THE UMD TP53 MUTATION DATABASE UPDATES AND BENEFITS … · 2019. 12. 12. · Data-driven unbiased...
Transcript of THE UMD TP53 MUTATION DATABASE UPDATES AND BENEFITS … · 2019. 12. 12. · Data-driven unbiased...
THE UMD TP53 MUTATION DATABASE
UPDATES AND BENEFITS
Pr. Thierry Soussi
TP53: 33 YEARS AND COUNTING
P. May
STRUCTURE FUNCTION RELATIONSHIP OF WILD AND MUTANT TP53
1983 Oren et al.
1984 Crawford et al.
1988 Soussi et al.
1987 Soussi et al.
1988 Soussi et al.
2000 Levine et al.
37°C
37°C
25°C
25°C
40°C
TP53: 33 YEARS AND COUNTING
P. May
STRUCTURE FUNCTION RELATIONSHIP OF WILD AND MUTANT TP53
1983 Oren et al.
1984 Crawford et al.
1988 Soussi et al.
1987 Soussi et al.
1988 Soussi et al.
2000 Levine et al.
2015 Soussi et al. A. Pompeii 60°C
Which TP53 residues are important for TP53 folding ? How these residues have evolved to ensure TP53 function from 0° to 60°C What is the status of these residues in human cancer ?
Wild type ? mutant ? associated with more deleterious clinical features ? http://p53.fr
37°C
37°C
25°C
25°C
40°C
TP53 MUTATIONS IN HUMAN CANCER
GENE MUTATION: FROM DISCOVERY TO APPLICATION
THE TP53 MUTATION DATABASE
TP53 MUTATION ANALYSIS IN THE NEXT DECADE
TP53 MUTATIONS IN HUMAN CANCER
ONCE UPON A TIME
OR
A NEW MUTATED GENE IN HUMAN CANCER
IT iS STORY TIME!
A NEW MUTATED GENE IN HUMAN CANCER!
TP53!
Inci
denc
e
Discovery PHASE I Causes
Total number of variants (cumulated)
Discovery rate of novel variants
Variant detection
Inci
denc
e In
cide
nce
Discovery
I.F.
PHASE I Causes
Total number of variants (cumulated)
Discovery rate of novel variants
Consequences
Variant detection
Publications Inconsistant
reports
Inci
denc
e
Discovery Consolidation PHASE II
Variant detection
Causes
Total number of variants (cumulated)
Discovery rate of novel variants
Clinical value
No clinical value X
Inci
denc
e In
cide
nce
Discovery
I.F.
Publications
Consolidation PHASE II
Variant detection
Causes
Total number of variants (cumulated)
Discovery rate of novel variants
Consequences
Inconsistant reports
Clinical value
No clinical value X
Inci
denc
e
Causes
Total number of variants (cumulated)
Discovery Application Consolidation PHASE III
Variant detection
Discovery rate of novel variants
Inci
denc
e In
cide
nce
Causes
Total number of variants (cumulated)
Discovery
Consequences I.F.
Publications Inconsistant
reports
Application Consolidation PHASE III
Variant detection
Discovery rate of novel variants
TP53 MUTATIONS IN HUMAN CANCER
GENE MUTATION: FROM DISCOVERY TO APPLICATION
THE TP53 MUTATION DATABASE
TP53 MUTATION ANALYSIS IN THE NEXT DECADE
THE p53 MUTATION DATABASE
October 2015
3,900 PUBLICATIONS 60,000 MUTATIONS
"unbiased" compilation of "every" TP53 mutations published in the literature
+ TCGA and ICGC unpublished data
http://p53.fr
Bernard Leroy and Thierry Soussi
7 200 TP53 VARIANTS 1750 missense variants 5450 indel variants
TP53 MUTATION HETEROGENEITY AND DATABASE FREQUENCY
TP53 MUTANTS (1,750 VARIANTS)
R175H (1 600 x) R273H (1 100x)
800 variants 1x 400 variants 2x
hot spot variants
rare variants
WHAT IS THE BIOLOGICAL SIGNIFICANCE OF THESE RARE VARIANTS ????
2,314 p53 mutants representing all possible amino acid substitutions caused by a point mutation throughout the entire protein (5.9 substitutions per residue) have been constructed The transcriptional activity of all these mutants was analyzed in a yeast based functional assay For each p53 mutant, a quantitative value of the remaining activity is available
TP53 MUTATION HETEROGENEITY
0
25
50
75
100
125
150
175
1x 2x 3-5x 6-9x 10-49x 50-99x >99
AC
TIVI
TY (%
wt p
53)
FREQUENCY
TP53 MUTATION HETEROGENEITY
ONLY TUMORS HAVE BEEN INCLUDED IN THE ANALYSIS
161_
+
81_1
60
41_8
0
21_4
09_
20 4-8
2_3 1
Tum
ors
cell l
ine
germ
line
-2
0
2
4
0
AC
TIVI
TY (%
)
100
REMAINING ACTIVITY OF MUTANT TP53 ACCORDING TO THEIR FREQUENCY IN THE DATABASE
FREQUENCY
NS
NS
NS
P<0.001
TP53 MUTATION HETEROGENEITY
Are they randomly distributed in the
literature ?
Are they associated with other unusual features ?
What is the contribution of these "rare" mutations to tumorigenesis
passenger mutations ? PCR and sequencing artefacts ? Weak mutations ?
TP53 MUTATION HETEROGENEITY
2,018 publications with 5 or more reported mutations
Frequency of each mutant in the db
Each publication was ranked according:
Remaining activity of each mutant
Number of tumors with multiple mutations
Number of tumors synonymous mutations
Tum 2x Tum 3x Tum >3x
Number of tumors with recurrent mutations
Edlund, K. et al. Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors. Proc Natl Acad Sci U S A 109, 9551-9556 (2012).
THE p53 MUTATION DATABASE
Included >90% of the publications
Outliers 7 % of the publications (2 sigma) or 1% (5 sigma) Multiple tumours with more than 1 TP53 mutations Multiple tumours with rare variants Multiple tumours with a high frequency of synonymous variants
PARAFFIN EMBEDDED TISSUE
THE p53 MUTATION DATABASE
Only 2 papers describing TP53 mutations in lymphoma have been flagged Both papers used DNA from paraffin embeded tissue
TP53 MUTATIONS IN HUMAN CANCER
GENE MUTATION: FROM DISCOVERY TO APPLICATION
THE TP53 MUTATION DATABASE
TP53 MUTATION ANALYSIS IN THE NEXT DECADE
THE TP53 PATHWAY: A COMPLEX NETWORK
1985-2005
2005-
TP53 activities are modulated by the ratio of the various isoforms
THE TP53 PATHWAY: A COMPLEX NETWORK
TP53 ISOFORMS: WHATS IMPORTANCE ?
6.6%
17.8%
p.P110L
TP53 exon 9 beta and gamma are poorly analyzed
They are not included in the majority of commercial exon selection kit
They are excluded from most analytical pipelines (labeled as intron)
They are excluded in custom arrays
TP53 ISOFORMS: WHATS IMPORTANCE ?
Revised guidelines for screening of TP53 gene mutations Bernard Leroy , Mandy L. Ballinger , Gareth L. Bond , Antony Braithwaite , Nicole Concin , Lawrence A. Donehower , Wafik S. El-Deiry , Pierre Fenaux , Gianluca Gaidano , Anita Langerød , Eva Hellstrom-Lindberg , Richard Iggo , Jacqueline Lehmann-Che , Phuong L. Mai , David Malkin , Ute M. Moll , Jeffrey N. Myers , Kim E. Nichols , Sarka Pospisilova , Davide Rossi, Sharon A. Savage, Louise C. Strong , Patricia N. Tonin , Robert Zeillinger , Thorsten Zenz ,Joseph F. Fraumeni Jr. , Pierre Hainaut and Thierry Soussi
TP53 ISOFORMS: WHATS IMPORTANCE ?
ASSESSING TP53 STATUS IN HUMAN CANCER
STRATEGY
MUTATION VALIDATION
METHODOLOGY
ANALYSIS OF TP53 MUTATIONS IN HUMAN CANCER
All coding exons with +/- 5 intronic extension Application phase
Intron 9
ANALYSIS OF TP53 MUTATIONS IN HUMAN CANCER
screening beta and gamma exons
Discovery phase
TP53 RE Int Promoter
ASSESSING TP53 STATUS IN HUMAN CANCER
Intron 4
Intron 4 promoter
Discovery phase
TP53 RE Int Promoter Intron 4
Intron 9
ASSESSING TP53 STATUS IN HUMAN CANCER
3'UTR
3’UTR ? Discovery phase
ASSESSING TP53 STATUS IN HUMAN CANCER
STRATEGY
MUTATION VALIDATION
METHODOLOGY
ASSESSING TP53 STATUS IN HUMAN CANCER
CONVENTIONAL SEQUENCING SANGER
HIGH-THROUGHPUT SEQUENCING
TUMOUR WITH MULTIPLE TP53 MUTATIONS
Multiple tumoral clones with different mutations
TUMOR HETEROGENEITY
ASSESSING TP53 STATUS IN HUMAN CANCER
STRATEGY
MUTATION VALIDATION
METHODOLOGY
Sequencing artefacts ? Passenger mutations ? Very rare neutral SNP ? Driver mutations ?
R72P R213R P47S
R283C R283H R156H P222L
?
N235S R290H
TP53 SNP CAN BE VERY UNFREQUENT
More than 150,000 TP53 gene have been sequenced
P36P
R72P R213R P47S
R283C R283H R156H P222L
?
N235S R290H
TP53 SNP CAN BE VERY UNFREQUENT
More than 150,000 TP53 gene have been sequenced
P36P
R72P R213R P36P
ASSESSING TP53 STATUS IN HUMAN CANCER
STRATEGY
MUTATION VALIDATION
METHODOLOGY
Sequencing artefacts ? Passenger mutations ? Very rare neutral SNP ? Driver mutations ?
Inci
denc
e In
cide
nce
Causes
Total number of variants (cumulated)
Discovery
Consequences I.F.
Publications Inconsistant
reports
Application Consolidation PHASE III
Variant detection
Discovery rate of novel variants
TP53 MUTATION HETEROGENEITY AND DATABASE FREQUENCY
TP53 MUTANTS (1,750 VARIANTS)
R175H (1 600 x) R273H (1 100x)
800 variants 1x 400 variants 2x
hot spot variants
rare variants
cut off: TP53 frequeny Remaining activity Frequency in outliers studies
THE p53 MUTATION DATABASE
http://p53.fr
TP53 Variants 7,200 Variants
TP53 Mutation 60,000 mutations
Each publication are flagged with a statistical index
cDNA variant
c.524G>A
Polyphen: Damaging Mutassessor: Damaging Condel: Damaging Provean: Damaging Splice assessor: Splice Neutral Variant
PREDICTION
wt
p.R175H
RESIDUAL ACTIVITY
Comment Isoforms
This mutation targets the 12 TP53 isoforms
Comment Frequency
This mutation is very frequent
Comment Activity
No activity
Comment Prediction
Damaging
Comment Outliers
No specific association
Comment Splice
No defect predicted
Frequency
2307
138
Hemopathies
38
CLL
14
MDS
for ERIC
Protein variant
p.R175H
ALL ISOFORMS
p.R175H p.R175H p.R136H p.R136H p.R136H p.R43H p.R43H p.R43H p.R16H p.R16H p.R16H
cDNA variant
c.375G>T
Protein variant
p.T125T
p.T125T p.T125T p.T86T p.T86T p.T86T p.= p.= p.= p.= p.= p.=
wt
p.T125T
Polyphen: No data Mutassessor: No data Condel: No data Provean: No data Splice assessor: Splice Neutral Variant
PREDICTION RESIDUAL ACTIVITY
ALL ISOFORMS
Frequency
74
4
Hemopathies
4
CLL
0
MDS
for ERIC
Comment Frequency
This mutation is not frequent
Comment Activity
No data
Comment Isoforms
This mutation targets 6 TP53 isoforms
Comment Prediction
No data
Comment Outliers
No specific association
Comment Splice
This exonic mutation, close to a splice site, has been predicted to impair splicing; high confidence index
No data
cDNA variant
c.704A>G
Protein variant
p.N235S
p.N235S p.N235S p.N196S p.N196S p.N196S p.N103S p.N103S p.N103S p.N76S p.N76S p.N76S
wt
p.N235S
Polyphen: Tolerated Mutassessor: Low Condel: Benign Provean: Damaging Splice assessor: Splice Neutral Variant
PREDICTION RESIDUAL ACTIVITY
ALL ISOFORMS
Frequency
39
8
Hemopathies
5
CLL
0
MDS
for ERIC
Comment Frequency
This mutation is no frequent
Comment Activity
Fully active
Comment Isoforms
This mutation targets the 12 TP53 isoforms
Comment Prediction
Probably Benign
Comment Outliers
No specific association
Comment Splice
No defect predicted
TP53 MUTATIONS ARE HETEROGENOUS
EXON 4 -9
R175H deficient for apoptosis and cell cycle arrest R175P deficient for apoptosis only
17p deletion Notch deletion association with another TP53 mutation early versus late
TP53 MUTATIONS AND ERIC
TP53 MUTATIONS IN CLL
ERIC program
Other parameters can be discussed
Ola Larsson
Thierry Soussi
Adam Ameur
Ignas Bunikis
Ulf Gyllensten
Bernard Leroy Jean L. Fournier
Karolina Edlund
Magnus Sundström
Patrick Micke
Johan Botling
ACKNOWLEDGEMENTS