Genome-wide approach to identify transcripts induced by DNA - - PowerPoint PPT Presentation

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Genome-wide approach to identify transcripts induced by DNA - - PowerPoint PPT Presentation

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Genome-wide approach to identify transcripts induced by DNA demethylation in tumor cells Axelle Loriot Computational Biology and Bioinformatics de Duve Institute Methylation profiles are profoundly altered in cancer cells 5m Cytosine Cytosine

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SLIDE 1

Genome-wide approach to identify transcripts induced by DNA demethylation in tumor cells

Axelle Loriot Computational Biology and Bioinformatics de Duve Institute

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SLIDE 2

SOMATIC CELL TUMOR CELL GERMLINE SPECIFIC GENES

HYPOMETYLATION HYPERMETYLATION

TUMOR SUPPRESSOR GENES

5mCytosine

Cytosine

Methylation profiles are profoundly altered in cancer cells

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SLIDE 3

TUMOR CELL

Genome-wide approach to uncover the set of transcripts activated by DNA demethylation in tumors

Other tissue specific genes?

GERMLINE SPECIFIC GENES

Ø Other tissue specific genes reactivated by demethylation in tumors ? Ø Tumor specific transcripts could be isoforms using demethylated alternative promoters

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SLIDE 4

OMICS CATALOGUE OF LUNG ADENOCARCINOMA CELL LINES

Accession: PRJDB2256

RNA-seq

fastq

26 LUAD cell lines

Transcripts activated in cell lines showing an inverse correlation between methylation and expression

de novo transcript assembling

hisat2 StringTie

Bisulfite-seq

fastq

Normal tissues

BisMark Ø Tissue specificity analysis Ø Methylation profile analysis

METHODOLOGY

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SLIDE 5

214 transcripts identified

Reference gene No gene reference

Normal transcripts Alternative transcripts Unknown transcripts

128 63 23

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SLIDE 6
  • chr1. T

Normal tissues Tumor cell lines

lung sperm testis esophagus skin keratinocytes adipose colon liver pancreas stomach intestine placenta thyroid cortex heart fibroblasts A427 A549 ABC1 H1437 H1648 H1703 H1819 H1975 H2126 H2347 H322 LC2ad PC9 RERF_LC_Ad1 RERF_LC_Ad2 RERF_LC_KJ RERF_LC_OK VMRC_LCD H2228 II18 PC7 H1650 PC3 RERF_LC_MS H1299 PC14

AGO1: an example of alternative transcript activated by demethylation

Normal transcripts Alternative transcripts Unknown transcripts

128 63 23

Tumor cell lines

RERF_LC_Ad1 RERF_LC_Ad2 RERF_LC_KJ RERF_LC_OK RERF_LC_MS

Normal tissues

k

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SLIDE 7

Reference gene

Tissue specificity

RNAseq of 53 normal tissues Multiple samples per tissues Processed data only => Expression values are given at Gene level Normal transcripts Alternative transcripts Unknown transcripts

128 63 23

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SLIDE 8

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Tissue specificity

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

26 LUAD cell lines 50 normal tissues from Gtex

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SLIDE 9

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Lung

Tissue specificity

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

26 LUAD cell lines 50 normal tissues from Gtex

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SLIDE 10

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Lung Testis

Testis specific genes

Tissue specificity

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

26 LUAD cell lines 50 normal tissues from Gtex

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SLIDE 11

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Lung Testis Colon (transverse) Small intestine Stomach Kidney (cortex) Kidney (medulla) Liver Pancreas

Testis specific genes Gut genes

Tissue specificity

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

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SLIDE 12

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Lung Skin Vagina Esophagus (mucosa)

Testis specific genes Gut genes

Tissue specificity

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

Stratified epithelium genes Squamous stratified epithelium

Testis

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SLIDE 13

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Is the activation of these genes in LUAD tumors associated to particular clinical features ? Ø tumor Stage Ø Tumor grade Ø Survival

Survival analyses

Testis specific genes Gut genes

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

Stratified epithelium genes

slide-14
SLIDE 14

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Is the activation of these genes in LUAD tumors associated to particular clinical features ? Ø tumor Stage Ø Tumor grade Ø Survival

Bad prognosis Goog prognosis

Survival analyses

AS1 SLC22A18AS

log1p(TPM) 2 4 6 matrix_4

Stratified epithelium genes

slide-15
SLIDE 15

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + ++ + p = 0.0026

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

ADGRF4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + ++ ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + p < 0.0001

0.00 0.25 0.50 0.75 1.00 2000 4000 6000

Time Survival probability

FAM83A + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0034

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time Survival probability

EPGN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.00018

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

KRT16 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + ++ ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0012

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

SERPINB5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + + p = 0.00027

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

TNS4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0031

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time Survival probability

DSG3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + + + p = 0.0036

0.00 0.25 0.50 0.75 1.00 2000 4000 6000

Time

GPR87 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + p = 4e−04

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

GPR78

Strata +

+

group=neg group=pos

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + p = 0.0058

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

GJB5

Bad prognosis Goog prognosis

Survival analyses

slide-16
SLIDE 16

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + ++ + p = 0.0026

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

ADGRF4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + ++ ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + p < 0.0001

0.00 0.25 0.50 0.75 1.00 2000 4000 6000

Time Survival probability

FAM83A + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0034

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time Survival probability

EPGN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.00018

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

KRT16 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + ++ ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0012

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

SERPINB5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + + p = 0.00027

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

TNS4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + p = 0.0031

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time Survival probability

DSG3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +++ + + + p = 0.0036

0.00 0.25 0.50 0.75 1.00 2000 4000 6000

Time

GPR87 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + p = 4e−04

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

GPR78

Strata +

+

group=neg group=pos

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + p = 0.0058

0.00 0.25 0.50 0.75 1.00 2000 4000 6000 8000

Time

GJB5

Bad prognosis Goog prognosis

Survival analyses

slide-17
SLIDE 17

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

CONCLUSION

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Ø Associated to bad prognosis Ø Prognosis biomarkers Ø Oncogenic functions ? Stratified epithelium genes

slide-18
SLIDE 18

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

CONCLUSION

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

Activation of “stratification” genes ?

Multilayer mass of cells Esophagus epithelium Skin epithelium Vagina epithelium

squamous stratified epithelium LUAD Ø Associated to bad prognosis Ø Prognosis biomarkers Ø Oncogenic functions ? Stratified epithelium genes

alveoli epithelium of lung

slide-19
SLIDE 19

LUAD cell lines Normal tissues (GTEx)

GDPD4 TDRD1 DNAH8 CCDC33 C9ORF84 LINC01511 MAGEA1 DDX53 MAGEA11 FTHL17 NAA11 MAGEC1 LINC01518 PASD1 MAGEA4 AC074389.2 RNF17 INSL6 MAGEC2 MAGEB2 DSCR8 TAF7L PRAME FMR1NB BRDT AC109635.4 COX7B2 CT83 AC063977.6 CCDC144NL ST8SIA6−AS1 AC010168.1 LINC00689 CCDC144NL−AS1 CSAG1 AC090502.1 AP002383.3 AL160408.1 POTEF AC092506.1 FAM9C ZBTB46−AS1 ANKRD62 Z98257.1 LINC00200 AC106771.1 AC100839.1 AC023824.3 AC087269.1 AC109635.2 LINC02492 AC097374.1 BAGE2 MKRN9P AC099520.1 MAGEA12 LIN28B BCAR4 INSL4 AC010894.3 PLCE1−AS1 MUC13 EPS8L3 PHGR1 ARL14 BCL2L15 DQX1 TFF1 HNF4A VIL1 SLC39A5 HGD DRAIC HAVCR1 HNF1A−AS1 HNF1A SLC22A18AS ABCC2 NPC1L1 ANGPTL3 XDH FAM25A ADGRF4 ABCA12 ZNF812P FAM83A EPGN TPRXL GPR78 KRT16 LY6D SERPINB5 ALDH3B2 DSG3 GPR87 GJB5 A2ML1 TNS4 MIR205HG C5ORF17 IGBP1P4 LINC01115 AC022733.1 LINC00355 LINC01194 LINC01446 DSCR4 AL929601.1 AC090809.1 LINC02008 LINC02438 MIR548XHG RPS4XP8 AC012363.1 BBOX1−AS1 FILNC1 CASC19 AL117329.1 CLDN10−AS1 TRPM2−AS1 LINC02526 AL109741.2 ZNF556 MKRN3 LINC00460 PNLDC1 TRIM55 KCTD4

log1p(TPM) matrix_4 Gr

CONCLUSION

H322 H1648 PC9 RERF_LC_Ad2 H1650 RERF_LC_KJ H1437 H2126 LC2ad H2347 RERF_LC_Ad1 H1975 II18 H2228 ABC1 A549 PC3 H1703 H1819 H1299 A427 RERF_LC_MS RERF_LC_OK PC14 VMRC_LCD PC7

MSTRG.26453.1

Lung Testis Adipose_subcut Adipose_visc Spleen Ovary Fallopian_tube Uterus Whole_blood Muscle Heart_2 Heart_1 Artery_tibial Artery_aorta Artery_coronary Brain_1 Brain_2 Brain_3 Brain_6 Brain_7 Brain_8 Brain_9 Brain_10 Brain_11 Brain_12 Brain_13 Brain_4 Brain_5 Pituitary Adrenal_gland Nerve Thyroid Colon_sigmoid Colon_transv Small_intestine Stomach Kidney_cortex Kidney_medulla Liver Pancreas Bladder Prostate Salivary_gland Breast Skin_1 Skin_2 Vagina Esophagus_mucosa Esophagus_gastr_junct Esophagus_musc

Group

alveoli epithelium of lung

Activation of “stratification” genes ?

Multilayer mass of cells

LUAD Ø Associated to bad prognosis Ø Prognosis biomarkers Ø Oncogenic functions ? Stratified epithelium genes Other epithelium stratified genes are also activated in LUAD tumors by a mechanism independent of DNA methylation Ø « Stratification » gene signature in LUAD tumors ? Preliminary results:

slide-20
SLIDE 20

Actions de Recherches concertées

Pr Charles De Smet Anna Diacofotakis

Genetics and Epigenetics Unit De Duve Institute belgium

Pr Laurent Gatto

Computational Biology and Bioinformatics de Duve Institute