001 <0.001 GCNP_SHH_UP_EARLY.V1_UP <0.001 <0.001 <0.001 TBK1.DF_UP <0.001 0.002 0.012 RB_DN.V1_UP <0.001 0.005 <0.001 ERB2_UP.V1_UP <0.001 0.002 0.001 GCNP_SHH_UP_LATE.V1_UP <0.001 <0.001 <0.001 PRC2_EZH2_UP.V1_UP <0.001 0.004 <0.001 VEGF_A_UP.V1_DN <0.001 <0.001 <0.001 ESC_V6.5_UP_LATE.V1_UP <0.001 0.229 0.172 RAF_UP.V1_UP 0.001 0.008 0.033 PDGF_UP.V1_UP 0.001 <0.001 0.002 P53_DN.V1_UP 0.001 0.001 0.001 IL21_UP.V1_DN 0.004 0.168 0.020 CRX_NRL_DN.V1_UP 0.005 0.215 0.017 KRAS.AMP.LUNG_UP.V1_UP 0.008 0.012 0.042 PRC2_SUZ12_UP.V1_UP 0.009 0.046 <0.001 PRC1_BMI_UP.V1_UP 0.013 0.008 0.001 ALK_DN.V1_DN 0.013 0.047 0.023 ATF2_UP.V1_UP 0.016 0.132 0.051 SRC_UP.V1_DN 0.031 0.024 0.042 PRC2_EZH2_UP.V1_DN 0.034 0.054 0.027 SIRNA_EIF4GI_DN 0.040 0.143 0.126 ATM_DN.V1_DN 0.043 0.228 0.011 TBK1.DN.48HRS_UP 0.055 0.116 0.052 PDGF_ERK_DN.V1_DN 0.085 0.106 <0.001 LEF1_UP.V1_UP 0.100 0.054 0.041 NRL_DN.V1_UP 0.148 0.171 0.010 Table S3. Signaling pathways identified by RNA seq to be controlled by MDK in lymphatic endothelial cells (LEC). Transcriptomic analyses were performed in MDK gain or loss of function studies (LoF and GoF) as indicated in Fig. 5a,b. Shown are Oncogenic Signatures found by gene set enrichment analyses (GSEA) to show a consistent (opposed) alterations in both settings. FDR for each gene set are shown. MDK/Neg, stands for comparative analyses of overexpressing MDK vs the parental (MDK negative control). shm1/shc and shm2/shc correspond to data from SK-Mel-147 expressing MDK sh1 or sh5, respectively, and analyzed with respect to the parental MDKexpressing cells transduced with shrna control. 4 WWW.NATURE.COM/NATURE

RESEARCH Supplementary Table 4 Log2(FC) - MDK/NEG SK-Mel-147 shm1/shc SK-Mel-147 shm5/shc Gene Replicate 1 Replicate 2 Replicate 3 Replicate 1 Replicate 2 Replicate 3 Replicate 1 Replicate 2 Replicate 3 mtor Inflammation Cell Cycle PHGDH 6.738 6.475 6.471-3.026-3.848-3.186-2.890-3.224-2.761 PHGDH SLC6A9 4.641 4.218 4.431-2.183-2.749-1.805-1.560-1.039-1.527 SLC6A9 CADM3 4.556 4.293 4.123-1.737-1.610-1.159-1.630-2.139-1.995 CADM3 HOXB9 4.239 4.107 4.134-1.258-1.442-1.564-1.439-1.657-1.358 HOXB9 CLDN1 3.763 3.829 3.980-1.694-1.562-1.227-1.211-1.312-1.961 CLDN1 ULBP1 4.010 3.668 3.865-2.180-1.812-1.780-1.379-0.773-1.015 ULBP1 CHAC1 3.944 3.626 3.768-2.016-2.441-1.973-1.647-1.242-1.535 CHAC1 SESN2 3.954 3.640 3.702-0.428-0.804-0.832-0.732-0.645-0.994 SESN2 STC2 3.868 3.619 3.765-1.139-1.140-1.157-0.762-0.826-0.894 STC2 CTH 3.684 3.586 3.875-1.233-0.876-1.163-0.793-1.173-0.642 CTH DDIT4 3.874 3.584 3.656-1.531-1.485-1.383-1.165-1.175-1.227 DDIT4 ASNS 3.633 3.652 3.695-1.916-1.971-1.999-1.394-1.307-1.388 ASNS SULT1E1 3.473 3.651 3.729-1.285-1.139-0.769-1.622-1.875-1.407 SULT1E1 LURAP1L 3.599 3.523 3.588-0.833-0.691-1.313-1.014-1.049-0.554 LURAP1L SLC7A11 3.376 3.405 3.652-1.020-0.841-1.104-0.788-1.144-0.995 SLC7A11 PSAT1 3.341 3.359 3.461-2.020-1.843-1.978-1.491-1.250-1.336 PSAT1 TRIB3 3.395 3.092 3.089-0.706-0.919-0.680-0.714-0.504-0.752 TRIB3 SLC3A2 3.160 2.880 2.963-0.751-0.903-0.761-0.622-0.549-0.673 SLC3A2 CCL20 2.786 2.657 2.865-1.141-1.390-1.300-0.793-0.816-0.938 CCL20 GGT5 2.936 2.655 2.606-0.713-1.078-0.661-0.714-1.473-1.117 GGT5 ADM2 2.835 2.615 2.622-1.083-1.380-1.343-0.808-0.755-0.777 ADM2 PCK2 2.693 2.503 2.420-1.054-1.125-1.033-0.982-0.767-0.960 PCK2 ABI3BP 2.398 2.488 2.601-0.907-1.003-0.853-0.891-1.108-0.817 ABI3BP MTHFD2 2.403 2.435 2.504-1.140-1.085-1.208-0.874-0.956-0.954 MTHFD2 VEGFA 2.605 2.353 2.368-0.697-0.874-0.973-0.533-0.550-0.823 VEGFA IL6 2.704 2.145 2.441-1.619-1.575-1.396-0.847-0.870-0.623 IL6 RNF144B 2.388 2.310 2.517-0.789-0.834-0.665-0.621-0.791-0.698 RNF144B SLC7A5 2.515 2.231 2.343-0.939-1.276-1.234-0.980-0.822-1.061 SLC7A5 NAV3 2.132 2.196 2.672-0.709-0.780-0.730-0.645-0.553-0.657 NAV3 MGC16121 2.316 2.368 2.302-1.500-2.391-1.634-1.297-1.619-1.620 MGC16121 CXCL5 2.337 2.318 2.300-2.026-1.839-1.688-1.199-1.452-0.960 CXCL5 SLC4A5 2.336 2.342 2.265-0.855-1.227-0.973-1.012-1.095-0.969 SLC4A5 GPT2 2.284 2.117 2.145-0.910-0.903-0.986-0.850-0.620-0.877 GPT2 SLC1A5 2.273 2.087 2.171-0.978-1.211-1.044-0.833-0.875-0.979 SLC1A5 PMAIP1 2.086 2.102 2.202-0.583-0.591-0.649-0.686-0.464-0.722 PMAIP1 PSTPIP2 2.038 1.984 2.225-1.032-1.013-0.964-0.840-0.788-0.575 PSTPIP2 CYFIP2 2.124 1.997 1.912-0.835-0.808-0.544-0.533-0.647-0.746 CYFIP2 EFNB1 2.168 1.898 1.954-0.693-0.777-0.594-0.515-0.635-0.708 EFNB1 AOX1 2.050 2.021 1.938-0.638-0.669-0.507-0.754-0.731-0.641 AOX1 GLIPR1 1.897 1.901 2.111-0.952-0.841-0.725-0.917-0.686-0.636 GLIPR1 TLR3 1.826 1.891 2.170-1.027-0.351-0.399-0.425-0.812-0.736 TLR3 ICAM1 2.071 1.810 1.960-0.647-0.736-0.598-0.529-0.753-0.701 ICAM1 EIF4EBP1 2.122 1.792 1.734-0.739-0.975-0.926-0.924-0.622-0.838 EIF4EBP1 FGL1 2.106 1.303 1.872-0.984-0.621-1.220-1.355-1.204-1.296 FGL1 NUPR1 1.906 1.603 1.487-0.994-1.146-1.258-0.862-0.679-0.827 NUPR1 GARS 1.661 1.630 1.688-0.816-0.792-0.806-0.652-0.585-0.656 GARS TMEM154 1.483 1.650 1.730-1.047-0.784-0.581-0.757-1.189-0.780 TMEM154 MRGPRX3 1.326 1.678 1.747-1.019-1.417-1.030-0.588-0.893-0.951 MRGPRX3 GPX8 1.624 1.573 1.545-1.254-1.230-0.993-1.311-1.833-1.014 GPX8 CBS 1.715 1.513 1.483-1.155-1.263-1.349-0.931-0.732-1.012 CBS TLR2 1.631 1.155 1.837-1.328-1.049-1.034-0.707-0.929-0.550 TLR2 JDP2 1.564 1.410 1.434-1.173-1.138-1.246-0.861-0.932-0.907 JDP2 LST1 1.194 1.633 1.562-1.234-0.964-1.054-1.035-0.665-0.446 LST1 ANXA3 1.565 1.317 1.142-0.614-0.734-0.503-0.877-0.721-0.755 ANXA3 SLC16A6 1.170 1.492 1.312-0.732-0.888-1.136-0.567-0.835-1.160 SLC16A6 PLD6 1.342 1.219 1.015-0.754-0.633-1.035-0.986-0.673-0.422 PLD6 LPCAT2 1.011 1.238 1.166-0.840-0.727-0.664-0.797-0.410-0.578 LPCAT2 FAM107A 1.092 1.011 1.102-1.068-1.146-0.830-0.955-1.494-1.085 FAM107A HNMT 1.100 1.133 0.876-1.145-0.958-0.726-0.929-0.577-0.488 HNMT NSUN5 1.199 0.871 1.031-0.323-0.654-1.132-0.362-0.910-0.844 NSUN5 C6orf115 1.013 0.739 0.989-1.039-0.665-0.708-0.661-0.620-0.567 C6orf115 CRTAC1 0.902 0.949 0.553-0.451-1.066-0.522-0.863-0.334-0.891 CRTAC1 APLN 0.884 0.535 0.694-1.694-2.019-1.565-1.577-1.709-1.613 APLN CENPQ -0.640-0.554-0.819 0.618 0.650 0.716 0.668 0.730 0.564 CENPQ PRICKLE4-0.876-0.868-0.908 0.611 0.768 0.662 0.779 0.818 0.223 PRICKLE4 SETBP1-1.143-0.758-1.223 0.963 0.941 0.787 0.809 1.024 0.649 SETBP1 TUBD1-1.053-0.956-1.123 0.507 0.715 0.759 0.396 0.626 0.890 TUBD1 ALDH3A2-1.096-0.995-1.056 0.653 0.752 0.566 0.746 0.742 0.744 ALDH3A2 GJA4-1.596-0.896-1.109 1.539 1.305 1.356 0.993 0.849 0.837 GJA4 UCP2-1.571-0.950-1.157 1.121 1.133 0.767 0.421 1.059 1.034 UCP2 RDH10-1.335-1.213-1.149 0.964 1.024 0.942 0.730 0.674 0.663 RDH10 PDK4-1.475-1.872-1.045 0.732 0.705 0.505 0.571 0.794 0.839 PDK4 RADIL -1.175-1.606-1.624 0.937 0.512 0.835 0.774 0.601 0.511 RADIL ATAD5-1.714-1.031-1.676 0.688 0.968 0.659 0.639 0.737 0.509 ATAD5 KHK -1.708-1.406-1.514 0.864 0.641 0.409 0.373 0.742 0.729 KHK GAB1-1.709-1.535-1.450 0.689 0.723 0.685 0.607 0.546 0.710 GAB1 PARD6G -1.572-1.557-1.607 0.815 0.782 0.622 0.566 0.622 0.748 PARD6G DCLK1-1.968-1.383-1.440 0.847 1.210 0.981 0.801 0.694 0.647 DCLK1 PPAP2A -1.674-1.563-1.735 1.120 1.073 0.936 0.676 0.760 0.707 PPAP2A DTX4-2.030-1.762-1.837 1.300 1.227 1.235 0.992 1.128 0.963 DTX4 PSG1-1.547-2.012-2.131 1.599 1.158 1.314 1.227 0.752 0.906 PSG1 HCRTR1-2.605-1.760-1.904 1.097 1.058 1.126 0.587 0.686 0.586 HCRTR1 ABCA4-2.382-2.188-2.062 1.237 1.183 1.044 1.232 1.239 0.976 ABCA4 SCNN1B -2.253-2.525-1.990 1.073 0.765 0.585 1.403 1.188 1.238 SCNN1B CLEC4M -2.547-2.239-2.233 1.045 1.032 0.703 0.641 1.358 1.181 CLEC4M SESN3-2.868-1.998-2.410 1.026 1.034 0.799 0.830 0.769 0.845 SESN3 RCN3-2.492-2.271-3.020 1.182 1.021 0.938 0.884 0.701 0.621 RCN3 CA2-2.824-2.784-2.950 0.775 1.432 0.694 1.003 0.830 1.063 CA2 FAM111B -3.465-2.966-2.936 0.685 1.008 0.795 0.565 0.647 0.770 FAM111B GUCY1A3-3.299-3.539-3.611 1.122 1.082 0.879 0.981 0.964 0.898 GUCY1A3 NTS -4.967-2.854-2.832 1.206 1.216 1.025 0.934 1.140 1.378 NTS Table S4. MDK-induced changes in the LEC transcriptome. Data corresponds to gene lists and the corresponding expression changes shown in the heatmap of Fig. 5b. Genes with the indicated functions are labeled in red in the right table. WWW.NATURE.COM/NATURE 5