Background
Methods
Patient population and ethics
Patient ID | Sample | PAM50 subtype | ER | PR | HER2 | HER2 CNV (exome data) | AdjCT | AdjHT | AdjRT | DFI | Relapse site | Relapse to death | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P1 |
Primary Tumor
Metastasis
| 3 |
NA
Luminal B | + - | + - | - - | HER2- HER2- | + | + | + | 3.3 | liver | 3.2 |
P2 |
Primary Tumor
Metastasis
| 3 |
NA
Basal like | -
NA
| -
NA
| -
NA
| HER2- HER2- | + | – | + | 1.4 | lymph | 4.9 |
P3 |
Primary Tumor
Metastasis
| 3 |
Na
Luminal B
| - - | + - | -
NA
| HER2- HER2- | – | – | + | 4.1 | liver | 1.5 |
P4 |
Primary Tumor
Metastasis
| 3 |
NA
Basal like | -
NA
| -
NA
|
NA
NA
| HER2+ (CN 3.5) HER2+ (CN 3.5) | + | + | + | 8.1 | lung | 6.0 |
P5 |
Primary Tumor
Metastasis
| N/A |
NA
Luminal A | + + | - - | -
NA
| HER2- HER2+ (CN 2.5) | – | + | + | 3.5 | liver | 5.7 |
P6 |
Primary Tumor
Metastasis
| 3 |
NA
HER2 enriched | + + | + - |
NA
- | HER2- HER2- | + | + | + | 2.6 | lymph | 1.1 |
P7 |
Primary Tumor
Metastasis
| 2 |
NA
Normal like | + + | + - |
NA
- | HER2- HER2- | + | + | + | 4.8 | skin | 0.8 |
P8 |
Primary Tumor
Metastasis
|
NA
NA
| + + | + + | - - | HER2+ (CN 2.4) HER2- (CN 0.8) | + | + | + |
5
a
| liver | 0.7 | |
P9 |
Primary Tumor
Metastasis
|
NA
NA
| - - | - - |
NA
- | HER2- HER2- | + | – | + |
11
a
| breast |
NA
| |
P10 |
Primary Tumor
Metastasis
|
NA
NA
| + + | + + | - - | HER2- HER2- | + | + | + |
4
a
| bone | 0.4 |
Cohort 1: DNA extraction and exome capture
Cohort 1: Variant detection
Cohort 2: DNA extraction and exome capture
Cohort 2: Variant detection
CNV calculations
LOH calculations
Microarray
Control experiment
Results
The number of somatic mutations was significantly different between primary tumor and metastatic lesion
Metastasis n = 10 (%) | Primary tumors n = 10 (%) | Primary tumors TCGA (%) | |
---|---|---|---|
KMT2C | 6 (60) | 1 (10) | 8 |
AFF2 | 3 (30) | 3 (30) | 2 |
KMT2A | 3 (30) | 1 (10) | 2 |
MED12 | 3 (30) | 1 (10) | 2 |
ASXL1 | 3 (30) | 1 (10) | 1 |
FBXO11 | 3 (30) | 0 | 1 |
TP53 | 2 (20) | 1 (10) | 35 |
ARID1A | 2 (20) | 1 (10) | 4 |
NF1 | 2 (20) | 1 (10) | 3 |
AKAP13 | 2 (20) | 0 | 2 |
APC | 2 (20) | 1 (10) | 2 |
ARID1B | 2 (20) | 1 (10) | 2 |
ATRX | 2 (20) | 1 (10) | 2 |
CDK12 | 2 (20) | 0 | 2 |
KDM6A | 2 (20) | 0 | 2 |
CDH1 | 1 (10) | 0 | 7 |
PIK3CA | 0 | 1 (10) | 36 |
AKAP12 | 2 (20) | 0 | 1 |
ALK | 2 (20) | 1 (10) | 1 |
ARID2 | 2 (20) | 1 (10) | 1 |
BAP1 | 2 (20) | 0 | 1 |
CAMTA1 | 2 (20) | 1 (10) | 1 |
CLTC | 2 (20) | 0 | 1 |
DICER1 | 2 (20) | 0 | 1 |
EML4 | 2 (20) | 0 | 1 |
EPS15 | 2 (20) | 0 | 1 |
GNAS | 2 (20) | 0 | 1 |
KDM5A | 2 (20) | 1 (10) | 1 |
KDR | 2 (20) | 0 | 1 |
MET | 2 (20) | 0 | 1 |
MYH11 | 2 (20) | 0 | 1 |
NIN | 2 (20) | 0 | 1 |
NUMA1 | 2 (20) | 0 | 1 |
NUP98 | 2 (20) | 0 | 1 |
PCSK7 | 2 (20) | 3 (30) | 1 |
PDGFRB | 2 (20) | 1 (10) | 1 |
Ti/Tv
Mutations in the AKAP gene family are enriched in metastases
Gene | Position | CytoBand | Mutation | Exon | A.A substitution | Protein region | SIFT Prediction | Primary VAF | Metastasis VAF | Patient |
---|---|---|---|---|---|---|---|---|---|---|
AKAP1 | ||||||||||
AKAP2 | ||||||||||
AKAP3 | ||||||||||
AKAP4 | ||||||||||
AKAP5 | chr14:64935761 | 14q23 | G > A | 2/2 | Asp217Asn | NA | damaging | 5.2% | 0% | P2 |
AKAP6 | chr14:33293693 | 14q12 | G > A | 13/14 | Gly2225Glu | NA | tolerated | 0% | 17% | P1 |
AKAP7 | ||||||||||
AKAP8 | chr19:15484018 | 19q13.12 | G > A | 1/11 | Gln169X | MCM2 binding domain | nonsense | 0% | 15% | P4 |
AKAP9 | chr7:91708964 | 7q21.2 | G > A | 31/50 | Ser2518Asn | close to PKA-R domain | tolerated | 0% | 9% | P1 |
AKAP10 | chr17:19861659 | 17p11.2 | A > G | 4/15 | Leu182Pro | RGS1 binding domain | damaging | 0% | 16% | P1 |
AKAP11 | ||||||||||
AKAP12 | chr6:151670403 chr6:151671474 | 6q25.1 | G > A G > A | 4/5 4/5 | Gly293Arg Ala650Thr | EGFR interaction domain EGFR interaction domain | damaging damaging | 0% 0% | 22% 15% | P5 P10 |
AKAP13 | chr15:86124141 chr15:86122728 | 15q25.3 | C > T G > A | 7/15 7/15 | Gln948X Asp477Asn | NA close to PKA-RII domain | nonsense damaging | 0% 0% | 10% 16% | P4 P5 |
AKAP14 |
Gene | Position | CytoBand | Mutation | Exon | A.A substitution | Protein region | SIFT Prediction | Primary VAF | Axillary lymph VAF | Metastasis 1 VAF | Metastasis 2 VAF | Patient |
---|---|---|---|---|---|---|---|---|---|---|---|---|
AKAP1 | ||||||||||||
AKAP2 | ||||||||||||
AKAP3 | chr12:4725047 | 12p13.32 | G > A | 5/5 | Ser807Leu | NA | damaging | 2% | – | 13% | 41%, 22%a | pat 19 |
AKAP4 | chrX:49958130 | Xp11.22 | A > G | 5/6 | Phe412Leu | NA | damaging | 0% | 0% | 22%b | 26% | pat 8 |
AKAP5 | ||||||||||||
AKAP6 | ||||||||||||
AKAP7 | ||||||||||||
AKAP8 | ||||||||||||
AKAP9 | chr7:91630327 | 7q21.2 | A > G | 8/50 | Ile366Val | close to bindning domain | tolerated | 4% | – | 24%, 36%a | pat 7 | |
AKAP10 | ||||||||||||
AKAP11 | chr13:42875448 | 13q14.11 | G > A | 8/13 | Asp856Asn | NA | tolerated | 0% | – | 8% | pat 12 | |
AKAP12 | ||||||||||||
AKAP13 | ||||||||||||
AKAP14 |
AKAP cytogenetics
P1 | P2 | P3 | P4 | P5 | P8 | # Amp in cohort 2 | # Del in cohort 2 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Chr region | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis | Primary | Metastasis |
AKAP1 | 17q22 | amp | 10 | 11 | |||||||||||||
AKAP5 | 14q23 | del | 0 | 1 | |||||||||||||
AKAP6 | 14q12 | del | 4 | 5 | |||||||||||||
AKAP7 | 6q23.2 | del | del | del | del | del | 1 | 4 | 0 | 2 | |||||||
AKAP8 | 19q13.12 | amp | 6 | 9 | 1 | ||||||||||||
AKAP11 | 13q14.11 | del | del | del | del | 0 | 2 | ||||||||||
AKAP12 | 6q25.1 | del | del | del | del | del | 0 | 2 | 2 | 3 |