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(1)

Titre:

Title :

Identifying biomarkers of Wharton's Jelly mesenchymal stromal cells using a dynamic metabolic model: the cell passage effect:

Suppléments Auteurs:

Authors : Benoît Laflaquière, Gabrielle Leclercq, Chandarong Choey, Jingkui Chen, Sabine Peres, Caryn Ito et Mario Jolicoeur

Date: 2018

Type: Article de revue / Journal article

Référence:

Citation :

Laflaquière, B., Leclercq, G., Choey, C., Chen, J., Peres, S., Ito, C. & Jolicoeur, M.

(2018). Identifying biomarkers of Wharton's Jelly mesenchymal stromal cells using a dynamic metabolic model: the cell passage effect. Metabolites, 8(1).

doi:10.3390/metabo8010018

Document en libre accès dans PolyPublie

Open Access document in PolyPublie

URL de PolyPublie:

PolyPublie URL:

https://publications.polymtl.ca/3564/

Version: Matériel supplémentaire / Supplementary material Révisé par les pairs / Refereed

Conditions d’utilisation:

Terms of Use

: CC BY

Document publié chez l’éditeur officiel Document issued by the official publisher

Titre de la revue:

Journal Title:

Metabolites (vol. 8, no 1) Maison d’édition:

Publisher:

MDPI URL officiel:

Official URL:

https://doi.org/10.3390/metabo8010018 Mention légale:

Legal notice:

Ce fichier a été téléchargé à partir de PolyPublie, le dépôt institutionnel de Polytechnique Montréal

This file has been downloaded from PolyPublie, the institutional repository of Polytechnique Montréal

http://publications.polymtl.ca

(2)

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(3)

Metabolites 2017, 7, x FOR PEER REVIEW 2 of 30

Table S1. Reaction equations (continued)

Reaction

number Reaction

name Reaction

18 G6PDH G6P + 2 NADP => R5P + 2 NADPH

19 GLDH GLU + NAD = AKG + NADH + NH4

20 GLN GLN = NH4 + GLU

21 GLNt EGLN + ATP => GLN + ADP

22 GLUt GLU + ADP => EGLU + ATP

23 GLYt EGLY + ATP => GLY + ADP

24 growth

0.06 EALA + 0.04 EARG + 0.03 EASN + 0.04 EASP + 0.02 ECYS + 0.03 EGLN + 0.04 EGLU + 0.06 EGLY + 0.02 EHIS + 0.03 EILE + 0.06 ELEU + 0.06 ELYS + 0.01 EMET + 0.02 EPHE + 0.03 EPRO + 0.05 ESER + 0.04 ETHR + 0.005 ETRP + 0.02 ETYR + 0.04 EVAL +

3.78 ATP + 0.03 G6P + 0.03 R5P + 0.09 CIT => X + 3.78 ADP

25 HISARGTA EHIS + EARG + AKG => 4 GLU + NH4

26 HK EGLC + ATP => G6P + ADP

27 IDO ETRP => KYN

28 iNOS ARG + NADP => CTR + NADPH + NO

29 KOT KYN + AKG => KYT + GLU

30 LDH PYR + NADH => ELAC + NAD

31 leak 2 NADH => 2 NAD

32 ME MAL + NAD => PYR + NADH

33 MLD MAL + NAD => OXA + NADH

34 NADPHox NADPH => NADP

35 NAT 2 R5P + 2 ATP + GLN => NAD + AMP + GLU

36 NHG NAD + ATP => NADP + ADP

37 OCT ORN => CTR

38 PC PYR + ATP => OXA + ADP

(4)

Metabolites 2017, 7, x FOR PEER REVIEW 3 of 30

Table S1. Reaction equations (continued)

Reaction

number Reaction

name Reaction

39 PYR + NAD => ACCOA + NADH

40 PFK F6P + ATP => 2 GAP + ADP

41 PGI G6P = F6P

42 PGK GAP + ADP + NAD => PEP + ATP + NADH

43 PK PEP + ADP => PYR + ATP

44 PPRibP R5P + 2 GLN + ASP + GLY + 5 ATP => 2 GLU + FUM + 4 ADP + 2 AMP

45 resp 2 NADH + 4 ADP => 2 NAD + 4 ATP

46 SCOAS SCOA + ADP => ATP + SUC

47 SDH SUC + 0.66 NAD + ADP => FUM + 0.66 NADH + ATP

48 SDHH ESER => PYR + NH4

49 TK 3 R5P => 2 F6P + GAP

(5)

Metabolites 2017, 7, x FOR PEER REVIEW 4 of 30

Table S2. Successive steps for model calibration

Step

number Used

metabolite Determined

reactions Step

number Used

metabolite Determined reactions

1 X growth 24 ASN ASN

2 PCr CK 25 ASP ASTA

3 EGLC HK 26 ACCOA CS & PDH

4 ELAC LDH 27 CIT CITS

5 ETRP IDO 28 AKG AKGDH & GLD

6 KYN KOT 29 SCOA SCOAS

7 ELEU AAtoSUC 30 SUC SDH

8 EHIS HISARGTA 31 NH4 GLN

9 EGLY GLYt 32 FUM FUM

10 UREA ARG1 33 GLN NAT

11 NO iNOS 34 AMP AK

12 R5P PPRibP 35 G6P G6PDH & PGI

13 R5P NAT. 36 NADPH NADPHox

14 EARG ARGt 37 NADP NHG

15 EGLU GLUt 38 F6P PFK & TK

16 EGLN GLNt 39 GAP PGK

17 EALA ALATA 40 PEP PK

18 ESER SDHH 41 R5P EP

19 EASN ASNt 42 MAL ME & MLD

20 EASP ASPt 43 OXA PC

21 ORN OCT 44 ADP ATPase & resp

22 CTR ASS 45 NAD leak

23 AS·ARG ASL

(6)

Metabolites 2017, 7, x FOR PEER REVIEW 5 of 30

Figure S1. Experimental data and model simulation of cofactors and nucleotides concentrations·

(A) Nicotinamide adenine dinucleotide concentration; (B) Nicotinamide adenine dinucleotide H

concentration; (C) Nicotinamide adenine dinucleotide phosphate concentration; (D) Nicotinamide

adenine dinucleotide phosphate H concentration; (E) Adenosine triphosphate concentration; (F)

Adenosine diphosphate concentration; (G) Adenosine monophosphate concentration. are P4

cells experimental data, are P9 cells experimental· Data Average values are shown for both

passages (n=3). Blue line is P4 cells simulation, red line is P9 cells simulation.

(7)

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(12)

Metabolites 2017, 7, x FOR PEER REVIEW 6 of 30 Table S3. Parameter values for average simulation (continued)

Parameters Values Units

!

,-'.&/0BCD

1.31 x 10

-04

mmol·10-6cells

!

,-'.&/EF1

8.79 x 10

-05

mmol·10

-6

cells

!

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-05

mM

(13)

Metabolites 2017, 7, x FOR PEER REVIEW 7 of 30 Table S4. MRM transition and retention time of each amino acid

Compound name IS Precursor ion Product ion frag CE polarity RT min

Cystine NO 241.3 241 76 0 pos 14.78

Homoarginine YES 189.2 144 92 12 pos 14.44

Tyrosine NO 182.2 136.1 66 8 pos 8.74

Homophenylalanine YES 180.2 134.1 75 8 pos 6.12

Arginine NO 175.2 70.1 95 24 pos 15.09

Phenylalanine NO 166.2 120.1 72 8 pos 6.92

Histidine NO 156.2 110.1 81 12 pos 16.84

Methionine-d3 YES 153.2 136.1 69 4 pos 8.22

Methionine NO 150.2 133 63 4 pos 8.18

Glutamic acid NO 148.1 84.1 72 16 pos 12.59

Lysine NO 147.2 84.1 66 12 pos 15.48

Glutamine NO 147.2 84.1 72 16 pos 11.3

Aspartic acid NO 134.1 74.1 61 12 pos 14.23

Asparagine NO 133.1 74 60 12 pos 11.87

Isoleucine NO 132.2 86.1 63 4 pos 7.431

Leucine NO 132.2 86.1 72 4 pos 7.431

Threonine NO 120.1 103.1 133 16 pos 6.94

Valine NO 118.2 72.1 55 8 pos 9

Proline NO 116.1 70.1 75 12 pos 9.6

Serine NO 106.1 60.1 60 8 pos 11.62

Alanine NO 90.1 44.1 42 8 pos 10.7

Glycine NO 76.1 30.1 39 4 pos 11.47

(14)

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´ ¶=

}„‚‡†~

* ¾+30¿¹

0@ B¾+58¿

BK µ ´=

go

³ =

gvv

³ =

rgw

³ ¼" * =

ttu{t

½´¶=

}„‚‡†~

*¾+58¿¹

1@ B¾+90¿

BK µ ´=

gulN

³ =

gul†

³ =

gvp

´=

rsv

´ ¶=

}„‚‡†~

*¾+90¿¹

2@ B¾+:¿

BK µ ´=

gvp

³ =

gvv

´ ¶=

}„‚‡†~

* ¾+:¿¹

3@ B¾+:6¿

BK µ ´=

gvr

³ =

gvr†

´ ¶=

}„‚‡†~

* ¾+:6¿¹

(26)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

)

) ))

4@ B¾+:8¿

BK µ =

gvr

³ =

gvt†

´ =

gvv

´=

gvwg

´ =

ttu{t

´¶=

}„‚‡†~

*¾+:8¿¹

5@

B¾+;8¿

BK µ ´=

gg†‚vxh

´=

go

´=

gul†

´=

gvr†

´ =

gvt†

´ =

gvv

´=

gwtz…|

³ =

ho

´ =

lpr†

³ =

lpx†

´=

lpy†

´ =

mo

´ ¼" *=

rgw

½´=

rml

´ =

th

´ =

tko

³ =

tlo

³ =

to

´ ¼% *=

ttu{t

½³ ¶$ *=

„|…ƒ

¹³ =

vhsgv

³ =

vim

´¶=

}„‚‡†~

*¾+;8¿¹´¶=

}„‚‡†~­ ª

*=

}„‚‡†~

¹

-,@ B¾,2;¿

BK µ ´=

hnwv

³ =

hv

´¶=

}„‚‡†~

*¾,2;¿¹´ ¶=

}„‚‡†~ž¤­

*=

}„‚‡†~

¹

--@ B¾/&8¿

BK µ ´=

tko

³ =

tln

³ ¼" * =

wo

½´¶=

}„‚‡†~

* ¾/&8¿¹

-.@ B¾/<5¿

BK µ =

gvp

´ =

kxq

³ =

ttu{t

³ =

vim

´ ¶=

}„‚‡†~

* ¾/<5¿¹

-/@ B¾&¿

µ ´

SOZRT

³

TV

´

ZSU

´ ¶

dc ea

* ¾&¿¹´¶

dc ea ‹

*

dc ea

¹

-0@ B¾0+8¿

BK µ ¼" * =

tko

½´=

tlo

³ =

wo

´ ¶=

}„‚‡†~

* ¾0+8¿¹

-1@ B¾046¿

BK µ ´=

lpr

³ =

lpr†

´ =

rgw

´ ¼" * =

ttu{t

½´¶=

}„‚‡†~

*¾046¿¹

(27)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

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) ))

-2@

B¾04<¿

BK µ ¼$ * =

gg†‚vxh

½´=

gpgwg

³ =

gvwg

´=

lpim

³ =

lpr

´ =

lpx†

³ ¼$ *=

mnvgulwg

½³ =

osw

³ =

rgw

³ ¼" *=

ttu{t

½

´¶=

}„‚‡†~

*¾04<¿¹

-3@ B ¾04?¿

BK µ =

lpy†

´ =

ttu{t

´ ¶=

}„‚‡†~

* ¾04?¿¹

-4@ B¾5+4¿

BK µ =

gg†‚vxh

³ =

kxq

´=

qj

´ =

qpi

´ ¶=

}„‚‡†~

* ¾5+4¿¹

-5@

B¾6+-¿

BK µ ´¼) *=

gg†‚vxh

½´=

golim

´=

hnwv

´ =

lpim

³ =

pim

³ ¼" *=

|z€

½´=

qj

´ =

qpi

³ =

rgw

´=

rml

´ =

tim

´=

tlo

³ ¶" * =

„|…ƒ

¹´ ¼ && * =

vim

½´¶=

}„‚‡†~

* ¾6+-¿¹

.,@

B¾6+-1¿

BK µ ¼) *=

gg†‚vxh

½³ =

golim

³ =

hnwv

³ =

lpim

´ =

pim

´ ¼" *=

|z€

½³ =

qj

³ =

qpi

³ =

tim

³ =

tlo

´ ¶" * =

„|…ƒ

¹³ ¼ && * =

vim

½´¶=

}„‚‡†~

* ¾6+-1¿¹

.-@ B¾6+-8¿

BK µ ´¼" * =

gg†‚vxh

½´ ¼" *=

lOtim

½´=

rsv

³ =

rgitm‚ˆ

³ =

rml

´ ¶=

}„‚‡†~

*¾6+-8¿¹

..@ B¾6+-81¿

BK µ ¼" *=

gg†‚vxh

½³ ¼" *=

lOtim

½³ =

rsv

´=

rgitm‚ˆ

´¶=

}„‚‡†~

*¾6+-81¿¹

./@ B¾7>+¿

BK µ =

gvwg

´=

hv

³ =

qpi

³ =

th

´ ¶=

}„‚‡†~

* ¾7>+¿¹

(28)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

)

) ))

.0@ B¾8,J¿

BK µ ´=

ho

´¶=

}„‚‡†~

*¾8,J¿¹

.1@ B¾8 8¿

BK µ =

tlo

´=

to

´ ¶=

}„‚‡†~

* ¾8 8¿¹

.2@ B¾8?9¿

BK µ ´=

gpgwg

´=

pim

³ =

qj

´=

th

´ =

tim

³ =

to

³ =

vimm

´¶=

}„‚‡†~

*¾8?9¿¹

.3@ B¾9%8¿

BK µ =

lOtim

´ ¼" * =

rgw

½´=

ttu{t

´ ¼ * =

wo

½´¶=

}„‚‡†~

* ¾9%8¿¹´ ¶=

}„‚‡†~«Šª

* =

}„‚‡†~

¹

.4@ B¾:,7+¿

BK µ =

golim

´ =

vhsgv

´¶=

}„‚‡†~

*¾:,7+¿¹

.5@ B¾:<,¿

BK µ ¼ *=

gg†‚vxh

½³ =

vhsgv

´=

vim

´¶=

}„‚‡†~

*¾:<,¿¹

/,@ B¾ +90¿

BK µ ¶´=

gul†

´=

mnvgulwg

´ =

}„‚‡†~ «¢

* =

}„‚‡†~

¹* ¼¾>¿ * ! ½

/-@ B¾796¿

BK µ ¼=

gulN

´=

shw

½*¼¾>¿ * ! ½

/.@ B¾,;9¿

BK µ ¼´=

gvv

³ =

rsv

³ =

shw

½*¼¾>¿ * ! ½

(29)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

)

) ))

//@ B¾ 04,¿

BK µ ¼´=

mo

½*¼¾>¿ * ! ½

/0@ B¾ 4+,¿

BK µ ¼=

pim

½*¼¾>¿ * ! ½

/1@ B¾ ¿

µ ¶´

URY

´

dc eaŽ —

*

dc ea

¹*¼¾¿ * ! ½

/2@ B¾¿

µ ¼

URY

´

VY

½*¼¾¿ * ! ½

/3@ B¾ ¿

µ ¼

VY

½*¼¾¿ * ! ½

/4@ B¾ ¿

µ ¶

S ^e

´

dc eaŽ ’š

*

dc ea

¹*¼¾¿ * ! ½

/5@ B¾ ¿

µ ¶´

S Xe

´

dc eaŽ ’”

*

dc ea

¹* ¼¾¿ * ! ½

0,@ B¾ ¿

µ ¶

P P P

´

dc eaŽŒ’Œ

*

dc ea

¹* ¼¾¿ * ! ½

0-@ B¾ ¿

µ ¶´

\RTT

´

dc eaŽ˜Ž—

*

dc ea

¹* ¼¾¿ * ! ½

(30)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

)

) ))

0.@ B¾ ¿

µ ¶´

P\Xe

´

dc eaŽŒ˜”

*

dc ea

¹* ¼¾¿ * ! ½

0/@ B¾ ¿

µ ¶´

P\Ze

´

dc eaŽŒ˜

*

dc ea

¹*¼¾¿ * ! ½

00@ B¾ ¿

µ ¶´

PPec\^Q

´

dc eaŽ‘’Ž

*

dc ea

¹*¼¾¿ * ! ½

01@ B¾ ¿

µ ¶´

PPec\^Q

´

dc eaŽ›Œ’

*

dc ea

¹* ¼¾¿ * ! ½

02@ B¾ ¿

µ ¶´

dc eaŽ —

*

dc ea

¹* ¼¾¿ * ! ½

03@ B¾ ¿

µ ¶´

PPec\^Q

´

dc eaŽ’Žš

*

dc ea

¹* ¼¾¿ * ! ½

04@ B¾ ¿

µ ¶´

PPec\^Q

´

dc eaŽ —

*

dc ea

¹*¼¾¿ * ! ½

05@ B¾ ¿

µ ¶´

dc eaŽ ˜

*

dc ea

¹* ¼¾¿ * ! ½

1,@ B¾ ¿

µ ¶´

PPec\^Q

´

dc eaŽ’ ˜

*

dc ea

¹*¼¾¿ * ! ½

(31)

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) '7@ %%@ %@! @&!&@! &$&! %@;! & '<@

)

) ))

1-@ B¾ ¿

µ ¶´

dc eaŽ —

*

dc ea

¹* ¼¾¿ * ! ½

1.@ B¾ ¿

µ ¶´

dc eaŽ“Ž

*

dc ea

¹* ¼¾¿ * ! ½

1/@ B¾ ¿

µ ¶´

dc eaŽ Ž

*

dc ea

¹* ¼¾¿ * ! ½

10@ B¾ ¿

µ ¶´

TU\P[S P

´

dc eaŽ‘˜

*

dc ea

¹*¼¾¿ * ! ½

11@ B¾$¿

µ ¼

P\X

³

S RT

³

S X

³

TU\P[S P

³

\RTT

½*¼¾¿ * ! ½

12@ B¾ ¿

µ ¶´

S _e

´

dc eaŽ ’

*

dc ea

¹*¼¾¿ * ! ½

13@ B¾ ¿

µ ¼

P[SN

½*¼¾¿ * ! ½

14@ B¾¿

µ ¶¾¿ *

dc ea

¹

15@ B¾¿

µ ¼

bXY\

½*¼¾¿ * ! ½

2,@ B¾¿

µ ¼

QV

½*¼¾¿ * ! ½

Figure

Table S1. Reaction equations (continued)
Table S1. Reaction equations (continued)
Table S2. Successive steps for model calibration
Figure S1. Experimental data and model simulation of cofactors and nucleotides concentrations·

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