SI Correction

SYSTEMS BIOLOGY Correction to Supporting Information for “miRNA proxy approach issue 23, June 9, 2015, of Proc Natl Acad Sci USA (112:7327–7332; reveals hidden functions of glycosylation,” by Tomasz Kurcon, first published May 26, 2015; 10.1073/pnas.1502076112). Zhongyin Liu, Anika V. Paradkar, Christopher A. Vaiana, Sujeethraj The authors note that Table S1, Table S3, and Table S4 ap- Koppolu, Praveen Agrawal, and Lara K. Mahal, which appeared in peared incorrectly. The SI has been corrected online.

Table S1. Classification of miR-200f predicted glycogenes according to the type of glycan synthesized (related to Table S3) N-linked O-linked NC-O-linked GAGs Glycolipid Other/terminal

ALG2 C1GALT1 B3GAT1 CSGALNACT2 B3GALT2 B3GALNT2 ALG5 GALNT2 B3GLCT B3GALT6 B3GALNT1 B3GNT1 ALG6 GALNT3 GXYLT1 CHST2 B3GNT4 B3GNT2 ALG8 GALNT4 LARGE CHST7 B3GNT5 FUT2 ALG11 GALNT10 LFNG CHST12 B4GALT6 FUT4 ALG14 GALNT11 OGT CHSY1 GAL3ST1 HAS2 DDOST GALNT12 POFUT1 CHSY3 ST3GAL5 HAS3 DPAGT1 GALNT14 EXTL2 ST3GAL6 ST3GAL2 MGAT2 GALNTL2 HS2ST1 ST6GALNAC3 ST3GAL3 MGAT3 GCNT2 HS3ST1 ST6GALNAC5 ST8SIA2 MGAT4A GCNT4 HS3ST3A1 UGCG ST8SIA4 MGAT4C HS3ST5 HS6ST1 HS6ST2 HS6ST3 NDST3 Count 12 11 7 16 11 11 % Total 17.6 16.2 10.3 23.5 16.2 16.2

miR-200f predicted glycogenes were classified according to the glycan they synthesize using the Kyoto Encyclopedia of Genes and Genomes. The % total represents the distribution of one type of glycan among all predicted targets. GAGs, glycosaminoglycans; NC O-linked, noncanonical O-linked.

E4632–E4635 | PNAS | August 18, 2015 | vol. 112 | no. 33 www.pnas.org Downloaded by guest on September 25, 2021 Table S3. miR-200f target glycogene transcript expression profile in MDA-MB-231 cells treated with miR-200a, miR-200b, or scramble mimics miR-200a treatment miR-200b treatment

Glycogene Fold change P values Glycogene Fold change P values Glycan type

Shared predicted targets MGAT4A 1.06 0.74 MGAT4A 1.17 0.31 N-linked C1GALT1 −1.19 0.050 C1GALT1 −1.10 0.40 O-linked GCNT2 1.04 0.86 GCNT2 1.20 0.36 B3GLCT −1.06 0.69 B3GLCT −1.61 4.18E-03 NC O-linked ST3GAL5 −1.61 6.37E-03 ST3GAL5 −2.13 2.11E-04 Glycolipid ST6GALNAC3 1.62 0.20 ST6GALNAC3 1.11 0.76 B3GNT2 1.07 0.66 B3GNT2 1.22 0.15 Other/terminal miR-200b/-200c/-429 predicted targets MGAT2 −1.08 0.72 MGAT2 1.01 0.98 N-linked MGAT3 −1.86 0.12 MGAT3 1.30 0.15 MGAT4C 1.93 0.20 MGAT4C −1.00 1.00 GALNT2 −1.09 0.52 GALNT2 −1.40 0.022 O-linked GALNT3 1.03 0.71 GALNT3 2.30 4.52E-04 GALNT10 −1.14 0.11 GALNT10 −1.68 1.22E-03 GALNT11 −1.11 0.29 GALNT11 −1.26 0.011 GALNT12 −1.40 7.38E-03 GALNT12 −1.52 6.32E-03 GALNT14 −1.49 0.011 GALNT14 −1.94 5.92E-03 GCNT4 −1.18 0.16 GCNT4 −1.05 0.79 LFNG −1.49 0.21 LFNG −2.14 0.074 NC O-linked CHST12 1.09 0.81 CHST12 1.22 0.66 GAGs CHSY3 1.15 0.36 CHSY3 −1.04 0.68 EXTL2 −1.05 0.78 EXTL2 1.07 0.71 HS3ST1 1.99 0.044 HS3ST1 3.28 0.014 HS3ST3A1 −1.11 0.74 HS3ST3A1 −1.24 0.39 NDST3 −2.87 3.16E-03 NDST3 −6.96 4.58E-04 B3GALNT1 −1.11 0.56 B3GALNT1 −1.16 0.46 Glycolipid ST6GALNAC5 2.23 0.033 ST6GALNAC5 4.79 0.010 B3GNT1 −1.04 0.80 B3GNT1 −1.47 0.039 Other/terminal ST3GAL2 −1.18 0.20 ST3GAL2 −1.59 1.23E-03 ST8SIA4 −1.23 0.013 ST8SIA4 −1.15 0.22 miR−/−200a/-141 predicted targets GALNT4 −1.16 0.20 GALNT4 −1.17 0.077 O-linked OGT −1.09 0.50 OGT −1.02 0.88 NC O-linked POFUT1 −1.00 0.98 POFUT1 −1.01 0.90 B3GALT6 1.05 0.83 B3GALT6 1.00 0.99 GAGs HS6ST1 −1.19 0.46 HS6ST1 −1.14 0.56 HS6ST3 1.13 0.59 HS6ST3 4.37 1.41E-03 B3GNT4 1.29 0.075 B3GNT4 2.42 6.44E-04 Glycolipid B3GNT5 1.25 0.11 B3GNT5 1.70 2.62E-03 ST3GAL6 −1.18 0.30 ST3GAL6 1.01 0.91 ST3GAL3 −1.42 0.051 ST3G AL3 −1.43 0.035 Other/terminal

MDA-MB-231 cells were treated with miR-200a, miR-200b. or scramble mimics (50 nM) for 7 d. The qRT-PCR was performed using RT2 Profiler PCR Array Human Glycosylation (Qiagen) or custom primers for genes not repre- sented on the array (Dataset S1). Fold change (miR-treated/scramble) was calculated by taking the average relative expression of miR-treated samples (n = 4 independent experiments, normalized to GAPDH) over the average SI CORRECTION relative expression of the scramble treated cells (n = 4 independent experiments, normalized to GAPDH). Where the fold change was less than 1, the negative inverse is shown. P values for treated vs. scramble were calculated using Student’s t test. Statistically significant (P ≤ 0.05) down-regulation is in bold; up-regulation is underlined. GAGs, glycosaminoglycans; NC O-linked, noncanonical O-linked; See Table S1 for glycan type distribution. *Genes for which luciferase data were obtained (Fig. 1).

PNAS | August 18, 2015 | vol. 112 | no. 33 | E4633 Downloaded by guest on September 25, 2021 Table S4. Expression profile of glycogenes not predicted to be targets of the miR-200 family in MDA-MB-231 cells treated with miR-200a, miR-200b, or scramble mimics miR-200a treatment miR-200b treatment

Glycogene Fold change P values Glycogene Fold change P values

A4GNT −1.41 7.17E-03 A4GNT −1.81 1.14E-03 AGA −1.37 2.50E-03 AGA −1.17 0.24 B3GNT3 13.51 5.78E-06 B3GNT3 67.80 1.35E-05 B3GNT8 −1.14 0.42 B3GNT8 1.01 0.95 B4GALT1 −1.17 0.20 B4GALT1 −1.15 0.16 B4GALT2 1.01 0.97 B4GALT2 −1.02 0.92 B4GALT3 1.21 0.43 B4GALT3 1.32 0.19 B4GALT5 1.11 0.62 B4GALT5 1.61 0.021 C1GALT1C1 −1.01 0.94 C1GALT1C1 1.02 0.80 EDEM1 −1.07 0.59 EDEM1 −1.05 0.65 EDEM2 −1.06 0.60 EDEM2 1.04 0.66 EDEM3 1.02 0.79 EDEM3 −1.10 0.23 FUCA1 −1.09 0.31 FUCA1 −1.12 0.19 FUCA2 −1.09 0.24 FUCA2 −1.03 0.61 FUT8 1.20 0.19 FUT8 −1.07 0.45 FUT11 1.03 0.79 FUT11 1.28 0.12 GALNT1 1.15 0.29 GALNT1 −1.12 0.30 GALNT6 2.14 3.74E-04 GALNT6 1.79 9.89E-05 GALNT7 −1.07 0.60 GALNT7 −1.09 0.39 GALNT8 −1.69 0.21 GALNT8 −2.07 0.18 GALNT9 −2.19 0.12 GALNT9 −1.90 0.17 GALNT13 −1.16 0.024 GALNT13 1.03 0.63 GALNTL1 −1.61 0.013 GALNTL1 −2.02 3.34E-03 GALNTL5 1.41 0.36 GALNTL5 1.08 0.36 GALNTL6 −2.06 0.12 GALNTL6 −3.08 0.048 GANAB −1.01 0.92 GANAB −1.02 0.80 GCNT1 −1.61 8.08E-05 GCNT1 −1.63 3.98E-03 GCNT3 −1.18 0.35 GCNT3 1.49 0.23 GLB1 −1.06 0.73 GLB1 −1.17 0.26 GNPTAB −1.15 0.19 GNPTAB −1.03 0.84 GNPTG −1.15 0.26 GNPTG −1.13 0.22 HEXA −1.11 0.36 HEXA −1.14 0.091 HEXB −1.13 0.24 HEXB −1.17 0.11 MAN1A1 1.09 0.54 MAN1A1 −1.14 0.45 MAN1A2 1.02 0.88 MAN1A2 −1.15 0.25 MAN1B1 −1.06 0.56 MAN1B1 −1.08 0.41 MAN1C1 −1.07 0.76 MAN1C1 −1.39 0.039 MAN2A1 −1.06 0.23 MAN2A1 1.13 0.23 MAN2A2 1.24 0.41 MAN2A2 1.43 0.12 MAN2B1 1.04 0.89 MAN2B1 1.01 0.97 MANBA −1.21 5.54E-04 MANBA −1.22 0.015 MGAT1 1.18 0.36 MGAT1 1.37 0.019 MGAT4B 1.13 0.39 MGAT4B 1.13 0.17 MGAT5 1.27 0.32 MGAT5 1.31 0.25 MGAT5B −1.29 0.15 MGAT5B −2.24 3.69E-03 MGEA5 −1.06 0.58 MGEA5 1.02 0.71 MOGS 1.10 0.63 MOGS 1.32 0.092 NAGPA −1.33 0.32 NAGPA −1.40 0.20 NEU1 −1.08 0.63 NEU1 1.25 0.10 NEU2 1.43 0.24 NEU2 1.62 0.032 NEU3 −1.05 0.63 NEU3 1.24 0.074 NEU4 −1.35 0.51 NEU4 −1.63 0.36 POFUT2 −1.14 0.18 POFUT2 −1.25 0.014 POMGNT1 1.06 0.71 POMGNT1 −1.05 0.59 POMT1 −1.18 0.33 POMT1 −1.07 0.61 POMT2 1.07 0.66 POMT2 1.02 0.85 PRKCSH 1.02 0.86 PRKCSH 1.07 0.39 ST3GAL1 1.19 0.056 ST3GAL1 1.21 0.027 ST6GAL1 −1.60 8.50E-03 ST6GAL1 −2.08 3.80E-04 ST6GALNAC1 4.57 0.044 ST6GALNAC1 9.10 6.11E-03

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Glycogene Fold change P values Glycogene Fold change P values

ST8SIA3 −1.11 0.91 ST8SIA3 −1.06 0.95 ST8SIA6 −1.72 0.017 ST8SIA6 −3.13 1.77E-03 UGGT1 −1.03 0.87 UGGT1 −1.15 0.30 UGGT2 −1.09 0.44 UGGT2 −1.18 0.093

MDA-MB-231 cells were treated with miR-200a, miR-200b, or scramble mimics (50 nM) for 7 d. The qRT-PCR was performed using RT2 Profiler PCR Array Human Glycosylation (Qiagen). Fold change (miR-treated/scramble-treated) was calculated by taking the average relative expression of miR-treated samples (n = 4 independent experiments, normalized to GAPDH) over the average relative expression of the scramble treated cells (n = 4 independent exper- iments, normalized to GAPDH). Where the fold change was less than 1, the negative inverse is shown. P values for treated vs. scramble were calculated using Student’s t test. Statistically significant (P ≤ 0.05) down-regulation is in bold type, and statistically significant up-regulation is underlined.

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