Cis-regulatory somatic mutations andgene-expression alteration in B-cell lymphomas

A. Mathelier, C. Lefebvre, A.W. Zhang, D.J. Arenilas, J. Ding,W.W. Wasserman, and S.P. Shah

Genome Biology, 2015, 16:84

2015 June 8th

anthony.mathelier@gmail.com @AMathelier

1

A cancer gene discovery gap

M.S. Lawrence et al.,Nature, 2013.

I Highly mutated cancer genes revealed through The CancerGenome Atlas project.

I Still a discovery gap in the search of new cancer genes.I We assert this gap can be partially filled through the analysis

of the non-coding genome.2

Cis-regulatory mutations may impact gene expression

Variation

TF

..GATCC.. ..GAACC..

TF

TFBS

adapted from W. Shi’s figure

One needs to accurately locate TFBSs to identify and characterizethe regulatory sequences controlling specific genes transcription.

3

Cis-regulatory mutations may impact gene expression

Variation

TF

..GATCC.. ..GAACC..

TF

TFBS

adapted from W. Shi’s figure

One needs to accurately locate TFBSs to identify and characterizethe regulatory sequences controlling specific genes transcription.

3

Predicting cis-regulatory elements genome wide

...gctaaGTAACAATgcgca......cttaaGTAAACATcgctc...

...ccaatGTAAACAAacgga...

MANTA

Adapted from Szalkowski and Schmid.Briefings in Bioinfomatics, 2010

Mathelier et al.,Nucleic Acids Research, 2014.

4

TFBSs defined as cis-regulatory elements

I 477 ChIP-seq data from ENCODE and literature

I 103 TFs with a JASPAR2014 TF binding profiles

I 76,160,599bp in TFBSs predicted in ChIP-seq peaks(∼2% of the human genome)

5

Somatic cis-regulatory mutations in B-cell lymphomas

I Whole genome sequence for 84 B-cell lymphoma patientsamples with matched control samples :

I cohort 1 : 40 diffuse large B-cell lymphomas (DLBCL)I cohort 2 : 44 of mixed histology – 14 Burkitt lymphomas, 15

DLBCLs, 1 primary mediastinal B-cell lymphoma (PMBCL),and 14 follicular lymphomas (FL)

I 406,611 SNVs and 15,739 indels in samples from cohort 1

I 282,636 SNVs and 8,080 indels in samples from cohort 2

I RNA-seq for the cancer samples

Richter et al., Nat. Genetics, 2012 ; Morin et al., Blood, 2013

6

Promoters are frequent targets of cis-regulatory mutationsA BCohort1 Cohort2

1

2

3

4

5

6

7

89

10

11

12

13

14

15

16

17

18

19

20

21

22

x

y

HIST1H1B

ST6GAL1

TMSB

4X

ZFP36L1

NEDD9

BCL7A

RHOH

BIRC3

CIITA

IGLL5

BTG

2

SGK1

CD74

BCL2

BCL6

1

2

3

4

5

6

7

89

10

11

12

13

14

15

16

17

18

19

20

21

22

x

y

HIST1H1C

HIST1H1E

TMSB

4X

ZFP36L1

BCL2L11

BZRAP1

DNMT1

ZNF860

NCOA3

FOXO

1

BACH2

CXCR4

DUSP2

RFTN1

TCL1A

BCL7A

SOCS1

SEPT9

P2RX5

S1PR2

RHOH

EPS15

BIRC3

CIITA

DTX1

IGLL5

BTG

2

BTG1 SGK1

CD74CD83

BCL2

BCL6

PIM1

MYC

B2M

IRF1IRF4

LTB

ID3

p = 1.16 x 10-75 p = 3.28 x 10-156

I 12 genes targeted in both cohorts independentlyI Additional 13 genes from combined cohorts not previously

described as hypermutated−→ 6 of them exclusively mutated in their promoters

7

Promoters are frequent targets of cis-regulatory mutationsA BCohort1 Cohort2

1

2

3

4

5

6

7

89

10

11

12

13

14

15

16

17

18

19

20

21

22

x

y

HIST1H1B

ST6GAL1

TMSB

4X

ZFP36L1

NEDD9

BCL7A

RHOH

BIRC3

CIITA

IGLL5

BTG

2

SGK1

CD74

BCL2

BCL6

1

2

3

4

5

6

7

89

10

11

12

13

14

15

16

17

18

19

20

21

22

x

y

HIST1H1C

HIST1H1E

TMSB

4X

ZFP36L1

BCL2L11

BZRAP1

DNMT1

ZNF860

NCOA3

FOXO

1

BACH2

CXCR4

DUSP2

RFTN1

TCL1A

BCL7A

SOCS1

SEPT9

P2RX5

S1PR2

RHOH

EPS15

BIRC3

CIITA

DTX1

IGLL5

BTG

2

BTG1 SGK1

CD74CD83

BCL2

BCL6

PIM1

MYC

B2M

IRF1IRF4

LTB

ID3

p = 1.16 x 10-75 p = 3.28 x 10-156

I 12 genes targeted in both cohorts independentlyI Additional 13 genes from combined cohorts not previously

described as hypermutated−→ 6 of them exclusively mutated in their promoters

7

Promoters of apoptic, B-cell, and cancer pathway genesare frequent targets of cis-regulatory mutations

Cohort1

lymphoma

small cell lung cancer

apoptosis

in apoptotic signaling

role of mitochondria

hiv-1 nef: negative

effector of fas and tnf

keratinocyte differentiation

ceramide signaling pathway

regulation of B cell

proliferation

positive regulation of B

cell proliferation

lymphocyte differentiation negative

regulation of lymphocyte apoptotic process

leukocyte activation

negative regulation of B cell apoptotic

process

regulation of B cell activation

leukocyte differentiation

positive regulation of lymphocyte proliferation

regulation of cell growth

lymphocyte activation

T cell differentiation

positive regulation of B cell activation

negative regulation of intracellular

signal transduction

positive regulation of leukocyte

proliferation

regulation of type 2 immune

response

regulation of B cell apoptotic

process

negative regulation of T

cell differentiation

positive regulation of mononuclear

cell proliferation

GO BiologicalProcess OMIM

KEGGPathway BioCarta

FDR < 0.05

8

Landscape of mutations and altered gene expression

mutationTFBSProtein-coding exon

TSS

A

B

C

xseq input

PC and disrupting TFBS

Protein coding (PC)

PC and TFBSDisrupting TFBS

TFBS

MYCEYS

TP53PTPRD

SMARCA4BCL6RYR2ITPKBWWC1

FCGBPSGK1

TBL1XR1ID3

CSMD3SIN3A

VPS13CUNC5D

NBASMTOR

PPP1R16BUSP25ASCC3GPHN

DHX35PEX2

XRCC4PXDNJRKL

WHSC1L1FBXW11

SRP72CRIM1FOXO1DGKDPHIP

PYGLUSP15BRD2

C2CD3LMO4FMN2

SRFBP1N4BP2CCNG1RHOA

DUSP2TGFBR2ARRDC3CADPS2

PIM1STIM2

GNA13

SA32

1012

SA32

0920

SA32

0824

SA32

0932

SA32

1004

SA32

0860

SA32

0992

SA32

0830

SA32

1030

SA32

0914

SA32

0842

SA32

0818

SA32

0980

SA32

0998

SA32

0848

SA32

0866

SA32

1106

SA32

0872

SA32

1119

SA32

0968

SA32

0962

SA32

0944

SA32

1050

SA32

1048

SA32

0956

SA32

1021

SA32

1103

SA32

0836

SA32

0902

SA32

1128

SA32

0974 0 2 4 6 8 10 12

0

5

10

15

20Cohort2

Ding et al., submitted.

9

Landscape of mutations and altered gene expression

mutationTFBSProtein-coding exon

TSS

A

B

C

xseq input PC and disrupting TFBS

Protein coding (PC)

PC and TFBSDisrupting TFBS

TFBS

MYCEYS

TP53PTPRD

SMARCA4BCL6RYR2ITPKBWWC1

FCGBPSGK1

TBL1XR1ID3

CSMD3SIN3A

VPS13CUNC5D

NBASMTOR

PPP1R16BUSP25ASCC3GPHN

DHX35PEX2

XRCC4PXDNJRKL

WHSC1L1FBXW11

SRP72CRIM1FOXO1DGKDPHIP

PYGLUSP15BRD2

C2CD3LMO4FMN2

SRFBP1N4BP2CCNG1RHOA

DUSP2TGFBR2ARRDC3CADPS2

PIM1STIM2

GNA13

SA32

1012

SA32

0920

SA32

0824

SA32

0932

SA32

1004

SA32

0860

SA32

0992

SA32

0830

SA32

1030

SA32

0914

SA32

0842

SA32

0818

SA32

0980

SA32

0998

SA32

0848

SA32

0866

SA32

1106

SA32

0872

SA32

1119

SA32

0968

SA32

0962

SA32

0944

SA32

1050

SA32

1048

SA32

0956

SA32

1021

SA32

1103

SA32

0836

SA32

0902

SA32

1128

SA32

0974 0 2 4 6 8 10 12

0

5

10

15

20Cohort2

9

Predicted genes and their deregulated interactors areenriched for pathways related to cancer

Cohort2

phosphatidylinositol signaling system

chronic myeloid leukemia

gliomahuntingtons disease

focal adhesion pancreatic cancer

small cell lung cancer

endometrial cancer

non small cell lung cancer

colorectal cancer

cell cycle

prostate cancer

calcium signaling pathway

inositol phosphate metabolism

erbb signaling pathway

mapk signaling pathway

vegf signaling pathway

long term potentiation

fc epsilon ri signaling pathway

gnrh signaling pathway

Cohort1

chronic myeloid

leukemia

erbb signaling pathway

acute myeloid leukemia

pancreatic cancer

prostate cancer

endometrial cancer glioma

ecm receptor interaction

focal adhesionepithelial cell signaling in helicobacter

pylori infection

renal cell carcinoma

small cell lung cancer

oxidative phosphorylation

colorectal cancer

WikiPathways

FDR < 0.05

10

Cis-regulatory mutation and associated gene with alteredexpression

Scor

e di

ffere

nce

−20

24

68

bits

1

2

1 2 3 4 5 6 7 8 9 10 11

ATATCTGTGGATTGATAAGAGTCAGAATCACATATCTGTGGATTGATACGAGTCAGAATCAC

ref.alt.

GATA3

ReferenceAlternative

GNA13

Expression

Den

sity

0 50 100 150 200 2500.00

00.

002

0.00

40.

006

Expression in sampleharbouring mutation

SOS1

F2RL3

CTNNA1ARHGEF2

AGTR1

ARHGAP4

ADRA1D

PLEKHG5ARHGEF1

RASGRF2

TBXA2R

FGD1

ESR1

PIK3CA

ECT2

PIK3R2

SOS2

GNG2

ARHGEF6

TIAM1

RAC2

PIK3R1

VAV1

GNA13

ARHGEF18ARHGEF9

RGS22 RHOB

CTNNB1S1PR4

11

Summary

I We analyzed ∼ 700, 000 somatic mutations from 84 B-celllymphoma samples

I We characterized a set of cis-regulatory elements fromChIP-seq

I Cis-regulatory mutations are enriched in promoter regions ofgenes involved in apoptosis or growth/proliferation

I We combined gene expression and mutation data from thecoding and non-coding spaces

I We highlight candidate regulatory-disrupting variationsdysregulating the gene expression program in cancer pathways

12

Acknowledgements

Wasserman lab :I Wyeth WassermanI David ArenillasI Allen ZhangI all the Wasserman lab members

Shah lab :I Sohrab ShahI Calvin LefebvreI Jiarui Ding

Funding :

Centre for Molecular Medicine and Therapeutics

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