Analysis of the clinical utility of gene expression profiling in relation to conventional prognostic markers in South African patients with breast carcinoma

Grant, Kathleen Ann (2014-12)

Thesis (PhD)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: Breast cancer is a heterogeneous disease characterised by marked inter-individual variability in presentation, prognosis and clinical outcome. The recognition that morphological assessment has limited utility in stratifying patients into prognostic subgroups led to clinico-pathological classification of tumour biology, based on receptor expression using immunohistochemical (IHC) techniques. This standard is currently complemented by the development of gene expression profiling methodology that led to the identification of intrinsic molecular subtypes, reflecting tumour genetics as the true driver of biological activity in breast cancer. The study was based on the hypothesis that molecular classification of breast carcinomas integrated with established clinico-pathological risk factors will improve current diagnostic and risk management algorithms used in clinical decision-making. A pathology-supported genetic testing strategy was used to evaluate microarray-based gene profiling against diagnostic pathology techniques as the current standard. Clinico-pathological factors including age, number of positive axillary nodes, tumour size, grade, proliferation index and hormone receptor status was documented for 141 breast cancer patients (143 tumours) referred for microarray-based gene expression profiling between 2007 and 2014. Subsets of patients were selected from the database based on the inclusion criteria defined for three phases in which the study was performed, in order to determine 1) the percentage of patients stratified as having a low as opposed to high risk of distant recurrence using the 70-gene MammaPrint profile within the inclusion criteria, 2) correlation of HER2 status as determined by IHC and fluorescence in situ hybridisation (FISH) with microarray-based mRNA readout (TargetPrint), and 3) the relationship between hormone receptor determination as reported by standard IHC and molecular subtyping using the 80-gene BluePrint profile. Similar distribution patterns for MammaPrint low- and high-risk profiles were obtained irrespective of whether fresh tumour biopsies or formalin-fixed paraffin embedded (FFPE) tissue was used. During the first phase of the study, 60% of the 106 tumour specimens analysed with MammaPrint were classified as low-risk and 40% as high-risk using a newly-developed MammaPrint pre-screen algorithm (MPA) aimed at cost-saving. In the second phase of the study, performed in 102 breast tumours, discordant or equivocal HER2 results were found in four cases. Reflex testing confirmed the TargetPrint results in discordant cases, achieving 100% concordance regardless of whether fresh tumour or FFPE tissue was used for microarray analysis. For the third phase of the study 74 HER2-negative tumour samples were selected for comparative analysis. Statistically significant positive correlations were found between protein expression (IHC score) and mRNA (TargetPrint) levels for estrogen receptor (ER) (R=0.53, p<0.0001) as well as progesterone receptor (PR) (R=0.62, p<0.0001), while combined ER/PR tumour status was reported concordantly in 82.4% of these tumours. BluePrint was essential for interpretation of these results used in treatment decision-making. The MPA developed in South Africa in 2009 was validated in this study as an appropriate strategy to prevent chemotherapy overtreatment in patients with early-stage breast cancer. The use of microarray-based analysis proved to be a reliable ancillary method of assessing HER2 status in breast cancer patients. Risk reclassification based on the TargetPrint results helped to avoid unnecessary high treatment costs in false-positive cases, in addition to providing potentially life-saving treatment to those for whom it was indicated. While neither IHC nor TargetPrint estimation of intrinsic subtype correlated independently with the molecular subtype as indicated by BluePrint profiling, the ability to distinguish between basal-like and luminal tumours was enhanced when the combined protein and mRNA values was considered. Genomic profiling provided information over and above that obtained from routine clinico-pathological assessments. This finding supports the relevance of a pathology-supported genetic testing approach to breast cancer management, whereby advanced genomic testing is combined with existing clinico-pathological risk stratification methods for improved patient management.

AFRIKAANSE OPSOMMING: Borskanker is „n heterogene siekte wat gekenmerk word deur merkbare inter-individuele variasie in kliniese beeld, prognose en uitkoms. Die beperkings van morfologiese klassifikasie vir identifikasie van prognostiese subgroepe het gelei tot klinies-patologiese tumor karakterisering op grond van reseptor uitdrukking deur gebruik van immunohistochemiese (IHC) toetse. Hierdie standaard word tans gekomplementeer deur ontwikkeling van geenuitdrukking tegnologie wat gelei het tot die identifikasie van intrinsieke molekulêre subtipes, wat die tumor genetika reflekteer as die ware drywer van biologiese aktiwiteit in borskanker. Die huidige studie is gebaseer op die hipotese dat integrasie van die molekulêre klassifikasie van borskanker met konvensionele risiko klassifikasie skemas huidige diagnostiese en behandelings algoritmes kan verbeter vir kliniese besluitneming. „n Patologie-gesteunde strategie is gebruik om mikroplaat-gebaseerde geen profilering te evalueer teen standaard patologie diagnotiese tegnieke. Kliniese-patologiese faktore insluitend ouderdom, aantal positiewe aksillêre limfnodes, tumor grootte, gradering, proliferasie indeks en hormoon reseptor status is gedokumenteer in 141 borskanker pasiente (143 tumore) wat verwys is vir mikroplaat-gebaseerde geenuitdrukking profilering tussen 2007 en 2014. Pasiënt subgroepe is geselekteer uit die databasis volgens die insluitingskriteria soos gedefiniëer in die drie fases waarvolgens hierdie studie uitgevoer is, om vas te stel 1) watter proporsie pasiënte geklassifiseer word as lae- of hoë-risiko vir latere herhaling van die borskanker deur gebruik van die 70-geen MammaPrint profile binne die insluitingskriteria, 2) hoe korreleer HER2 status soos vasgestel deur IHC en fluoreserende in situ hybridisasie (FISH) toetsing met mikroplaat-gebaseerde RNA lesings (TargetPrint), en 3) wat die verwantskap is tussen hormoon reseptor status soos deur standaard IHC gerapporteer en molekulëre klassifikasie volgens die 80-geen BluePrint profiel. Soortgelyke verdelingspatrone vir MammaPrint lae- teenoor hoe-risiko profiele is waargeneem ongeag of vars tumor biopsies of formalien-gefikseerde paraffin bevattende weefsel gebruik is. Tydens die eerste fase van die studie is 60% van die 106 tumore as lae-risiko en 40% as hoë-risiko geklassifiseer met toepassing van die nuwe MammaPrint Presifting Algoritme (MPA) wat ontwikkel is met die doel op kostebesparing. In die tweede fase van die studie waar 102 tumore ingesluit is, het die resultate van vier gevalle verskil van mekaar of was onbepaald ten opsigte van HER2 status. Refleks herevaluering het die TargetPrint resultate bevestig in alle nie-ooreenstemmende gevalle, en 100% ooreenstemming is bereik ongeag of vars tumor biopsies of formalien-gefikseerde paraffin bevattende weefsel gebruik is vir mikroplaat analise. In die derde fase van die studie is 74 HER2-negative tumore selekteer vir vergelykende analise. Statisties beduidende positiewe korrelasies is waargeneem tussen proteïen uitdrukking (IHC) en mRNA (TargetPrint) vlakke vir die estrogeen reseptor (ER) (R=0.53, p<0.0001) sowel as progesteroon reseptor (PR) (R=0.62, p<0.0001), terwyl gekombineerde ER/PR reseptor status ooreenstemming getoon het in 82.4% tumore. BluePrint was noodsaaklik vir die korrekte interpretasie van die resultate wat gebruik is in kliniese besluitneming vir behandeling van pasiënte. The MPA wat in Suid Africa ontwikkel is in 2009, is gedurende hierdie studie bevestig as n toepaslike strategie om onnodige handeling met chemoterapie te voorkom in pasiënte met vroeë stadium borskanker. Die gebruik van mikroplaat-gebaseerde analise is aangetoon as „n betroubare aanvullende metode om HER2 status te evalueer. Risiko herklassifikasie gebaseer op TargetPrint resultate het onnodige hoë behandelingskoste in vals-positiewe gevalle vermy, sowel as om die verskaffing van potensieël lewensreddende behandeling vir die toepaslike pasiënte te verseker. Genomiese profilering het inligting addisioneel tot dit wat met roetine klinies-patologies metodes verkry kan word verskaf. Hierdie bevinding ondersteun die relevansie van „n patologie-gesteunde genetiese toets benadering tot hantering van borskanker, waardeur genomiese toetsing gekombineer word met bestaande klinies-patologiese risiko stratifisering metodes om pasiënt behandeling te verbeter.

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