resin (TAAB Laboratories Equipment Ltd., Aldermaston, UK). Semi-thin sections were stained with toluidine blue, and areas of the sections were selected for ...
Cell Reports, Volume 19
Supplemental Information
Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS Claire E. Hall, Zhi Yao, Minee Choi, Giulia E. Tyzack, Andrea Serio, Raphaelle Luisier, Jasmine Harley, Elisavet Preza, Charlie Arber, Sarah J. Crisp, P. Marc D. Watson, Dimitri M. Kullmann, Andrey Y. Abramov, Selina Wray, Russell Burley, Samantha H.Y. Loh, L. Miguel Martins, Molly M. Stevens, Nicholas M. Luscombe, Christopher R. Sibley, Andras Lakatos, Jernej Ule, Sonia Gandhi, and Rickie Patani
Supplementary Figure 1. Trancriptional evidence of VCP-mutant motor neuron perturbations in synapse structure and assembly, and ion channel expression. Related to Figure 2.
A
Synapse assembly and structure SLITRK4 ENST00000356928
TPM [log2]
3.0 2.5 2.0 1.5 1.0 0.5 0.0
SLITRK2 ENST00000335565
**
3 2 1 d3MN
d17MN
0
TPM [log2]
***
**
4 3 2 1 0
B
d3MN
d3MN
d17MN
3.0 2.5 2.0 1.5 1.0 0.5 0.0
PTPN5 ENST00000396168
NLGN4Y ENST00000382872 5
***
4
d17MN
7 6 5 4 3 2 1 0
Key CBLN2 ENST00000269503
Control VCP mutant
***
*,**,*** P-val < 0.1,0.05,0.01
d3MN
d17MN
ACHE ENST00000440755
**
**
4 3 2 1
d3MN
d17MN
0
d3MN
d17MN
Voltage-gated Ca+ channels CACNA1B ENST00000371357
TPM [log2]
CACNA1A ENST00000360228 3.0 2.5 2.0 1.5 1.0 0.5 0.0
5 4 3 2 d3MN
d17MN
1
d3MN
d17MN
CACNB1 ENST00000394303 6 5 4 3 2 1 0
d3MN
d17MN
CACNB3 ENST00000551544 3.0 2.5 2.0 1.5 1.0 0.5 0.0
CACNG2 ENST00000300105 4
*
3 2 1 0 d3MN
d17MN
d3MN
d17MN
Delayed rectifier K+ channels KCNA6 ENST00000280684
KCNA2 ENST00000633222
TPM [log2]
4 3
**
**
4
0.8
3
0.6
2
KCNB1 ENST00000371741
1.0
2
0.4
1
0.2
1
0
0.0
0
d3MN
d17MN
d3MN
d17MN
d3MN
d17MN
KCNH2 ENST00000330883 6.0 5.5 5.0 4.5 4.0 3.5 3.0
KCNQ2 ENST00000626839 6 5 4 3 2
d3MN
d17MN
1
d3MN
d17MN
Inward rectifier K+ channels KCNJ3 ENST00000295101
TPM [log2]
2.0 1.5 1.0 0.5 0.0
d3MN
d17MN
KCNJ5 ENST00000529694
KCNJ4 ENST00000303592 4.0 3.5 3.0 2.5 2.0 1.5 1.0
4 3
d3MN
d17MN
**
***
4 3
2
2
1
1
0
d3MN
d17MN
KCNJ11 ENST00000339994
KCNJ9 ENST00000368088
0
d3MN
d17MN
3.0 2.5 2.0 1.5 1.0 0.5 0.0
d3MN
d17MN
Na* channels and synaptic density SCN2A ENST00000480032
SCN9A ENST00000454569
*
TPM [log2]
2.0
3
1.0
2
0.5
1
0.0
0
d3MN
d17MN
***
4
1.5
d3MN
d17MN
DLG4 ENST00000399506
SLC12A5 ENST00000243964
SYNPO ENST00000307662
5
8
2.0
4
7
1.5
3
6
2
5
1
4
0
3
d3MN
d17MN
1.0 0.5 d3MN
d17MN
0.0
d3MN
d17MN
Glutamate receptor GRIN2A ENST00000396575
**
TPM [log2]
4
GRM3 ENST00000361669
**
5 4
3
3
2
GRIK2 ENST00000369134
GRM7 ENST00000389335
GRIK5 ENST00000301218
2.0
4
5
1.5
3
4
**
1.0
2
3
1
1
0.5
1
2
0
0
0.0
0
2
d3MN
d17MN
d3MN
d17MN
d3MN
d17MN
d3MN
d17MN
1
*
d3MN
d17MN
Supplementary Figure 1. (A) We provide transcriptional evidence for mutation-dependent effects on synapse assembly and structure, predominantly at a later differentiation stage (d17 motor neurons) with the following genes: SLITRK4, SLITRK2, CBLN2, NLGN4Y, PTPN5, ACHE. (B) Looking at an array of different ion channels, we find further specific evidence of perturbation, specifically in the delayed rectifier potassium channel KCNA2, the inward rectifier potassium channel KCNJ5, the sodium channel SCN2A and glutamate receptors GRIN2A and GRM7. Technical n=6, across 5 different cell lines (2 x control and 3 x VCP mutant). Transcripts that showed a log twofold differential expression and a P-value < 0.05, and that were reliably expressed in either VCP mutant or control condition were considered as changing significantly. *** = p
