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PDF file - 109K, Derivation of samples for microarray analysis.

CDK4/6 inhibition partly overcomes NF1 loss in T47D cells

Supplementary Table 1. Targets of The Breast NGS v1.0 capture panel. Supplementary Table 2. Gene list of NanoString nCounter{trade mark, serif} custom codeset. Supplementary Table 3. Gene list of Human Estrogen Receptor RT2 Profiler PCR Array (330231, PAHS-005ZA-24, Qiagen) Supplementary Table 4. Lines of treatment of patients with ESR1 and NF1 mutations. Supplementary Table 5. Disease free survival for mutated genes with incidence {greater than or equal to}5% presented by HR+/HER2-, HER2+ and TNBC subtype. Supplementary Table 6. Advanced overall survival for mutated genes with incidence {greater than or equal to}5% presented by HR+/HER2-, HER2+ and TNBC subtype

Purpose: Estrogen withdrawal by treatment with aromatase inhibitors is the most effective form of endocrine therapy for postmenopausal estrogen receptor–positive (ER+) breast cancer. However, response to therapy varies markedly and understanding of the precise molecular effects of aromatase inhibitors and causes of resistance is limited. We aimed to identify in clinical breast cancer those genes and pathways most associated with resistance to aromatase inhibitors by examining the global transcriptional effects of AI treatment.Experimental Design: Baseline and 2-week posttreatment biopsies were obtained from 112 postmenopausal women with ER+ breast cancer receiving neoadjuvant anastrozole. Gene expression data were obtained from 81 baseline and 2-week paired samples. Pathway analysis identified (i) the most prevalent changes in expression and (ii) the pretreatment genes/pathways most related to poor antiproliferative response.Results: A total of 1,327 genes were differentially expressed after 2-week treatment (false discovery rate < 0.01). Proliferation-associated genes and classical estrogen-dependent genes were strongly downregulated whereas collagens and chemokines were upregulated. Pretreatment expression of an inflammatory signature correlated with antiproliferative response to anastrozole and this observation was validated in an independent study. Higher expression of immune-related genes such as SLAMF8 and TNF as well as lymphocytic infiltration were associated with poorer response (P < 0.001) and validated in an independent cohort.Conclusions: The molecular response to aromatase inhibitor treatment varies greatly between patients consistent with the variable clinical benefit from aromatase inhibitor treatment. Higher baseline expression of an inflammatory signature is associated with poor antiproliferative response and should be assessed further as a novel biomarker and potential target for aromatase inhibitor-treated patients. Clin Cancer Res; 19(10); 2775–86. ©2013 AACR.

Supplementary Figure Legend

PDF File - 438K, HER2 : EFTUD2 copy number ratio in validation cohort.

XLSX file - 250K, Excel file of differentially expressed and correlated genes.

PDF file - 87K, Lymphocytic infiltration in tumours.

Purpose: Digital PCR is a highly accurate method of determining DNA concentration. We adapted digital PCR to determine the presence of oncogenic amplification through noninvasive analysis of circulating free plasma DNA and exemplify this approach by developing a plasma DNA digital PCR assay for HER2 copy number.Experimental Design: The reference gene for copy number assessment was assessed experimentally and bioinformatically. Chromosome 17 pericentromeric probes were shown to be suboptimal, and EFTUD2 at chromosome position 17q21.31 was selected for analysis. Digital PCR assay parameters were determined on plasma samples from a development cohort of 65 patients and assessed in an independent validation cohort of plasma samples from 58 patients with metastatic breast cancer. The sequential probability ratio test was used to assign the plasma DNA digital PCR test as being HER2-positive or -negative in the validation cohort.Results: In the development cohort, the HER2:EFTUD2 plasma DNA copy number ratio had a receiver operator area under the curve (AUC) = 0.92 [95% confidence interval (CI), 0.86–0.99, P = 0.0003]. In the independent validation cohort, 64% (7 of 11) of patients with HER2-amplified cancers were classified as plasma digital PCR HER2–positive and 94% (44 of 47) of patients with HER2-nonamplified cancers were classified as digital PCR HER2–negative, with a positive and negative predictive value of 70% and 92%, respectively.Conclusion: Analysis of plasma DNA with digital PCR has the potential to screen for the acquisition of HER2 amplification in metastatic breast cancer. This approach could potentially be adapted to the analysis of any locus amplified in cancer. Clin Cancer Res; 19(12); 3276–84. ©2013 AACR.

PDF File - 694K, Comparison between EFTUD2 and UBBP4 reference probes on patient plasma samples.

PDF file - 826K, Clustering of the tumours based on immunohistochemical parameters.

Genetic profile of advanced breast cancer subtypes

NCOR expression following NF1 loss

PDF file - 46K, Prediction analysis of correlated genes.

PDF file - 68K, Multivariable analysis of inflammatory metagene, grade, ER H-score, baseline Ki67 and proportional change in Ki67.

PDF file - 44K, Patient demographics.

PDF File - 854K, Digital PCR analysis by droplet digital PCR.

PDF File - 1282, Digital PCR assay for HER2 on 384 well microplates.

Purpose:Advanced breast cancer (ABC) has not been subjected to the same degree of molecular scrutiny as early primary cancer. Breast cancer evolves with time and under the selective pressure of treatment, with the potential to acquire mutations with resistance to treatment and disease progression. To identify potentially targetable mutations in advanced breast cancer, we performed prospective molecular characterization of a cohort of patients with ABC.Experimental Design:Biopsies from patients with advanced breast cancer were sequenced with a 41 genes targeted panel in the ABC Biopsy (ABC-Bio) study. Blood samples were collected at disease progression for circulating tumor DNA (ctDNA) analysis, along with matched primary tumor to assess for acquisition in ABC in a subset of patients.Results:We sequenced 210 ABC samples, demonstrating enrichment compared with primary disease for potentially targetable mutations in HER2 (in 6.19% of samples), AKT1 (7.14%), and NF1 (8.10%). Of these enriched mutations, we show that NF1 mutations were frequently acquired in ABC, not present in the original primary disease. In ER-positive cancer cell line models, loss of NF1 resulted in endocrine therapy resistance, through both ER-dependent and -independent mechanisms. NF1 loss promoted ER-independent cyclin D1 expression, which could be therapeutically targeted with CDK4/6 inhibitors in vitro. Patients with NF1 mutations detected in baseline circulating tumor DNA had a good outcome on the CDK4/6 inhibitor palbociclib and fulvestrant.Conclusions:Our research identifies multiple therapeutic opportunities for advanced breast cancer and identifies the previously underappreciated acquisition of NF1 mutations.

PDF File - 832K, Example Digital PCR analysis in 384 well plate.

NCOR expression in NF1 mutated cancers

Genetic profile of ER positive primary breast cancers that 'switch' to triple negative recurrent advanced breast cancer

PDF file - 81K, IPA analysis and genes in the inflammatory immune response signature.

PDF File - 883K, Bio-informatic comparison of different reference probes.

PDF File - 177K, Supplementary methods, tables, and figures legends.

Background CDK4/6 inhibitors may trigger anti-tumour immunity, both through tumour cell intrinsic and extrinsic mechanisms, which can be enhanced by immune checkpoint blockade in pre-clinical studies. Although most triple negative breast cancers (TNBC) are resistant to CDK4/6 inhibition, palbociclib (palbo) has activity in pre-clinical models of the luminal androgen receptor (LAR) subtype. Here we report the dose finding phase Ib cohort A of the PAveMenT trial combining avelumab and palbociclib Methods The PAveMenT phase 1b trial consists of a dose finding phase (cohort A), to be followed by an expansion in androgen receptor positive (AR+) TNBC (Cohort B). The phase 1B phase investigated palbo dosing schedules (75mg intermittent dosing (ID), 100mg continuous dosing (CD) and 125mg ID) in combination with the anti-PD-L1 antibody, avelumab 10mg/kg 2-weekly (cohort A) to determine the optimal schedule for cohort B. The CD dose-level was pre-specified as the preferred schedule if tolerated, due to the proliferative nature of TNBC and potential for tumour re-growth with ID. Patients with previously treated advanced breast cancer (ABC) of any histology with measurable disease and adequate organ function, who had not received prior immunotherapy or CDK4/6 inhibitors or more than 2 lines of chemotherapy for ABC, were eligible for cohort A. Dose-limiting toxicities (DLTs) were defined as Grade(G) 4 neutropenia, complicated G3 neutropenia or G4 thrombocytopenia, or ≥G3 immune toxicity during cycle 1. AR staining of ≥10% using the SP107 antibody (Ventana) was considered AR+. PD-L1 was evaluated using CC23 Pharma Dx antibody (DAKO) and PD-L1 positive defined as CPS score of ≥10%. Results Fourteen patients were recruited to Part A, all female, 12 with TNBC, two with ER positive/HER2 negative ABC, median age 53.5 years. Three evaluable patients received palbo 75mg/day ID without DLTs, therefore two further dose levels were opened in parallel. Three evaluable patients received palbo 125mg/day ID without DLTs. Due to a DLT of fever with G3 neutropenia in one of 3 patients receiving palbo 100mg CD, 3 further evaluable patients received 100mg CD without DLTs. Two patients were not evaluable for DLTs having not received a full cycle of treatment so were replaced. One case of grade 3 colitis and one case of grade 2 hypothyroidism (both 100mg CD) occurred outside the DLT period. Amongst 12 patients with TNBC, metastatic tissue was available for 11, archival breast tissue for one. Four of 12 patients were AR+. Five of 10 TNBC patients with sufficient tissue were PD-L1 positive, all of whom had previously tested negative with the SP142 antibody (Ventana). One of the 5 PD-L1+ and 2/5 PD-L1 negative TNBC cases were also AR+. TNBC patients received a median of 2 cycles of treatment (range 1-17). Both ER+ patients were AR+ and PD-L1 negative; one progressed after 4 cycles, the other remains on treatment at 12 cycles. The 100mg CD schedule was selected for cohort B. Conclusions All schedules were tolerable, with activity observed in patients with both ER positive and TNBC cancers. Cohort B of the study is open to recruitment for patients with AR+ TNBC. NCT04360941. Citation Format: Alicia F. Okines, Houman Moghadam, Laura Sparks, Kabir Mohammed, Kathryn Dunne, Ashutosh Nerurkar, Peter Osin, Claire Swift, Ruth Sardinha, Nicholas Turner. Results from a dose escalation phase 1b study of palbociclib and avelumab in advanced breast cancer in the PAveMenT Trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-01-02.