Cancer RNA BiomarkersA cancer RNA biomarker refers to a coding or non-coding RNA that is indicative of the presence of cancer—either expressed by a tumor or expressed as a specific response of the body to the presence of cancer. Cancer researchers apply RNAscope® in situ hybridization to study the following:

Tumor heterogeneity—There is a tremendous amount of inter-tumor and intra-tumor heterogeneity. RNAscope’s single-molecule sensitivity with single-cell resolution along with intact morphological context allows for visualization of differential gene expressions in morphologically similar tumor cells.

Tumor microenviroment—A tumor is a complex organ comprised of many different cell types. Its communication with neighboring normal cells, extracellular matrix, and signaling molecules like chemokines, cytokines and growth factors is a major driver of cancer progression and metastasis. RNAscope ISH is particularly suited for dissecting complex autocrine and paracrine communication mechanisms.

Circulating tumor cells—The unprecedented high-fidelity signal amplification and multiplexing capability of RNAscope make it possible to simultaneously detect and characterize viable CTCs in the background of millions of blood cells.

RNAscope ISH enables visualization of RNA biomarkers while preserving tissue context with single-cell resolution. It is an essential solution in a multitude of cancer research applications

including risk assessment, diagnosis, prognosis, patient stratification, therapy and epidemiology.

Figure 1. Human breast cancer: EPCAM1 (red) & EGFR (green) expression in FFPE tissue; RNAscope 2-plex Chromogenic Kit

Above: Human breast cancer: HPRT1, POLR2A, PPIB and PGK mRNA expression in FFPE tissue

Figure 2: Human breast cancer: PanCK, uPA and PAI-1 expression in FFPE tissue; RNAscope Multiplex Fluorescent Kit

Product Overview

Partial list of publications using RNAscope® Technology in cancer research:

A collagen-remodeling gene signature regulated by TGF-ß signaling is associated with metastasis and poor survival in serous ovarian cancer. Cheon et al. (2014) PMID: 24218511

Possible role of Cdx2 in the serrated pathway of colorectal cancer characterized by BRAF mutation, high-level CpG Island methylator phenotype and mismatch repair-deficiency. Dawson et al. (2014) PMID: 24166180

In situ Tumor PD-L1 mRNA expression is associated with increased TILs and better outcome in breast carcinomas. Schalper et al. (2014) PMID: 24647569

The PAS positive material in gastric cancer cells of signet ring type is not mucin. Sørdal et al. (2014) PMID: 24589859

Utility of PAX8 mouse monoclonal antibody in the diagnosis of thyroid, thymic, pleural, and lung tumors: a comparison with polyclonal PAX8 antibody. Toriyama et al. (2014) PMID: 24592933

Visualize RNA biomarkers in your cancer tissues today acdbio.com/cancer

RNAscope®Probe List: Cancer RNA Biomarkers

RNAscope® Probes for Cancer RNA Biomarkers Get molecular detection with morphological context in a single assay.

CAT No. Gene

401191 ABCB1

404701 ACACA

408301 ACSL4

311811 ACTA2

310141 ACTB

559661 ADAM10

319711 ADRM1

602841 AGTR1

521761 AICDA

600941 ALB

310151 ALDH1A1

310151-C3 ALDH1A1

528741 ALDH1A2

314191 ALK

317841 ALK

314731 ALK

311841-C3 ALK

311841-C4 ALK

405671 ALOX12

405451-C2 AMACR

594511 ANGPT2

402881 ANKRD30A

400101 ANXA10

558931 ANXA6

314311 APOA1

560521 APOBEC3A

561751 APOBEC3B

405761 APOC3

404691 APOH

400491 AR

313111 AREG

313111-C3 AREG

401581 ARG1

401591 ARG2

538341 ARID1A

477211 ARPC5

406521 ASAP1

311011 ASCL2

405741 ATF4

494481 ATP4A

401361 AVP

400241 AXIN2

319641 AXL

602131 AXL

401861 AZGP1

310161 B2M

310161-C2 B2M

319841 BACH1

CAT No. Gene

407731 BBC3

407771 BCAR4

591721 BCL2

591721-C3 BCL2

408271-C4 BCL2L1

407251 BCL6

319931 BCR

409041 BDNF

560311 BIN1

562551 BIRC7

591931 BMI1

595251 BRAF

485471 BRCA1

485471-C2 BRCA1

401371 BRCA2

408681-C2 BRD4

464291 BTC

464291-C2 BTC

408431 BTG2

401601 BTLA

406161 BTLA

559341 CA9

559341-C2 CA9

605551-C2 CALCA

598461-C2 CALR

314401 CAST

557641 CAST

314411 CAST

314391 CAST

406001 CBFA2T3

496861 CBR3

539041 CCK

485911 CCKAR

311101 CCKBR

549171 CCL5

591821 CCND1

406901 CCR1

401881 CCR1

601501 CCR5

601501-C4 CCR5

403911 CCR6

488071 CCR8

407361 CD22

313021 CD24

313021-C3 CD24

316271 CD274

600861 CD274

311211 CD274

CAT No. Gene

539251-C2 CD34

560821-C2 CD34

539251-C4 CD34

560821-C4 CD34

555241 CD38

555241-C4 CD38

586341 CD3G

605601 CD4

408061 CD4

605601-C3 CD4

408071-C3 CD4

578471 CD40

542341 CD40LG

311271 CD44

311271-C4 CD44

555111 CD47

560591 CD68

560591-C2 CD68

560391 CD8A

560391-C2 CD8A

559231 CDA

311091 CDH1

311091-C2 CDH1

311091-C3 CDH1

310171 CDH2

407201 CDH3

403021 CDH9

311401 CDKN1A

607061 CDKN1B

408201 CDKN1C

310181 CDKN2A

401621 CDKN3

406261 CDX2

403031 CEACAM6

313661 CELA2A

313671 CELA3B

404351 CES1

404361 CES2

402101 CFB

317551 CFLAR

317561 CFLAR

603291 CFTR

311111 CHGA

311111-C2 CHGA

408121 CHI3L1

407951 CHRM1

310101 CHRNA7

492131 CLDN6

CAT No. Gene

606241 CLU

554801 CMKLR1

591521 CNR1

596021 CNR2

400741 COL11A1

401891 COL1A1

549431 COL3A1

549431-C3 COL3A1

313001 CSF1

310111 CSF1R

310811 CSF1R

313981 CSF2

402891 CTAG1B

560581 CTGF

554341 CTLA4

311731 CTNNB1

403981 CXADR

311851 CXCL10

311851-C2 CXCL10

311321 CXCL13

539251 CXCR3

310511 CXCR4

547161 CYP3A43

550331 CYP3A5

406171 DCBLD1

602031 DCK

593011 DCLK1

593011-C2 DCLK1

589521 DCN

312371 DDB2

311131 DDIT3

593591 DDR1

593591-C2 DDR1

551011 DDR2

316631 DEFA6

316631-C2 DEFA6

400751 DEFB4A

403041 DES

403051 DICER1

603001 DLL4

553991 DRD2

553991-C2 DRD2

561361 DUOX2

561361-C2 DUOX2

401261 DUOXA2

401261-C2 DUOXA2

402181 DUSP22

405361 DUSP6

CAT No. Gene

528301 EDNRB

408471 EDNRB

400621 EFNA3

557791 EFNA4

469161 EFNB3

605771 EGF

605771-C2 EGF

314001 EGFL7

319461 EGFR

310061 EGFR

310061-C2 EGFR

402911 EN2

601051 ENPP2

310281 EPCAM

310281-C5 EPCAM

463241-C2 EPGN

407441 EPHA2

406251 EPHB2

528991 EPHB3

516401 EPHB4

312191 EPOR

312671 ERBB2

310081 ERBB2

310081-C2 ERBB2

310081-C3 ERBB2

310081-C4 ERBB2

311941 ERBB3

311941-C2 ERBB3

407831-C2 ERBB4

310291 ERCC1

313081 EREG

604021 ERG

310301 ESR1

310301-C2 ESR1

310301-C4 ESR1

311411 ETV1

491521 ETV4

590371 ETV5

408971-C2 EWSR1

528941 EZH1

405491 EZH2

319861 F2RL1

407611 F3

593511 FBLN5

405801 FBXW7

555921 FCGR2A

401381 FDXR

584671 FERMT2

RNAscope® Human Cancer RNA Biomarker Probe List

Partial publications list (continued)

Programmed death ligand-1 expression in non-small cell lung cancer. Velcheti et al. (2014) PMID: 24217091

Application of circulating tumor cells scope technique on circulating tumor cell research. Yang et al. (2014)doi:10.1186/2052-8426-2-8

Monitoring Tumorigenesis and Senescence In Vivo with a p16 INK4a Luciferase Model. Burd et al. (2013) PMID: 23332765

The utility of immunohistochemistry for providing genetic information on tumors. Chan et al. (2013) PMID: 24065374

Cell-Autonomous and Non–Cell-Autonomous Mechanisms of HGF/MET–Driven Resistance to Targeted Therapies: From Basic Research to a Clinical Perspective. Corso, S, Giordano, S (2013) PMID: 23901039

Validation of esophageal squamous cell carcinoma candidate genes from high-throughput transcriptomic studies. Du Q et al. (2013) PMID: 23977449

The effects of unilateral truncal vagotomy on gastric carcinogenesis in hypergastrinemic Japanese female cotton rats. Fossmark et al. (2013) PMID: 23499800

Fibroblast growth factor receptor 1 as a putative therapy target in colorectal cancer. Göke et al. (2013) PMID: 24135816

Distribution of LGR5+ Cells and Associated Implications during the Early Stage of Gastric Tumorigenesis. Jang BG, Lee BL, Kim WH. (2013) PMID: 24340024

In situ analysis of HER2 mRNA in gastric carcinoma: comparison with fluorescence in situ hybridization, dual-color silver in situ hybridization, and immunohistochemistry. Kim et al. (2013). PMID: 23084583

CAT No. Gene

528301 EDNRB

408471 EDNRB

400621 EFNA3

557791 EFNA4

469161 EFNB3

605771 EGF

605771-C2 EGF

314001 EGFL7

319461 EGFR

310061 EGFR

310061-C2 EGFR

402911 EN2

601051 ENPP2

310281 EPCAM

310281-C5 EPCAM

463241-C2 EPGN

407441 EPHA2

406251 EPHB2

528991 EPHB3

516401 EPHB4

312191 EPOR

312671 ERBB2

310081 ERBB2

310081-C2 ERBB2

310081-C3 ERBB2

310081-C4 ERBB2

311941 ERBB3

311941-C2 ERBB3

407831-C2 ERBB4

310291 ERCC1

313081 EREG

604021 ERG

310301 ESR1

310301-C2 ESR1

310301-C4 ESR1

311411 ETV1

491521 ETV4

590371 ETV5

408971-C2 EWSR1

528941 EZH1

405491 EZH2

319861 F2RL1

407611 F3

593511 FBLN5

405801 FBXW7

555921 FCGR2A

401381 FDXR

584671 FERMT2

CAT No. Gene

312321 FFAR1

553981 FGF19

312111 FGF2

557241 FGF23

310071 FGFR1

311171 FGFR2

310791 FGFR3

405281 FLG

311221 FLI1

408981 FLI1

560701 FLT1

552441 FLT4

310311 FN1

310311-C2 FN1

310311-C3 FN1

580751 FOLR1

580751-C2 FOLR1

479871 FOLR2

319901 FOS

313201 FOXC2

406941 FOXM1

407231 FOXP1

407261 FOXP2

400501 FSHR

408101 FSHR

315051 FTL

317631 GAL

493901 GALR1

310321 GAPDH

310321-C4 GAPDH

403551 GATA3

579821 GATA4

486841 GATA5

603131 GATA6

600301 GDF15

499521 GDF2

499521-C2 GDF2

499711 GDF3

311801 GFAP

311801-C2 GFAP

489201 GLDC

310991 GLI1

310991-C2 GLI1

519821 GLP1R

519821-C3 GLP1R

407371-C2 GNLY

553421 GNRHR

310331 GRB7

CAT No. Gene

312831 GREM1

310621 GUCA2A

310601 GUCY2C

400771 H19

400771-C3 H19

607081 HAS2

316051 HAVCR2

560681 HAVCR2

524821 HBEGF

524821-C2 HBEGF

311191 HES1

311201 HEY1

310761 HGF

314331 HIF1A

605221 HIF1A

594851 HMGB2

594851-C3 HMGB2

319851 HMOX1

312341 HOTAIR

400221 HOXA13

400781 HOXB13

312211 HOXC6

583651 HPGD

310341 HPRT1

402191 HRH3

310681 HTR3A

560621 HTRA1

402951 ICAM1

407141-C2 ICOS

537491 IDH1

537791 IDH2

602681 IDO1

559781 IFNG

310501 IFNG

310501-C2 IFNG

412341 IFNL1

314641 IGF1

313031 IGF1

594361 IGF2

594361-C2 IGF2

558011 IGF2BP3

558011-C2 IGF2BP3

313061 IGFBP2

310351 IGFBP3

310351-C2 IGFBP3

316681 IGFBP7

312551 IGKC

602051 IL10

CAT No. Gene

316061 IL10

402061 IL12A

402071 IL12B

586241 IL13

546221 IL13RA2

310931 IL17A

310941 IL17F

400301 IL18

556791 IL1A

310361 IL1B

603491 IL1RL1

402041 IL2

404291 IL20RB

401251 IL21

560811 IL22

403811 IL22RA1

562851 IL23A

406891 IL23A

406881 IL23A

554761 IL23R

404301 IL24

542211 IL3

400111 IL33

315191 IL4

319391-C2 IL5

310371 IL6

310371-C2 IL6

557201 IL6R

408841 IL7R

310381 IL8

492041-C2 ILDR1

313571 INS

313571-C3 INS

406411 INSR

522691 IRAK1

457751 ITGA11

559021 ITGA6

559021-C3 ITGA6

555091 ITGAM

555091-C2 ITGAM

312491 ITGB6

605941 ITGB7

506871 ITGB8

546181 JAG1

403791 JAK2

403921 KCNA3

407741 KDM5A

312121 KDR

CAT No. Gene

591611 KDR

606401 KIT

606401-C2 KIT

407671 KITLG

601181 KLF5

582551 KLF9

582551-C2 KLF9

555151 KLK3

555151-C2 KLK3

310741 KLRC1

595101 KRAS

310201 KRT17

310211 KRT18

310211-C5 KRT18

310221 KRT19

549681 KRT20

310241 KRT5

547901 KRT5

310241-C2 KRT5

310241-C3 KRT5

550151 KRT7

550151-C3 KRT7

310261 KRT8

310261-C5 KRT8

316071 LAG3

553931 LAG3

408081 LAPTM4B

559441 LCN2

406371 LEPR

311021 LGR5

311021-C2 LGR5

311021-C3 LGR5

588991 LIN28A

596361 LIN28B

596361-C2 LIN28B

311341 LOXL2

483881 LPAR1

407421 LRIG1

310461 LTA

596391 MACC1

402921 MAGEA10

402931 MAGEB2

400811 MALAT1

603161 MAP3K5

402751 MAP3K8

408991 MAPT

601731 MCAM

588851 MCL1

CAT No. Gene

311781 MDM2

403711 MDM4

400821 MEG3

310051 MET

310051-C2 MET

588941 MGMT

310951 MITF

591771 MKI67

403411-C3 MMP13

408011 MMP14

311751 MMP2

403421-C2 MMP3

311331 MMP9

313811 MMP9

311331-C2 MMP9

603091 MPO

312461 MST1R

408421 MTA2

310631 MTNR1A

310391 MUC1

310391-C2 MUC1

310391-C3 MUC1

312911 MUC13

312871 MUC2

312871-C2 MUC2

312881 MUC4

312891 MUC5AC

312901 MUC6

311761 MYC

311761-C2 MYC

599311 NAMPT

604491 NANOG

604491-C2 NANOG

491071 NCSTN

582241 NDRG4

549451 NGF

406331 NGFR

583321 NID1

311861 NOTCH1

558991 NOTCH3

558991-C2 NOTCH3

555671 NQO1

582621 NR4A2

538501 NRF1

311181 NRG1

311181-C2 NRG1

313171 NTM

402631 NTRK1

CAT No. Gene

406391 NTRK1

402621 NTRK2

406341 NTRK3

406511 OCLN

498831 OGN

311041 OLFM4

594211 OSGIN1

554091 P2RX7

531491 PAF1

588881-C2 PAX6

402361 PAX8

403311 PBRM1

312201 PCA3

312201-C2 PCA3

312201-C3 PCA3

313851 PCAT1

553071 PCNA

316281 PDCD1

602021 PDCD1

316291 PDCD1LG2

551891 PDCD1LG2

406721 PDGFA

406701 PDGFB

404281 PDGFC

406711 PDGFD

604481 PDGFRA

604481-C2 PDGFRA

548991 PDGFRB

539751 PDPN

548451 PECAM1

548451-C2 PECAM1

311771 PGF

310401 PGK1

589751 PGR

312381 PHLDA3

435301 PIF1

603041 PIK3CA

603041-C4 PIK3CA

520981 PIK3CD

520981-C2 PIK3CD

590471 PIK3CG

590471-C2 PIK3CG

401901 PIM1

542701 PLAUR

599121 PMP22

402431-C3 PODXL

310451 POLR2A

310451-C2 POLR2A

CAT No. Gene

310451-C3 POLR2A

310451-C4 POLR2A

310451-C5 POLR2A

409181 POSTN

592861 POU5F1

592861-C2 POU5F1

592861-C3 POU5F1

313901 PPIB

313901-C2 PPIB

602231 PPM1D

401851 PRAME

407381-C3 PRF1

561721 PRKAB1

315811-C2 PRL

315811 PRL

542551 PRLR

542551-C2 PRLR

409331 PRNCR1

605331 PROCR

311261 PROM1

311261-C2 PROM1

530241 PROX1

530241-C2 PROX1

432791 PRUNE2

405781 PTCH1

310121 PTEN

408511 PTEN

407761 PTENP1

406791 PTGER2

406771 PTGER4

406781 PTGES2

406811 PTGS1

406801 PTGS2

537131 PTH1R

404141 PTK7

601991 PTPRC

601991-C4 PTPRC

403071 PVRL1

406951 PVT1

407641 PYCARD

559121 RAF1

545401 RARRES3

310551 REG1A

312051 REG1B

312061 REG3A

312071 REG4

586581 RIPK1

401181 RLN1

This document is provided for informational use only.For Molecular Biology Applications (MBA), not intended for diagnosis. Refer to appropriate regulations. RNAscope® is a registered trademark of Advanced Cell Diagnostics, Inc. in the United States or other countries. All rights reserved. ©2014 Advanced Cell Diagnostics, Inc. Doc#: 321088/040214/revA

Advanced Cell Diagnostics

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Visualize RNA biomarkers in your cancer tissues today acdbio.com/cancer

RNAscope® Human Cancer RNA Biomarker Probe List (continued)

Partial publications list (continued)

Intestinal Tumorigenesis. Méniel et al. (2013) PMID: 23935526

Deregulation of the cell polarity protein Lethal giant larvae 2 (Lgl2) correlates with gastric cancer progression. Nam et al. (2013) PMID: 24337435

The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Prensner et al. (2013) PMID: 24076601

Pin1 modulates ERß levels in breast cancer through inhibition of phosphorylation-dependent ubiquitination and degradation. Rajbhandari et al. (2013). PMID: 23542176

Cyclin D1̶a prognostic marker in oropharyngeal squamous cell carcinoma that is tightly associated with high-risk human papillomavirus status. Scantlebury et al. (2013) PMID: 23566410

High Heregulin Expression is Associated with Activated HER3 and

in Patients with Squamous Cell Carcinomas of the Head and Neck. Shames et al. (2013) PMID: 23468880

A mouse model of chronic prostatic

prostate cancer-derived isolate of Propionibacterium acnes. Shinohara et al. (2013) PMID: 23389852

Myeloid cell receptor LRP1/CD91 regulates monocyte recruitment and angiogenesis in tumors. Staudt et al. (2013) PMID: 23633492

CAT No. Gene

400251 RNF43

402831 ROR1

408601 ROR2

311061 RORC

556991 RORC

316871 ROS1

314321 ROS1

316861 ROS1

314751 ROS1

312391 RPS27L

310411 RRM1

402211 RTN4

400861 S100A11

310971 S100B

401931 S100P

491201 S1PR1

537881 S1PR3

475601 S1PR4

313421 SAT1

562251 SCN9A

315071 SEC61B

401941 SERPINB5

555961 SERPINE1

555961-C3 SERPINE1

313351 SFRP4

600951 SHH

600951-C2 SHH

311431 SLC18A2

588291 SLC24A4

606431 SLC29A1

407101 SLC34A2

407101-C3 SLC34A2

315831 SLC39A6

604741 SLC6A4

310561 SLC6A4

404371 SLFN11

CAT No. Gene

404231 SMAD2

404241 SMAD3

404251 SMAD4

521561 SMC1A

405831 SMO

560421 SNAI1

554581 SNAI2

605681 SNCA

409021 SNCA

408411 SOS1

400871 SOX2

404221 SOX9

405321 SPRY2

546711 SPRY4

310591 SST

310591-C2 SST

310581 SSTR1

310571 SSTR2

312841 SSTR3

312851 SSTR4

312861 SSTR5

498361 ST8SIA1

405851 STK39

408671 STK4

403581 SULF1

311421 SYP

310711 TAC1

551641-C2 TACC3

310701 TACR1

405471 TACSTD2

498961 TAGLN

405571 TAS2R38

601121 TBK1

314291 TBP

406561-C2 TCF7

312361 TERC

CAT No. Gene

605511 TERT

407431 TFF2

403101 TFF3

313131 TGFA

400881 TGFB1

407121 TGFB1

404581 TGFB2

407941 TGFBR2

403111 TLR2

605951 TLR3

311281 TLR4

541441 TLR7

542521 TLR8

402221 TMEM45A

310421 TNF

310421-C2 TNF

310721 TNFRSF10B

310801 TNFRSF12A

406961 TNFRSF13C

319731 TNFRSF14

319721 TNFRSF14

585791 TNFRSF17

400611 TNFRSF1A

310831 TNFRSF8

593451 TNFRSF8

406981 TNFSF13

406971 TNFSF13B

403121 TNFSF15

605201 TP53

601891 TP63

405481 TPBG

403931 TPBG

495221 TRIM23

319871 TRIM29

311951 TRPA1

312731 TSC2

CAT No. Gene

403541 TSLP

402841 TSPY1

403561 TTF1

588791 TUBB

318901 TUBB3

318901-C2 TUBB3

310431 TWIST1

602381 TXNIP

602381-C4 TXNIP

407341 UBB

402241 UBB

310041 UBC

310041-C2 UBC

310041-C3 UBC

594281 UCHL1

403131 UNC5C

405811 UPK2

311351 VEGFA

401951 VHL

310441 VIM

560461 VWF

560461-C2 VWF

560461-C4 VWF

584071 WNT2

604921 WNT5A

408231 WNT7A

313191 ZEB1

313191-C4 ZEB1

404271 ZEB2

Advanced Cell Diagnostics offers an ever-growing selection of RNA biomarker probes for virtually ANY genes from ANY species in ANY tissues.

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