Perez, EA

Abstract Background: While previous study showed that the enrichment of immune-related gene expression was associated with outcome in HER2+ patients receiving sequential or concurrent trastuzumab (H), stromal tumor infiltrating lymphocytes (sTIL) have not been consistently shown to associate with outcome in this group of patients. Given that TIL scoring may be subjective, we analyzed molecular signatures of different subsets of tumor infiltrating immune cell populations, using NanoStringTM gene expression data to assess molecular TIL (mTIL) signature enrichment and intrinsic subtype as a function of relapse-free survival (RFS). Methods: NanoStringTM technology was used to quantify mRNA in samples from 1,280 patients in N9831, 168 patients in FinHer, and 170 patients in FinXX. In N9831, patients in arm A were treated with chemotherapy alone (AC-T), arm B received chemotherapy followed by sequential H (AC-T-H), and arm C received H concurrently with chemotherapy (AC-TH). In the FinHer trial, H was given concurrently for 9 weeks and either 1 year or 9 weeks in FinXX trial. Cox proportional hazard ratio (HR) was used to determine the association of each gene signature with RFS. Different immune subset signatures, including CD45, B-cells, CD8 T-cells, cytotoxic-cells, and T-cells were analyzed using algorithms developed by NanoString. Results: In N9831, CD45, cytotoxic-cell, and T-cell signatures were significantly associated with improved RFS in patients receiving chemotherapy alone and AC-T-H. However, none of the mTIL signatures were significantly associated with outcome in patients receiving AC-TH. Patients lacking CD45 enrichment had better outcome when H was given concurrently with chemotherapy. The 10-year Kaplan-Meier estimates for RFS in arm B patients with CD45 enrichment or no enrichment were 81.3% and 72.6%, respectively (HR 0.63 [95% CI, 0.42-0.93]; p = 0.02), and in arm C were 83.6% and 79.8%, respectively (HR 0.79, 95%CI 0.49-1.28; p = 0.34). Among patients with HER2-enriched subtype, all of the mTIL signatures were associated with improved RFS in arm A (AC-T) and B (AC-T-H) but remained non-significant in arm C (AC-TH). In patients with luminal subtypes, mTIL signatures were not significantly associated with outcome in patients treated with chemotherapy alone. Similar findings were observed in the FinHer and FinXX trials, in which, none of mTIL signatures were significantly associated with outcome among patients who received H. Conclusion: This analysis sheds light on previous discrepancy between immune-related gene signature and sTIL findings. Our data also suggests that the poor prognosis associated with lack of infiltrating immune cells can be partly overcome by the concomitant administration of H with chemotherapy. mTIL signatures, specifically CD45, cytoxic, and T cells, were prognostically associated with improved outcome in patients receiving chemotherapy without concurrent trastuzumab. Understanding the role of the immune system in response to H will require a higher degree of granularity than can be achieved by histological quantification of TILs. Further studies are needed to validate the significance of mTIL signatures as predictive or prognostic biomarker in HER+ patients. Citation Format: Chumsri S, Serie DJ, Mashadi-Hossein A, Tenner KS, Lauttia SL, Moreno-Aspitia A, McLaughlin SA, Nassar A, Warren S, Danaher P, Colon-Otero G, Lindman H, Joensuu H, Perez EA, Thompson EA. Prognostic value of molecular tumor infiltrating lymphocyte (mTIL) signatures in HER2-positive breast cancer patients in N9831 and FinHer/FinXX trials [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD5-06.

Abstract Fusion transcript 24analysis by five groups, each using "in house" analytical workflow to analyze RNA-seq data from 813 breast tumors from The Cancer Genome Atlas project detected 2514 high confidence RNA fusions (2 or more junction spanning reads detected by 2 or more groups). A subset of tumors with fusions were evaluated for chromosomal rearrangement using whole genome sequence data (WGS), and about half of the high confidence fusions could be validated, with the remainder likely subclonal and therefore below the limits of detection by WGS at the relatively low depth of coverage (30X) available. The majority of tumors contained one or more fusion transcript (range 0-24 fusions/tumor), but recurrence of specific chimaeric transcripts was low. Only ESR1->CCDC170, C20orf3->ACSS1, and USP22->MYH10 fusions were detected in 10 or more tumors. Additional ESR1 fusions were detected with AKAP12, BNC2, C6orf211, GNAS, POLH, USP25, and UTRN, within 19 tumors, primarily of the Luminal B subtype. RARA was the second most common 5' fusion partner with 17 tumors, predominately of the HER2-enriched subtype, expressing out of frame RARA fusions to 19 different 3' fusion partners. Other common 5' fusion partners included FBXL20, USP22, USP32, BCAS3, MED1, BPTF, ERBB2, MED24, and PPF1A1 (expressed in 10 or more tumors each). The most common 3' fusion partners were ERBB2, CCDC170, PITPNC1, ACSS1, MYH10, IKZF3, and RAB6A (10 or more tumors each). HER2-enriched tumors expressed significantly more fusions than other subtypes (4.9 fusions/tumor vs 3.3 for Basal-like, 1.3 for LumA, and 3.2 for LumB). Almost all HER2-enriched tumors expressed fusions (97%), whereas 85% of Basal-like tumors and 79% of Luminal B tumors expressed one or more fusions. Among Luminal A tumors, only 48% expressed one or more fusion transcript. Those Luminal A tumors with multiple fusion transcripts contained significantly more copy number aberrations and were enriched for expression of mitotic cell cycle genes (p=3.07E-18), characteristic of the recently described high risk CNH subclass of Luminal A tumors. We conclude that, consistent with other observations, breast tumors generally exhibit a high level of genomic instability, associated with multiple copy number alterations and multiple fusion transcripts. However, recurrence of specific fusion transcripts is low. About half of Luminal A tumors express fusion transcripts; and these tumors exhibit multiple copy number events, consistent with high level genomic instability, as well as enriched expression of mitotic cell cycle genes. These tumors appear to be related to the relatively high risk Luminal A CNH subclass, and express high levels of aurora kinases and polo-like kinases, which might be considered as therapeutic targets. Given the increasing emphasis on transcript profiling of clinical samples and the clinical significance of high risk Luminal A tumors, it may be timely to consider inclusion of fusion transcripts in such analyses as surrogate markers of genomic instability and potential therapeutic and/or prognostic indicators. Citation Format: Thompson EA, Asmann YW, Su X, Ellis MJ, Shao J, Hu Y, White KP, Cherniack AD, Hoadley KA, Serie DJ, Perez EA, Perou CM. A comprehensive analysis of fusion transcripts in breast cancer reveals associations between number of fusion transcripts, copy number events, gene expression profiles, and potentially clinical outcome. [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 S4-02.

Abstract Background: The need remains for novel agents that prolong survival and/or improve QOL in women with aBC. EP is a long-acting topoisomerase 1 inhibitor engineered to produce sustained exposure to irinotecan and its active metabolite SN38. Given previous efficacy seen in an earlier phase II trial in MBC, EP 145 mg/m2 every 3 weeks was compared to TPC (one of 7 single-agent regimens) in the randomized phase 3 BEACON study (NCT01492101). As reported at ASCO 2015 (abstract 1001), EP prolonged median overall survival by 2.1 months, although this did not reach statistical significance (12.4 vs 10.3 months; HR 0.87, p=0.08). Grade ≥ 3 adverse events were significantly less common with EP (48% vs 63% with TPC, p<0.001). We now present results of the QOL analyses. Methods: Patients completed validated health-related QoL (HRQoL) questionnaires, EORTC QLQ-C30 (version 3.0) and breast cancer-specific QLQ-BR23, pretreatment and every 8 weeks until progression, death or withdrawal of consent. Questionnaires were scored according to the EORTC manual. For each scale, raw scores were standardized via a linear transformation to a range from 0 to 100. Absolute scores and changes from baseline were analyzed longitudinally and categorically using a 5-point difference calculated by treatment group. Comparisons between treatment groups were conducted to evaluate the differences in global health status, functional scores and symptoms over time. Results: The majority of patients who were randomized (total: 733/852 [86%], EP: 378/429 [88%], TPC: 355/423 [84%]) completed at least one post-baseline HRQoL questionnaire. In the EORTC QLQ-C30, grade ≥ 3 AEs significantly impacted HRQoL measured by global health status and 5 additional functional domains. Of the six domains, compared to TPC in a longitudinal analysis, EP was statistically superior in the mean treatment effect through Week 32 in global health status p=0.02 and physical functioning scale p=0.01. EP was also numerically superior in all other scales. In EORTC QLQ-C30 and BR-23, a total of 13 symptoms were measured and categorically analyzed. There were no treatment differences in 7 of 13 symptom scales. EP was associated with worsening of 3 symptom scales: appetite loss, nausea/vomiting, and diarrhea. TPC was associated with worsening of 2 symptom scales: dyspnea and systemic side effects. Conclusions: In the phase 3 BEACON trial comparing EP to TPC, the more favorable toxicity profile of EP resulted in an improvement in global health status and physical function (results of the symptom scales confirmed the different toxicities of the two arms). EP remains a promising investigational therapy for aBC. Citation Format: Cortes J, Awada A, Perez EA, Rugo HS, Twelves C, Im S-A, Zhao C, Hoch U, Ney J, Hannah AL, O'Shaughnessy J. Impact of treatment on quality of life (QOL) in the BEACON study, a randomized phase III trial of etirinotecan pegol (EP) versus treatment of physician's choice (TPC) in patients (pts) with advanced breast cancer (aBC) whose disease has progressed following anthracycline (A), taxane (T) and capecitabine (C). [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 P4-11-08.

Abstract Background: The role of fusion genes and associated fusion transcripts has long been recognized in hematopoietic malignancies. Until quite recently it has been difficult to detect such events on a genomic scale in solid tumors. Consequently, little is known about the potential role of fusion genes, transcripts, and proteins as driver mutations, biomarkers, or therapeutic targets in breast cancer. Methods: We have developed a novel analytical pipeline, Snowshoes-FTD, for detection of fusion transcripts in breast cancer cell lines and tumor samples (Asmann, et al. NAR 2011; May 27 ePub ahead of print). Preliminary analyses have been carried out with a panel of 8 each ER+, HER2+, and triple negative (TN) primary breast tumors, 8 primary human mammary epithelial cell (HMEC) lines from biopsy samples, plus 16 normal tissues from the Illumina Body Map dataset. Results: We have identified 120 redundant, tumor-specific fusion transcripts, expressed in two or more tumors and in no non-transformed samples. Sixteen of these represent intrachromosomal fusions and 104 arise from fusion of transcripts that map to two different chromosomes. Every breast tumor expressed one or more fusion transcripts. Twenty-nine fusion transcripts appeared to be tumor subtype specific. Among these, we have identified 2 HER2+, 10 ER+, and 17 triple negative specific redundant transcripts. In general, HER2+ tumors expressed fewer fusion transcripts (range 4 to 28/tumor) compared to TN (range11 to 44/tumor). Chromosomal distribution patterns were also markedly different among the tumor subtypes. For example, ER+ tumors expressed a preponderance of redundant fusion transcripts that involve chr1 and 2, whereas TN tumors had no fusion transcripts that map to either chromosome. Conversely, the predominant locus for TN fusion transcripts was chr19, which contains only one HER2+ fusion and no ER+ fusion transcripts. Conclusions: Primary breast tumors express many chimaeric transcripts, which we presume to arise primarily from genomic rearrangements. The majority of these transcripts are redundant, and a subset are tumor subtype specific. These transcripts may mark regions of chromosomal instability. HER2+ tumors, in general, appear to evidence less chromosomal instability, as inferred from fusion transcripts; although some HER2+ tumors appear to be quite unstable. TN tumors contain many more redundant fusion transcripts, implying increased genomic instability, particularly in chr19. We conclude that these fusion transcripts represent a class of heretofore unrecognized biomarkers that may be used for sub-classification of breast tumors. Some of these transcripts appear to encode proteins that may function as tumor-subtype-specific driver mutations and may have potential as therapeutic targets in breast cancer. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-02.

Abstract Background: NKTR-102, a topoisomerase 1 inhibitor-polymer conjugate with reduced peak concentrations and a continuous concentration profile, demonstrated evidence of anti-tumor activity in a broad range of tumors in phase 1 (Von Hoff; EORTC-NCI-AACR 2008, abstract #595), including three patients (pts) with triple negative breast cancer (one confirmed PR by RECIST, one 20% reduction in tumor burden and one 50%+ reduction in CA 27.29). We now report data of a randomized phase 2 study in pts with MBC following progression to taxane-based therapy. Methods: This open-label, phase 2 study enrolled pts to receive NKTR-102 intravenously (IV) at a target dose of 145 mg/m2. Eligible patients had progressive MBC following taxane therapy, ECOG PS 0-1, adequate renal, hepatic, and marrow function. The study randomized pts to receive NKTR-102 q14d or q21d; each schedule followed a two-stage Simon design to ensure adequate response rate prior to proceeding to full enrollment. The primary endpoint was objective response rate (ORR) by RECIST v1.0; secondary endpoints were safety and PFS. Results: 70 pts were randomized from Feb09 to Apr10 and treated (35 on each schedule); 20 patients remain active on study as of 14Jun2010. Median age was 55 (range 33-83); all but 1 pt was female. ECOG PS 0/1 equaled 40%/60%. Prior neo-adjuvant and adjuvant therapy had been administered in 15 and 39 patients respectively; 23 pts had received prior hormonal therapy. Median number of prior non-hormonal regimens for metastatic disease was 2 (range 0-4). All pts had received prior taxane therapy; 11 in the adjuvant setting and 60 in the metastatic setting). 45 pts had received only prior anthracycline/taxane therapy (“AT”); an additional 14 pts had received prior AT/capecitabine therapy (“ATC”). 42 were estrogen or progesterone receptor positive and 20 pts had triple negative disease. Best RECIST response rate (confirmed and unconfirmed) equaled 27% (9 pts; 2 awaiting confirmation) and 24% (8 pts; 4 awaiting confirmation) for the q14d and q21d schedules (n=33 and 34, respectively; 3 patients had not undergone first on-study CT exam). As ORR results were similar for each schedule, the combined best RECIST ORR for in AT/ATC pts equaled 23%/29%, respectively and in pts with triple negative disease, this equaled 25%. Common related Grade 3/4 toxicities (q14d/q21d schedules; n=67 pts with AE data available): diarrhea (15%/12%), neutropenia (15%/9%),fatigue (12%/3%), and dehydration (6%/3%). One pt in each schedule died due to septic shock and acute renal failure secondary to hypovolemia. Conclusion: Single-agent NKTR-102 demonstrates significant anti-tumor activity in pts with MBC, including pts having tumor progression after ATC-based therapy and pts with triple negative disease, with a tolerable toxicity profile. Mature ORR and median PFS will be available by December 2010. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-11-01.

Abstract Background: Trastuzumab (H) improves disease-free survival (DFS) in patients (pts) with HER2 positive breast cancer (BR Ca) when used with adjuvant chemotherapy. We herein compare the rates of local regional recurrence (LRR) in pts randomized to adjuvant chemotherapy with or without adjuvant H. Methods: The phase 3 randomized trial NCCTG N9831 enrolled 3505 pts with high risk HER2 positive Br Ca to evaluate the effect of adjuvant H on DFS. Pts were randomized to either doxorubicin (A) and cyclophosphamide (C) followed by paclitaxel (T); or AC→TH→H. RT was given concurrently with H after ACT chemotherapy. Pts analyzed underwent lumpectomy (L) + radiotherapy (RT), mastectomy (M) alone, or M+RT. All pts underwent sentinel lymph node biopsy alone and/or axillary dissection. 2816 pts were eligible for competing risk analysis of LRR as a first event (competing risks were distant recurrence, contralateral Br Ca, second primary cancer, or death). Median follow-up is 5.3 years. Results: Primary breast therapy included L+RT 1062 (38%), M 711 (25%), and M+RT 1043 (37%). Axillary dissection was performed in 90% of pts but less frequently with L+RT (83%) compared to M (88%) or M+RT (98%), chi-sq P<0.001. Stage at presentation was I 41%, II 51%, and III 8% with a significant greater proportion of higher stage pts undergoing M+RT, chi-sq P<0.001. Overall the 5-year LRR rate was 4.1% (95% CI 3.5-4.9%) and similar among the treatment groups: L+RT 4.7% (95% CI 3.6-6.1%), M 3.5% (95% CI 2.4-5.1%), and M+RT 2.3% (95% CI 1.6-3.4%). Among pts with a LRR, 66% were local recurrence only, 11% were local-regional, and 23% were regional only. In the L+RT patients with a LRR, the corresponding rates were 74%, 7%, and 19%, respectively. In the M patients with a LRR, the corresponding rates were 40%, 23%, and 37%, respectively. In the M+RT patients with LRR, the rates were 79%, 4%, and 17%, respectively. H is associated with a non-statistically significant reduction in the risk of LRR for pts who receive L+RT or M+RT (Table 1). No such trend was seen in the M alone group but the number of events was low. Table 1. LRR According to Local and Adjuvant Treatment Groups Conclusion: The LRR as the first reported site of failure was low with a median 5. 3 year follow-up. Adjuvant H was associated with a trend of lower LRR in the pts treated with L + RT or M+RT. This observation suggests an additive effect of RT and H on LRR that warrants further investigation. The small number of local-regional events in this one randomized trial supports further investigation of LRR across other adjuvant trastuzumab trials. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-13-02.

Abstract Abstract #6037 Background: Tamoxifen (Tam) is biotransformed to the potent antiestrogen, endoxifen, by the CYP2D6 enzyme. We previously demonstrated that patients (pts) receiving adjuvant TAM with impaired CYP2D6 metabolism due to CYP2D6 (*4) and/or concurrent administration of a CYP2D6 inhibitor had a higher risk of recurrence. Other studies suggest CYP2C19*17 (Schroth JCO 2007) and SULT1A1*2 (Nowell JNCI 2002) may be associated with treatment outcome. With extended follow-up, we sought to evaluate the importance of comprehensive CYP2D6 genotyping as well as the potential association between CYP2C19*17 and SULT1A1 copy number with clinical outcome in pts randomized to TAM in NCCTG 89-30-52.
 Methods: Using DNA derived from paraffin embedded sections, CYP2D6 and SULT1A1 genotype were determined using quantitative multiplex PCR and CYP2C19 by sequencing. Pts administered the following CYP2D6 inhibitors (fluoxetine, paroxetine, sertraline, cimetidine, amiodarone, doxepin, ticlopidine and haloperidol) were considered as intermediate (IM) or poor metabolizers (PM) based on the potency of CYP2D6 inhibition. CYP2D6 phenotype was defined as follows: extensive metabolizers (EM) were pts not administered an inhibitor who did not carry a null allele (*3, *4, *6) and who were not homozygous for an IM allele (*10, *17, *41). CYP2D6 IM were either heterozygous for a null allele or homozygous for an IM allele but not administered an inhibitor or CYP2D6 EM administered a weak inhibitor. PM were pts homozygous for a null allele, or any patient administered a potent inhibitor. The association between genotype or CYP2D6 phenotype and clinical outcome was determined using the log-rank test. Multivariate Cox modeling was performed using traditional prognostic factors.
 Results: The median follow-up of living pts is now 14.5 years. Of 256 pts. randomized to TAM, genotype was determined for CYP2D6 (n=210), CYP2C19*17 (n=170), and SULT1A1 (n=169) with the following allele frequencies: CYP2D6 *3 (.02), *4(.20), *6 (.01), *10 (.03), *17 (.00), *41(.08), and CYP2C19*17 (.22). The frequency of SULT1A1 copy number alleles (CNA) was 1 (4%), 2 (67%), 3 (20%), and 4+ (9%). 14/227 patients (6%) were administered an inhibitor. A multivariate analysis accounting for nodal status and tumor size demonstrated that compared to CYP2D6 EM, CYP2D6 PM had significantly shorter time to recurrence (TTR) (HR 4.0, p=0.001) and DFS (HR 2.0, p=0.02) and CYP2D6 IM tended to have shorter TTR (HR 1.8, p=0.08) and DFS (HR 1.4, p=0.10). DFS did not differ by SULT1A1 copy number (p=0.62) or CYP2C19 *17 (p=0.47)
 Conclusion: Long term follow-up of pts in NCCTG 89-30-52 confirms the importance of CYP2D6 metabolism and further demonstrates the importance of comprehensive genotyping and phenotyping with CYP2D6 inhibitors. We could not identify an association between CYP2C19*17 or SULT1A1 copy number with recurrence but further evaluation is needed in larger cohorts. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 6037.