Citations

Abstract Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a life-time risk of 1 in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry GWAS in ALS including 29,612 ALS patients and 122,656 controls which identified 15 risk loci in ALS. When combined with 8,953 whole-genome sequenced individuals (6,538 ALS patients, 2,415 controls) and the largest cortex-derived eQTL dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, repeat expansions or regulatory effects. ALS associated risk loci were shared with multiple traits within the neurodegenerative spectrum, but with distinct enrichment patterns across brain regions and cell-types. Of the environmental and life-style risk factors obtained from literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.

Abstract Background: Cyclin dependent 4/6 kinase inhibitors (CDK4/6i) and endocrine therapy (ET) have improved progression-free survival (PFS) and overall survival in hormone-receptor (HR)-positive metastatic breast cancer (MBC), but progression of disease is inevitable. Serum thymidine kinase-1 (TK1) is a secreted marker of proliferation that is prognostic in patients (pts) with HR-positive, HER2-negative MBC and may be predictive of ET and CDK 4/6i response. PROMISE (NCT0281902) is a prospective study enrolling women with HR-positive MBC starting palbociclib (Pb) + letrozole (L) (1st line) or Pb + fulvestrant (2nd line). We undertook a comprehensive “omic” assessment of blood, tumor, urine and the fecal microbiome in order to identify novel genomic variants and pathways associated with an early decline in TK1 (measured after 2 months) and PFS. Additionally, patient derived xenografts/organoids were generated at baseline and progression to test new therapeutic approaches to overcome resistance to CDK4/6i and ET. We report the initial association between the baseline genomic landscape and baseline TK1 levels. Methods: FFPE tumor biopsies were obtained for DNA/RNA sequencing (TempusTM) and blood samples for TK1 (Divitum® assay, Biovica) were collected pretreatment (pre-Pb) and after 2 cycles of Pb + ET (post-Pb2). Both whole-exome (exome capture) sequencing (WES) and RNA-Seq used the Integrated DNA Technologies xGen Exome Research Panel v1.0 capture kit. TK1+ disease was defined as > 200 Du/L and TK1- disease as below limit of detection up to 200 Du/L. We tested the association between genomic and transcriptomic characteristics with baseline TK1 data in pretreatment samples where both WES and RNA-seq and TK1 was available. The data were analyzed using bioinformatics pipelines for somatic and germline mutations and copy number alterations. The current analysis focuses on baseline 1st-line pre-Pb omics data in conjunction with baseline TK1 levels. The database was locked for analysis on 5/29/2020. Results: Thirty-three pts (median age: 59 yrs.) were evaluable, with paired samples for TK1 in 32. Six pts had TK1+ disease pre-Pb and post-Pb2. Twenty-two pts had TK1- disease pre-Pb and post-Pb2. Four pts had a decrease in TK1 after 2 cycles of treatment that altered the classification from TK1+ to TK1-. Both baseline RNA seq and serum TK1 (n=16) were available for 4 TK1+ and 12 TK1- pts. In this group, 476 genes were differentially regulated (398 upregulated; 78 downregulated). Pathway analysis demonstrated enrichment in complement and coagulation cascade pathway, PPAR signaling pathway, and metabolism-related pathways related to up-regulation of CYP and UGT gene families. Further testing for the association of WES data with baseline TK1+ (n=8) and TK1- (n=16) disease demonstrated somatic copy number variations on chromosomes 6, 11, 12 and 15. CDK4 copy number gains were observed in 3/8 TK1+ pts and 0/16 TK1- pts. We also observed that somatic mutations (LOH, copy number and/or SNV/INDELs) were more prevalent in the TK1+ compared to the TK1- pre-Pb group in several cancer-associated genes (FAS [p=0.06] PTEN, PIK3CB, NAB2, SOX9 and FAT1 [p=0.08], TP53, and MAP2K4 [p=0.22]). Conversely, we also noted that 6/7 pts with GATA3 mutations had TK1- disease (p=0.23). Conclusions: Using a comprehensive “omics” approach, our data suggest that a secreted biomarker of proliferation (TK1) obtained prior to initiating CDK4/6i and ET for the first line treatment of HR+ MBC is associated with established and novel genes and pathways associated with prognosis of pts receiving ET and CDK 4/6i. Analysis of on-treatment (after 2 cycles) tumor RNA seq and its association with change in TK1 as well as data from the 2nd-line cohort will be presented at the meeting. Citation Format: Ciara C O Sullivan, Krishna R Kalari, Vera J Suman, Peter T Vedell, Ann Moyer, Abraham D Eyman Casey, Jason Sinnwell, Xiaojia Tang, Kevin Thompson, Alvaro Moreno-Aspitia, Donald W Northfelt, Minetta C Liu, Tufia C Haddad, Saranya Chumsri, Prema Peethambaram, Kathryn J Ruddy, Karthik V Giridhar, Roberto A Leon-Ferre, Adrian Nordmark, Mattias Bergqvist, Brendan P McMenomy, Richard M Weinshilboum, Liewei Wang, Matthew P Goetz. Novel genomic variants and pathways associated with baseline serum thymidine kinase 1 levels in HR-positive HER2-negative MBC patients commencing palbociclib and letrozole [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-24.

Abstract Background: The tamoxifen (TAM) metabolite, ENDX, demonstrated promising antitumor activity in endocrine resistant breast cancer (BC) in both phase I and phase II settings. Furthermore, ENDX resulted in superior in vivo antitumor activity compared to TAM and letrozole in aromatase-expressing aromatase inhibitor-sensitive and resistant MCF7AC1 models. Recently, we identified protein kinase C beta 1 (PKCβ1), which regulates cell proliferation and tumorigenic transformation, as a novel target of ENDX. ENDX-bound PKCβ1 at concentrations achieved in phase I/II ENDX studies (100-300 nM). In contrast, TAM binding to PKCβ1 occurred at concentrations 7-10 folds higher (2 μM) than achievable with TAM 20 mg/day dosing. However, the clinical relevance of targeting PKCβ1 kinase activity is unclear, since drugs that target PKCβ1 (enzastaurin) have been ineffective in BC and other solid tumors. Therefore, we sought to understand how ENDX altered PKCβ1 and to further compare and contrast ENDXs effects to that of PKCβ1 kinase inhibition in ERα+ BC. Methods: The effects of PKCβ1 silencing and ENDX treatment on gene expression was analyzed by RNAseq in MCF7AC1 cells. The impact of PKCβ1-silencing on cell cycle was evaluated by flow cytometry. Protein expression of cell cycle regulators in PKCβ1 and ENDX-treated MCF7AC1 and T47D cells were compared to TAM and enzastaurin in vitro and to letrozole, TAM or control in vivo. The effects of PKCβ1 and drugs on growth were analyzed by cell proliferation assays. PRKCB gene amplification was assessed in primary tumors using TCGA data and in metastatic tumors using whole-exome sequencing data from patients enrolled in the PROMISE study (NCT 03281902). Results: RNAseq analysis revealed E2F targets and G2M checkpoints as the top hallmark genesets significantly downregulated in both PKCβ1-silenced and ENDX-treated MCF7AC1 cells. Flow cytometry demonstrated that PKCβ1 silencing increased G1 and reduced S phases of the cell cycle. Western blot analyses of PKCβ1-silenced MCF7AC1 and T47D cells displayed reduced protein levels of the cell cycle regulators Cyclin D1, Retinoblastoma (Rb), phospho-RbS807/811, CDK4, Chk1 and E2F1 that regulate G1/S transition. While short term ENDX (48 hours) treatment did not alter PKCβ1 levels, prolonged in vitro ENDX treatment profoundly reduced PKCβ1 protein levels and the aforementioned cell cycle regulators, faithfully replicating PKCβ1 silencing effects. In contrast, enzastaurin had no impact on proliferation or cell cycle proteins in either model. Consistent with this finding, ENDX, but not TAM or letrozole, reduced protein levels of ERα and cell cycle regulators in vivo. Overexpression of PKCβ1 induced TAM, but not ENDX, resistance and had little impact on responsiveness to enzastaurin. While PRKCB gene amplification was uncommon in newly diagnosed ERα+/HER2- BC (5%, TCGA), PRKCB was amplified in 40% of metastatic ERα+/HER2- BC (PROMISE study). Conclusion: We have confirmed the relevance of a new ENDX target, PKCβ1, in ERα+/HER2- BC. While targeting PKCβ1 kinase activity elicited no anticancer effects in ERα+ cells, PKCβ1 downregulation, either by siRNA or ENDX, resulted in profound ERα turnover, reduced protein levels of essential cell cycle mediators and profoundly inhibited cell proliferation. Furthermore, PKCβ1 protein expression is associated with TAM, but not ENDX, resistance, a finding whose clinical relevance is further magnified by identification of PRKCB amplification in metastatic ERα+ BC, confirming its potential importance in progression. Efforts are currently underway to elucidate the mechanistic basis for ENDX-induced PKCβ1 and ERα degradation and the contribution of these effects to the superior antitumor activity of ENDX in ERα+ BC. Citation Format: Swaathi Jayaraman, Mary J Kuffel, Krishna R Kalari, Kevin J Thompson, Xiaojia Tang, Vera J Suman, Elizabeth S Bruinsma, Ciara C O'Sullivan, Liewei Wang, Richard Weinshilboum, James N Ingle, John R Hawse, Matthew P Goetz. Antitumor activity of Z-endoxifen (ENDX) is mediated via PKCβ1-dependent ERα loss and cell cycle arrest in ERα-positive breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD8-04.

Abstract Introduction: The immune microenvironment of high-risk HR+ breast cancer (BC) is poorly understood. BEAUTY is a prospective neoadjuvant chemotherapy (NAC) study of stage I-III BC patients treated with neoadjuvant weekly taxane followed by anthracycline-based chemotherapy. Among clinical luminal B BC (St. Gallen criteria) from BEAUTY, we used high-plex digital spatial profiling (DSP) to characterize the intra-epithelial tumor and stromal immune landscapes to 1) assess the impact of NAC on these landscapes and 2) identify immune biomarkers predictive of response to NAC. Methods: The tissue set included FFPE sections of resected tumors from 35 patients (median 51y; range: 21-71y) with clinically-defined luminal B BC (ER > 10%/grade 2/Ki67 ≥ 15% or ER > 10%/grade 3), and 16 paired pre-NAC biopsies. Nanostring GeoMX DSP was used to quantitate 58 immune and BC biomarker proteins in intra-epithelial, cytokeratin-positive tumor segments and adjacent stromal (cytokeratin-negative/SYTO13 (nuclear stain)-positive) segments. Data were normalized using the geometric mean of two negative controls (RbIgG and MsIgG1). A general linear model with negative binomial identified differentially-expressed (DE) proteins in pre/post-NAC tumors. Based on DE protein data and biologic function, a targeted protein subset (N=19) was evaluated in pre-NAC biopsies for associations between protein abundance and residual cancer burden (RCB) class (0-II vs. III) (Wilcoxon-rank sum test: p-value < 0.025 considered significant) or RCB ‘breast only’ index (Spearman correlation). Results: Comparing tumor segments in pre-NAC specimens, intra-epithelial segments were predictably enriched in cytokeratin, ER, PR and Ki-67, but also CD127 and NY-ESO-1; whereas stromal segments were enriched in proteins associated with T cell subsets (e.g. CD3, CD4, CD8), macrophages (CD68 and CD163), antigen presentation/dendritic cells (CD11c, HLA-DR) and immune checkpoint proteins (PD-L1, PD-L2, B7-H3, TIM-3, VISTA) among others. While NAC did not alter the spatial distribution of proteins (intra-epithelial vs. stromal segments), it markedly attenuated the immune landscape, with decreased abundance of functionally-diverse immune proteins (e.g. CD45, CD3, CD4, CD127, granzyme B, CTLA4; STING, B7-H3, CD11c, and CD68, log2FC: 0.27-1.52 p < 0.05), including low abundance proteins PD-1, PD-L1, PD-L2, CD20, and OX40L (log 2FC: 0.15-1.16, p < 0.05). Both PR and Ki-67 decreased in post-NAC tumors whereas ER was not significantly altered (p < 0.05). CD8, CD14, CD163, HLA-DR, IDO-1 and TIM-3 were not significantly altered by NAC. In the pre-NAC biopsies (which had subsequent residual tumor burdens of RCB class 0 or I (n=1 each), II (n=6), and III (n=8), and median RCB ‘breast only’ index of 3.39 (range: 0.00-38.02), 19 proteins were used for RCB analysis (CD3, CD4, CD8, CD14, CD34, CD44, CD45, CD68, CD127, CD163, CTLA4, granzyme B, STING, B7-H3, fibronectin, Ki-67, HLA-DR, SMA and TIM3). Among them, stromal CD127 was significantly higher in RCB class III than RCB class 0-II (p=0.021) and RCB ‘breast only’ index was positively correlated with intra-epithelial granzyme B (rho = 0.61; p=0.012), and negatively correlated with intra-epithelial Ki-67 (rho= -0.71; p=0.0022). Conclusion: In this series of clinical luminal B BC, NAC markedly attenuated the tumoral immune landscapes with a small set of “NAC-resistant” immune proteins. Among a targeted set, stromal CD127 was significantly higher in RCB III, and RCB breast-only index was positively correlated with intra-epithelial granzyme B. These data provide insight into the impact of NAC on HR+ BC, and identify potential immune biomarkers to predict response to neoadjuvant chemotherapy. Citation Format: Jodi M Carter, Judy C Boughey, Jun He, Vera J Suman, Xue Wang, Jennifer M Kachergus, Krishna R Kalari, Liewei Wang, Richard Weinshilboum, Ann M Moyer, Sarah A McLaughlin, Alvaro Moreno-Aspitia, Donald W Northfelt, Richard J Gray, James N Ingle, E. Aubrey Thompson, Matthew P Goetz. Neoadjuvant chemotherapy selectively alters spatially-defined immune landscapes in clinical luminal B HR+/HER2- breast cancers: Analysis of the breast cancer genome guided therapy study (BEAUTY) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD7-05.

Abstract Background: Patient derived xenografts are a standard tool used to study cancer biology and evaluate drug response phenotypes. It is well known that PDX take rate is associated with more aggressive clinical features [higher grade, biologic subtype (e.g. TNBC vs luminal)]. Previous data from a small retrospective cohort of patients (pts) with no prior chemo (n=24) suggested that primary breast tumor PDX take rate was associated with reduced overall survival. (Derose Nat Med. 2011) However, whether take rate is prognostic in newly diagnosed pts receiving standard of care neoadjuvant chemotherapy (NAC) is unknown. From the prospective BEAUTY clinical trial of pts treated with NAC in which PDX was attempted from pre-NAC as well as after chemo (post-NAC), we recently reported no difference in take rate comparing pts with or without a pathologic complete response (pCR) (Yu Breast Canc Res 2018). Herein we report the association between PDX take rate and recurrence from tumor samples implanted pre-NAC as well as post-NAC (time of surgery). Methods: The BEAUTY study is a prospective NAC study which enrolled breast cancer pts (Stage I-III; n=140) treated with neoadjuvant weekly taxane +/-trastuzumab followed by anthracycline-based chemotherapy. Percutaneous tumor biopsies were obtained prior to NAC and tumor samples from residual disease at surgery were additionally used to establish PDXs. Tumor take rate was defined as percent of pts with the development of at least one stably transplantable (passed at least for four generations) xenograft that was pathologically confirmed as breast cancer. Time to breast cancer recurrence was defined as the time from surgery to documentation of a local, regional, or distant recurrence. Gray’s test was used to assess whether the cumulative incidence (CI) of a breast cancer recurrence differs with respect to either pre-NAC PDX take or post-NAC PDX take. Results: Of 140 pts enrolled in the BEAUTY study, tumor tissue for PDX from the pre-NAC tumor was available for implantation in 113. As previously published, PDX take rate from pre-NAC tumor was 27.4% (31/113), and varied according to tumor clinical subtype [51.3% (20/39) in triple negative breast cancer (TNBC), 26.5% (9/34) in HER2+, 5.0% (2/40) in Luminal]. With median follow up of 5.7 years (range: 3 months to 6.75 years), 17 pts developed local, regional or distant disease relapse (4 of whom had a PDX established pre-NAC). The cumulative incidence of breast cancer relapse after surgery was not found to differ according to pre-NAC PDX take (5 yr CI rate: 13.6% no take; 13.4% take; p=0.8911). In pts with TNBC, the group with the highest take rate, there was also no significant difference in incidence of BC recurrence between those without PDX take and those with PDX take (5 yr CI rate: 21.4% vs 16.2% p=0.7314). PDXs were established from residual tissue from surgery (post-NAC) in 6 of 34 pts (17.6%), [specifically, TNBC: 5/9; Her2+: 1/8; and Luminal: 0/17]. Nine of these 34 pts developed a local, regional or distant recurrence. There was a tendency for pts who had a PDX established from their residual disease to have a higher incidence of a breast event (p=0.1092). The 5 year cumulative incidence of a breast event was 19.6% for pts whose post-NAC PDX did not take and 50.0% for pts whose post-NAC PDX took. Discussion: In pts receiving NAC for breast cancer, we observed no significant difference between establishment of a pre-NAC PDX and breast cancer relapse. In contrast, post-NAC PDX take rate (from residual tumor obtained from the breast at surgery) was associated with a tendency to have a higher incidence of a breast cancer event. PDXs remain a valuable tool for the evaluation of tumor biology and development of new therapeutics, especially those models established from pts with chemotherapy resistance. Citation Format: Judy C. Boughey, Vera J. Suman, Jia Yu, Katelyn Santo, Jason P. Sinnwell, Jodi M. Carter, Krishna R. Kalari, Xiaojia Tang, Sarah A. McLaughlin, Alvaro Moreno Aspitia, John A. Copland, III, Donald W. Northfelt, Richard J. Gray, Katie N. Hunt, Amy Lynn Conners, Richard Weinshilboum, Liewei Wang, Matthew P. Goetz. Association between patient derived xenograft (PDX) take rate and breast cancer recurrence in the prospective breast cancer genome guided therapy study (BEAUTY) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD7-04.

Abstract Background: NET is offered to postmenopausal patients (pts) with clinical stage 2/3 ER+/HER2- BC to promote breast-conserving surgery. Also limited surgical accessibility during the COVID19 pandemic has increased NET utility. Inability to identify ET-resistant disease at diagnosis risks disease progression (PD) and delays more effective treatments. Dowsett et al. recently demonstrated that baseline levels of ER, progesterone receptor (PR), Ki67 (>15% vs ≤15%), and Ki67 (>10% vs ≤10%) 2-4 weeks (wks) after starting NET may improve appropriate patient (pt) selection for NET (PMC7280290). The ER, PR and Ki67-based prediction model divides pts with primary ER+/HER2- BC into 3 groups for appropriateness for NET: (Group 1) NET is likely to be inappropriate (Allred ER <6 or ER 6 and PgR <6), (Group 2) NET may be appropriate and a biopsy for on-treatment Ki67 analysis may be considered after 2-4 wks of NET (2A: ER 7 or 8 and PgR <6 and 2B: ER 6 or 7 and PgR ≥6) given that on-treatment Ki67 >10% has been associated with worse outcome (PMC5455353), or (Group 3) NET is appropriate (ER 8 and PgR ≥6). The ALTERNATE trial (NCT01953588) randomized postmenopausal women with clinical stage II or III, ER+ (Allred score 6-8)/HER2- BC to receive anastrozole (ANA), fulvestrant (FUL), or ANA + FUL for 6 months, unless Ki67 was >10% on wk 4 or 12 biopsy, in which case pts were triaged to receive neoadjuvant chemotherapy (NCT) or surgery. As previously reported, the ET-sensitive disease (mPEPI 0 plus pCR) rates were similar across the treatment arms and overall 22% (286 of 1,299) pts had Ki67 >10% at wk 4 or 12. The ALTERNATE trial therefore provides a large independent data set to evaluate the NET appropriateness model. Results: Among 1,299 eligible pts randomized to receive 6 months of NET, 214 were excluded due to absent HR Allred score (n=41) or absence of pre-treatment and wk 4 Ki67 determinations (n=173). The proportions of the remaining 1,085 pts in Group 1, 2 and 3 were 1% (n=10), 43% (n= 468), and 56% (n=607), respectively. On-study Ki67 >10% prompting conversion from NET to NCT/Surgery occurred in: Group 1 90% (9 of 10), Group 2 30% (141 of 468), and Group 3 17% (104 of 607) (Table 1). Among the 1,075 pts in Groups 2 and 3, 260 (24%) pts had Ki67 ≤15% at baseline (BL), among whom only 14 (5.4%) had Ki67 >10% at wk 4, compared to 231 of the 815 (28.3%) who had BL Ki67 >15% and subsequent Ki67 >10% at wk 4. 2% of pts who remained on NET due to on-treatment Ki67 <10% had PD. Response and PEPI-0 rates by group will be reported. Conclusion: ALTERNATE trial data support a model whereby levels of ER, PR and Ki67 at diagnosis can be used for the identification of postmenopausal pts with primary ER+/HER2- BC who are appropriate for NET. When baseline ER Allred scores are >6 and Ki67 ≤15%, there is a low likelihood of ET-resistant disease. When BL Ki67 is >15%, ET sensitivity is variable, and on-treatment biopsy for Ki67 may assist in triaging regarding NET appropriateness, particularly given the extremely low local PD rates seen in ALTERNATE when on-treatment Ki67 was <10%. Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG); NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org; Clinical Trials.gov Identifier: NCT01953588 Table 1 Baseline levels of ER, PR, and Ki67 in Relation to Wk 4 Ki67 (N=1,085)BaselineWeek 4GroupNERAllred ScorePRAllred ScoreKi67Ki67 ≤10%N (%)Ki67 >10%N (%)1N=26<6≤15%0 (0%)2 (100%)9 (90)N=86<6>15%1 (12.5%)7 (87.5%)2AN=647 or 8<6≤15%61 (95.3%)3 (4.7%)90 (30.1)N=2357 or 8<6>15%148 (63%)87 (37%)2BN=466 or 7≥6≤15%42 (91.3%)4 (8.7%)51 (30.2)N=1236 or 7≥6>15%76 (61.8%)47 (38.2%)3N=1508≥6≤15%143 (95.3%)7 (4.7%)104 (17.1)N=4578≥6>15%360 (78.8%)97 (21.2%) Citation Format: Matthew J Ellis, Vera Suman, A. Marilyn Leitch, Souzan Sanati, Kiran Vij, Gary W Unzeitig, Jeremy Hoog, Mark Watson, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erika Crouch, Horacio Maluf, Mitch Dowsett, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J Hieken, Yang Wang, Travis Dockter, Jo Anne Zujewski, Anna Weiss, Clifford Hudis, Eric P Winer, Kelly Hunt, Ann H Partridge, Cynthia X Ma, Lisa A Carey. Validation of a predictive model for potential response to neoadjuvant endocrine therapy (NET) in postmenopausal women with clinical stage II or III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC): An ALTERNATE trial analysis (Alliance A011106) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD2-10.

Abstract Background: In ER+ breast cancer (BC) models, Aurora A kinase (AURKA) activation is associated with expansion of CD44+/CD24low/- tumor initiating cells, down-regulation of ERα, and endocrine therapy resistance. Alisertib, a selective AURKA inhibitor, can restore ERα expression and endocrine sensitivity. Early phase studies evaluating alisertib alone or with fulvestrant for ER+ metastatic BC (MBC) demonstrated a favorable safety profile and promising antitumor activity [Haddad, Breast Cancer Res Treat. 2018]. A phase II trial was conducted to determine if the addition of fulvestrant to alisertib improved objective response rate (ORR) and to assess clinical activity of alisertib alone or with fulvestrant in patients (pts) with prior fulvestrant and CDK 4/6 inhibitor (CDK 4/6i). Methods: Pts were randomized 1:1 to Arm A, alisertib (50 mg PO BID Days 1-3, 8-10, 15-17 q 28 days) or Arm B, alisertib with fulvestrant (500 mg IM Day 1, 15 for Cycle 1 and q 28 days thereafter). Eligibility included postmenopausal women, history of ER+ BC, prior fulvestrant, ≤ 2 prior chemotherapy lines, and measurable disease. Stratification factors included prior CDK4/6i, ER level (<10%, ≥10%), and primary/secondary endocrine resistance. Pts on Arm A could cross over to Arm B at progression. With 45 pts per arm, a one sided alpha=0.15 sequential binomial test would have an 85% chance of detecting an increase of ≥ 20% in the ORR of ArmB when the true ORR for Arm A is ≤ 20%. ORR was defined as a partial response (PR) + complete response (CR) by RECIST v.1.1 criteria. Secondary endpoints include progression free survival (PFS), 24-week clinical benefit rate (CBR = CR + PR + absence of progression for> 6 cycles), overall survival, duration of response (DoR), and safety. Blood and tumor specimens were collected at baseline, end of Cycle 1, and progression. Results: Pts enrolled July 2017 - November 2019 with 118 pre-registered, 96 registered, and 90 evaluable for the primary endpoint (Arm A: 45, Arm B: 45). Median age was 60 (range 33, 85). Nearly all received prior fulvestrant (n=89, 98.9%), aromatase inhibitor (n=83, 92.2%), and CDK4/6i (n=88, 97.8%). Most had secondary endocrine resistance (n=71, 78.9%). Pre-registration biopsy for ER was positive in 84 pts (86.7%) and negative in 6 pts (13.3%). More pts on Arm B had prior everolimus (A: 35.6%, B: 57.8%) and prior chemotherapy (A: 44.4%, B: 55.6%) for MBC. The ORR for alisertib and fulvestrant was 20.0% (90% CI: 10.9-32.3%), not significantly greater than alisertib alone 17.8% (90% CI: 9.2-29.8%). The 24-week CBR for Arm A was 42.2% (90% CI: 29.7-55.6%; n=19, including 7 PR) and Arm B was 31.1% (90% CI: 19.9-44.3%; n=14, including 8 PR). As of July 1, 2020, the median DoR was not reached in either arm. The median PFS time was 5.6 months (95% CI: 3.9 - 9.3) for Arm A and 5.1 months (95%CI: 3.8 - 7.6) for Arm B. Seventeen pts (18.9%) remain on treatment (A: 12, B: 5) having received at least 11 cycles (range up to 32+ cycles). At least one dose reduction was required for pts (A: 19, B: 18), most commonly due to neutropenia. The most common severe (grade ≥3) adverse events included neutropenia (n=19, 42.2% in each arm), anemia (A: 15.6%, B: 8.8%), and fatigue (n=5, 11.1% Arm B only). Pts discontinued therapy due to disease progression equally in each arm (n=28, 62.2%), however more pts on Arm B (n=12) than Arm A (n=5) discontinued therapy due to toxicity, refusal or other reasons. Conclusion: While the addition of fulvestrant to alisertib did not improve ORR, promising clinical activity with alisertib monotherapy was observed overall and notably for pts with endocrine and CDK 4/6i-resistant MBC. More severe toxicities and treatment discontinuation were observed in pts receiving combination therapy. Correlative blood (CTC/cfDNA) and tissue (AURKA, ERα, and stemness biomarkers) studies are underway. Citation Format: Tufia Haddad, Antonino D'Assoro, Vera Suman, Jodi Carter, Brendan McMenomy, Erica Mayer, Meghan Karuturi, Aki Morikawa, Paul Marcom, Claudine Isaacs, Sun Young Oh, Amy Clark, Ingrid Mayer, Khandan Keyomarsi, Roberto Leon-Ferre, Karthik Giridhar, Ciara O'Sullivan, Prema Peethambaram, Timothy Hobday, Minetta Liu, James Ingle, Matthew Goetz. Randomized phaseII trial to evaluate alisertib alone or combined with fulvestrant for advanced, endocrine-resistant breast cancer (TBCRC 041) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD2-05.

Abstract Background: Ki67 values >10% 2-4 weeks (wks) after starting neoadjuvant ET (NET) indicates persistent cell proliferation, resistance to ET, and is associated with increased risk of recurrence. The ACOSOG Z1031 trial suggested that these tumors are also relatively chemotherapy (chemo) resistant with a low pathologic complete response (pCR) rate to NCT. The ALTERNATE trial (NCT01953588) is a randomized study of neoadjuvant anastrozole (ANA), fulvestrant (FUL), or ANA + FUL in postmenopausal patients (pt) with newly diagnosed clinical stage II or III ER+ (Allred score 6-8)/HER2- BC. Ki67 >10% at wk 4 or 12 after starting NET triggered triage to NCT of physician choice or weekly paclitaxel. Pts who refused protocol-directed therapy, were not candidates for NCT, or decided to undergo immediate surgery are being followed per protocol. Here we report the rates of pCR and residual cancer burden (RCB) following NCT for pts triaged to NCT due to Ki67 >10% at wk 4 or 12. Results: Of the 1,299 eligible pts randomized to receive ANA, FUL, or ANA + FUL, 286 (22%) had Ki67 >10% at wk 4 or 12. 168 of these 286 pts (58.7%) chose to switch to NCT, 32 went to surgery (11.2%), and 86 discontinued further protocol-directed therapy (30.1%). Among the 168 pts who underwent NCT, the presenting clinical T stages were cT2 (n=113; 67.26%), cT3 (n=47; 27.98%) and cT4 (n=8; 4.76%) and N stages were cN0 (n=82; 48.8%), cN1 (n=75; 44.6%), cN2/3 (n=9; 5.4%) and cNx (n=2; 1.2%). Central ER testing was performed on pre-treatment biopsies and confirmed ER Allred score 6-8 in 155 of 168 (92.2%) pts, with the rest being ER Allred score 4-5 (n=5; 3%), ER- (Allred score 0) (n=2; 1.2%), or not tested (n=6; 3.6%). Most (n=139; 82.7%) were ER+/PR+, while 17.3% (n=29) were ER+/PR-, and tumor grades were G1 (n=10; 6%), G2 (n=99; 58.9%), G3 (n=54; 32.1%), not reported (n=5; 3%). Baseline Ki67 levels prior to NET were >10% in 94% (n=158), ≤10% in 3% (n=5), and not done in 3% (n=5). NCT regimens administered included doxorubicin/cyclophosphamide (AC) followed by paclitaxel (T) (n=60; 35.71%); weekly paclitaxel (n=56; 33.33%), docetaxel/cyclophosphamide (TC) (n=33; 19.65%), other doxorubicin and/or taxane containing regimen (n=17; 10.12%), and cyclophosphamide/methotrexate/fluorouracil (CMF) (n=2; 1.19%). 35 (20.8%) pts did not complete planned course of NCT due to toxicity (n=27) or refusal (n=8). 154 NCT pts underwent surgery (mastectomy in 40.3%, and breast conserving surgery in 59.7%). The path ypT stages were Tis/0 (n=10; 6.5%), T1 (n=62; 40.3%), T2 (n=61; 39.6%), and T3/4 (n=21; 13.6%), and the ypN stages were N0 (n=66; 42.9%), N1 (n=57; 37%), N2/3 (n=30; 19.5%), and Nx (n=1; 0.6%). Among the 168 pts who started on NCT (intent to treat population), there were 8 pCRs (no invasive disease in the breast or lymph nodes) (4.8%; 95% CI: 2.1% to 9.2%). Residual Cancer Burden (RCB) categories include RCB 0 (n=8; 4.8%), RCB 1 (n=15; 8.9%), RCB 2 (n=82; 48.8%), RCB 3 (n=42; 25.0%), and not determined (n=21; 12.5%). Correlations of baseline pt and tumor characteristics with pathology response to NCT will also be presented. Conclusion: In pts with NET-resistant ER+/HER2- BC, salvage NCT is not likely to induce a complete or near complete response. More effective treatments are needed for this high-risk ER+/HER2- pt population. Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG); NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. Clinical Trials.gov Identifier: NCT01953588 Citation Format: Cynthia X Ma, Vera Suman, A. Marilyn Leitch, Souzan Sanati, Kiran Vij, Gary W Unzeitig, Jeremy Hoog, Mark Watson, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erika Crouch, Horacio Maluf, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J Hieken, Yang Wang, Travis Dockter, Jo Anne Zujewski, Anna Weiss, Kelly Hunt, Clifford Hudis, Eric P Winer, Matthew J Ellis, Lisa A Carey, Ann H Partridge. Neoadjuvant chemotherapy (NCT) response in postmenopausal women with clinical stage II or III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) resistant to endocrine therapy (ET) in the ALTERNATE trial (Alliance A011106) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr GS4-05.

Background Activating mutations in JAK2 are the molecular hallmark of PV. However, achieving molecular remission is not a validated endpoint in PV, as its correlation with patient-relevant endpoints, such as thrombotic events or disease progression, is not well established. The expression of MDM2, a negative regulator of wild-type p53, is significantly higher in CD34+ cells from patients with PV vs those from healthy controls. Therefore, MDM2 antagonists such as idasanutlin (idasa) may have selective and potentially disease-modifying effects in PV. This exploratory analysis reports baseline mutational profiling and serial measurements of JAK2 V617F variant allele frequency (VAF) from patients treated with idasa in the Phase II NP39761 study (NCT03287245). Methods Patients with PV, as defined by the 2016 World Health Organization criteria, were eligible for inclusion if their disease was HU resistant/intolerant according to European LeukemiaNet criteria and they were phlebotomy dependent (≥ 1 phlebotomy in the 16-wk period prior to screening). Prior PV therapy with ruxolitinib and/or interferon was allowed. Idasa was given orally once daily on days 1-5 of 28-day cycles for up to 24 mo. The starting dose was 150 mg, but dose increase (to 200 mg) or decrease (to 100 mg) was allowed per protocol-defined criteria. The primary efficacy endpoints were hematocrit control (HTC), defined as maintaining acceptable hematocrit levels with ≤ 1 phlebotomy between cycle 1, day 1 (C1D1) and wk 8 and no phlebotomy after wk 8, and complete hematologic remission (CHR), defined as HTC together with platelets < 400 × 109/L and white blood cell count < 109/L on the day of response assessment (or most recent test). JAK2 V617F VAF was analyzed at screening and at C3D28, C5D28 and wk 32. The JAK2 V617F VAF was determined using quantitative polymerase chain reaction. Baseline blood samples were sequenced using the Foundation Medicine FoundationOne Heme next-generation sequencing panel, which interrogates > 400 DNA-sequenced genes, to explore the genetic landscape of PV beyond JAK2 V617F. Results All 27 patients enrolled in the study harbored JAK2 V617F. Baseline and ≥ 1 later JAK2 VAF measurements were available in 23 patients, allowing for analysis. The median age was 56 y (range, 34-74), and 7 patients (26%) had been previously treated with ruxolitinib. Median treatment duration was 257 days (range, 5-677), and the median number of treatment cycles was 8 (range, 1-22). JAK2 V617F VAFs at baseline were highly variable, ranging from 7% to 96% (median, 66%). A reduction in JAK2 V617F VAF was observed as early as after 3 cycles (median reduction, 39%; n = 19) and was sustained in patients receiving treatment, with a median reduction of 58% at C5D28 (n = 17) and of 76% at wk 32 (n = 13). The median reductions in JAK2 V617F VAF were significantly higher for patients with CHR and HTC than in nonresponders on C3D28 (CHR, P < 0.01; HTC, P = 0.04) and C5D28 (CHR, P < 0.01; HTC, P = 0.03), with a similar trend also at wk 32 (CHR, P = 0.06; HTC, P = 0.19) (Figures). Baseline targeted sequencing (n = 16) identified several additional subclonal mutations. However, no TP53 mutations were detected. Variants in TET2 and ASXL1 were detected in 37% (6 of 16) and 20% (3 of 16) of patients, with VAFs of 2%-51% and 38%-50%, respectively. Notably, 68% of the patients had variants detected in 1 to 3 DNA repair genes, including ATM (VAF, 47%-52%), ATR (VAF, 49%), BRCA2 (VAF, 47%-51%), PARP1 (VAF, 52%), PARP3 (VAF, 48%), FANCM (VAF, 47%-50%), BLM (VAF, 48%) and MSH3 (VAF, 49%). In the absence of sequencing of patient-matched non-hematologic tissue and the VAFs being ≈50%, it is possible some of these variants are germline. Whether such variants predispose to PV is unknown. Conclusions Idasa has relevant clinical activity in patients with PV who are resistant to or intolerant of HU and showed rapid JAK2 V617F VAF reduction in a subset of patients as early as after 3 treatment cycles. The median JAK2 VAF reduction was significantly greater in patients who achieved CHR and HTC after 3 and 5 cycles of idasa treatment, suggesting that early molecular response was associated with higher likelihood of clinical response. Baseline mutations were seen in several genes commonly mutated in PV. A high frequency of variants in DNA repair genes has not previously been reported in PV and may contribute to genomic instability in this disease. Figure Disclosures Passamonti: Roche: Other: Support of parent study and funding of editorial support; BMS: Speakers Bureau; Novartis: Speakers Bureau. El-Galaly:F. Hoffmann-La Roche: Current Employment, Other: Support of parent study and funding of editorial support. Gerds:Celgene: Consultancy, Research Funding; Gilead Sciences: Research Funding; CTI Biopharma: Consultancy, Research Funding; Imago Biosciences: Research Funding; AstraZeneca/MedImmune: Consultancy; Roche/Genentech: Research Funding; Incyte Corporation: Consultancy, Research Funding; Pfizer: Research Funding; Apexx Oncology: Consultancy; Sierra Oncology: Research Funding. Gupta:Incyte: Honoraria, Research Funding; Bristol MyersSquibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Sierra Oncology: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy. Higgins:Roche: Current Employment, Current equity holder in publicly-traded company, Other: Support of parent study and funding of editorial support. Huw:Roche: Current Employment, Other: Support of parent study and funding of editorial support. Maffioli:Roche: Other: Support of parent study and funding of editorial support. Mesa:Sierra Oncology: Consultancy; Incyte: Research Funding; Samus Therapeutics: Research Funding; Promedior: Research Funding; Genentech: Research Funding; Novartis: Consultancy; CTI BioPharma: Research Funding; LaJolla Pharmaceutical Company: Consultancy; AbbVie: Research Funding; Bristol Myers Squibb: Research Funding. Rambaldi:Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Support of parent study and funding of editorial support. Received travel support., Research Funding; Sanofi: Honoraria, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company); Astellas: Honoraria, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company); Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company); Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel support from Gilead.; BMS/Celgene: Honoraria, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company); Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company). Advisory board and speaker fees from Pfizer.; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company). Research grant from Amgen Inc.; Omeros: Honoraria, Other: TRAVEL, ACCOMMODATIONS, EXPENSES (paid by any for-profit health care company); University of Milan: Current Employment. Vannucchi:Novartis: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Incyte: Membership on an entity's Board of Directors or advisory committees; Blueprint: Membership on an entity's Board of Directors or advisory committees; Celgene/BMS: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Yacoub:Incyte: Speakers Bureau; Hylapharm: Current equity holder in private company; Cara Therapeutics: Current equity holder in publicly-traded company; Dynavax: Current equity holder in publicly-traded company; Agios: Honoraria, Speakers Bureau; Novartis: Speakers Bureau; Roche: Other: Support of parent study and funding of editorial support; Ardelyx: Current equity holder in publicly-traded company. Mascarenhas:Celgene, Prelude, Galecto, Promedior, Geron, Constellation, and Incyte: Consultancy; Incyte, Kartos, Roche, Promedior, Merck, Merus, Arog, CTI Biopharma, Janssen, and PharmaEssentia: Other: Research funding (institution).

Introduction: Polycythemia Vera (PV), Essential Thrombocythemia (ET), and Primary Myelofibrosis (PMF) are BCR/ABL1-negative myeloproliferative neoplasms (MPN) that are associated with morbidity and increased mortality. Limited data regarding population-based outcomes for these MPNs have been reported. Our aim was to use the Surveillance, Epidemiology, and End Results (SEER) registry to investigate population based outcomes for PV, ET, and PMF. Methods: The SEER 18 registries were used to identify patients with ICD-O-3 diagnosis codes for PV (9950/3), ET (9962/3), and PMF (9961/3) from 2001-2015. For ET and PMF, histologic diagnosis was required for inclusion. Incidence was age-adjusted to the U.S. 2000 standard population. Causes of death were obtained and MPN-related death was defined as death from any myeloid disorder (ET, PV, PMF, acute myeloid leukemia [AML], acute monocytic leukemia, other myeloid/monocytic leukemia, and aleukemic, subleukemic and NOS). Relative survival (RS) was defined as the ratio of the proportion of observed survivors in a cohort of PV, ET, PMF patients to the proportion of expected survivors in a comparable set of individuals that did not respectively have PV, ET, or PMF, adjusting for the general survival of the US population for race, sex, age, and time when the diagnosis was established. Time to leukemic transformation was calculated using the left-truncated life tables session with a 3-month latency period used to prevent misattribution. Overall survival (OS) was calculated between the date of diagnosis and the date of death, date last known to be alive, or date of the study cut-off (31 December 2018). Variables significant in univariate analysis were included in a multivariate analysis. The Kaplan-Meier method was used to calculate overall survival (OS), and Cox regression model was used to identify predictors of survival. Statistical analyses were performed using JMP version 14.0. Results: 10,988 patients with PV, 9,146 with ET, and 4,022 with PMF were identified in SEER. The median age of diagnosis (interquartile range [IQR]) was 65 years (IQR 54-76), 67 years (IQR 54-77), and 69 years (IQR 60-78) for PV, ET, and PMF respectively. Overall incidence rates (cases/100,000) were 0.86 for PV, 0.72 for ET, and 0.30 for PMF. With a median follow up (in years, 95% confidence interval [CI]) of 7.6 (7.4-7.8), 7.9 (7.8-8.2), and 7.25 (7.0-7.5), the median OS was 11.4 (11.2-11.7), 11.75 (11.3-12.0), and 3.5 (3.3-3.7), for PV, ET, and PMF respectively. RS was better than expected survival for PV and ET, while less than expected survival for PMF (Figure 1). 3853 of PV patients died (35.1%) by the end of the study period, with 4.1% and 34.1% of deaths from PV-related and cardiovascular disease respectively (Table 1). 3142 of ET patients died (34.4%), with 7.2% and 32.2% of deaths from ET-related and cardiovascular disease respectively. 2578 patients with MF died (64.1%), with 13.2%, and 51.9% of deaths from PMF-related and other malignancies respectively. 106 patients (1.0%) with PV, 135 patients (1.5%) with ET, and 127 patients (3.2%) with PMF transformed to AML. Median time to transformation was 4.8, 6.3, and 2.3 years for PV, ET, and PMF respectively. Factors indicating inferior OS on multivariate analysis (Table 2) included age ≥ 65, female sex, and year of diagnosis for PV, age ≥ 65, male sex, and year of diagnosis for ET, and age ≥ 65, and male sex for PMF. Conclusion: Incidence rates for PV, ET, and PMF were similar to previous reports. RS was better than expected survival for PV and ET, while less than expected survival for PMF. The majority of deaths in ET and PV occurred from cardiovascular disease; a finding likely related to these MPNs. Patients with PMF were more likely to die from their disease or a subsequent malignancy. Transformation to AML occurred less frequently than prior large case series, noting a limitation in the current study. Patients with PMF were more likely to transform to AML with a shorter time interval. Older age was associated with worse OS in all patients. Male sex was predictive of worse survival for ET and PMF, while female sex was associated with worse survival in PV. Over the years, survival has improved for PV and remained essentially unchanged for ET and PMF. Figure Disclosures Shah: Dren Bio: Consultancy.