www.sciencesignaling.org/cgi/content/full/12/571/eaau5755/DC1

Supplementary Materials for

Excitatory neuron–specific SHP2-ERK signaling network regulates synaptic

plasticity and memory

Hyun-Hee Ryu, TaeHyun Kim, Jung-Woong Kim, Minkyung Kang, Pojeong Park, Yong Gyu Kim, Hyopil Kim, Jiyeon Ha, Ja Eun Choi, Jisu Lee, Chae-Seok Lim, Chul-Hong Kim, Sang Jeong Kim, Alcino J. Silva,

Bong-Kiun Kaang, Yong-Seok Lee*

*Corresponding author. Email: yongseok7@snu.ac.kr

Published 5 March 2019, Sci. Signal. 12, eaau5755 (2019)

DOI: 10.1126/scisignal.aau5755

The PDF file includes:

Fig. S1. The second probe trials after extended trainings. Fig. S2. Short-term memory test in object place recognition. Fig. S3. Effects of expressing SHP2D61G in excitatory or inhibitory neurons on basal synaptic transmission and PPF ratio. Fig. S4. Effect of SHP2D61G on ERK activation in PV+ neurons. Fig. S5. The total number of p-ERK1/2+ neurons and viral vector–expressing cells were not significantly different between EYFP- and SHP2D61G-infected hippocampi. Fig. S6. Validation of the quality of cell sorting and bioinformatic workflow. Fig. S7. Comparison of GAB1 protein abundance in vGAT+ and vGAT– neurons in vGAT-Cre;tdTomato mice. Fig. S8. The effect of GAB1Y627F on the interaction of SHP2D61G with GAB1 and ERK activation. Fig. S9. The second probe trials after extended trainings in rescue experiments. Legends for tables S1 to S4

Other Supplementary Material for this manuscript includes the following: (available at www.sciencesignaling.org/cgi/content/full/12/571/eaau5755/DC1)

Table S1 (Microsoft Excel format). List of 3482 DEGs. Table S2 (Microsoft Excel format). Functional annotation of 3482 DEGs. Table S3 (Microsoft Excel format). Expression profile of RASopathy-associated genes. Table S4 (Microsoft Excel format). Primer sequences for qRT-PCR validation.

Fig. S1. The second probe trials after extended trainings. (A) Swim speed during the 1st

probe test, αCaMKII-Cre::EYFP, n = 7 mice; αCaMKII-Cre::SHP2D61G

, n = 7 mice, unpaired

t-test, P = 0.597 (B) Distance moved during the 1st probe test, EYFP, n = 7; SHP2

D61G, n = 7,

unpaired t-test, P = 0.952 (C) Performance of αCaMKII-Cre::SHP2D61G

and αCaMKII-

Cre::EYFP mice in the 2nd

probe test. Time spent in each quadrant, αCaMKII-Cre::EYFP, n =

7 mice; αCaMKII-Cre::SHP2D61G

, n = 7 mice, two-way repeated measure ANOVA,

interaction between virus and quadrant, F3, 36 = 0.374, P = 0.772. (D) Mean distance

(proximity) to platform for the probe test with mice described in (C), unpaired t-test, P =

0670. (E) Performance of vGAT-IRES-Cre::SHP2D61G

and vGAT-IRES-Cre::EYFP mice in

the 2nd

probe test. Time spent in each quadrant, vGAT-IRES-Cre::EYFP, n = 11 mice; vGAT-

IRES-Cre::SHP2D61G

, n = 16 mice; two-way repeated measure ANOVA, interaction between

virus and quadrant, F3, 75 = 1.144, P = 0.337. (F) Mean distance to platform, unpaired t-test, P

= 0.435.

Fig. S2. Short-term memory test in object place recognition. Both αCaMKII-

Cre::SHP2D61G

and αCaMKII-Cre::EYFP mice showed preference for the relocated object in

short-term object place recognition test. EYFP, n = 6 mice, one sample t-test, hypothetical

value 50 %, **P < 0.01; SHP2D61G

, n = 7 mice, ***P < 0.005.

Fig. S3. Effects of expressing SHP2D61G

in excitatory or inhibitory neurons on basal

synaptic transmission and PPF ratio. (A and B) αCaMKII-Cre::SHP2D61G

and αCaMKII-

Cre::EYFP showed comparable basal synaptic transmission and paired-pulse facilitation ratio.

(A) Plots show the fEPSP as a function of stimulation intensity. αCaMKII-Cre::EYFP, n = 58

slices from 25 mice; αCaMKII-Cre::SHP2D61G

, n = 60 slices from 26 mice, two-way repeated

measure ANOVA, effect of virus, F1, 57 = 3.383, P = 0.071 (B) Plots show the paired-pulse

facilitation ratio. αCaMKII-Cre::EYFP, n = 58 slices from 25 mice; αCaMKII-Cre::SHP2D61G

,

n = 60 slices from 26 mice, two-way repeated measure ANOVA, effect of virus, F1, 57 = 1.444,

P = 0.234 (C-D) vGAT-IRES-Cre::SHP2D61G

and vGAT-IRES-Cre::EYFP showed similar

basal synaptic transmission and paired-pulse facilitation ratio. (C) Plots show the fEPSP as a

function of stimulation intensity. vGAT-IRES-Cre::EYFP, n = 32 slices from 15 mice; vGAT-

IRES-Cre::SHP2D61G

, n = 38 slices from 19 mice; two-way repeated measure ANOVA, effect

of virus, F1, 680 = 0.573, P = 0.452 (D) Plots show the paired-pulse facilitation ratio. vGAT-

IRES-Cre::EYFP, n = 32 slices from 15 mice; vGAT-IRES-Cre::SHP2D61G

, n = 38 slices from

19 mice, two-way repeated measure ANOVA, effect of virus, F1, 340 = 0.239, P = 0.627.

Fig. S4. Effect of SHP2D61G

on ERK activation in PV+ neurons. (A) PV-Cre::SHP2

D61G

and PV-Cre::EYFP mouse hippocampal CA1 region immunostained for p-ERK1/2 and HA.

(B) Proportions of hippocampal neurons that were p-ERK-positive were comparable between

PV mice infused with SHP-2D61G

-HA vector and in PV-Cre mice infused with EYFP. PV-

Cre::EYFP, n = 7 slices from 4 hippocampi; PV-Cre::SHP2D61G

, n = 13 slices from 4

hippocampi; unpaired t-test, P = 0.900, Scale bar, 20 μm. Data are expressed as the mean ±

SEM.

Fig. S5. The total number of p-ERK1/2+ neurons and viral vector–expressing cells were

not significantly different between EYFP- and SHP2D61G

-infected hippocampi. (A to C)

The total numbers of p-ERK1/2 positive neurons. (A) αCaMKII-Cre::EYFP, n = 14 slices

from 4 hippocampi; αCaMKII-Cre::SHP2D61G

, n = 16 slices from 4 hippocampi; unpaired t-

test, P = 0.111. (B) vGAT-IRES-Cre::EYFP, n = 9 slices from 4 hippocampi; vGAT-IRES-

Cre::SHP2D61G

, n = 9 slices from 4 hippocampi; unpaired t-test, P = 0.478. (C) vGAT-IRES-

Cre::EYFP, n = 8 slices from 4 hippocampi; vGAT-IRES-Cre::KRASG12V

, n = 6 slices from 4

hippocampi; unpaired t-test, P = 0.635. (D to F) The numbers of viral vector-expressing cells.

(D) αCaMKII-Cre::EYFP, n = 14 slices from 4 hippocampi; αCaMKII-Cre::SHP2D61G

, n = 16

slices from 4 hippocampi; unpaired t-test, P = 0.101. (E) vGAT-IRES-Cre::EYFP, n = 9 slice

from 4 hippocampi; vGAT-IRES-Cre::SHP2D61G

, n = 9 slice from 4 hippocampi; unpaired t-

test, P = 0.194. (F) vGAT-IRES-Cre::EYFP, n = 8 slices from 4 hippocampi; vGAT-IRES-

Cre::KRASG12V

, n = 6 slices from 4 hippocampi; unpaired t-test, P = 0.559.

Fig. S6. Validation of the quality of cell sorting and bioinformatic workflow. (A)

Validation of the quality of cell sorting by qualitative real-time polymerase chain reaction

(qRT-PCR). Relative expression levels of known marker genes for αCaMKII+

excitatory (red)

and vGAT+

inhibitory (blue) neuron. Two independent cDNA libraries per cell type were

used with triple technical repeats. Error bars represent the mean ± SEM. (B) Bioinformatic

workflow. Diagram showing the steps for filtering and defining the differentially expressed

genes from the RNA-seq data. (C) Density plot shows the distribution of gene expression

level in each cell type and a comparison before (black) and after filtering the RNA-seq data

(blue or red). (D) PCA analysis showing clear segregation of two cell types.

Fig. S7. Comparison of GAB1 protein abundance in vGAT

+ and vGAT

– neurons in

vGAT-Cre;tdTomato mice. (A) Representative image of immunohistochemistry in vGAT-

Cre;tdTomato mouse. Alexa 488 (green), Gab1. White arrows indicate tdTomato+/Gab1

+ cells.

Scale bar, 20 μm. (B) Bar graph represents proportions of neurons that were Gab1-positive

either in tdTomato+ or tdTomato

- neurons. Numbers of counted cells are indicated. Unpaired

t-test, ***P < 0.005, Data are mean ± SEM.

Fig. S8. The effect of GAB1Y627F

on the interaction of SHP2D61G

with GAB1 and ERK

activation. (A) Western blot assessing the interaction with SHP2D61G

in HEK293T cells were

transfected with CMV-GFP, CMV-Flag-SHP2D61G

-MYC, GAB1WT

-MYC or GAB1Y627F

-

MYC as indicated. Input samples were immunoblotted for MYC (GAB1

WT or GAB1

Y627F)

and Flag (SHP2D61G

). Cell lysates were immunoprecipitated using Flag. Unpaired t-test, *P <

0.05. Blots are representative of three biological replicates. (B) Western blot for MYC

(GAB1), SHP2, p-ERK1/2, and total ERK1/2 in cell lysates from the transfected HEK293T

cells described in (A). The cells were treated with EGF (1mg/ml, 5min) for ERK activation.

Blots are representative of three biological replicates. Data are mean ± SEM, analyzed by

unpaired t-test, **P < 0.01, *** P < 0.005.

Fig. S9. The second probe trials after extended trainings in rescue experiments. (A)

αCaMKII-Cre::EYFP, αCaMKII-Cre::GAB1Y627F

, αCaMKII-Cre::SHP2D61G

, and αCaMKII-

Cre::SHP2D61G

/GAB1Y627F

mice spent similar time in the TQ during the 2nd

probe tests.

αCaMKII-Cre::EYFP, n = 9 mice; αCaMKII-Cre::GAB1Y627F

, n = 10 mice; αCaMKII-

Cre::SHP2D61G

, n = 14 mice; αCaMKII-Cre::SHP2D61G

/GAB1Y627F

, n = 12 mice; two-way

repeated measure ANOVA, interaction between virus and training days, P = 0.993. (B) All

groups of mice had a similar average distance from the platform location during the 2nd

probe

tests. αCaMKII-Cre::EYFP, n = 8 mice; αCaMKII-Cre::GAB1Y627F

, n = 10 mice; αCaMKII-

Cre::SHP2D61G

, n = 14 mice; αCaMKII-Cre::SHP2D61G

/GAB1Y627F

, n = 12 mice; one-way

ANOVA, P = 0.995. Data are mean ± SEM.

Table S1. List of 3482 DEGs. Excel spreadsheet file showing the list of differentially

expressed genes (fold change > 2, P < 0.015) in hippocampal αCaMKII+ neurons or vGAT

+

neurons.

Table S2. Functional annotation of 3482 DEGs. Excel spreadsheet file showing results

from the pathway enrichment analyses of the differentially expressed genes listed in Table S1.

Table S3. Expression profile of RASopathy-associated genes. Excel spreadsheet file

showing the expression profile of RASopathy-associated genes in hippocampal αCaMKII+

and vGAT+ neurons. NS, Noonan syndrome; CS, Costello syndrome; CFC, cardio-facio-

cutaneous syndrome; NSML, Noonan syndrome with multiple lentigines; NFLS,

Neurofibromatosis Type 1-like syndrome; NF1, neurofibromatosis type 1.

Table S4. Primer sequences for qRT-PCR validation. Primer sequences for quantitative

real time PCR (pRT-PCR). Provided as an Excel file.