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  • Microarray studies show that luminal types express high amounts of luminal cytokeratins and genetic markers of luminal epithelial cell of normal breast tissue
    Basal-like  no ER, PR, or ER related genes; high levels of EGFR, c-kit, and growth factors such as hepatocyte growth factor and IGF
  • 34 with distant mets at <5 yrs, 44 disease-free at >5 years, and 18 BRCA1/2 BRCA2 germline mutations; 19 to validate signature
    Statistical analysis called “supervised classification,” the expression of 231 genes seemed to be significantly correlated with disease outcome (distant mets within 5 years). They were ranked on the basis of their correlation coefficient with disease outcome; the top 70 genes were shown to most accurately classify tumors in either good or poor prognosis categories.
    Pts with correlation coefficient >0.4 were in the good prognosis group
    Odds ratio of distant mets in the poor prognosis group compared to the good prognosis group = 15
  • Prognosis profile was significantly associated with the histological grade of the tumor, the ER status, and age, but not with tumor diameter, extent of vascular invasion, the number of positive LNs, or treatment.
    The odds ratio for the development of distant mets within 5 years was similar to prior study (15.3 and 15)
  • Estimated hazard ratio for distant mets as a first event in the poor-prognosis group as compared to the good-prognosis group over the entire follow-up period was 5.1 (p<0.001)
    The hazard ratio for overall survival was 8.6 (p<0.001)
  • The poor prognosis signature was by far the strongest predictor of the likelihood of distant mets, with an overall hazard ratio of 4.6
    Low-risk pts identified by gene-expression profiling had a higher likelihood of mets-free survival than those classified according to St. Galen or NIH criteria, and high-risk pts identified by profiling tended to have a higher rate of distant mets than did the high-risk pts identified by the St Gallen or NIH criteria.
    Both sets of criteria currently misclassify a significant number of patients
    This shows that a number of patients are either overtreated or undertreated by these criteria.
    NPV of 96% for new pts, but PPV of 38%...the profile was built to have a minimum of misclassified pts with a poor disease outcome and therefore avoid undertreatment.
  • low – clinical risk group would be defined as patients with 10-year
    overall survival probabilities (as calculated by Adjuvant! software,
    version 7.0) of at least 88% if 10% or more of the tumor
    cells expressed detectable ER (i.e., ER-positive tumors) and of
    at least 92% if ER expression was seen in less than 10% of the
    tumor cells (i.e., ER-negative tumors). These two cutoffs were
    chosen to reflect the fact that patients with ER-positive tumors
    routinely receive adjuvant endocrine therapy [with an estimated
    absolute 10-year survival benefi t of approximately 4% overall
  • The signature remained a statistically significant prognostic factor for time to distant
    metastases and survival even after adjustment for various risk classifications that take into account all clinicopathologic factors known to have prognostic value in this disease.
    (The lack of statistical significance for disease-free survival is not surprising because the signature was
    developed using only time to distant metastases as an endpoint.)
    These results indicate that the gene signature adds independent
    prognostic information to that provided by a risk assessment
    based solely on clinicopathologic factors.
    As Fig. 4 shows, the behavior of the adjusted hazard ratio of the gene signature shows substantial
    variation over time, suggesting that the ability of the gene signature to identify those who will develop distant relapse is greatestwithin 5 years of diagnosis.
    The gene signature hazard ratio also remained much higher after adjustment in the
    original series ( 6 ) than in the current validation series. It has previously
    been noted ( 12 ) that the inclusion in the original series of patients whose data were used in the development of the 70-gene signature may have infl ated the discriminatory power of the signature in that study
  • Patient’s age and tumor size are routinely used as predictors of recurrence in breast cancer
    When the recurrence score was combined with data pertaining to age and tumor size to predict risk of distant mets…only the recurrence score remained statistically significant
    Decreased risk with age may be in part related to increased ER expression in older patients’ tumors – this is captured in recurrence score
    For tumor size -- >1/3 of patients (tumors smaller than 1 cm) had intermediate-risk or high-risk recurrence scores and a 15-20% risk of distant recurrence.
    The subgroup analysis of age and tumor size should be interpreted cautiously
    Concordance b/w pathologists on poorly diff tumors was moderate and for the well-diff and moderately diff grades is low
    Traditional measures of ER and HER2 expression were only weakly predictive of the risk of distant recurrence (this information was encompassed in the RT-PCR assay)
    They concluded that they did not know whether the genes used correlate with recurrence in this population b/c they predict responsiveness to tamoxifen, b/c they show a relation with the natural history of breast cancer, or both
  • At 10 years, risk of death: low 2.8%, intermediate 10.7%, & high 15.5%
  • NSABP Protocol B20, “A Clinical Trial to Determine the Worth of
    Chemotherapy and Tamoxifen Over Tamoxifen Alone in the Management of
    Patients with Primary Invasive Breast Cancer, Negative Axillary Nodes and
    Estrogen-Receptor-Positive Tumors,” enrolled 2,363 patients between October
    17,1988, and March 5, 1993, who were randomly assigned to tamoxifen
    versus tamoxifen plus either CMF or MF
  • Kaplan-Meier plots for distant recurrence comparing treatment with tamoxifen (Tam) alone versus treatment with tamoxifen plus chemotherapy (Tam chemo).
    (A) All patients; (B) low risk (recurrence score [RS] 18); (C) intermediate risk (RS 18-30); (D) high risk (RS 31). The number of patients at risk and the number of
    distant recurrences (in parentheses) are provided below each part of the figure.
    Similar trends were seen when analyzed for freedom from locoregional and/or distant recurrence and OS
  • No interaction of chemotherapy treatment with the clinical variables and with all the individual genes and gene group scores
    The likelihood ratio test for interaction between chemo and RS (p=0.038)
    Patients with low recurrence scores derived minimal, if any, benefit from chemo
    Patients with intermediate risk tumors no substantial benefit..difficult to conclude
  • Taxane or non-taxane group  intermediate groups
    Tailorx was developed by the North American Breast Cancer Intergroup
    It was developed for ER+/ LN- patients
    Chemotherapy usually recommended if residual risk of recurrence exceeds 5-10% despite adjuvant hormonal tx
    Adding chemo reduces the risk of recurrence on average by 25-30%; but absolute benefit is 1-5%
    Recurrence scores were adjusted so to avoid undertreatment
    Te intermediate risk group was randomize to hormonal v chemohormonal tx
  • FFPE – Formalin fixed and paraffin-embedded
    Of the 60 patients: 28 were LN-, 25 were LN+, and 7 not evaluated
    In 20 patient cohort, 19 were LN-
  • As Fig. 4 shows, the behavior of the adjusted hazard ratio of the gene signature shows substantial
    variation over time, suggesting that the ability of the gene signature to identify those who will develop distant relapse is greatestwithin 5 years of diagnosis.
  • All risk classifications for patients with early breast cancer attempt to
    identify reliably patients at low risk of metastasis or death, i.e., to achieve high sensitivity, even if this comes at the cost of very low specificity. In this respect, the gene signature performed better than any of the classifications based on clinicopathologic factors
  • On multivariate analysis including (ER status, grade, nodal status, age, tumor diameter, and treatment status), all but the 2 gene signature were significant predictors of RFS and OS
    Results were highly concordant except for the two-gene ratio
    RS and 70 gene agreed with 81% of all pts and 77% of ER+ cancer (only 1 gene overlaps)
  • Personalized Therapy for Breast Cancer: Gene Expression ...

    1. 1. In Pursuit of Personalized Therapy for Breast Cancer: Gene Expression Signatures Jane S. Chawla, M.D. November 6, 2009
    2. 2. Objectives <ul><li>Case: Chemotherapy or NOT </li></ul><ul><li>Who should receive adjuvant chemotherapy? </li></ul><ul><li>The birth of gene-expression signatures: Intrinsic breast cancer subtypes </li></ul><ul><li>Gene Expression Signatures under development </li></ul><ul><ul><li>70-gene Signature </li></ul></ul><ul><ul><li>21-gene Signature </li></ul></ul><ul><ul><li>2-gene Signature </li></ul></ul><ul><ul><li>50-gene signature </li></ul></ul><ul><li>Case revisited </li></ul>
    3. 3. Clinical Case <ul><li>30 y/o WF with newly diagnosed IDC R breast </li></ul><ul><li>MMG / Ultrasound  1.2 x 1.2 cm mass at 10 o’clock + surrounding microcalcifications + several suspicious axillary LNs </li></ul><ul><li>s/p bilateral mastectomies at OSH </li></ul><ul><li>Surgical Path - 4.6 cm lesion consisting of IDC mixed with DCIS; intermediate grade; + lymphovascular invasion ; 11 (-) LNs; ER+/PR+/HER-2-; T2N0M0 </li></ul><ul><li>Oncotype DX - -> low risk for recurrence </li></ul><ul><li>Based on oncotype results her oncologist recommended adjuvant tamoxifen x 5 years </li></ul><ul><li>Pt presents for a second opinion </li></ul>Should the patient receive chemotherapy?
    4. 4. Who Should Receive Adjuvant Chemotherapy? <ul><li>65% of women with invasive breast cancer have LN(-) disease </li></ul><ul><li>Adjuvant chemotherapy improves DFS and OS in pre- and postmenopausal women <70 with LN+/- breast cancer </li></ul><ul><li>NSABP B-14 & B-20 showed the benefit of tamoxifen & chemo in ER+/LN- breast cancer </li></ul><ul><ul><li>Likelihood of distant mets at 10 years is about 15% </li></ul></ul><ul><ul><li>85% of pts are overtreated if chemo given to all patients </li></ul></ul><ul><li>Those with poor prognostic features benefit most from chemotherapy </li></ul><ul><li>Main clinical prognostic factors: age, tumor size, axillary LN status, tumor histology, grade, and hormone-receptor status </li></ul>How else can we differentiate these tumors?
    5. 5. Sotiriou, C. et al. NEJM, 2009. Luminal A Luminal B HER2+ Basal-like Intrinsic Breast Cancer Subtypes described by Perou et al. Express ↑ amounts Of luminal cyto- Keratins & genetic Markers of luminal Epithelial cells of Normal tissue Express ↑ levels of EGFR, c-kit, & growth factors like hepatocyte growth factor and IGF
    6. 6. Gene Expression Profiles or “Signatures” <ul><li>Composed of a selection of genes felt to provide prognostic or predictive information about tumors </li></ul><ul><li>A number of gene expression signatures have been developed to help identify those patients at highest risk for recurrent disease </li></ul><ul><li>This may avoid chemotherapy administration to patients at low risk </li></ul>
    7. 7. The 70-gene Assay: MammaPrint
    8. 8. Mammaprint: Development of the 70-Gene Signature <ul><li>DNA microarray analysis of 78 breast primary tumors (untreated) </li></ul><ul><ul><li>Pts were <55 years of age with T1-2/N0 disease </li></ul></ul><ul><ul><li>Pts selected based on outcome: Distant metastases within 5 years </li></ul></ul><ul><li>Statistical analysis, “supervised classification,” identified 231 genes correlated with disease outcome  Top 70 genes selected </li></ul><ul><li>Genes that regulate cell cycle, invasion, metastasis, & angiogenesis </li></ul><ul><li>Patients categorized as “good prognosis” or “poor prognosis.” </li></ul><ul><li>Found to be a better predictor of distant metastases within 5 years than all clinical variables in this study </li></ul><ul><li>Odds ratio (distant metastases): poor to good prognosis groups = 15 </li></ul>Van ’t Veer, L. Nature , 2002.
    9. 9. Retrospective Validation of the 70-Gene Signature <ul><li>295 women ages ≤ 52 with T1-2, LN-/+ breast cancer </li></ul><ul><ul><li>226 ER+ / 69 ER- </li></ul></ul><ul><ul><li>chemo 31%; hormonal 7%; both 7% </li></ul></ul><ul><li>61 pts included in the analysis were used to develop 70-gene signature </li></ul>Van de Vijver. NEJM , 2002.
    10. 10. Prognosis Signature Predictive of End Points (10 years) 995% ±2.6% 555% ±4.4% 85 % ±4.3% 51 % ±4.5% Probability of Remaining Metastasis-free Overall Survival
    11. 11. Multivariate Analysis Independent predictors of risk of distant metastasis as a 1 st event <ul><li>70-gene signature </li></ul><ul><li>Tumor diameter </li></ul><ul><li>Chemotherapy </li></ul><ul><li>Lymph node status </li></ul><ul><li>Vascular invasion </li></ul>Authors report that gene signature is predictive of distant mets in LN+ pts Multivariate analysis argues that LN status is independent of gene signature as a predictor Van de Vijver. NEJM, 2002.
    12. 12. TRANSBIG Independent Retrospective Validation Study <ul><li>Retrospective evaluation of 302 pts from several sites in Europe (age<60, T1-2, LN-) previously untreated </li></ul><ul><li>Aim: to examine whether the 70-gene signature had prognostic value independent of the best clinical risk classifications ( St Gallens, Nottingham Prognostic Index, & adjuvant online) </li></ul>Buyse, M. J of NCI , 2006.
    13. 13. Does 70-gene Signature have Independent Prognostic Value? <ul><li>Gene signature adds independent prognostic information to that provided by various risk classifications </li></ul><ul><li>The signature remained a statistically significant prognostic factor for time to distant metastases & OS even after adjustment for various risk classifications (HR 2.15 & 2.15, respectively) </li></ul>Buyse, M. J of NCI , 2006.
    14. 14. Forrest Plot of HR for Time to Distant Metastases <ul><li>Although, average HR of 2.32 is significant…there was wide variation in the HRs among clinical sites. </li></ul><ul><li>Therefore model is very sensitive to variation in patient population </li></ul>Clinical Sites Buyse, M. J of NCI , 2006.
    15. 15. Conclusions of Validation Studies <ul><li>Studies were retrospective </li></ul><ul><li>Concern for overfitting with supervised analysis of relatively small sample sizes and large numbers of genes </li></ul><ul><li>The first validation study contained 61 patients from study on which the classifier was built </li></ul><ul><li>Claims exceed evidence? </li></ul>
    16. 16. Prospective Validation of Mammaprint: The MINDACT Trial Accrual started 2/07 and is expected to be finished within 3 years 6,000 LN- patients High risk  Chemo + Endocrine Risk assessed via Clinicopathological Factors (adjuvant) + Mammaprint Low risk  Endocrine Discordant cases: random assignment to follow genomic vs clinicopathologic result Cardoso, F. JCO, 2008.
    17. 17. The 21-gene Recurrence Score: Oncotype DX
    18. 18. Oncotype Dx: The 21-Gene Assay <ul><li>Designed to quantify the risk of distant recurrence in patients with LN(-), ER(+) tumors receiving tamoxifen </li></ul><ul><li>RT-PCR was used to quantify gene expression from fixed, parafin-embedded tumor tissue </li></ul><ul><li>250 candidate genes selected based on published literature, genomic databases, & experiments based on DNA arrays on fresh-frozen tissue </li></ul><ul><li>Analyzed data from 3 independent studies (447 patients) including tamoxifen-only arm of NSABP trial B-20 to test relation b/w 250 genes and recurrence of breast cancer </li></ul><ul><li>From these studies, 21 genes were selected that correlated with proliferation and endocrine response </li></ul>
    19. 19. Levels of Gene Expression Determine Recurrence Score 21-gene assay = 16 outcome-related genes + 5 reference genes Higher expression levels of “ favorable” genes = ↓ RS Higher expression levels of “ unfavorable” genes = ↑ RS A risk score is calculated from 0 -100 Cutoff points chosen based on Results of NSABP trial B-20 Sparano, J & Paik, S. JCO , 2008.
    20. 20. Prospective Validation Study of 21-Gene Assay <ul><li>Analyzed tumor blocks of 668 patients on NSABP trial B-14 study that were randomized to tamoxifen </li></ul><ul><li>RS was significantly correlated with relapse free interval & OS (p<0.001) </li></ul><ul><li>Rate of distant recurrence at 10 years: </li></ul><ul><ul><li>Low risk – 6.8% </li></ul></ul><ul><ul><li>Intermediate risk – 14.3% </li></ul></ul><ul><ul><li>High risk – 30.5% (similar risk to LN+ patients) </li></ul></ul>No distant recurrence (low risk) = 93.2% No distant recurrence (high risk) = 69.5% p<0.001 Paik, S. JCO, 2004.
    21. 21. Other End Points RS predicted distant recurrence independent of age & tumor size The likelihood of distant recurrence ↑ continuously as the RS ↑ Multivariate Cox Analysis Distant Recurrence as a Function of RS Paik, S. JCO, 2004.
    22. 22. Does RS Have Prognostic or Predictive Value? <ul><li>Oncotype was evaluated in both TAM (n=290) & placebo (n=355) arms of the NSABP B-14 trial to determine its prognostic value in an untreated population </li></ul><ul><ul><li>Patients with low (p=0.02) and intermediate (p=0.04) RS derived benefit from tamoxifen, whereas those with high RS (p=0.82) did not </li></ul></ul><ul><ul><li>Although sample size limited, seems to indicate that ↓ RS predicts greater benefit to TAM </li></ul></ul><ul><li>Population-based external validation study of women with ER+/LN- breast cancer in The Northern California Kaiser Permanente tumor registry, age <75, untreated & TAM </li></ul><ul><ul><li>RS was associated with risk of breast cancer death in tamoxifen-treated (p=0.003) and untreated patients (p=0.03) </li></ul></ul><ul><ul><li>Prognostic in TAM-treated and untreated pts </li></ul></ul>Paik, S. ASCO Abstract, 2005. Habel, L. Breast Cancer Research, 2006.
    23. 23. Does the 21-Gene Assay Predict Response to Chemotherapy? <ul><li>NSABP B20 trial: 651 ER+/LN- pts randomized to chemo + TAM (n=424) v. TAM alone (n=227) (ALL PATIENTS) </li></ul><ul><ul><li>Chemo – CMF or MF </li></ul></ul><ul><ul><li>No distant recurrence - 92.2% (chemo + TAM) v. 87.7% (TAM) </li></ul></ul><ul><ul><li>No local/distant relapse - 90.1% (chemo + TAM) v. 83.5% (TAM) </li></ul></ul><ul><ul><li>Overall Survival – 89.5% (chemo + TAM) v. 86.4% (TAM) </li></ul></ul><ul><li>The TAM alone arm was used in the training set in development of the 21-gene assay </li></ul>Paik, S. JCO , 2006.
    24. 24. Kaplan-Meier Plots for Distant Recurrence All patients Low Risk RS <18 Intermediate Risk RS 18-30 High Risk RS ≥ 31 88% 60% 92.2% 87.7% Paik, S. JCO , 2006.
    25. 25. Relative & Absolute Benefit of Chemotherapy as a Function of RS 27.6% Low RS  mean absolute decrease in distant recurrence rate of -1.1% High RS  mean absolute decrease in Distant recurrence rate of 27.6% Intermediate RS  no substantial benefit, But the uncertainty in the estimate cannot Exclude a clinically important benefit Paik, S. JCO , 2006.
    26. 26. Prospective Validation of Oncotype DX: The TAILORX Trial Dowsett, M. & Dunbier, A. Clin Cancer Res, 2008. Low RS: Hormonal Therapy High RS: Chemo + Hormonal Therapy Hormonal Therapy Chemo + Hormonal 11,248 ER+/LN- patients
    27. 27. The Two-gene Ratio: HOXB13:IL17BR
    28. 28. Two-Gene Expression Ratio: HOXB13:IL17BR <ul><li>Developed to predict response to tamoxifen in ER+/PR+, early stage , LN+/- breast cancers </li></ul><ul><li>Performed microarray gene expression analysis of tumors from 60 women treated with adjuvant tamoxifen </li></ul><ul><ul><li>Patients selected based on outcome: early relapse or not </li></ul></ul><ul><ul><li>RNA isolated from frozen tumor-tissue  9 genes were identified with p<0.001  2 selected </li></ul></ul><ul><ul><li>HOXB13 was overexpressed in tamoxifen recurrences & IL17BR was overexpressed in tamoxifen nonrecurrences </li></ul></ul><ul><ul><li>HOX family of genes implicated in tumor invasion and metastases </li></ul></ul><ul><ul><li>HOXB13 is expression is often up-regulated in breast cancer cells </li></ul></ul>Ma, X. Cancer Cell, 2004.
    29. 29. HOXB13:IL17BR Predicts Response to Tamoxifen <ul><li>HOXB13 & IL17BR outperformed other predictive markers (quant-itative ER and PR, ERBB2, & EGFR) </li></ul><ul><li>HOXB13:IL17BR ratio was a better composite predictor of tamoxifen response </li></ul><ul><li>HOXB13:IL17BR was an indepen-dent predictor of treatment outcome when controlled for tumor size & expression of PGR and ERBB2 </li></ul><ul><li>HOXB13:IL17BR ratio was highly correlated with clinical outcome in an independent 20 pt cohort </li></ul>Ma, X. Cancer Cell, 2004.
    30. 30. Lack of Consistency of 2-gene Signature STUDY PATIENTS HAZARD RATIOS OUTCOME CUT POINTS Goetz et al. 206 ER+, LN+/- adjuvant TAM RFS – 1.98 DFS – 2.03 OS – 2.4 (LN- pts) <ul><li>Prognostic in TAM-treated LN- pts only </li></ul>TAM -1.849 Ma et al. 852 pts ( 66% untreated & 34% TAM-treated ) RFS – 3.9 (p=.007) in TAM and untreated pts combined <ul><li>Prognostic in ER+/LN- pts </li></ul><ul><li>Unable to compare TAM & untreated groups </li></ul>TAM -0.06 Untreated – 1.0 Jansen et al. 1,252 LN+/-, 32% adj tx(44% hormonal, 53% chemo, & 3% both) DFS (LN-, no tx) – 1.74 (p=.006) DFS (TAM) – 2.97 (p<.001) <ul><li>Prognostic in untreated, LN- </li></ul><ul><li>Predicts response to TAM </li></ul>Untreated – 1.0 TAM – 0.06
    31. 31. Limitations of These Studies <ul><li>Extreme sensitivity to training set since there is such variability in the cut point </li></ul><ul><li>Does not seem to be effective in LN+ patients </li></ul><ul><li>Needs prospective validation </li></ul>
    32. 32. Intrinsic Subtypes: PAM50
    33. 33. Intrinsic Subtypes: PAM50 <ul><li>Training set =189 breast tumor + 29 normal samples  qRT-PCR </li></ul><ul><li>An expanded gene set of 1,906 genes from other microarray studies  analyzed by hierarchical clustering  significant clusters correlated to known intrinisic subtypes  narrowed to 50 significant genes ( PAM50) </li></ul><ul><li>Intrinsic subtypes are useful in predicting RFS of untreated patients & those stratified by ER status </li></ul><ul><li>Cox models tested using intrinsic subtypes alone and together with clinical variables (ER status, tumor size, & node status) </li></ul><ul><ul><li>ROR-S  Subtypes alone </li></ul></ul><ul><ul><li>ROR-C  Subtype + clinical variables </li></ul></ul><ul><ul><li>Models containing both subtype & clinical variables better than either clinical variables (p<0.0001) or subtype alone (p<0.0001) </li></ul></ul>
    34. 34. ROR-C Predicts RFS in Untreated LN- Patients Only Luminal A group contained low risk patients ROR-C Scores Stratified by Subtype Kaplan-Meier Plots of RFS of Risk Groups High Risk Medium Risk Low Risk Risk Groups Predict RFS
    35. 35. PAM50 Predicts Response to Neoadjuvant T/FAC ROR-S v Probability of pCR Low-risk tumors (luminal A)  chemo-insensitive tumors with ↓ probability of pCR Plateau  chemo- resistance among high risk tumors Sensitivity 94% & NPV 97% for identifying nonresponders to Neoadjuvant chemo ROCC of ROR-S v pCR ↑ Probability of pCR with ↑ ROR-S
    36. 36. PAM50 Prognostic in TAM-treated Patients <ul><li>786 ER+ TAM treated pts  qRT-PCR, PAM50, and ROR calculation done </li></ul><ul><ul><li>Multivariate analysis – Intrinsic subtype and ROR score were independently prognostic (Grade and HER2 were not) </li></ul></ul><ul><ul><li>Low ROR score  good outcomes (even if +LN) </li></ul></ul><ul><ul><li>Found to be superior to immunohistochemical markers & adjuvant! Online as a prognosticator </li></ul></ul>Ellis, M. ASCO, 2009 .
    37. 37. 5 Gene Signatures Compared
    38. 38. Is There Concordance Between Gene Expression Profiles? 295 Stage I/II ER +/- Analyzes done with All pts & ER+ only 165 untreated 20 TAM 20 TAM + chemo 90 chemo Fan, C. NEJM , 2006.
    39. 39. Relapse-free Survival Overall Survival Intrinsic Subtype Recurrence Score 70-Gene Profile Wound Response Two-Gene Ratio All models except the two-gene ratio model were significant predictors of both RFS and OS.
    40. 40. Summary of Gene Signatures
    41. 41. 70-gene Signature 21-gene Signature 2-Gene Ratio Intrinsic Subtypes Analysis Approach Supervised Supervised Supervised Unsupervised Tissue Type Fresh or Frozen Formalin-Fixed, Parafin-embedded Formalin-Fixed, Parafin-embedded Formalin-Fixed, Parafin-embedded Technique DNA microarrays Q-RT-PCR Q-RT-PCR Q-RT-PCR Prognostic Untreated pts age<60, T1-2, LN- Untreated & TAM-treated ER+/LN- TAM-treated, ER+/LN- untreated TAM-treated Predictive NO Benefit to TAM +/- CMF/MF Response to TAM NO Validation Retrospective Retrospective Retrospective Retrospective Prospective Trials MINDACT TAILORX NONE NONE
    42. 42. Case Revisited <ul><li>Pathology report showed a poor-risk feature: lymphovascular invasion </li></ul><ul><ul><li>Lee et al showed that those with peritumoral lymphatic and blood vessel invasion had a 4.7x higher risk of relapse </li></ul></ul><ul><li>Therefore, her oncotype DX results disregarded  started on chemotherapy. </li></ul>
    43. 43. Conclusions <ul><li>No gene signature is currently able to replace all clinicopathological variables in assessing risk of recurrence </li></ul><ul><li>What patient populations should be evaluated with gene signatures is actively being investigated </li></ul><ul><li>NCCN guidelines suggest that oncotype DX is an option for risk evaluation in 0.6-1 cm tumors with unfavorable characteristics or in >1 cm LN-, ER+/HER2 tumors </li></ul>
    44. 44. Resources <ul><li>Dowsett, M. & Dunbier, A. Emerging Biomarkers and New Understanding of Traditional Markers in Personalized Therapy for Breast Cancer. Clinical Cancer Research 2008; 14: 8019-26. </li></ul><ul><li>Sotiriou, C et al. Gene-Expression Signatures in Breast Cancer. New England Journal of Medicine 2009; 360: 790-800. </li></ul><ul><li>Van’t Veer, L et al. Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer. Nature 2002; 415: 530-36. </li></ul><ul><li>Van de Vijver, M. et al. A Gene-Expression Signature as a Predictor of Survival in Breast Cancer. The New England Journal of Medicine 2002; 347: 1999-2009. </li></ul><ul><li>Paik, S. et al. A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer. The New England Journal of Medicine 2004; 351: 2817-2826. </li></ul><ul><li>Sparano, J and Paik, S. Development of the 21-Gene Assay and Its Application in Clinical Practice and Clinical Trials. Journal of Clinical Oncology 2008; 26: 721-728. </li></ul><ul><li>Paik, S. et al. Gene Expression and Benefit of Chemotherapy in Women With Node-Negative, Estrogen-Receptor-Positive Breast Cancer. Journal of Clinical Oncology 2006; 24: 3726-3734. </li></ul><ul><li>Paik, S. et al. Expression of the 21 genes in the Recurrence Score assay and tamoxifen clinical benefit in the NSABP study B-14 of node negative, estrogen receptor positive breast cancer. Journal of Clinical Oncology 2005; 23: suppl abstr 510. </li></ul>
    45. 45. Resources <ul><li>Ma, X. et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell, 2004; 5: 607-16. </li></ul><ul><li>Ma X. et al. The HOXB13:IL17BR Expression Index Is a Prognostic Factor in Early-Stage Breast Cancer. Journal of Clinical Oncology , 2006; 24: 4611-4619. </li></ul><ul><li>Jansen, M. et al. HOXB13-to-IL17BR Expression Ratio Is Related With Tumor Aggressiveness and Response to Tamoxifen of Recurrent Breast Cancer: A Retrospective Study. Journal of Clinical Oncology , 2007; 25: 662-668. </li></ul><ul><li>Cardosa, F. et al. Clinical Application of the 70-Gene Profile: The MINDACT Trial. Journal of Clinical Oncology , 2008; 26: 729-735. </li></ul>
    46. 46. Intrinsic Subtype & Response to Paclitaxel <ul><li>CALGB 9344  adding T to AC in the adjuvant setting led to a 5% absolute improvement in DFS </li></ul><ul><li>Of the 42% of pts with complete data, no benefit in the ER+/HER2- pts </li></ul><ul><li>Microarray done in 2039 pts and pts were categorized into intrinsic subtypes: 790 luminal A, 340 luminal B, 221 HER2-enriched, 444 basal, and 93 ER-/HER2-/nonbasal </li></ul><ul><li>Intrinsic subtype was prognostically significant in multivariate analysis (p<0.001) </li></ul><ul><li>No significant interaction of Ki67 with paclitaxel among ER+/HER2- patients </li></ul><ul><li>Basal subtype predicted benefit from paclitaxel in multivariate analysis (HR 0.75, p=0.033) </li></ul>
    47. 47. Variation in Hazard Ratios over Time Cardoso, F. JCO, 2008. Substantial variation over time of adjusted hazard ratio ability of gene signature to identify those who will develop distant relapse is greatest within 5 years of diagnosis.
    48. 48. Sensitivity & Specificity of 70-gene Signature <ul><li>Sensitivity is as good as other risk classification models </li></ul><ul><li>Specificity is slightly better than the other risk classification models </li></ul>Buyse, M. J of NCI , 2006.
    49. 49. Classification of Tumor Samples According to Model <ul><li>Basal-like, HER2+ and ER-, & luminal B all had a poor outcome by 70-gene, recurrence score, and wound –response models </li></ul><ul><li>Normal-like and luminal A had variability in the outcomes </li></ul>

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