188 2
1 78
351 2 365 2
1 288 3 116
65 3 100 2 116 7
1 42 3 25 4 51
39 10 38 6 26 33 59 2
4 27 5 13 10 38 0 18
35 9 30 3 50 8 34 3 25 3
2 54 14 26 9 34 5 10 3 10
OFC
vmPFC
aINS
NAc
vSUB
dlPFC OFC vmPFC aINS NAc
130 2
2 260
86 3 174 8
1 111 4 115
52 4 88 5 88 1
0 125 2 94 1 72
89 15 71 25 103 3 66 1
1 40 21 25 3 25 0 30
42 5 149 6 134 2 75 1 70 2
0 141 6 131 1 79 4 72 3 22
OFC
vmPFC
aINS
NAc
vSUB
dlPFC OFC vmPFC aINS NAc
Females
1.3
Males >25
20
15
10
5
0 -lo
g(co
rrec
ted
p-v
alu
e)
a b >25
20
15
10
5
0 -lo
g(co
rrec
ted
p-v
alu
e)
1.3
Supplementary Figure 1.
Nature Medicine: doi:10.1038/nm.4386
Supplementary Figure 2.
1321 1427
211
1058 2432
258
1131
3030
419
BA46
Hippocampus
Striatum
Fem
ale
Male
23
1
18
5
13
9
92
46
0
-log(p-value)
Nature Medicine: doi:10.1038/nm.4386
0
40
80
120
160
Female Male
# o
f M
odule
s
Conserved LOC GOC
Chartreuse Blue Cyan 2
Gold 2
Khaki Lightyellow
Navy
Purple
Wheat
a b c Rhodopsin-like rc act.
Cholesterol Biosynt.
Transcrip. fact bind.
Glucuronosyltransf act.
Inflammatory resp.
Reg. lymph act.
Axoneme
Reg. Catechol. met.
Amine rc act.
Nerve Ensheath.
Olfactory rc act.
Cell projection
Synaptic transm.
Chromatin
GTP metabolism 1 210 1
0
500
1000
1500
2000
2500
3000
3500
5000
10000
Module
siz
e
MDC 1
Fem
ale
MD
D M
odule
s
Male MDD Modules
Pi3k-Akt signal.
Ca2+ signal.
Neurotrans. rc act.
Neurotransmission
Neuron differentiation
Reg. of catechol. met.
Transcription factor
Inflammatory resp.
Amine rc. act.
Neuropeptide rc act.
Nerve ensheathment
0
400
800
1200
1600
0 5 10
Module
siz
e
MDC
d e
20 40 60
Fold Enrichment
Supplementary Figure 3.
Nature Medicine: doi:10.1038/nm.4386
GOC Conserved
Neuron (2.2E-18)
Neuron (2.2E-4)
Neuron (4.6E-8)
Neuron (5.1E-3)
Microglia (1.0E-110)
Endoth Cells (4.1E-14)
Astrocyte (5.2E-46)
Neuron (1.1E-8)
Neuron (1.3E-15)
Neuron (1.4E-5)
Astrocyte (5.1E-3)
Neuron (8.6E-4)
Neuron (9.5E-4)
LOC
Myel.Oligod (1.3E-56)
Neuron (1.0E-2) 5000
0
10000
15000
20000
25000
Male CTRL vs Male MDD Modules
Mo
du
le S
ize
Conserved GOC
Neuron (1.2E-2)
Neuron (8.0E-3)
Neuron (6.6E-4)
Neuron (1.5E-13)
Neuron (6.0E-2)
Neuron (6.0E-2)
Neuron (1.3E-3)
5000
0
10000
15000
20000
25000
Neuron (2.4E-5)
Neuron (1.9E-4)
Astrocyte (1.0E-4)
Neuron (4.6E-6)
Astrocyte (1.6E-81)
Neuron (2.2E-10)
Astrocyte (8.8E-6)
Neuron (8.6E-18)
Endo Cell (7.4E-4)
Myel. Oligo. (2.0E-71)
Neuron (3.9E-2)
Neuron (1.4E-2)
Neuron (2.0E-5)
Microglia (9.7E-38)
Neuron (1.1E-8)
Microglia (2.3E-3)
Microglia (3.8E-3)
Mo
du
le S
ize
Female CTRL vs Female MDD Modules a b
Supplementary Figure 4.
Nature Medicine: doi:10.1038/nm.4386
2.7e-11 4.1e-8
1.4e-5 5.3e-3
5.1e-6 4.4e-5
Female NAc
Female NAc
Male NAc
Male NAc
Female vmPFC
Female vmPFC
Male vmPFC
Male vmPFC
↑
↓
↓
↓
↓
↑
↑
↑
1 2 3 4
Odd Ratio
Supplementary Figure 5.
Nature Medicine: doi:10.1038/nm.4386
75
50
37
25
Phospho-Erk (Green line indicates lanes for mouse male in main figure)
75
50
37
25
Total Erk (Green line indicates lanes for mouse male in main figure)
50
37
Actin (Green line indicates lanes for mouse male in main figure)
75
50
37
25
Phospho-Erk (Green line indicates lanes for mouse female in main figure)
75
50
37
25
Toal Erk (Green line indicates lanes for mouse female in main figure)
Actin (Green line indicates lanes for mouse female in main figure)
50
37
Supplementary Figure 6.
Nature Medicine: doi:10.1038/nm.4386
100 75
50
37 50
37
Phospho-Erk (Green line indicates lanes for human male in main figure)
50
37
Toal Erk (Green line indicates lanes for human male in main figure)
100 75
50
37
Actin (Green line indicates lanes for human male in main figure)
50
37
Phospho-Erk (Green line indicates lanes for human female in main figure)
100 75
50
37
Toal Erk (Green line indicates lanes for human female in main figure)
Actin (Green line indicates lanes for human female in main figure)
100 75
50
37
Supplementary Figure 7.
Nature Medicine: doi:10.1038/nm.4386
a
b
c
d
Supplementary Figure 8.
20 m m
GAD67
pERK
GF P
*
Female GFP+/pERK
GAD+/pERK
% o
f C
ells
Male
% o
f C
ells
GFP+/pERK
GAD+/pERK
*
e
Nature Medicine: doi:10.1038/nm.4386
*
Peru
Habituation
1 week
D1 D2 D3 D7 D0 D4 D5 D6
Males
1217 2778
195
d
f
i
h
CVS 21 Days
Emx1 OE
CVS 21 Days
Emx1 OE
1 -1 Log FC
Supplementary Figure 9.
Hub/node
↑ DEG / ↓ DEG in
Emx1 OE/Dusp6 KD
16 13 10 7 3 0
-log(p value)
Male
Em
x1 O
E
Male CVS
Gray26
Females
Habituation
1 week
D1 D2 D3 D4 D0
c
g
b
e
a
1350 5364
781
Translation
Precursor metabolites…
Phosphate metabolic…
sGTPase mediated…
Ras protein signal…
Ribosome
Cytosol
Ribonucleoprotein…
Mitochondrial part
Mitochondrial…
0 2 4 6 8 10
Constituent of ribosome
Ribonucleotide binding
Cation transmemb.…
ATP binding
ATPase coupled activity
-log10(Benjamini pval)
Biological
processes
Cellular
components
Molecular
functions
CVS 21 Days
Dusp6 KD
CVS 21 Days
Dusp6 KD 1
-1
Log F
C
164 131 98 66 33 0
-log(p value)
Fem
ale
Dusp6 K
D
Female CVS
Nature Medicine: doi:10.1038/nm.4386
Supplementary Figure 10.
Nature Medicine: doi:10.1038/nm.4386
Supplementary Table 1. Postmortem sample demographics
* Prescribed for sleep disorders
Legend: PMI: postmortem interval; OFC: orbitofrontal cortex; dlPFC: dorsolateral prefrontal
cortex; vmPFC: ventromedial prefrontal cortex; aINS: anterior insula; Nac: nucleus accumbens;
vSUB: ventral subiculum.
Male CTRL Male MDD Female CTRL Female MDD
Age 41.2 ± 11.3 46.7 ± 15.7 58.1 ± 19.5 43.7 ± 11.6
pH 6.53 ± 0.28 6.68 ± 0.31 6.59 ± 0.32 6.65 ± 0.19
PMI 25.0 ± 14.4 31.8 ± 13.8 29.8 ± 31.9 22.5 ± 18.1
RIN OFC 7.02 ± 0.79 7.11 ± 1.20 7.31 ± 1.27 7.55 ± 0.72
RIN dlPFC 7.39 ± 0.54 7.34 ± 0.76 6.90 ± 0.63 7.29 ± 0.45
RIN vmPFC 6.88 ± 1.04 6.43 ± 0.89 6.41 ± 0.74 6.42 ± 0.95
RIN aINS 6.48 ± 0.92 6.18 ± 1.05 6.98 ± 1.27 6.62 ± 1.15
RIN Nac 7.08 ± 0.54 7.65 ± 0.92 7.74 ± 0.43 8.00 ± 0.51
RIN vSUB 6.79 ± 0.54 7.61 ± 0.93 7.00 ± 0.97 7.18 ± 0.60
Smoking
(NA/No/Moderate/Heavy) 6/4/0/3 5/3/0/5 1/4/0/4 3/3/1/6
Alcool 0 0 2 2
Drug of abuse 0 0 0 0
Antidepressant 0 4 2* 9
History of abuse 2 3 3 2
Cause of death
(Accident/Natural/Suicide) 3/3/7 0/0/13 1/3/5 0/0/13
Nature Medicine: doi:10.1038/nm.4386
Supplementary Table 5. Postmortem validation cohort sample socio-demographics
Male NanoString validation cohort
Male CTRL Male MDD
N 17 15
Age 41.8 ± 12.1 42.0 ± 17.3
pH 6.6±0.3 6.6±0.3
PMI 18.7 ± 4.0 21.6 ± 3.1
Smoking
(NA/ No/Moderate/Heavy) N/A N/A
Alcohol (NA/Yes) 1/4 1/6
Drug of abuse (NA/Yes) 0/2 1/6
Antidepressant 0 9
History of abuse (NA/Yes) 3/1 3/2
Cause of death
(NA/Accident/Natural/Suicide) 1/0/16/0 0/1/14/0
Legend: PMI: postmortem interval
Nature Medicine: doi:10.1038/nm.4386
Supplementary Table 6. Postmortem validation cohort sample socio-demographics
Female NanoString validation cohort
Legend: PMI: postmortem interval
Female
CTRL
Female
MDD
N 12 6
Age 61.6 ± 9.5 42.0 ± 11.6
pH 6.2 ± 0.4 6.6 ± 0.4
PMI 20.7 ± 5.4 23.7 ± 10.8
Smoking
(NA/No/Moderate/Heavy) 0/7/2/3 0/3/0/3
Alcohol (Yes/NA) 0/1 4/0
Drug of abuse 1 4
Antidepressant 0 4
History of abuse 1 4
Cause of death
(NA/Accident/Natural/Suicide) 0/0/11/1 0/1/1/4
Nature Medicine: doi:10.1038/nm.4386
Extended Table 12. Transcriptional overlap in DEG from male MDD and female MDD is
maintained for genes that are sexually dimorphic at baseline
Sexually dimorphic (Sex. Dimorp.) genes: DEG in male CTRL vs female CTRL
Male MDD: DEGs in male MDD vs male CTRL
Female MDD: DEGs in female MDD vs CTRL
Male and Female MDD: DEGs in males and females with MDD
Nature Medicine: doi:10.1038/nm.4386