Multiparameter Gene Expression Assays Research Articles

Predictive value of DNA repair gene expression for response to neoadjuvant chemotherapy in breast cancer.

e12538 Background: Genome-wide analysis using microarrays has revolutionized the field of breast cancer (BC) research, classifying breast cancer by gene expression profiling. In patients with BC, a substantial body of evidence supports the clinical utility of gene expression profiling. For example, the 21-gene assay (Oncotype DX) and 70-gene assay (MammaPrint) predict BC recurrence and the magnitude of chemotherapy benefit. However, there is currently no gene-expression profiling able to predict chemosensitivity and chemoresistance to neoadjuvant chemotherapy (NACT) during BC treatment. Therefore, the development of specific predictive biomarkers for chemoresistance and chemosensitivity is desirable. In the present study, we explored the predictive value of DNA repair gene expression for response to NACT in BC by evaluating the mRNA expression of 11 selected genes which have a key role in DNA repair mechanisms. Methods: We selected 98 patients with BC treated with NACT. We assessed DNA repair expression in 98 formalin-fixed, paraffin-embedded core biopsy fragments used at diagnosis and in 32 formalin-fixed, paraffin-embedded post-NACT residual tumors using quantitative reverse transcription-polymerase chain reaction. The following genes were selected: BRCA1, PALB2, RAD51C, BRCA2, ATM, FANCA, MSH2, XPA, ERCC1, PARP1 and SNM1. We used the mean of 2 reference genes (GAPDH and ACTB) to minimize the risk of normalization bias that can result from variations in the expression of any single reference gene. Results: Of 98 patients, 33 (33.7%) achieved pathologic complete response (pCR). The DNA expression of 2 genes assessed in pre-NACT biopsies (PALB2 and ERCC1) was lower in pCR than in non-pCR patients (p=0.005 and p=0.009, respectively). After adjustment for tumor grade and molecular subtype, a linear regression model with rank transformation showed that the DNA expression of 2 genes (PALB2 and ERCC1) assessed in pre-NACT biopsies was lower in the pCR group than in the non-pCR group (p=0.014 and p=0.040 respectively). The genes BRCA2 (p=0.009), ATM (p=0.004), FANCA (p=0.001), and PARP1 (p=0.011) showed a lower expression in post-NACT residual tumor samples (n=32) than in pre-NACT biopsy samples (n=98). Conclusions: In the genomics era, treatment should be tailored to the individual patient. The present study showed that PALB2 and ERCC1 expressions, assessed in pre-NACT biopsies, were lower in pCR patients. These alterations in DNA repair could be considered suitable targets for cancer therapy. In addition, BRCA2, ATM, FANCA, and PARP1 expressions were lower in post-NACT residual tumor samples than in pre-NACT biopsies. The use of recently developed multiparameter gene-expression assays, based on the expression of genes involved in different DNA repair pathways, should be further explored in future studies, as they may facilitate the selection of patients most likely to benefit from NACT.

Abstract OT1-06-01: OPTIMA: A prospective randomized trial to validate the predictive utility and cost-effectiveness of gene expression test-directed chemotherapy decisions in early breast cancer

Abstract Background: Multi-parameter gene expression assays (MPAs) are widely used to estimate individual patient residual risk in hormone-sensitive HER2-negative node-negative early breast cancer, allowing patients with low risk to safely avoid chemotherapy. Evidence for MPA use in node-positive breast cancer is limited. OPTIMA (Optimal Personalised Treatment of early breast cancer usIng Multi-parameter Analysis) aims to validate MPA's as predictors of chemotherapy sensitivity in a largely node-positive breast cancer population. Methods: OPTIMA is a partially blinded multi-center, phase 3 randomized controlled trial with an adaptive two-stage design. The main eligibility criteria are women or men aged 40 or older with resected ER-positive, HER2-negative breast cancer and up to 9 involved axillary lymph nodes. Randomization is to standard management (chemotherapy and endocrine therapy) or to MPA-directed treatment. Those with a “high risk” tumor MPA score receive standard management whilst those at “low risk” are treated with endocrine therapy alone. The preliminary phase (OPTIMA prelim) evaluated the performance of several MPAs to select a test to be used in the main efficacy trial based on economic analysis, and assessed the feasibility and acceptability of a large UK trial. OPTIMA prelim used Oncotype DX as the primary discriminator; the main trial will use Prosigna (PAM50) with Prosigna Score ≤60 defined as “low-risk”. The co-primary outcomes are (1) Invasive Disease Free Survival (IDFS) and (2) cost-effectiveness of test-directed therapy. Secondary outcomes include IDFS in “low-risk” patients, quality of life and additional survival measures. An integrated qualitative recruitment study will identify and address challenges to recruitment and informed consent. Tumor blocks from all consenting participants will be banked allowing the performance of alternative MPA technologies to be evaluated. Recruitment of 4500 patients will permit demonstration of 3% non-inferiority of test-directed treatment, with 5% significance and 85% power, assuming 3 years follow-up and a control arm 5-year IDFS of at least 85%. The addition of patients from OPTIMA prelim will allow non-inferiority to be assessed with 2.5% significance. Results: OPTIMA-prelim recruited 412 patients in 23 months from 35 sites with a 47% acceptance rate. The main study opened in January 2017. Early progress indicates that the recruitment target is achievable in the intended 46-month timescale through the participation of >100 sites Conclusion: OPTIMA, as one of two large scale prospective trials validating the use of test-guided chemotherapy decisions in node-positive early breast cancer, is expected to have a global impact on breast cancer treatment. Experience from OPTIMA prelim showed that patient advocate support and close engagement with sites will aid trial success. Funding: The project is funded in the UK by the NIHR HTA Programme (10/34/501). Views expressed are those of the authors and not those of the HTA Programme, NIHR, NHS or the DoH. Citation Format: Stein RC, Makris A, Hughes-Davies L, Macpherson IR, Hall PS, Cameron DA, Earl HM, Pinder SE, Poole CJ, Rea DW, McIntosh S, Harmer V, Morgan A, Rooshenas L, Conefrey C, Donovan JL, Hulme C, McCabe C, Stallard N, Campbell A, Higgins H, Bartlett JMS, Marshall A, Dunn JA. OPTIMA: A prospective randomized trial to validate the predictive utility and cost-effectiveness of gene expression test-directed chemotherapy decisions in early breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT1-06-01.

OPTIMA (Optimal Personalised Treatment of early breast cancer usIng Multi-parameter Analysis): A prospective trial to validate the predictive utility and cost-effectiveness of gene expression test-directed chemotherapy decisions.

TPS623Background: Multi-parameter gene expression assays (MPAs) are widely used to estimate individual patient residual risk and guide chemotherapy use in hormone sensitive HER2-ve early breast cancer, but prospective validation data are not available. OPTIMA aims to validate the use of MPA testing to predict chemotherapy sensitivity in a largely node-positive breast cancer population. Methods: OPTIMA is a partially blinded multi-center, phase 3 RCT with an adaptive two-stage design. The preliminary phase (OPTIMA prelim) evaluated the performance of MPAs to identify a suitable test to be used in the main efficacy trial, and demonstrated the feasibility and acceptability of a large UK trial. Eligible patients (pts) are men or women aged ≥ 40 years who have surgically resected early stage ER+ve and HER2-ve breast cancer, and have either 1-9 involved axillary lymph nodes or tumors of ≥ 30mm diameter. Randomization is to standard management (chemotherapy followed by endocrine therapy) or to MPA-directed thera...

Abstract OT3-02-12: OPTIMA (optimal personalised treatment of early breast cancer usIng multi-parameter analysis), a prospective trial to validate the predictive utility and cost-effectiveness of gene expression test-directed chemotherapy decisions

Abstract Background: Multi-parameter gene expression assays (MPAs) are widely used to estimate individual patient residual risk and to guide chemotherapy use in hormone-sensitive HER2-negative node-negative early breast cancer. These uses of MPAs have not yet been prospectively validated. OPTIMA aims to validate the use of MPA testing to predict chemotherapy sensitivity in a largely node-positive breast cancer population. Methods: OPTIMA is a partially blinded multi-center, phase 3 randomized controlled trial with an adaptive two-stage design. The preliminary phase (OPTIMA prelim) evaluated the performance of MPAs to identify a suitable test(s) to be used in the main efficacy trial and assessed the feasibility and acceptability of a large UK trial. Eligible patients are men or women aged 40 years or older who have surgically resected early stage breast cancer, which is ER-positive and HER2-negative and who have either 1-9 involved axillary lymph nodes or tumors of at least 30mm diameter. Randomization is to standard management (chemotherapy followed by endocrine therapy) or to MPA-directed treatment. Those with a tumor categorized as "high-risk" by the test will be assigned to standard management whilst those at "low-risk" will be treated with endocrine therapy alone. OPTIMA prelim used Oncotype DX as the primary discriminator; the main trial will use Prosigna (PAM50). The co-primary outcomes are (1) Invasive Disease Free Survival (IDFS) and (2) cost-effectiveness of test-directed therapy compared to standard practice. Secondary outcomes include IDFS in "low-risk" patients, distant disease free survival, breast cancer specific survival, overall survival and quality of life. An integrated qualitative recruitment study will identify and address challenges to recruitment and informed consent. Tumor blocks from all consenting participants will be banked allowing the performance of alternative MPA technologies to be evaluated. Recruitment of 4500 patients over 4 years will permit demonstration of 3% non-inferiority of test-directed treatment, with 5% significance and 85% power, assuming 3 years follow-up and a control arm 5-year IDFS of at least 85%. The addition of patients from OPTIMA prelim will allow non-inferiority to be assessed with 2.5% significance. Results: OPTIMA-prelim recruited 412 patients in 23 months from 35 sites. It confirmed the acceptability of randomization to patients with a 47% acceptance rate, and to clinicians and hence the feasibility of a large prospective trial of test-directed treatment running in 100-plus UK sites. It showed that investment into research on test-directed therapy, especially with Prosigna, should be of substantial value to the NHS. Conclusion: OPTIMA, as one of two large scale prospective trials validating the use of test-guided chemotherapy in node-positive hormone-sensitive early breast cancer will have a global impact on patient treatment. Recruitment into the main efficacy trial will commence in October 2015. Funding: Project funded by the UK NIHR HTA Programme (10/34/501). Views expressed are those of the authors and not those of the HTA Programme, NIHR, NHS or the DoH. Citation Format: Stein RC, Marshall A, Hall PS, Bartlett JMS, Rooshenas L, Campbell A, Cameron DA, Rea D, Macpherson I, Earl HM, Poole CJ, Francis A, Morgan A, Harmer V, Pinder SE, Stallard N, Donovan J, Hulme C, McCabe C, Hughes-Davies L, Makris A, Dunn JA. OPTIMA (optimal personalised treatment of early breast cancer usIng multi-parameter analysis), a prospective trial to validate the predictive utility and cost-effectiveness of gene expression test-directed chemotherapy decisions. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT3-02-12.

Abstract ES5-1: Predictive gene expression profiles in breast cancer, where are we?

Abstract Successful sequencing of the entire human genome offered an enormous potential for improving human health, especially in oncology. Nearly 20 years after successful completion of the human genome project, the Cancer Genome Atlas (TCGA) has catalogued the most common mutations in most cancers, including breast. Further, the technical advances that facilitate the ability to fully analyze both germline and somatic DNA and RNA has resulted in rapid (<4 weeks) and relatively inexpensive (<$3000) assays to emerge. Indeed, the NCI-sponsored Lung MAP and Cancer MATCH, and the ASCO-sponsored TAPUR, trials are now opening in the U.S., testing whether knowledge of somatic genetic changes improves patient outcomes. However, arguably, the most clinically useful product of the Human Genome Project to date has been the emergence of multiparameter gene expression assays that can be used to direct cancer care, particularly in breast cancer. The 21-gene assay was the first of these to be shown to have sufficiently high analytical validity and clinical utility to be used to identify patients with node negative, ER positive early stage breast cancer who, assuming adequate adjuvant endocrine therapy, could be spared the toxicity of adjuvant chemotherapy based on prognosis alone. Subsequently, several other assays have now been reported to be equally satisfactory for this same use context. The Oxford Overview has suggested that adjuvant chemotherapy reduces the odds of distant recurrence and death by approximately 1/3, regardless of initial prognosis. However, many retrospective correlative studies over the last 4 decades have suggested that chemotherapy may have differing relative activities within distinct biological, or more recently designated “intrinsic,” subtypes, based mostly on expression of estrogen receptor and proliferation genes. Preliminary, prospective retrospective studies by the NSABP in B20 and SWOG in S8814 have, indeed, suggested that patients with ER positive breast cancer with low recurrence scores, as determined by the 21-gene assay, not only have better prognosis than those with intermediate or higher RS, but that chemotherapy may simply not work in this category. However, these studies were both confounded by a number of biases. Therefore, before potentially life-saving chemotherapy is with-held from node positive breast cancer patients based on prediction alone, a prospective clinical trial, SWOG S1007 (the RxPonder Trial), was initiated. The primary objective of the RxPonder trial is to determine if women with node positive, ER positive breast cancer with RS <25 may not benefit from adjuvant chemotherapy even if their prognosis is worse than those with node negative disease. This trial, which is now fully accrued, will not only tell us if we can spare yet another group of women from receiving unnecessary or inactive chemotherapy, it also offers the promise of identification of targets that could be further interrogated with newer biological treatments in the future. Citation Format: Hayes DF. Predictive gene expression profiles in breast cancer, where are we?. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr ES5-1.

Practicalities of using an adaptive design for decision making within the optima trial: optimal personalized treatment of early breast cancer using multi-parameter tests

Multi-parameter gene expression assays (MPA) to aid selection of chemotherapy in hormone-sensitive early breast cancer have not been prospectively validated. This field of personalised medicine is rapidly evolving. There is currently no “best test”. OPTIMA is an adaptive trial of MPA-based chemotherapy assignment in a largely node-positive breast cancer population.

Progress in adjuvant chemotherapy for breast cancer: an overview.

Breast cancer is the most common cause of cancer and cancer death worldwide. Although most patients present with localized breast cancer and may be rendered disease-free with local therapy, distant recurrence is common and is the primary cause of death from the disease. Adjuvant systemic therapies are effective in reducing the risk of distant and local recurrence, including endocrine therapy, anti-HER2 therapy, and chemotherapy, even in patients at low risk of recurrence. The widespread use of adjuvant systemic therapy has contributed to reduced breast cancer mortality rates. Adjuvant cytotoxic chemotherapy regimens have evolved from single alkylating agents to polychemotherapy regimens incorporating anthracyclines and/or taxanes. This review summarizes key milestones in the evolution of adjuvant systemic therapy in general, and adjuvant chemotherapy in particular. Although adjuvant treatments are routinely guided by predictive factors for endocrine therapy (hormone receptor expression) and anti-HER2 therapy (HER2 overexpression), predicting benefit from chemotherapy has been more challenging. Randomized studies are now in progress utilizing multiparameter gene expression assays that may more accurately select patients most likely to benefit from adjuvant chemotherapy.

Abstract P2-11-03: A tumor microenvironment of metastasis (TMEM) biomarker in early breast cancer provides prognostic information that is complementary to IHC4: A prospective validation study

Abstract Background: Multiparameter gene expression assays (eg, Oncotype DX®) provide prognostic and predictive information in estrogen receptor (ER)+ Her2- negative disease, but are driven largely by proliferation and ER signaling captured by immunohistochemistry (IHC) assays such as IHC4 (Cuzick et al. J Clin Oncol. 2011 10;29:4273-8). However, these assays do not reflect the capacity of individual tumor cells to metastasize, nor interaction with their microenvironment. Using a bench-to-bedside approach, we have identified in animal models and human breast cancer by IHC methods a microanatomic landmark (TMEM) precisely where Mena-overexpressing invasive tumor cells intravasate and hematogenously metastasize by directly interacting with endothelial cells and macrophages (Robinson et al. Clin Cancer Res 2009;15:2433-41). In the present study, we performed a prospective validation study to establish analytic and clinical validity of TMEM in comparison with IHC4 in accordance with recommended guidelines (Simon et al. JNCI 2009;101:1446-52). Methods: A case-control study was performed nested within a cohort of 3760 invasive ductal breast carcinomas, in which cases (subsequent distant recurrence) and controls (no recurrence) were selected using incidence density sampling matched on age at and calendar year of primary diagnosis, resulting in 481 subjects (259 case-control pairs). TMEM and IHC4 were performed as previously reported, and stained slides were read independently by 5 pathologists blinded to outcome. Odds ratios (OR)(95% CI) for the association with TMEM were estimated using logistic regression, with adjustment for clinical variables, including age, tumor size, grade, number of positive lymph nodes, ER, PR, and Her2 expression, lymphovascular invasion (LVI), and use of chemotherapy or hormonal therapy. The ORs for TMEM was compared with those for IHC4. Results: in a multivariate model adjusted for other covariates, TMEM was associated with increased risk of distant metastasis in 62% of subjects with ER+/Her2- tumors (OR [95%CI]high vs. low tertile = 2.70 [1.39-5.26], Ptrend = 0.004), whereas IHC4 had a borderline positive association (OR10 unit increase = 1.06 [1.00-1.13]); the association for TMEM persisted after adjustment for IHC4 (OR [95%CI]high vs. low tertile = 2.68 [1.31-5.49], Ptrend = 0.004). TMEM scores ranged up to a nearly 200-fold from lowest to highest, and did not correlate with tumor size, number of positive lymph nodes, nor IHC4 score (Spearman correlation 0.12 for IHC4). The AUC for a TMEM composite score (0.77), derived from a multivariate logistic regression model with TMEM and clinical variables, was significantly higher than those for TMEM alone (0.65) and for IHC4 (0.62). Neither TMEM nor IHC4 was independently associated with metastatic risk in the triple negative (20%) or HER2+ (18%) tumors. Conclusion: TMEM score, a mechanism-based assay, is positively associated with risk of distant metastasis in ER+/Her2- breast cancer and provides prognostic information that is complementary to IHC4 and other clinicopathologic risk factors. Additional validation studies designed to establish clinical validity are currently being planned. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-11-03.

Defining the Clinical Utility of Gene Expression Assays in Breast Cancer: The Intersection of Science and Art in Clinical Decision Making

Defining the Clinical Utility of Gene Expression Assays in Breast Cancer: The Intersection of Science and Art in Clinical Decision Making

American Society of Clinical Oncology 2007 Update of Recommendations for the Use of Tumor Markers in Breast Cancer

To update the recommendations for the use of tumor marker tests in the prevention, screening, treatment, and surveillance of breast cancer. For the 2007 update, an Update Committee composed of members from the full Panel was formed to complete the review and analysis of data published since 1999. Computerized literature searches of MEDLINE and the Cochrane Collaboration Library were performed. The Update Committee's literature review focused attention on available systematic reviews and meta-analyses of published tumor marker studies. In general, significant health outcomes (overall survival, disease-free survival, quality of life, lesser toxicity, and cost-effectiveness) were used for making recommendations. Recommendations and Thirteen categories of breast tumor markers were considered, six of which were new for the guideline. The following categories showed evidence of clinical utility and were recommended for use in practice: CA 15-3, CA 27.29, carcinoembryonic antigen, estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, urokinase plasminogen activator, plasminogen activator inhibitor 1, and certain multiparameter gene expression assays. Not all applications for these markers were supported, however. The following categories demonstrated insufficient evidence to support routine use in clinical practice: DNA/ploidy by flow cytometry, p53, cathepsin D, cyclin E, proteomics, certain multiparameter assays, detection of bone marrow micrometastases, and circulating tumor cells.