Resolving Equivocal HER2 Status in Breast Cancer by Automated and Quantitative RNA Chromogenic In Situ Hybridization (CISH)

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1 Resolving Equivocal HER2 Status in Breast Cancer by Automated and Quantitative RNA Chromogenic In Situ Hybridization (CISH) USCAP, Vancouver, Canada, March 2012 Zhen Wang 1, Son Bui 2, Hongwei Wang 2, Nan Su 2, Xiao-Jun Ma 2, Yuling Luo 2, and Raymond Tubbs 1 1 Department of Molecular Pathology, Cleveland Clinic, Cleveland, OH, United States 2 Advanced Cell Diagnostics, Hayward, CA, United States

2 Resolving Equivocal HER2 Status in Breast Cancer by Automated and Quantitative RNA Chromogenic In Situ Hybridization (CISH) Zhen Wang 1, Son Bui 2, Hongwei Wang 2, Nan Su 2, Xiao-Jun Ma 2, Yuling Luo 2, and Raymond Tubbs 1 1 Department of Molecular Pathology, Cleveland Clinic, Cleveland, OH, United States USCAP Advanced Cell Diagnostics, Hayward, CA, United States March 17-23, 2012 Abstract Background: Fluorescence in situhybridization (FISH )forher2 gene am plification and im m unohistochem istry (IHC)forHER2 protein overexpression both can generate equivocal HER2 results (FISH HER2/CEP17 ratio orihc score 2+ ),and som e cases generate equivocal results by both methods.this study explores the potentialofa novelautom ated and quantitative HER2 mrna CISH assay based on the recently developed RNAscope technology forresolving equivocalher2 status. Design: Formalin-fixed,paraffin-em bedded (FFPE)breastcancerspecimens from a non-consecutive series of73 cases were analyzed forher2 mrna using a fully autom ated RNAscope CISH assay. There were 30 negative and 22 positive cases based on the com bined FISH and IHC results,and 21 cases were equivocalby both methods ( dualequivocals ).These cases were pre-allocated into a training set(n= 38)and a validation set(n= 35).Autom ated image analysis ofher2 mrna staining was used to countthe num berofpunctate dots percell,each dotcorresponding to a single HER2 RNA transcript.and correlated to HER2 FISH,IHC and HER2 mrna RT-PCR.A probabilistic linear discriminantanalysis modelforher2 status based on the training setwas builtand applied to the validation set. Results: Evaluable HER2 mrna CISH results were obtained for67 cases (92% ).HER2 mrna dots percellcorrelated strongly to FISH (Spearman r=0.81)and RT-PCR (r=0.86)and definitively separated HER2 positive and negative cases in the training set.a predictive modelbased on HER2 mrna dots/cellin the training setcorrectly identified 11/12 negative and 5/5 positive cases (concordance= 94% )in the validation set.the only discrepantcase was review ed and found to have both am plified ductalcarcinom a in situ(dcis)and Non-am plified invasive com ponents;the HER2 RNA CISH results were from the DCIS.W hen analyzed on the invasive com ponentonly,this case was correctly classified as HER2 negative.the modelclassified all16 double equivocalcases in the validation setinto positives (n= 2)and negatives (n= 14). Conclusions: This quantitativeher2 mrna CISH assay was highly accurate in assessing HER2 status and may provide an effective means to resolve FISH /IHC dualequivocalcases.the walk-aw ay autom ation and image analysis-based quantification should minimize both analyticaland postanalyticalvariability in HER2 testing.quantification ofsingle RNA transcripts in situin routine clinical specim ens dem onstrates gra greatpotentialin al n prd predictive biom arkeranalysis. ranaly Background This study assesses the feasibility ofusing a novelautom ated and quantitative HER2 mrna CISH assay based on the recently developed RNAscope technology 1 to resolve H ER 2 am plification/overexpression status in invasive breastcancercases thatfailresolution via im m unohistochem istry (IHC) and fluorescence in situhybridization (FISH )testing follow ing ASCO/CAP guidelines 2.The two most widely utilized methods forher2 detection include IHC,which detects protein over-expression and FISH,which detects gene am plification.both IHC and FISH are slide-based,sem i-quantitative assays thatareperform performed ed on formalin-fixed,paraffin em bedded tissue.while hileprim primary aryand and reflextesting utilizing eitherihc orfish resolves HER2 status in the majority ofpatients,there rem ains a population ofpatients thatare equivocalby both IHC and FISH,ie. Double Equivocal (1.6% atccf) 3.Itis this double equivocalpopulation thatrepresents a unique diagnostic challenge forboth pathologistand oncologists due to the lack ofclearevidence based guidelines fordouble equivocal patientmanagement. Therefore,double equivocalher2 patients representa realand significantdeficiency in current laboratory testing forher2.her2 gene am plification directly leads to HER2 mrna over-expression. HER2 mrna has been show n to be highly correlated with HER2 gene status by many studies,and it is thus a validated targetforher2 testing.in this study,we dem onstrated thata HER2 mrna CISH assay separated HER2 positive from HER2 negative cases in a population thatfailed classification by both FISH and IHC.One strength ofthis assay is the ability to directly visualize and quantify individual molecules oftargetmrna in single cells.this is preformed in the contextoftissue,which allow s quantification ofher2 mrna in invasive tum orcells withoutinterference from surrounding strom a or adjacentin situneoplasm s and also allow s the identification ofregions ofheterogeneity.this autom ated assay can be integrated into existing HER2 testing work flow as a reflex testforcases with equivocalresults by traditionalfish /IHC testing.this dow nstream placem entofthe assay would also offera costsavings by 1)limiting application ofthe testto a sm allpre-selected population and 2) yielding diagnostic information when traditionaltesting fails which would spare patient s from a second invasive procedure simply to obtain additionaldiagnostic material.furtherstudies correlating response to anti-her2 therapy and HER2 status by HER2 mrna CISH assay are warranted. Materials and Methods Selection of cases: Cases were selected from the Cleveland Clinic electronic records from 1/2008 to 12/2010.A totalof73 cases with FISH and IHC forher2 were selected forthe study (30 FISH /IHC negative,22 FISH /IHC positive,and 21 FISH /IHC equivocal;perasco/cap guidelines).these cases were pre-allocated into a training set(n= 38)and a validation set(n= 35). HER2 mrna CISH assay: Allsteps ofrnascope staining ofthe slides were performed on a Ventana DISCOVERY XT autom ation system.autom ated image analysis software,rnascope TargetQuant,was developed in the Definiens Cognition Network Technology gyfa fram ework (Definiens Defiie AG,M unich,germ any) to countthe num berofpunctate ca e dots in individualcells,each ii dot corresponding to a single HER2 RNA transcript. Results Figure 3. Determination of HER2 status by automated quantitative HER2 mrna CISH Assay. Training Set Validation Set Figure 1. Automated RNAscope HER2 mrna CISH assay. HER2mRNA dots percellcorrelated strongly to FISH (Spearman r=0.81)and RT- A B PCR (r=0.86)and definitively separated HER2 positive and ndnegative cases in the training setaccording to a lineardiscrim inantanalysis model. Figure 2. Principle of in situ RNA quantification by RNAscope TargetQuant image analysis software A HER2 positive exam ple. Exam ple image ofrnascope-stained slide detecting POLR2A m RNA.Brow n punctate dots are DAB signals,with each dotrepresenting a single target RNA molecule.nucleiare couterstained blue. B H ER2 negative exam ple. Single-celllevelquantification ofmrna.green squares denote individualsignaldots identified by RNAscope TargetQuant.Black lines outline cell boundaries A predictive modelbased on HER2 mrna dots/cellin the training setcorrectly identified 11/12 negative and 5/5 positive cases (overallconcordance= 94% )in the validation set. HER2mRNA CISH applied to the 16 IHC/FISH double equivocalcases identified 2 cases as positive and 14 cases as negative with high confidence. Conclusions 1. The originalm anualrnascope assay has been fully autom ated on the Ventana Discovery instrum ents. 2. The single-m olecule detection sensitivity ofrnascope enables directquantification of targetrna molecules in single cells,which can be autom ated by im age analysis software. 3. The autom ated quantitative HER2 mrna CISH assay dem onstrated high concordance with FISH /IHC testing in unequivocalcases ofbreastcarcinom as. 4.TheHER2 mrna CISH assay dem onstrated capacity to resolve double equivocal cases resulted from currentihc/fish testing. Furtherstudies correlating RN Ascope HER2 mrna scores with response to trastuzum ab therapy are warranted. References 1. W ang,f.etal.rnascope:a Novelin Situ RNA Analysis Platform forformalin-fixed,paraffin-em bedded Tissues.The JournalofMolecularDiagnostics 14,22-29 (2012). 2. W olff,a.c.etal.am erican Society ofclinicaloncology/college ofam erican Pathologists guideline recommendations forhum an epidermalgrow th factorreceptor2 testing in breastcancer.journalof clinicaloncology:officialjournalofthe Am erican Society ofclinicaloncology 25, (2007) 3. Grimm,E.E.,Schm idt,r.a.,sw anson,p.e.,dintzis,s.m.& Allison,K.H.Achieving 95% crossmethodologicalconcordance in HER2 testing:causes and implications ofdiscordantcases.am erican journalofclinicalpathology 134, (2010).

3 Abstract Background: Fluorescence in situ hybridization (FISH) for HER2 gene amplification and immunohistochemistry (IHC) for HER2 protein overexpression both can generate equivocal HER2 results (FISH HER2/CEP17 ratio or IHC score 2+), and some cases generate equivocal results by both methods. This study explores the potential of a novel automated and quantitative HER2 mrna CISH assay based on the recently developed RNAscope technology for resolving equivocal HER2 status. Design: Formalin-fixed, paraffin-embedded (FFPE) breast cancer specimens from a non- consecutive series of 73 cases were analyzed for HER2 mrna using a fully automated RNAscope CISH assay. There were 30 negative and 22 positive cases based on the combined FISH and IHC results, and 21 cases were equivocal by both methods ( dual equivocals ). These cases were pre- allocated into a training i set (n=38) and avalidation set (n=35). Automated t image analysis of HER2 mrna staining i was used to count the number of punctate dots per cell, each dot corresponding to a single HER2 RNA transcript. and correlated to HER2 FISH, IHC and HER2 mrna RT-PCR. A probabilistic linear discriminant analysis model for HER2 status based on the training set was built and applied to the validation set. Results: Evaluable HER2 mrna CISH results were obtained for 67 cases (92%). HER2 mrna dots per cell correlated strongly gyto FISH (Spearman r=0.81) and RT-PCR (r=0.86) and definitively separated HER2 positive and negative cases in the training set. A predictive model based on HER2 mrna dots/cell in the training set correctly identified 11/12 negative and 5/5 positive cases (concordance=94%) in the validation set. The only discrepant case was reviewed and found to have both amplified ductal carcinoma in situ (DCIS) and Non-amplified invasive components; the HER2 RNA CISH results were from the DCIS. When analyzed on the invasive component only, this case was correctly classified as HER2 negative. The Amodel classified all 16 double equivocal cases in the validation set into positives (n=2) and negatives (n=14). Conclusions: This quantitative HER2 mrna CISH assay was highly accurate in assessing HER2 status and may provide an effective means to resolve FISH/IHC dual equivocal cases. The walk-away automation and image analysis-based quantification should minimize both analytical and post-analytical variability in HER2 testing. Quantification of single RNA transcripts in situ in routine clinical specimens demonstrates great potential in predictive biomarker analysis. 2

4 Background This study assesses the feasibility of using a novel automated and quantitative HER2 mrna CISH assay based on the recently developed RNAscope technology 1 to resolve HER2 amplification/over-expression status in invasive breast cancer cases that fail resolution via immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) testing following ASCO/CAP guidelines 2. The two most widely utilized methods for HER2 detection include IHC, which detects protein overexpression and FISH, which detects gene amplification. Both IHC and FISH are slide-based, semi-quantitative assays that are performed on formalin-fixed, paraffin embedded tissue. While primary and reflex testing utilizing either IHC or FISH resolves HER2 status in the majority of patients, there remains a population of patients that are equivocal by both IHC and FISH, ie. Double Equivocal (1.6% at CCF) 3. It is this double equivocal population p that represents a unique diagnostic challenge for both pathologist and oncologists due to the lack of clear evidence based guidelines for double equivocal patient management. Therefore, double equivocal HER2 patients represent a real and significant deficiency in current laboratory testing for HER2. HER2 gene amplification directly leads to HER2 mrna over-expression. HER2 mrna has been shown to be highly correlated with HER2 gene status by many studies, and it is thus a validated target for HER2 testing. In this study, we demonstrated that a HER2 mrna CISH assay separated HER2 positive from HER2 negative cases in a population thatt failed classification by both FISH and IHC. One strength of this assay is the ability to directly visualize and quantify individual molecules of target mrna in single cells. This is preformed in the context of tissue, which allows quantification of HER2 mrna in invasive tumor cells without interference from surrounding stroma or adjacent in situ neoplasms and also allows the identification of regions of heterogeneity. This automated assay can be integrated into existing HER2 testing work flow as a reflex test for cases with equivocal results by traditional FISH/IHC testing. This downstream placement of the assay would also offer a cost savings by 1) limiting application of the test to a small pre-selected population and 2) yielding diagnostic information when traditional testing fails which would spare patient s from a second invasive procedure simply to obtain additional diagnostic material. Further studies correlating response to anti-her2 therapy and HER2 status by HER2 mrna CISH assay are warranted. 3

5 Materials and Methods Selection of cases: Cases were selected from the Cleveland Clinic electronic records from 1/2008 to 12/2010. A total of 73 cases with FISH and IHC for HER2 were selected for the study (30 FISH/IHC negative, 22 FISH/IHC positive, and 21 FISH/IHC equivocal; per ASCO/CAP guidelines). These cases were pre-allocated into a training set (n=38) and a validation set (n=35). HER2 mrna CISH assay: All steps of RNAscope staining of the slides wereperformedonaventanadiscoveryxt automation system. Automated image analysis software, RNAscope TargetQuant, was developed in the Definiens Cognition Network Technology framework (Definiens AG, Munich, Germany) to count the number of punctate dots in individual cells, each dot corresponding to a single HER2 RNA transcript. 4

6 Results Figure 1. Automated RNAscope HER2 mrna ISH assay on Ventana Discovery. A B HER2 positive example. HER2 negative example. 5

7 Results Figure 2. Principle of in situ RNA quantification by RNAscope SpotQuant image analysis software. A B Example image of RNAscope-stained slide detecting POLR2A mrna. Brown punctate dots are DAB signals, with each dot representing a single target RNA molecule. Nuclei are couterstained blue. POLR2A RNA expression: 5-10 copies/cell Single-cell level quantification of mrna. Green squares denote individual signal (RNA) dots identified by RNAscope SpotQuant. Black lines outline cell boundaries 6

8 Results Figure 3. Determination of HER2 status by automated quantitative HER2 RNAscope ISH assay. RNAscope HER2 Scoring Training Set HER2 mrna dots per cell correlated strongly to FISH (Spearman r=0.81) and RT-PCR (r=0.86) and definitively separated HER2 positive and negative cases in the training set according to a linear discriminant analysis model. 7

9 Results Figure 3 (cont.). Determination of HER2 status by automated quantitative HER2 RNAscope ISH assay. RNAscope HER2 Scoring Validation Set A predictive model based on HER2 mrna dots/cell in the training set correctly identified 11/12 negative and 5/5 positive cases (overall concordance=94%) in the validation set. HER2 RNAscope quantification applied to the 16 IHC/FISH double equivocal cases identified 2 cases as positive and 14 cases as negative with high confidence. 8

10 Conclusions 1. The original manual RNAscope assay has been fully automated on the Ventana Discovery instruments. 2. The single-molecule detection sensitivity of RNAscope enables direct quantification of target RNA molecules in single cells, which can be automated by image analysis software. 3. The automated quantitative HER2 mrna CISH assay demonstrated high concordance with FISH/IHC testing in unequivocal cases of breast carcinomas. 4. The HER2 mrna CISH assay demonstrated capacity to resolve double equivocal cases resulted from current IHC/FISH testing. Further studies correlating RNAscope HER2 mrna scores with response to trastuzumab therapy are warranted. References 1. Wang, F. et al. RNAscope: A Novel in Situ RNA Analysis Platform for Formalin-Fixed, Paraffin-Embedded Tissues. The Journal of Molecular Diagnostics 14, (2012). 2. Wolff, A.C. et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. Journal of clinical oncology: official journal of the American Society of Clinical Oncology 25, (2007) 3. Grimm, E.E., Schmidt, R.A., Swanson, P.E., Dintzis, S.M. & Allison, K.H. Achieving 95% cross-methodological concordance in HER2 testing: causes and implications of discordant cases. American journal of clinical pathology 134, (2010). 9

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