SUPPLEMENTARY NFORMATON Artcles https://do.org/10.1038/s41551-017-0181-y n the format provded by the authors and unedted. Engneered commensal mcrobes for detmedated colorectal-cancer chemopreventon Chun Loong Ho 1,2, Hu Qng Tan 3, Koon Jew Chua 1,2, Aram Kang 1,2, Kat Hon Lm 4, Khoon Ln Lng 3, Wen Shan Yew 1,2, Yung Seng Lee 2,5, Jean Paul Thery 1,2 and Matthew Wook Chang 1,2 * 1 Department of Bochemstry, Yong Loo Ln School of Medcne, Natonal Unversty of Sngapore, Sngapore, Sngapore. 2 NUS Synthetc Bology for Clncal and Technologcal nnovaton (SynCT), Lfe Scences nsttute, Natonal Unversty of Sngapore, Sngapore, Sngapore. 3 Department of Gastroenterology and Hepatology, Sngapore General Hosptal, Sngapore, Sngapore. 4 Department of Pathology, Sngapore General Hosptal, Sngapore, Sngapore. 5 Department of Paedatrcs, Yong Loo Ln School of Medcne, Natonal Unversty of Sngapore, Sngapore, Sngapore. *e-mal: matthew_chang@nuhs.edu.sg Nature Bomedcal Engneerng www.nature.com/natbomedeng 2018 Macmllan Publshers Lmted, part of Sprnger Nature. All rghts reserved.
TABLE OF CONTENTS Fgure / Table Fgure Legends Pages Fgure S1 Cytoscape-generated dstrbuton of putatve 3 myrosnase/beta-glucosdase Table S1 Myrosnase actvty assay screenng under varous 4 ph and temperature condtons Table S2 Ant cancer actvty levels n varous cancer cell lnes 5 treated separately wth sulforaphane, allyl sothocyanate (ATC) and myrosnase 1-converted ATC Fgure S2 Surface charges of modelled structures of varous 6 myrosnases Fgure S3 Dsassocaton constant determnaton of GFP-HlpA 7 and GFP aganst varous cancer cell lnes Fgure S4 Mcroscopc mage of GFP-tagged HlpA bndng on 8 varous cancer cell lnes nclusve of control groups Fgure S5 Localzaton of E. col Nssle 1917 (EcN) expressng 9 RFP and surfaced tagged NP-HlpA proten on the surfaces of varous cancer cell lnes nclusve of control groups Fgure S6 Rato of localzaton of E. col Nssle 1917 (EcN) 10 expressng RFP and surfaced tagged NP-HlpA proten n each cancer cell nclusve of control groups Fgure S7 SDS-PAGE gel ndcatng expresson of secreted 11 myrosnase and surface presentng NP-HlpA Fgure S8 Varous CRC cell lnes treated wth Eda-1-HlpA 12 and/or sngrn staned wth a LVE/DEAD kt Fgure S9 Preparaton of cancer cells and Eda-1-HlpA cocultured 13 sldes Fgure S10 Percentage of Rectal Bleedng ncdences n Eda-1-13 fed mce and Eda-1-HlpA-fed mce Fgure S11 Hstology of colorectal tssue from AOM/DSS treated 14 and untreated mce Fgure S12 Hstology of colorectal tssue from AOM/DSS treated 15 mce fed wth Eda-1 Fgure S13 Hstology of colorectal tssue from AOM/DSS treated 16 mce fed wth Eda-1-HlpA Fgure S14 Separaton of mce blood serum and detecton of N- 17 acetyl-cystene ATC usng Hgh Performance Lqud Chromatography Fgure S15 Hstology of colorectal tssue from AOM/DSS treated 18 19 mce fed wth Eda-1-HlpA, staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant- Syndecan 2 antbody Fgure S16 Hstology of colorectal tssue from AOM/DSS treated 20 21 mce fed wth Eda-1, staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant- Syndecan 2 antbody Fgure S17 Hstology of colorectal tssue from untreated mouse 22 23 1
Fgure S18 Fgure S19 Fgure S20 Fgure S21 Fgure S22 staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant-syndecan 2 antbody Fluorescence mage analyss of murne colorectal tssue staned wth Alexa Fluor 488 conjugated ant- E. col, ant-syndecan 1 or ant-syndecan 2 antbody Hstology of colorectal tssue from AOM/DSS treated and untreated mce staned wth GFP-HlpA or GFP Hstology of colorectal tssue from AOM/DSS treated mouse ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant-syndecan 1 or ant-syndecan 2 antbody Hstology of colorectal tssue from untreated mouse ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant-syndecan 1 or ant-syndecan 2 antbody Fluorescence mage analyss of of murne colorectal tssue ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant-syndecan 1 or ant- Syndecan 2 antbody 23 24 25 26 27 28 29 29 2
Fgure S1 Cytoscape-generated dstrbuton of putatve myrosnase/beta-glucosdase. 3
Table S1 Myrosnase actvty assay screenng under varous ph and temperature condtons (n=3 ndependent experments, each measurement performed n trplcates; mean ± s.d.). Myrosnase Condton k cat (1/s) K m (μm) K cat /K m (1/s) BMY1 ph 7.4, 34 ᵒC 6.9 ± 0.4 76 ± 6 89.7 ± 7.4 ph 7.4, 37 ᵒC 6.0 ± 0.7 67 ± 1 88.6 ± 2.5 ph 7.4, 40 ᵒC 9.1 ± 0.8 342 ± 67 26.5 ± 5.2 ph 6.0, 37 ᵒC 5.7 ± 0.8 158 ± 17 36.15 ± 3.9 ph 6.5, 37 ᵒC 11.8 ± 0.4 399 ± 86 29.6 ± 6.4 ph 8.0, 37 ᵒC 5.6 ± 0.6 217 ± 67 25.6 ± 7.9 TGG1 ph 7.4, 34 ᵒC 6.9 ± 1.6 78 ± 8 88.2 ± 9.7 ph 7.4, 37 ᵒC 6.4 ± 1.1 71 ± 3 89.9 ± 4.2 ph 7.4, 40 ᵒC 6.5 ± 0.2 88 ± 9 73.7 ± 7.6 ph 6.0, 37 ᵒC 10.2 ± 0.6 361 ± 11 28.3 ± 0.9 ph 6.5, 37 ᵒC 8.6 ± 1.6 198 ± 20 43.7 ± 4.6 ph 8.0, 37 ᵒC 4.3 ± 0.7 137 ± 69 31.2 ± 15.7 A6 ph 7.4, 34 ᵒC 7.2 ± 1.3 47 ± 5 153.5 ± 18.1 ph 7.4, 37 ᵒC 5.2 ± 0.9 44 ± 4 118.3 ± 11.1 ph 7.4, 40 ᵒC 9.7 ± 1.3 189 ± 39 51.6 ± 10.7 ph 6.0, 37 ᵒC 6.6 ± 1.3 68 ± 2 96.3 ± 4.7 ph 6.5, 37 ᵒC 15.0 ± 1.5 187 ± 13 80.4 ± 5.6 ph 8.0, 37 ᵒC 9.3 ± 1.2 142 ± 22 65.4 ± 10.2 C9 ph 7.4, 34 ᵒC 11.2 ± 2.4 384 ± 28 29.1 ± 2.4 ph 7.4, 37 ᵒC 3.4 ± 0.6 38 ± 2 88.8 ± 5.6 ph 7.4, 40 ᵒC 9.0 ± 0.9 352 ± 68 25.6 ± 4.9 ph 6.0, 37 ᵒC 5.6 ± 0.8 439 ± 97 12.7 ± 2.8 ph 6.5, 37 ᵒC 9.0 ± 0.9 290 ± 31 31.1 ± 3.4 ph 8.0, 37 ᵒC 10.7 ± 1.3 842 ± 80 12.7 ± 1.2 1 ph 7.4, 34 ᵒC 3.4 ± 0.7 49 ± 4 69.5 ± 6.3 ph 7.4, 37 ᵒC 15.0 ± 1.5 87 ± 7 173.2 ± 13.7 ph 7.4, 40 ᵒC 15.2 ± 1.5 87 ± 9 174.0 ± 15.2 ph 6.0, 37 ᵒC 6.6 ± 0.7 192 ± 40 41.1 ± 8.5 ph 6.5, 37 ᵒC 7.9 ± 1.1 183 ± 19 61.6 ± 6.5 ph 8.0, 37 ᵒC 6.6 ± 3.1 192 ± 17 96.4 ± 9.1 Q5 ph 7.4, 34 ᵒC 2.9 ± 1.4 225 ± 13 13.0 ± 1.3 ph 7.4, 37 ᵒC 2.1 ± 1.6 25 ± 7 82.7 ± 24.1 ph 7.4, 40 ᵒC 3.7 ± 1.6 49 ± 14 75.2 ± 22.2 ph 6.0, 37 ᵒC 4.6 ± 1.1 184 ± 15 25.3 ± 2.3 ph 6.5, 37 ᵒC 4.9 ± 1.2 127 ± 21 39.0 ± 6.8 ph 8.0, 37 ᵒC 2.8 ± 1.1 154 ± 24 18.4 ± 3.1 Q9 ph 7.4, 34 ᵒC 13.0 ± 3.5 1301 ± 280 10 ± 2.2 ph 7.4, 37 ᵒC 3.8 ± 1.5 130 ± 9 29.1 ± 3.9 ph 7.4, 40 ᵒC 12.8 ± 3.9 693 ± 23 18.5 ± 10.2 ph 6.0, 37 ᵒC 3.0 ± 0.6 111 ± 3 27.3 ± 10.4 ph 6.5, 37 ᵒC 7.8 ± 0.8 291 ± 5 26.9 ± 6.0 ph 8.0, 37 ᵒC 4.4 ± 1.0 473 ± 6 9.2 ± 1.3 4
Table S2 Ant cancer actvty levels n varous cancer cell lnes treated separately wth sulforaphane, allyl sothocyanate (ATC) and myrosnase 1-converted ATC. NA represents unquantfable values based on the expermental parameters (n=3 ndependent experments, each measurement performed n trplcates; mean ± s.d.). Table a. Varous cell lnes treated wth L-sulforaphane Type Prmary Gastrc Colorectal Breast cells Cell lne SMC AGS LoVo CT26 HCT116 MCF7 G 50 value (μm) 375 ± 113 15 ± 3 23 ± 2 45 ± 3 30 ± 7 29 ± 3 Complete nhbton (hour) NA < 24 < 24 < 24 < 24 < 3 Table b. Varous cell lnes treated wth ATC Type Prmary Gastrc Colorectal Breast cells Cell lne SMC AGS LoVo CT26 HCT116 MCF7 G 50 value (μm) 589 ± 219 18 ± 1 74 ± 5 15 ± 4 116 ± 9 104 ± 17 Complete nhbton (hour) NA < 24 < 24 < 24 < 24 < 3 Table c. Varous cell lnes treated wth YebF-1- converted ATC Type Prmary Gastrc Colorectal Breast cells Cell lne SMC AGS LoVo CT26 HCT116 MCF7 G 50 value (μm) NA 26 ± 2 232 ± 18 46 ± 10 155 ± 32 139 ± 21 Complete nhbton (hour) NA < 24 < 24 < 24 < 24 < 24 5
90 o 180 o Modelled TGG1 structure 90 o 180 o Modelled 1 structure 90 o 180 o Fgure S2 Surface charges of modelled structures of varous myrosnases. 6
a b c d e f Fgure S3 Dsassocaton constant determnaton of GFP-HlpA and GFP aganst varous cancer cell lnes. a. HCT116 b. CT26 c. LoVo d. SMC e. MCF7 f. AGS (n=3 ndependent experments, each measurement performed n trplcates; mean ± s.d.). 7
sgfp sgfp-hlpa sgfp sgfp-hlpa LoVo CT26 HCT116 SMC AGS MCF7 Fgure S4 Mcroscopc mage of GFP-tagged HlpA bndng on varous cancer cell lnes nclusve of control groups. GFP-tagged HlpA or GFP (green); DAP staned nucleus (blue) (Bar: 20 μm). 8
Eda Eda-np-HlpA Eda Eda-np-HlpA LoVo CT26 HCT116 SMC AGS MCF7 Fgure S5 Localzaton of E. col Nssle 1917 (EcN) expressng RFP and surfaced tagged NP-HlpA proten (ndcated by whte arrows) on the surfaces of varous cancer cell lnes nclusve of control groups. EcN expressng RFP (red); Alexa Fluor 488 conjugated ant- HSPG antbody (green); DAP staned nucleus (blue) (Bar: 10 μm). 9
Fgure S6 Rato of localzaton of E. col Nssle 1917 (EcN) expressng RFP and surfaced tagged NP-HlpA proten n each cancer cell nclusve of control groups. Ratos were establshed usng fluorescence emsson of RFP and DAP converted nto cell count based on pre-establshed standard curves, where * p 0.05, ** p 0.01, ***p 0.001 (n=5 ndependent experments, each measurement performed n trplcates; mean ± s.d.). 10
250 130 100 70 55 kda 1 2 3 4 5 6 7 * 35 ** 25 15 Fgure S7 SDS-PAGE gel ndcatng expresson of secreted myrosnase (*) and surface presentng NP-HlpA(**). Lane 1 s the pulled down purfed proten from solublzed ncluson body, Lane 2 and 3 the crude solublzed ncluson body, Lane 4 the crude ntracellular lysate, Lane 5 the crude extracellular medum, Lane 6 the pulled down purfed proten from the ntracellular lysate and Lane 7 the pulled down purfed proten from the extracellular medum. 11
Eda-1-HlpA Eda-1-HlpA Sngrn +Sngrn Eda-1-HlpA Eda-1-HlpA Sngrn +Sngrn LoVo CT26 HCT116 SMC AGS MCF7 Fgure S8 Varous CRC cell lnes treated wth Eda-1-HlpA and/or sngrn staned wth a LVE/DEAD kt. Lve cells are staned green and dead cells n red (Bar: 15 μm). 12
a b c d Fgure S9 Preparaton of cancer cells and Eda-1-HlpA co-cultured sldes. a. Cells were grown on the surfaces of glass sldes untl 80% confluent. b. Eda-1-HlpA was ntroduced to the medum for 30 mnutes before beng washed twce wth 1x PBS. c. Sldes were nverted facedown n antbotc-free culture meda contanng sngrn. d. Sldes were ncubated for 24 hours pror to stanng wth a LVE/DEAD kt and vewed under a fluorescence mcroscope. Fgure S10 Percentage of Rectal Bleedng ncdences n Eda-1-fed mce (left) and Eda-1- HlpA-fed mce (rght) 13
a b Fgure S11 Hstology of colorectal tssue from AOM/DSS treated and untreated mce. a. Tssue secton from mouse not treated wth AOM/DSS, scale bar: 5 mm. b. Tssue secton from mouse treated wth AOM/DSS, scale bar: 5 mm (nset: boxes ndcated wth captal roman numerals ndcate 2x magnfcaton, scale bar: 500 μm. Boxes ndcated wth small roman numerals ndcate 20x magnfcaton, scale bar: 50 μm)(whte arrows ndcate GALT). 14
a b Fgure S12 Hstology of colorectal tssue from AOM/DSS treated mce fed wth Eda-1. a. Tssue secton from mouse treated wth AOM/DSS and fed wth Eda-1 and sngrn, scale bar: 5 mm. b. Tssue secton from mouse treated wth AOM/DSS and fed wth Eda-1 and broccol, scale bar: 5 mm (nset: boxes - ndcate 2x magnfcaton, scale bar: 500 μm. Boxes - ndcate 20x magnfcaton, scale bar: 50 μm)(whte arrows ndcate GALT). 15
a b Fgure S13 Hstology of colorectal tssue from AOM/DSS treated mce fed wth Eda-1- HlpA. a. Tssue secton from mouse treated wth AOM/DSS and fed wth Eda-1-HlpA and sngrn, scale bar: 5 mm. b. Tssue secton from mouse treated wth AOM/DSS and fed wth Eda-1-HlpA and broccol, scale bar: 5 mm (nset: boxes - ndcate 2x magnfcaton, scale bar: 500 μm. Boxes - ndcate 20x magnfcaton, scale bar: 50 μm)(whte arrows ndcate GALT). 16
Fgure S14 Separaton of mce blood serum and detecton of N-acetyl-cystene ATC usng Hgh Performance Lqud Chromatography. NAC-ATC maxma retenton volume s 8.8 ml, ATC maxma retenton volume s 10.9 ml. 17
a b c Fgure S15 Hstology of colorectal tssue from AOM/DSS treated mce fed wth Eda-1- HlpA, staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant- Syndecan 2 antbody. a. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated mouse fed wth Eda-1-HlpA staned wth Alexa Fluor 488 conjugated ant-e. col (green), scale bar: 10 mm. b. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated 18
mouse fed wth Eda-1-HlpA staned wth Alexa Fluor 488 conjugated ant-syndecan 1 (green), scale bar: 10 mm. c. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated mouse fed wth Eda-1-HlpA staned wth Alexa Fluor 488 conjugated ant-syndecan 2 (green), scale bar: 10 mm. (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes - ndcate 100x objectve magnfcaton, scale bar: 100 μm). Fluorescence mage analyss s shown n Supplementary Fgure 18. 19
a b c Fgure S16 Hstology of colorectal tssue from AOM/DSS treated mce fed wth Eda-1, staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant-syndecan 2 antbody. a. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated mouse fed wth Eda-1 staned wth Alexa Fluor 488 conjugated ant-e. col (green), scale bar: 10 mm. b. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated mouse fed wth Eda-1 20
staned wth Alexa Fluor 488 conjugated ant-syndecan 1 (green), scale bar: 10 mm. c. Tssue secton wth DAP-staned nucleus (blue) from AOM/DSS treated mouse fed wth Eda-1 staned wth Alexa Fluor 488 conjugated ant-syndecan 2 (green), scale bar: 10 mm. (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes - ndcate 100x objectve magnfcaton, scale bar: 100 μm). Fluorescence mage analyss s shown n Supplementary Fgure 18. 21
a b c Fgure S17 Hstology of colorectal tssue from untreated mouse staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant-syndecan 2 antbody. a. Tssue secton wth DAP-staned nucleus (blue) from untreated mouse staned wth Alexa Fluor 488 conjugated ant-e. col (green), scale bar: 10 mm. b. Tssue secton wth DAP-staned nucleus (blue) from untreated mouse staned wth Alexa Fluor 488 conjugated ant-syndecan 1 (green), 22
scale bar: 10 mm. c. Tssue secton wth DAP-staned nucleus (blue) from untreated mouse staned wth Alexa Fluor 488 conjugated ant-syndecan 2 (green), scale bar: 10 mm. (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes - ndcate 100x objectve magnfcaton, scale bar: 100 μm). Fluorescence mage analyss s shown n Supplementary Fgure 18. Fgure S18 Fluorescence mage analyss of murne colorectal tssue staned wth Alexa Fluor 488 conjugated ant-e. col, ant-syndecan 1 or ant-syndecan 2 antbody. Fluorescence mages were evaluated by measurng the corrected total fluorescence for DAP, GFP and RFP. The values are expressed as GFP or RFP emsson per unt DAP, where * p 0.05, ** p 0.01, ***p 0.001, NS represents non- sgnfcant (n=10 ndependent experments, each measurement performed n trplcates; mean ± s.d.). 23
a c b d e Fgure S19 Hstology of colorectal tssue from AOM/DSS treated and untreated mce staned wth GFP-HlpA or GFP. a. Tssue secton wth DAP-staned nucleus(blue) from mouse treated wth AOM/DSS staned wth GFP-HlpA (green), scale bar: 10 mm. b. Tssue secton wth DAP-staned nucleus(blue) from mouse not treated wth AOM/DSS staned wth GFP-HlpA (green), scale bar: 10 mm. c. Tssue secton wth DAP-staned nucleus (blue) from mouse treated wth AOM/DSS staned wth GFP (green), scale bar: 10 mm. d. Tssue secton wth DAP-staned nucleus (blue) from mouse not treated wth AOM/DSS staned wth GFP (green), scale bar: 10 mm (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes 24
- ndcate 100x objectve magnfcaton, scale bar: 100 μm) (red dotted lnes annotates the tumor tssue).e. Fluorescence mages were evaluated by measurng the corrected total fluorescence for DAP, GFP and RFP. The values are expressed as GFP or RFP emsson per unt DAP, where * p 0.05, ** p 0.01, ***p 0.001, NS represents non-sgnfcant (n=10 ndependent experments, each measurement performed n trplcates; mean ± s.d.). 25
a b c d Fgure S20 Hstology of colorectal tssue from AOM/DSS treated mouse ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant-syndecan 1 or ant-syndecan 2 antbody. Alexa Fluor 488 conjugated 26
ant-syndecan 1 (green) staned tssue sectons from mouse treated wth AOM/DSS ncubated wth a. RFP expressng EcN (red) and b. NP-HlpA expressng EcN (red). Alexa Fluor 488 conjugated ant-syndecan 2 (green) staned tssue sectons from mouse treated wth AOM/DSS ncubated wth c. RFP expressng EcN (red) and d. NP-HlpA expressng EcN (red). All nucleus n tssue sectons were staned wth DAP (blue).scale bar: 10 mm (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes - ndcate 100x objectve magnfcaton, scale bar: 100 μm). Fluorescence mage analyss s shown n Supplementary Fgure 21. 27
a b c d Fgure S21 Hstology of colorectal tssue from untreated mouse ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant- Syndecan 1 or ant-syndecan 2 antbody. Alexa Fluor 488 conjugated ant-syndecan 1 (green) staned 28
tssue sectons from untreated mouse ncubated wth a. RFP expressng EcN (red) and b. NP-HlpA expressng EcN (red). Alexa Fluor 488 conjugated ant-syndecan 2 (green) staned tssue sectons from untreated mouse ncubated wth c. RFP expressng EcN (red) and d. NP-HlpA expressng EcN (red). All nucleus n tssue sectons were staned wth DAP (blue).scale bar: 10 mm (nset: boxes - ndcate 20x objectve magnfcaton, scale bar: 20 μm. Boxes - ndcate 100x objectve magnfcaton, scale bar: 100 μm). Fluorescence mage analyss s shown n Supplementary Fgure 21. Fgure S22 Fluorescence mage analyss of of murne colorectal tssue ncubated wth E. col Nssle (EcN) expressng RFP wth or wthout NP-HlpA, co-staned wth Alexa Fluor 488 conjugated ant-syndecan 1 or ant-syndecan 2 antbody. Fluorescence mages were evaluated by measurng the corrected total fluorescence for DAP, GFP and RFP. The values are expressed as GFP or RFP emsson per unt DAP, where * p 0.05, ** p 0.01, ***p 0.001, NS represents non-sgnfcant (n=10 ndependent experments, each measurement performed n trplcates; mean ± s.d.). 29