Germline predictors for bevacizumab induced hypertensive crisis in ECOG-ACRIN 5103 and BEATRICE

BACKGROUND

Bevacizumab is a beneficial therapy in several advanced cancer types. Predictive biomarkers to better understand which patients are destined to benefit or experience toxicity are needed. Associations between bevacizumab induced hypertension and survival have been reported but with conflicting conclusions.

METHODS

We performed post-hoc analyses to evaluate the association in 3124 patients from two phase III adjuvant breast cancer trials, E5103 and BEATRICE. Differences in invasive disease-free survival (IDFS) and overall survival (OS) between patients with hypertension and those without were compared. Hypertension was defined as systolic blood pressure (SBP) ≥ 160 mmHg (n = 346) and SBP ≥ 180 mmHg (hypertensive crisis) (n = 69). Genomic analyses were performed to evaluate germline genetic predictors for the hypertensive crisis.

RESULTS

Hypertensive crisis was significantly associated with superior IDFS (p = 0.015) and OS (p = 0.042), but only IDFS (p = 0.029; HR = 0.28) remained significant after correction for prognostic factors. SBP ≥ 160 mmHg was not associated with either IDFS or OS. A common single-nucleotide polymorphism, rs6486785, was significantly associated with hypertensive crisis (p = 8.4 × 10-9; OR = 5.2).

CONCLUSION

Bevacizumab-induced hypertensive crisis is associated with superior outcomes and rs6486785 predicted an increased risk of this key toxicity.

A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

SIGNIFICANCE

Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.

Molecular and clinical effects of aromatase inhibitor therapy on skeletal muscle function in early-stage breast cancer

We evaluated biochemical changes in skeletal muscle of women with breast cancer initiating aromatase inhibitors (AI), including oxidation of ryanodine receptor RyR1 and loss of stabilizing protein calstabin1, and detailed measures of muscle function. Fifteen postmenopausal women with stage I-III breast cancer planning to initiate AI enrolled. Quadriceps muscle biopsy, dual-energy x-ray absorptiometry, isokinetic dynamometry, Short Physical Performance Battery, grip strength, 6-min walk, patient-reported outcomes, and serologic measures of bone turnover were assessed before and after 6 months of AI. Post-AI exposure, oxidation of RyR1 significantly increased (0.23 ± 0.37 vs. 0.88 ± 0.80, p < 0.001) and RyR1-bound calstabin1 significantly decreased (1.69 ± 1.53 vs. 0.74 ± 0.85, p < 0.001), consistent with dysfunctional calcium channels in skeletal muscle. Grip strength significantly decreased at 6 months. No significant differences were seen in isokinetic dynamometry measures of muscle contractility, fatigue resistance, or muscle recovery post-AI exposure. However, there was significant correlation between oxidation of RyR1 with muscle power (r = 0.60, p = 0.02) and muscle fatigue (r = 0.57, p = 0.03). Estrogen deprivation therapy for breast cancer resulted in maladaptive changes in skeletal muscle, consistent with the biochemical signature of dysfunctional RyR1 calcium channels. Future studies will evaluate longer trajectories of muscle function change and include other high bone turnover states, such as bone metastases.

Racial Disparities in Breast Cancer: from Detection to Treatment

PURPOSE OF REVIEW

Update on current racial disparities in the detection and treatment of breast cancer.

RECENT FINDINGS

Breast cancer remains the leading cause of cancer death among Black and Hispanic women. Mammography rates among Black and Hispanic women have surpassed those among White women, with studies now advocating for earlier initiation of breast cancer screening in Black women. Black, Hispanic, Asian, and American Indian and Alaskan Native women continue to experience delays in diagnosis and time to treatment. Further, racial discrepancies in receipt of guideline-concordant care, access to genetic testing and surgical reconstruction persist. Disparities in the initiation, completion, toxicity, and efficacy of chemotherapy, endocrine therapy, and targeted drug therapy remain for racially marginalized women. Efforts to evaluate the impact of race and ethnicity across the breast cancer spectrum are increasing, but knowledge gaps remain and further research is necessary to reduce the disparity gap.

"How is it going to help?": Exploring Black breast cancer patients' questions about biomarker testing to predict chemotherapy-induced peripheral neuropathy

Objective

Many Black breast cancer patients experience chemotherapy-induced peripheral neuropathy (CIPN). Our study assessed Black breast cancer patients' questions about a biomarker test that can predict likelihood of CIPN.

Methods

Nineteen Black women who were previous/current breast cancer patients participated in focus groups. Researchers briefly explained CIPN and the biomarker test, and then participants were asked what questions they would have about the test and its use in treatment decisions. These participant-voiced questions composed the data for this study and were analyzed using thematic analysis.

Results

Participants' questions centered on six themes: reasons for the test, effect on timeline of breast cancer treatment, testing procedure, limits of test (including accuracy), research done to develop this test (including research participants), and concerns about personal information connected to the test (including DNA).

Conclusion

This study provides an exploratory look at questions that Black breast cancer patients may have about toxicity biomarker testing use in breast cancer treatment decisions.

Innovation

These findings provide a starting point for developing patient-centered approaches for integrating this precision medicine tool into clinical care. The methodological choice to generate participants' questions (rather than answers to a question) led to robust, actionable data.

Clinically significant germline pathogenic variants are missed by tumor genomic sequencing

A germline pathogenic variant may be present even if the results of tumor genomic sequencing do not suggest one. There are key differences in the assay design and reporting of variants between germline and somatic laboratories. When appropriate, both tests should be completed to aid in therapy decisions and determining optimal screening and risk-reduction interventions.

Cytochrome P450 Oxidoreductase (POR) Associated with Severe Paclitaxel-Induced Peripheral Neuropathy in Patients of European Ancestry from ECOG-ACRIN E5103

PURPOSE

Paclitaxel is a widely used anticancer therapeutic. Peripheral neuropathy is the dose-limiting toxicity and negatively impacts quality of life. Rare germline gene markers were evaluated for predicting severe taxane-induced peripheral neuropathy (TIPN) in the patients of European ancestry. In addition, the impact of Cytochrome P450 (CYP) 2C8, CYP3A4, and CYP3A5 metabolizer status on likelihood of severe TIPN was also assessed.

EXPERIMENTAL DESIGN

Whole-exome sequencing analyses were performed in 340 patients of European ancestry who received a standard dose and schedule of paclitaxel in the adjuvant, randomized phase III breast cancer trial, E5103. Patients who experienced grade 3-4 (n = 168) TIPN were compared to controls (n = 172) who did not experience TIPN. For the analyses, rare variants with a minor allele frequency ≤ 3% and predicted to be deleterious by protein prediction programs were retained. A gene-based, case-control analysis using SKAT was performed to identify genes that harbored an imbalance of deleterious variants associated with increased risk of severe TIPN. CYP star alleles for CYP2C8, CYP3A4, and CYP3A5 were called. An additive logistic regression model was performed to test the association of CYP2C8, CYP3A4, and CYP3A5 metabolizer status with severe TIPN.

RESULTS

Cytochrome P450 oxidoreductase (POR) was significantly associated with severe TIPN (P value = 1.8 ×10-6). Six variants were predicted to be deleterious in POR. There were no associations between CYP2C8, CYP3A4, or CYP3A5 metabolizer status with severe TIPN.

CONCLUSIONS

Rare variants in POR predict an increased risk of severe TIPN in patients of European ancestry who receive paclitaxel.

Computational pharmacogenotype extraction from clinical next-generation sequencing

Background

Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively.

Methods

Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1.

Results

Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort.

Conclusion

Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.

Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development

In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic BRCA1 and BRCA2 mutations.

A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, MEGA, to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of 9 cancer centers in the Oncology Research Information Exchange Network (ORIEN). This package has 3 unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2704 tumor RNA-seq samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

Abstract PD18-01: Adjuvant Trastuzumab Emtansine Versus Paclitaxel plus Trastuzumab for Stage I HER2+ Breast Cancer: 5-year results and correlative analyses from ATEMPT (TBCRC033)

Background: The ATEMPT trial primary analysis found that one year of adjuvant trastuzumab emtansine (T-DM1) achieved a 3-year iDFS of 97.8% for patients with stage I HER2+ breast cancer, but was not associated with fewer clinically relevant toxicities (CRTs) compared with paclitaxel and trastuzumab (TH). In this end-of-study analysis, we report 5-year survival outcomes and correlative analyses from the trial. Methods: Patients with stage I centrally confirmed HER2+ breast cancer were randomly assigned 3:1 to adjuvant T-DM1 for one year or TH and received T-DM1 3.6 mg/kg IV every 3 weeks for 17 cycles or paclitaxel 80 mg/m2 IV with weekly trastuzumab IV followed by trastuzumab for 9 months. The co-primary objectives were to compare the incidence of CRTs between the 2 arms and to evaluate iDFS in patients receiving T-DM1. To investigate proteomic correlates of recurrence, spatial proteomic analyses were performed on samples from 13 patients experiencing iDFS events (cases) and 24 matched controls using the NanoString GeoMx Digital Spatial Profiler. The impact of HER2 heterogeneity on outcomes was investigated among 17 cases and 51 matched controls by fluorescence in-situ hybridization (FISH). HER2 genetic heterogeneity was assessed by scrutinizing the whole tumor area and defined as the occurrence of HER2 gene amplification in &gt;5% but &lt; 50% invasive tumor cells. The risk of recurrence was evaluated centrally with the HER2DX genomic assay from 225 primary tumor samples. Germline whole genome sequencing (WGS) was conducted among 55 patients experiencing T-DM1-induced thrombocytopenia and/or bleeding and 55 matched controls to identify genomic correlates for this side effect. Results: A total of 497 patients who initiated protocol therapy were included in this analysis (383 T-DM1 and 114 TH). After a median follow up 5.8 years, among patients receiving T-DM1 there were a total of 11 iDFS events, with 3 distant recurrences. The 5-year iDFS for T-DM1 was 97.0% (95% CI, 95.3-98.8%), the 5-year recurrence-free interval (RFI) was 98.6% (95% CI: 97.4-99.8%) and the 5-year overall survival (OS) for T-DM1 was 97.8 % (95% CI, 96.3-99.3%). Although the study was not powered to evaluate the efficacy of TH, among the 114 patients receiving TH, a total of 9 iDFS events were observed, including 2 distant events; the 5-year iDFS with TH was 91.3% (95% CI: 86.0-96.9%), 5-year RFI was 93.3% (95% CI: 88.6-98.2%) and 5-year OS was 97.9% (95% CI: 95.2-100%). A total of 56 samples were evaluable for heterogeneity analyses, among which 14% (n=8) harbored HER2 genetic heterogeneity. Spatial proteomic analyses found that NF1 (adjusted p=0.72 × 10-6) and CTLA-4 (adjusted p=0.15 × 10-3) were significantly upregulated in primary samples from cases, while cleaved caspase 9, CD25, GITR, ICOS, p53 and PD-L2 were significantly upregulated in controls (all with adjusted p&lt; 0.05). Germline WGS found that the top gene associations with thrombocytopenia and thrombocytopenia or bleeding were ALMS1 (p=0,19 × 10-3) and APBA3 (p=0,23 × 10-3), respectively, although none reaching the threshold for genome wide significance. rs62143195 and rs114169776 were the top single nucleotide polymorphisms associated with thrombocytopenia and thrombocytopenia or bleeding, respectively. Data on the impact of HER2 heterogeneity and of HER2DX score on survival outcomes will be presented. Conclusion: With longer follow-up, adjuvant T-DM1 confirmed outstanding long-term outcomes among patients with stage I HER2+ breast cancer, demonstrating a 5-year RFI of 98.6%. Spatial proteomic analyses identified a potential association between NF1 and CTLA-4 expression with recurrence. Details on the impact of HER2 heterogeneity and HER2DX assay on prognosis will be presented.

Citation Format: Paolo Tarantino, Nabihah Tayob, Chau T Dang, Denise Yardley, Steven J. Isakoff, Vicente Valero, Meredith Faggen, Therese Mulvey, Ron Bose, Douglas Weckstein, Antonio C. Wolff, Katherine Reeder-Hayes, Hope Rugo, Bhuvaneswari Ramaswamy, Dan Zuckerman, Lowell Hart, Vijayakrishna K. Gadi, Michael Constantine, Kit Cheng, Audrey Merrill Garrett, Paul K. Marcom, Kathy S. Albain, Patricia DeFusco, Nadine Tung, Blair Ardman, Rita Nanda, Rachel C. Jankowitz, Mothaffar Rimawi, Vandana Abramson, Paula R. Pohlmann, Catherine Van Poznak, Andres Forero-Torres, Minetta C. Liu, Kathryn Ruddy, Yue Zheng, Romualdo Barroso-Sousa, Adrienne Waks, Michelle K. DeMeo, Molly K. DiLullo, Giuseppe Curigliano, Harold Burstein, Ann Partridge, Eric Winer, Giuseppe Viale, Winnie Hui, Elizabeth A. Mittendorf, Bryan P. Schneider, Aleix Prat, Ian Krop, Sara Tolaney. Adjuvant Trastuzumab Emtansine Versus Paclitaxel plus Trastuzumab for Stage I HER2+ Breast Cancer: 5-year results and correlative analyses from ATEMPT (TBCRC033) [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 PD18-01.

Abstract PD8-06: Incidence of Acute and Persistent Clinically Meaningful Chemotherapy Induced Peripheral Neuropathy in Patients with Early-Stage Breast Cancer Receiving Taxane Therapy: SWOG S1714 (NCT# 03939481)

Background: Taxanes play an important role in the treatment of early-stage breast cancer. Chemotherapy induced peripheral neuropathy (CIPN) is a complication of taxane therapy and can lead to treatment dose reduction or discontinuation, which may ultimately affect overall survival, and can substantially impact quality of life and functional status in survivors. The trajectory of CIPN symptoms is not well described. Methods: SWOG S1714 enrolled participants 18 years or older with Stage I-III primary non-small cell lung, primary breast, or primary ovarian/fallopian tube/peritoneal cancer starting treatment with a taxane-based regimen. Participants with baseline neuropathy were eligible to enroll. Neuropathy was assessed with the patient-reported European Organization for Research and Treatment of Cancer QLQ-CIPN20 (CIPN-20). The occurrence of clinically meaningful sensory neuropathy was defined as an increase of 8 or more points (on a 0-100 scale, with a higher score indicating more severe symptoms) between baseline and follow-up in the sensory neuropathy subscale of the CIPN-20. Assessments occurred at baseline and at 4, 8, and 12 weeks +/- 14 days and 24, 52, 104, and 156 weeks +/- 28 days after registration. Results: Among N=1336 enrolled participants, 1321 were eligible (99%). Of the eligible participants, we will report on the 1198 (90.7%) with breast cancer. The median age was 55 years (range 23-84) and 99.3% were female. The breast cancer cohort included 72.2% White, 11.7% Black, 4.9% Asian, and 11.0% Hispanic/Latino participants. Paclitaxel (every week for 12 weeks or every 2 weeks for 8 weeks) was administered to 56.2% and docetaxel (every 3 weeks for 12-18 weeks) to 43.8%. The mean baseline patient-reported CIPN-20 sensory neuropathy subscale score was 6.2 (standard deviation 12.0). Through one full year of follow up, 1084 participants (90.5%) were evaluable for sensory neuropathy at any time point. At individual assessment times, clinically meaningful sensory neuropathy was reported by 18.7% of participants at week 4, 33.0% at week 8, 46.3% at week 12, 44.8% at week 24, and 47.4% at week 52. Clinically meaningful sensory neuropathy at one or more assessments was reported by 67.8% of participants. Conclusions: In this large prospective cohort of racially/ethnically diverse participants with breast cancer receiving taxane-based therapy, 2 out of every 3 experienced clinically meaningful sensory neuropathy symptoms during the first year of treatment and nearly 50% continue to experience clinically meaningful sensory neuropathy symptoms at the end of the first year. Given the high incidence of symptoms during taxane treatment and persistence of symptoms after treatment completion, it is critical to develop effective methods to predict, prevent, and treat this toxicity. Follow up of data at 104 and 156 weeks will further characterize the trajectory of long term CIPN symptoms. Funding: NIH/NCI/NCORP grant UG1CA189974

Citation Format: Meghna S. Trivedi, Joseph M. Unger, Dawn Hershman, Amy K. Darke, Daniel L. Hertz, Thomas H. Brannagan, Stephanie J. Smith, Bryan P. Schneider, William J. Irvin Jr, Amanda R. Hathaway, Amy C. Vander Woude, Vinay K. Gudena, N. Lynn Henry, Michael J. Fisch. Incidence of Acute and Persistent Clinically Meaningful Chemotherapy Induced Peripheral Neuropathy in Patients with Early-Stage Breast Cancer Receiving Taxane Therapy: SWOG S1714 (NCT# 03939481) [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 PD8-06.

Genomic alterations in metastatic renal cell carcinoma (mRCC): Impact on survival and clinical outcomes

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Background: Genomic alterations in RCC can serve as biomarkers for response to therapy. Wild type VHL has shown inferior response to VEGF inhibitors, while patients (pts) with mutated VHL have improved outcomes with immunotherapy (IO)/tyrosine kinase inhibitor (TKI) therapy. We describe the impact of genomic alterations on outcomes and response to front-line therapy. Methods: Pts with mRCC who underwent genomic sequencing between 2015-2022 at Indiana University and were treated with front-line therapy were included. Kaplan-Meier method was used to analyze progression free survival (mPFS) and overall survival (OS) using the log rank test to compare groups. Results: 141 pts were included. Median age was 58yrs (range, 24-81). Tumor histology was 68% clear cell, 10% papillary, 9% unclassified, 1% chromophobe, 1% poorly differentiated, and 9% other. 18% of pts had sarcomatoid features; 13% had rhabdoid. 47% pts had metastasis at diagnosis and 53% at relapse. Metastasis sites were lungs 60%, regional lymph nodes (LNs) 41%, bone 36%, distant LNs 21%, liver 17%, and brain 8%. IMDC risk was 18% good, 48% intermediate, 17% poor, and 17% unknown. Front-line therapy was IO/IO in 21%, IO/TKI in 18%, single-agent TKI in 29%, single-agent IO in 6%, and other in 26%. Genetic alterations included VHL in 50%, PBRM1 in 29%, SETD2 in 23%, BAP1 in 16%, and TP53 in 15%. Median follow-up was 2.74yrs (range 0.1-18.6). Overall mPFS with first line therapy was 1.2yrs (95%CI 0.9-1.5). 2-yr OS was 80% (95%CI: 71-86). For pts with a VHL mutation, mPFS was 1.4yrs (95% CI; 0.9-1.8) compared to 0.9yrs (0.5-1.4) for pts without (p=0.38). 2-yr OS for pts with a VHL mutation was 93% (95% CI: 82-97) vs. 68% (95%CI: 54-78) for pts without (p=0.01). No other mutations impacted overall mPFS or 2-yr OS. mPFS for pts treated with IO/IO was 0.6yrs (95%CI 0.3-0.9) vs. 0.9yrs (95%CI 0.5-1.4) for IO/TKI (p=0.09). 2-yr OS for pts treated with IO/IO was 70% (95% CI 44-85) compared to 94% (95% CI 65-99) for IO/TKI (p=0.29). For pts with SETD2 mutations treated with IO/IO, mPFS was 0.7yrs (95%CI 0.3-1.2) vs. 1.4yrs (95%CI 0.8-1.9) for IO/TKI (p=0.01). For pts with BAP1 mutations treated with IO/IO, mPFS was 0.4yrs (95%CI 0.2-1.2) vs. NE (95%CI 0.2-NE) for IO/TKI (p=0.04). The table outlines outcomes by genomic mutation and therapy. Conclusions: VHL mutation was associated with improved 2-yr OS. Pts with SETD2 and BAP1 mutations treated with IO/TKI had improved mPFS, though no differences in OS. [Table: see text]

Clinicogenomic Landscape of Metastatic Thymic Epithelial Tumors

BACKGROUND

Despite favorable clinical outcomes, a subset of patients with thymic epithelial tumors (TETs) develop metastasis. The Cancer Genome Atlas (TCGA) provides genomic data on primary TETs (pTETs). This study assessed the molecular alterations and uncovered targetable pathways in metastatic TETs (mTETs).

METHODS

From 2015 to 2020, 49 patients with stage IV TETs underwent Clinical Laboratory Improvement Amendments-based sequencing using whole-exome sequencing (n = 33), panel-based testing (n = 12), and/or liquid biopsy (n = 24). Specimens were obtained from a metastatic organ (n = 36) or relapsed primary mediastinal mass (n = 10), whereas four patients underwent a liquid biopsy only. Data on pTETs were derived from the TCGA.

RESULTS

Compared with the pTET data set, patients with mTETs were younger (54 years v 60.5 years, P = .009) and had more aggressive histologies, with the most common tumor type being thymic carcinoma (n = 22, 40.7%) and B3 thymoma (n = 15, 27.8%). GTF2I was the most altered gene in primary thymomas (48.80%, n = 60). In metastatic thymoma and thymic carcinoma, TP53 was the most common genetic alteration (31% and 36%, respectively). In mTETs, the genomic alteration occurred in the TP53/CDK, EGFR/RAS, and PI3K/mTOR pathways. Biopsies obtained from distant metastasis were more commonly found to contain targetable mutations. There was an overlap of 61% (22 of 36) between tissue and liquid biopsy genomic alterations.

CONCLUSION

Clinically actionable genomic alterations are frequently observed in mTETs, indicating a value of repeat biopsy (preferably from a metastatic site of TETs for sequencing at the time of recurrence (TCGA data).

Association of QT interval-prolonging drugs with clinical trial eligibility in patients with advanced cancer

Introduction

Drug-induced prolongation of the heart rate-corrected QT interval (QTc) is associated with increased risk for the potentially fatal arrhythmia torsades de pointes. Due to arrhythmia risk, clinical trials with cancer therapeutics often exclude patients based on thresholds for QTc prolongation. Our objective was to assess associations between prescriptions for QT-prolonging drugs and the odds of meeting cancer trial exclusionary QTc thresholds in a cohort of adults with advanced cancer.

Methods

Electronic health records were retrospectively reviewed for 271 patients seen at our institutional molecular solid tumor clinic. Collected data included demographics, QTc measurements, ventricular arrhythmia-related diagnoses, and all inpatient and outpatient prescriptions. Potential associations were assessed between demographic and clinical variables, including prescriptions for QT-prolonging drugs, and QTc measurements.

Results

Women had longer median QTc measurements than men (p = 0.030) and were prescribed more QT-prolonging drugs during the study (p = 0.010). In all patients, prescriptions for QT-prolonging drugs were associated with longer median and maximum QTc measurements at multiple assessed time points (i.e., for QT-prolonging drugs prescribed within 10, 30, 60, and 90 days of QTc measurements). Similarly, the number of QT-prolonging drugs prescribed was correlated with longer median and maximum QTc measurements at multiple time points. Common QTc-related exclusionary criteria were collected from a review of ClinicalTrials.gov for recent cancer clinical trials. Based on common exclusion criteria, prescriptions for QT-prolonging drugs increased the odds of trial exclusion.

Conclusion

This study demonstrates that prescriptions for QT-prolonging drugs were associated with longer QTc measurements and increased odds of being excluded from cancer clinical trials.

Passage number affects differentiation of sensory neurons from human induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) are a valuable resource for neurological disease-modeling and drug discovery due to their ability to differentiate into neurons reflecting the genetics of the patient from which they are derived. iPSC-derived cultures, however, are highly variable due to heterogeneity in culture conditions. We investigated the effect of passage number on iPSC differentiation to optimize the generation of sensory neurons (iPSC-dSNs). Three iPSC lines reprogrammed from the peripheral blood of three donors were differentiated into iPSC-dSNs at passage numbers within each of the following ranges: low (5-10), intermediate (20-26), and high (30-38). Morphology and pluripotency of the parent iPSCs were assessed prior to differentiation. iPSC-dSNs were evaluated based on electrophysiological properties and expression of key neuronal markers. All iPSC lines displayed similar morphology and were similarly pluripotent across passage numbers. However, the expression levels of neuronal markers and sodium channel function analyses indicated that iPSC-dSNs differentiated from low passage numbers better recapitulated the sensory neuron phenotype than those differentiated from intermediate or high passage numbers. Our results demonstrate that lower passage numbers may be better suited for differentiation into peripheral sensory neurons.

Initial Phase I Safety Study of Gedatolisib plus Cofetuzumab Pelidotin for Patients with Metastatic Triple-Negative Breast Cancer

PURPOSE

The PI3K pathway is dysregulated in the majority of triple-negative breast cancers (TNBC), yet single-agent inhibition of PI3K has been ineffective in TNBC. PI3K inhibition leads to an immediate compensatory upregulation of the Wnt pathway. Dual targeting of both pathways is highly synergistic against TNBC models in vitro and in vivo. We initiated a phase I clinical trial combining gedatolisib, a pan-class I isoform PI3K/mTOR inhibitor, and cofetuzumab pelidotin, an antibody-drug conjugate against the cell-surface PTK7 protein (Wnt pathway coreceptor) with an auristatin payload.

PATIENTS AND METHODS

Participants (pt) had metastatic TNBC or estrogen receptor (ER) low (ER and PgR < 5%, HER2-negative) breast cancer, and had received at least one prior chemotherapy for advanced disease. The primary objective was safety. Secondary endpoints included overall response rate (ORR), clinical benefit at 18 weeks (CB18), progression-free survival (PFS), and correlative analyses.

RESULTS

A total of 18 pts were enrolled in three dose cohorts: gedatolisib 110 mg weekly + cofetuzumab pelidotin 1.4 mg/kg every 3 weeks (n = 4), 180 mg + 1.4 mg/kg (n = 3), and 180 mg + 2.8 mg/kg (n = 11). Nausea, anorexia, fatigue, and mucositis were common but rarely reached ≥grade 3 severity. Myelosuppression was uncommon. ORR was 16.7% (3/18). An additional 3 pts had stable disease (of these 2 had stable disease for >18 weeks); CB18 was 27.8%. Median PFS was 2.0 months (95% confidence interval for PFS: 1.2-6.2). Pts with clinical benefit were enriched with genomic alterations in the PI3K and PTK7 pathways.

CONCLUSIONS

The combination of gedatolisib + cofetuzumab pelidotin was well tolerated and demonstrated promising clinical activity. Further investigation of this drug combination in metastatic TNBC is warranted.

Impact of African ancestry on the relationship between body mass index and survival in an early-stage breast cancer trial (ECOG-ACRIN E5103)

BACKGROUND

African ancestry (AA) and obesity are associated with worse survival in early-stage breast cancer. Obesity disproportionately affects women of AA; however, the intersection between ancestry and obesity on breast cancer outcomes remains unclear.

METHODS

A total of 2854 patients in the adjuvant trial E5103 were analyzed. Genetic ancestry was determined using principal components from a genome-wide array. The impact of continuous or binary body mass index (BMI) on disease-free survival (DFS) and overall survival (OS) was evaluated by multivariable Cox proportional hazards models in AA patients and European ancestry (EA) patients.

RESULTS

There were 2471 EA patients and 383 AA patients. Higher BMI was significantly associated with worse DFS and OS only in AA patients (DFS hazard ratio [HR], 1.25; 95% CI, 1.07-1.46; OS HR, 1.38; 95% CI, 1.10-1.73), not in EA patients (DFS HR, 0.97; 95% CI, 0.90-1.05; OS HR, 1.03; 95% CI, 0.93-1.14). Severe obesity (BMI ≥40) was significantly associated with worse survival in AA patients (DFS HR, 2.04; 95% CI, 1.21-3.43; OS HR, 2.21; 95% CI, 1.03-4.75) but had no impact on that of EA patients. In the estrogen receptor-positive (ER+) and triple-negative breast cancer subgroups, BMI was significantly associated with worse outcomes only in those AA patients with ER+ disease. Within the AA group, BMI remained associated with worse survival regardless of the AA proportion.

CONCLUSIONS

Higher BMI was statistically significantly associated with worse breast cancer outcomes in AA but not EA patients. This association was most significant for severe obesity and those with ER+ disease. These observations help define optimal populations for weight change interventions designed to affect disparities and survival in early-stage breast cancer.

LAY SUMMARY

African ancestry and obesity are both risk factors for worse survival after early-stage breast cancer. Women of African descent are also disproportionately affected by obesity; however, it is unclear what impact body weight has on racial disparities in breast cancer. Data from a large phase 3 clinical trial in high-risk, early-stage breast cancer were used to determine how body weight affects survival outcomes in European versus African Americans. Study results demonstrate that a higher body mass index is associated with increased risk of breast cancer recurrence and worse survival in women of African ancestry but not in women of European ancestry.

DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden in a nationwide cohort

e17634

Background: DACH1 is a novel transcriptional repressor and tumor suppressor gene. DACH1 mutations are associated with poor prognostic features and reduced overall survival in endometrial cancer, with an increased prevalence in the Appalachian region of Kentucky. Preliminary studies have suggested an association with an increase in tumor mutation burden. In this follow up study, we utilized the nationwide Oncology Research Information Exchange Network (ORIEN) to determine the frequency of DACH1 mutations in patients with endometrial cancer through a multi-institution analysis and evaluate its impact on RNA expression, clinical correlates, and outcomes. Methods: We obtained clinical and genomic data for 691 patients with endometrial cancer from nine U.S. institutions within the ORIEN collaborative. We examined the clinical attributes of the cancers with DACH1 status by comparing whole-exome sequencing (WES), RNA Sequencing (RNASeq), microsatellite instability (MSI), and tumor mutational burden (TMB). Results: Appalachian women with endometrial cancer had an increased frequency of DACH1 mutations (6/41 patients, 15%) compared to the non-Appalachian endometrial cancer population (24/581 patients, 4.1%) with p-value = 0.010, with the non-Appalachian DACH1 mutation frequency mirroring the rate of DACH1 gene mutation seen in TCGA at 3.8%. DACH1 mutated patients have a higher tumor mutation burden compared to DACH1 wild-type (32.2 vs. 4.62, p-value = 0.001) though no differences in microsatellite instability between DACH1 mutated and wild-type were present (p-value = 0.350). DACH1 mutations showed significant gene co-occurrence patterns with POLE, MLH1, MSH2, MSH6 and PMS2. Conclusions: DACH1 mutations are prevalent in Kentucky patients with endometrial cancer, particularly those from the Appalachian region. These results were again reflected in the TCGA PanCancer Atlas as well as the ORIEN multi-institution cohort. These mutations are associated with high tumor mutational burden and co-occur with genome destabilizing gene mutations. These findings suggest DACH1 as a candidate biomarker for future trials with immunotherapy, particularly in endometrial cancers.

Abstract PD9-10: BRE12-158: A post-neoadjuvant, randomized phase 2 trial of personalized therapy vs. treatment of physician’s choice for patients with residual triple negative breast cancer

Purpose: Patients with triple negative breast cancer (TNBC) with residual disease after neoadjuvant chemotherapy (NAC) have high risk of recurrence with prior data suggesting improved outcomes with capecitabine. Targeted agents have demonstrated activity across multiple cancer types. BRE12-158 was a phase 2, multicenter trial that randomized TNBC patients with residual disease after NAC to genomically-directed therapy vs. treatment of physician choice (TPC). Patients and Methods: From March 2014 to December 2018, 197 patients were enrolled. Residual tumors were sequenced using a next generation sequencing (NGS) test. A molecular tumor board adjudicated all results. Patients were randomized to 4 cycles of genomically-directed therapy (arm A) vs. TPC (arm B). Patients without a target were assigned to arm B. Primary endpoint was 2-year disease free survival (DFS) among randomized patients. Secondary/exploratory endpoints included: distant disease free survival (DDFS), overall survival (OS), toxicity assessment, time-based evolution of therapy, and drug-specific outcomes. Results: 193 patients were randomized or were assigned to arm B. The estimated 2-year DFS was 56.6% (95%CI:0.45-0.70) for arm A vs. 62.4% (95%CI:0.52-0.75) for randomized arm B. No difference was seen in DFS, DDFS, or OS for the entire or randomized populations. There was increased uptake of capecitabine for TPC over time. Patients randomized later had less distant recurrences. ctDNA status remained a significant predictor of outcome with some patients demonstrating clearance with post-neoadjuvant therapy. Conclusion: Genomically directed therapy was not superior to TPC for patients with residual TNBC after NAC. Capecitabine should remain the standard of care; however, the activity of other agents in this setting provides rationale for testing optimal combinations to improve outcomes for this high-risk population. ctDNA should be considered a standard covariate for trials in this setting.

Citation Format: Bryan P Schneider, Guanglong Jiang, Tarah J Ballinger, Fei Shen, Christopher Chitambar, Rita Nanda, Carla Falkson, Filipa C Lynce, Christopher Gallagher, Claudine Isaacs, Marcelo Blaya, Elisavet Paplomata, Radhika Walling, Karen Daily, Reshma Mahtani, Michael A Thompson, Robert Graham, Maureen E Cooper, Dean C Pavlick, Lee A Albacker, Jeffery Gregg, Jeffery P Solzak, Yu-Hsiang Chen, Casey L Bales, Erica Cantor, Bradley A Hancock, Nawal Kassem, Paul Helft, Bert O'Neil, Anna Maria Storniolo, Sunil Badve, Kathy D Miller, Milan Radovich. BRE12-158: A post-neoadjuvant, randomized phase 2 trial of personalized therapy vs. treatment of physician’s choice for patients with residual triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD9-10.

Abstract P1-08-02: Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103

Introduction: Paclitaxel induced peripheral neuropathy (TIPN) is one of the most important survivorship issues of cancer patients with the potential to substantially impact quality of life. TIPN can lead to dose reductions, early cessation, and has the potential to compromise treatment efficacy. We previously reported both rare (SBF2) and common germline (FCAMR) predictors for TIPN in patients of African descent through whole-exome sequencing (WES) and a genome-wide association study (GWAS), respectively, in the adjuvant, randomized phase III breast cancer trial, E5103. These predictors are now being evaluated in the prospective ECOG-ACRIN trial EAZ171 (NCT04001829). We have also previously reported our evaluation of common germline variants for patients of European descent through GWAS in E5103 with validation in another adjuvant breast cancer trial, E1199. Herein, we evaluated for rare variants that were associated with risk of TIPN in patients of European ancestry from WES in E5103. Methods: Gene-based rare variant analyses using SKAT were performed to compare select cases of severe TIPN (n=172) and controls without any evidence of TIPN (n=170) derived from E5103. Cases were defined as those with at least grade 3 TIPN and controls were optimally. matched by demographic and risk factors and had no reported evidence for TIPN of any grade. Germline WES was conducted using Ion Proton™ Sequencers from Life Technologies with an average &gt;100X coverage of the exome. Rare variants with a minor allele frequency &lt;3% predicted to be deleterious by protein prediction programs were retained for the analysis. 7,278 genes passed quality control and were included in the analysis, setting the threshold for significance at a p-value &lt; 6.87 ×10-6 after Bonferroni correction. Results: Cytochrome P450 oxidoreductase (POR) was significantly associated with an increased risk of grade 3+ TIPN (p =1.82 ×10-6). Six variants predicted to be deleterious in POR were identified in the study population. Paclitaxel is predominately metabolized by cytochrome P450 (CYP) 2C8 and 3A4. A functional cytochrome P450 oxidoreductase is required for the catalytic activities of all 57 CYP family members to metabolize drugs, xenobiotics, and steroid hormones. Conclusion: Rare variants in cytochrome P450 oxidoreductase predicted an increased risk of severe TIPN in patients receiving paclitaxel. These rare variants in POR may modulate the catalytic activities of P450 enzymes that are responsible for paclitaxel metabolism and have a striking biological rationale as contributors to TIPN. Work is ongoing to validate these findings mechanistically and to identify strategies to nullify the impact of these deleterious variants.

Citation Format: Fei Shen, Guanglong Jiang, Laura Gardner, Gloria Xue, Santosh Philips, Reynold Ly, Osei Wilberforce, Xi Wu, Erica Cantor, Chau Dang, Donald Northfelt, Todd Skaar, Kathy D. Miller, George Sledge, Bryan P Schneider. Cytochrome P450 reductase gene, POR, associated with paclitaxel induced peripheral neuropathy in patients of European ancestry from the adjuvant breast cancer trial, ECOG-ACRIN E5103 [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-02.

Bevacizumab-induced hypertension and proteinuria: a genome-wide study of more than 1000 patients

BACKGROUND

Hypertension and proteinuria are common bevacizumab-induced toxicities. No validated biomarkers are available for identifying patients at risk of these toxicities.

METHODS

A genome-wide association study (GWAS) meta-analysis was performed in 1039 bevacizumab-treated patients of European ancestry in four clinical trials (CALGB 40502, 40503, 80303, 90401). Grade ≥2 hypertension and proteinuria were recorded (CTCAE v.3.0). Single-nucleotide polymorphism (SNP)-toxicity associations were determined using a cause-specific Cox model adjusting for age and sex.

RESULTS

The most significant SNP associated with hypertension with concordant effect in three out of the four studies (p-value <0.05 for each study) was rs6770663 (A > G) in KCNAB1, with the G allele increasing the risk of hypertension (p-value = 4.16 × 10-6). The effect of the G allele was replicated in ECOG-ACRIN E5103 in 582 patients (p-value = 0.005). The meta-analysis of all five studies for rs6770663 led to p-value = 7.73 × 10-8, close to genome-wide significance. The most significant SNP associated with proteinuria was rs339947 (C > A, between DNAH5 and TRIO), with the A allele increasing the risk of proteinuria (p-value = 1.58 × 10-7).

CONCLUSIONS

The results from the largest study of bevacizumab toxicity provide new markers of drug safety for further evaluations. SNP in KCNAB1 validated in an independent dataset provides evidence toward its clinical applicability to predict bevacizumab-induced hypertension. ClinicalTrials.gov Identifier: NCT00785291 (CALGB 40502); NCT00601900 (CALGB 40503); NCT00088894 (CALGB 80303) and NCT00110214 (CALGB 90401).

Clinical Opportunities for Germline Pharmacogenetics and Management of Drug-Drug Interactions in Patients With Advanced Solid Cancers

PURPOSE

Precision medicine approaches, including germline pharmacogenetics (PGx) and management of drug-drug interactions (DDIs), are likely to benefit patients with advanced cancer who are frequently prescribed multiple concomitant medications to treat cancer and associated conditions. Our objective was to assess the potential opportunities for PGx and DDI management within a cohort of adults with advanced cancer.

METHODS

Medication data were collected from the electronic health records for 481 subjects since their first cancer diagnosis. All subjects were genotyped for variants with clinically actionable recommendations in Clinical Pharmacogenetics Implementation Consortium guidelines for 13 pharmacogenes. DDIs were defined as concomitant prescription of strong inhibitors or inducers with sensitive substrates of the same drug-metabolizing enzyme and were assessed for six major cytochrome P450 (CYP) enzymes.

RESULTS

Approximately 60% of subjects were prescribed at least one medication with Clinical Pharmacogenetics Implementation Consortium recommendations, and approximately 14% of subjects had an instance for actionable PGx, defined as a prescription for a drug in a subject with an actionable genotype. The overall subject-level prevalence of DDIs and serious DDIs were 50.3% and 34.8%, respectively. Serious DDIs were most common for CYP3A, CYP2D6, and CYP2C19, occurring in 24.9%, 16.8%, and 11.7% of subjects, respectively. When assessing PGx and DDIs together, approximately 40% of subjects had at least one opportunity for a precision medicine-based intervention and approximately 98% of subjects had an actionable phenotype for at least one CYP enzyme.

CONCLUSION

Our findings demonstrate numerous clinical opportunities for germline PGx and DDI management in adults with advanced cancer.

Quality of Life Following Receipt of Adjuvant Chemotherapy With and Without Bevacizumab in Patients With Lymph Node-Positive and High-Risk Lymph Node-Negative Breast Cancer

IMPORTANCE

Breast cancer treatment can impact not only short-term health but may also affect longer-term quality of life (QOL).

OBJECTIVE

To describe and evaluate factors associated with diminished QOL following completion of active treatment.

DESIGN, SETTING, AND PARTICIPANTS

This was a secondary analysis of a randomized clinical trial included patients with lymph node-positive or high-risk lymph node-negative breast cancer who had undergone definitive surgery and were enrolled in ECOG-ACRIN E5103, a multisite phase 3 trial. A survey was administered 18 months after enrollment to patients enrolled between January and June 2010. Final analysis of the data took place from March to December 2021.

INTERVENTIONS

Patients received adjuvant doxorubicin, cyclophosphamide, and paclitaxel with either bevacizumab or placebo.

MAIN OUTCOMES AND MEASURES

QOL and health status assessed with the EuroQol 5-Dimension 3-Levels (EQ-5D-3L), EQ-visual analog scale (EQ-VAS), and the Functional Assessment of Cancer Therapy-Breast Cancer, with arm subscale (FACT-B+4). Groups were compared by Fisher exact test, Wilcoxon rank sum, or Kruskal-Wallis test. Multivariable linear regression was used to assess factors independently associated with FACT-B scores.

RESULTS

Data at 18 months were available from 455 of 519 patients (87.7%) enrolled in the trial. Median (range) age at enrollment was 52 (25-76) years. No differences in QOL (median [range] FACT-B scores: group A, 123 [67-146]; group B, 114 [54-148]; group C, 117 [42-148]; P = .23) or health status (median [range] EQ-5D-3L index scores: group A, 0.83 [0.28-1.00]; group B, 0.83 [0.20-1.00]; group C, 0.83 [0.17-1.00], P = .80; median EQ-VAS: group A, 85 [20-100]; group B, 85 [0-100]; group C, 85 [0-100]; P = .79) were observed across treatment groups; results for subsequent analyses were therefore reported irrespective of primary treatment. Overall, half of patients (258 of 444 [58%]) reported at least some pain or discomfort; 170 (38%) reported symptoms of anxiety or depression. In multivariable analyses, mastectomy with radiation (vs breast conserving surgery) and Asian, Black, or American Indian or Alaska Native race (vs White race) were associated with lower QOL (mastectomy with radiation: coefficient: -5.5; 95% CI, -10.1 to -0.9; Asian, Black, or American Indian or Alaska Native race: coefficient: -7.3; 95% CI, -13.2, -1.4).

CONCLUSIONS AND RELEVANCE

In this study, the addition of bevacizumab to chemotherapy was not negatively associated with QOL at 18 months. A substantial proportion of participants reported problems related to pain or discomfort and anxiety or depression, demonstrating persistent consequences for physical and psychosocial well-being in this heavily treated population. Many problems reported are amenable to intervention, underscoring the need for timely referral to supportive resources, especially for women of color and those who have more extensive local therapy.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT00433511.

Life-Threatening Docetaxel Toxicity in a Patient With Reduced-Function CYP3A Variants: A Case Report

Docetaxel therapy occasionally causes severe and life-threatening toxicities. Some docetaxel toxicities are related to exposure, and inter-individual variability in exposure has been described based on genetic variation and drug-drug interactions that impact docetaxel clearance. Cytochrome P450 3A4 (CYP3A4) and CYP3A5 metabolize docetaxel into inactive metabolites, and this is the primary mode of docetaxel clearance. Supporting their role in these toxicities, increased docetaxel toxicities have been found in patients with reduced- or loss-of-function variants in CYP3A4 and CYP3A5. However, since these variants in CYP3A4 are rare, little is known about the safety of docetaxel in patients who are homozygous for the reduced-function CYP3A4 variants. Here we present a case of life-threatening (grade 4) pneumonitis, dyspnea, and neutropenia resulting from a single dose of docetaxel. This patient was (1) homozygous for CYP3A4*22, which causes reduced expression and is associated with increased docetaxel-related adverse events, (2) heterozygous for CYP3A4*3, a rare reduced-function missense variant, and (3) homozygous for CYP3A5*3, a common loss of function splicing defect that has been associated with increased docetaxel exposure and adverse events. The patient also carried functional variants in other genes involved in docetaxel pharmacokinetics that may have increased his risk of toxicity. We identified one additional CYP3A4*22 homozygote that received docetaxel in our research cohort, and present this case of severe hematological toxicity. Furthermore, the one other CYP3A4*22 homozygous patient we identified from the literature died from docetaxel toxicity. This case report provides further evidence for the need to better understand the impact of germline CYP3A variants in severe docetaxel toxicity and supports using caution when treating patients with docetaxel who have genetic variants resulting in CYP3A poor metabolizer phenotypes.

The impact of SBF2 on taxane-induced peripheral neuropathy

Taxane-induced peripheral neuropathy (TIPN) is a devastating survivorship issue for many cancer patients. In addition to its impact on quality of life, this toxicity may lead to dose reductions or treatment discontinuation, adversely impacting survival outcomes and leading to health disparities in African Americans (AA). Our lab has previously identified deleterious mutations in SET-Binding Factor 2 (SBF2) that significantly associated with severe TIPN in AA patients. Here, we demonstrate the impact of SBF2 on taxane-induced neuronal damage using an ex vivo model of SBF2 knockdown of induced pluripotent stem cell-derived sensory neurons. Knockdown of SBF2 exacerbated paclitaxel changes to cell viability and neurite outgrowth while attenuating paclitaxel-induced sodium current inhibition. Our studies identified paclitaxel-induced expression changes specific to mature sensory neurons and revealed candidate genes involved in the exacerbation of paclitaxel-induced phenotypes accompanying SBF2 knockdown. Overall, these findings provide ex vivo support for the impact of SBF2 on the development of TIPN and shed light on the potential pathways involved.

Abstract PO-219: The implications of genetic ancestry and allostatic load on clinical outcomes in the ECOG-ACRIN adjuvant breast cancer trial E5103

Introduction: Elevated allostatic load (AL) has been associated with poor tumor prognostic features in Black breast cancer patients and worse disease specific and overall survival among cancer patients. To date, there are no studies evaluating the relationship between genetic ancestry, allostatic load and clinical trial endpoints such as completion of chemotherapy per protocol or overall survival. Prior evaluations of the ECOG-ACRIN adjuvant breast cancer trial E5103 suggests African ancestry is associated with a worse invasive disease-free survival and lower odds of chemotherapy completion. The objective of this study is to evaluate the association of genetic ancestry and AL with trial completion per protocol and with overall survival among patients in E5103. Methods: ECOG-ACRIN E5103 was a clinical trial that compared doxorubicin and cyclophosphamide (AC) for four cycles, followed by 12 weeks of weekly paclitaxel with placebo (Arm A) to the same chemotherapy with either concurrent bevacizumab (Arm B) or with concurrent plus sequential bevacizumab (Arm C) among women with node positive or high-risk node negative HER2 negative disease. Genetic ancestry groups of African ancestry (AA), European ancestry (EA) and other ancestry (OA) were determined using genome-wide single nucleotide polymorphisms. AL, at trial entry, was comprised of the biomarkers body mass index, systolic blood pressure, diastolic blood pressure, creatinine, IL6, IL10, and TNF alpha. To calculate AL, patients were awarded a point if their biomarker value was above the 75 percentile of the study sample. Logistic regression and Cox-Proportional Hazard models (odds ratio(OR) and hazard ratio (HR) estimates with corresponding 95% confidence intervals (CI)) were used to assess association with chemotherapy completion and with overall mortality. Estimates for AL were adjusted for genetic ancestry. Results: There were 348 patients in the study. The majority of the sample was of EA (EA 80%, AA 10%, OA 10%). Median (range) of AL was 2(0-6). Patients of AA (2.1(1.3)) and EA (1.88(1.4)) had a higher mean (SD) AL score compared to OA patients (0.91(1.1). On adjusted analysis, a 1 unit increased in AL was associated with a 15% reduction in the odds of completing chemotherapy per protocol (OR 0.85, 95% CI 0.72-0.99). Additionally, a 1 unit increase in AL was associated with a 14% increase in the hazard of death (HR 1.14, 95%CI 1.02-1.29). There was no association between ancestry and chemotherapy completion (AA OR 0.95, 95%CI 0.47-1.93; OA 1.82, 95%CI 0.78-4.23; ref EA) or survival (AA HR 1.40, 95% CI 0.85-2.31), OA 0.89 (0.46-1.73; ref EA). Moreover, there was no interaction between AL and ancestry. Conclusion: Among patients enrolled in E5103, AL appeared to be a better predictor of chemotherapy completion and overall survival than genetic ancestry. These results suggest life course exposure to chronic stress has implication in clinical outcomes even within the context of equivalent access to and quality of care.

Citation Format: Samilia Obeng-Gyasi, Anne ONeill, Kathy D. Miller, Bryan P. Schneider, Ann H. Patridge, Lava R. Timsina, George W. Sledge, Lynne Wagner, Ruth C. Carlos. The implications of genetic ancestry and allostatic load on clinical outcomes in the ECOG-ACRIN adjuvant breast cancer trial E5103 [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-219.

BRE12-158: A Postneoadjuvant, Randomized Phase II Trial of Personalized Therapy Versus Treatment of Physician's Choice for Patients With Residual Triple-Negative Breast Cancer

PURPOSE

Patients with triple-negative breast cancer (TNBC) with residual disease after neoadjuvant chemotherapy (NAC) have high risk of recurrence with prior data suggesting improved outcomes with capecitabine. Targeted agents have demonstrated activity across multiple cancer types. BRE12-158 was a phase II, multicenter trial that randomly allocated patients with TNBC with residual disease after NAC to genomically directed therapy versus treatment of physician choice (TPC).

PATIENTS AND METHODS

From March 2014 to December 2018, 193 patients were enrolled. Residual tumors were sequenced using a next-generation sequencing test. A molecular tumor board adjudicated all results. Patients were randomly allocated to four cycles of genomically directed therapy (arm A) versus TPC (arm B). Patients without a target were assigned to arm B. Primary end point was 2-year disease-free survival (DFS) among randomly assigned patients. Secondary/exploratory end points included distant disease-free survival, overall survival, toxicity assessment, time-based evolution of therapy, and drug-specific outcomes.

RESULTS

One hundred ninety-three patients were randomly allocated or were assigned to arm B. The estimated 2-year DFS for the randomized population only was 56.6% (95% CI, 0.45 to 0.70) for arm A versus 62.4% (95% CI, 0.52 to 0.75) for arm B. No difference was seen in DFS, distant disease-free survival, or overall survival for the entire or randomized populations. There was increased uptake of capecitabine for TPC over time. Patients randomly allocated later had less distant recurrences. Circulating tumor DNA status remained a significant predictor of outcome with some patients demonstrating clearance with postneoadjuvant therapy.

CONCLUSION

Genomically directed therapy was not superior to TPC for patients with residual TNBC after NAC. Capecitabine should remain the standard of care; however, the activity of other agents in this setting provides rationale for testing optimal combinations to improve outcomes. Circulating tumor DNA should be considered a standard covariate for trials in this setting.

An organoid-based screen for epigenetic inhibitors that stimulate antigen presentation and potentiate T-cell-mediated cytotoxicity

In breast cancer, genetic heterogeneity, the lack of actionable targets and immune evasion all contribute to the limited clinical response rates to immune checkpoint blockade therapy. Here, we report a high-throughput screen based on the functional interaction of mouse- or patient-derived breast tumour organoids and tumour-specific cytotoxic T cells for the identification of epigenetic inhibitors that promote antigen presentation and potentiate T-cell-mediated cytotoxicity. We show that the epigenetic inhibitors GSK-LSD1, CUDC-101 and BML-210, identified by the screen, display antitumour activities in orthotopic mammary tumours in mice, that they upregulate antigen presentation mediated by the major histocompatibility complex class I on breast tumour cells and that treatment with BML-210 substantially sensitized breast tumours to the inhibitor of the checkpoint programmed death-1. Standardized measurements of tumour-cell killing activity facilitated by tumour-organoid-T-cell screens may help with the identification of candidate immunotherapeutics for a range of cancers.

Inhibiting Fatty Acid Synthase with Omeprazole to Improve Efficacy of Neoadjuvant Chemotherapy in patients with Operable TNBC

PURPOSE

Fatty acid synthase (FASN) is overexpressed in 70% of operable triple negative breast cancer (TNBC) and is associated with poor prognosis. Proton pump inhibitors selectively inhibit FASN activity and induce apoptosis in TNBC cell lines.

EXPERIMENTAL DESIGN

Patients with operable TNBC were enrolled in this single arm Phase II study. Patients began omeprazole (OMP) 80 mg PO BID for 4-7 days prior to neoadjuvant anthracycline- taxane based chemotherapy (AC-T) and continued until surgery. The primary endpoint was pathologic complete response (pCR) in patients with baseline FASN overexpression (FASN+). Secondary endpoints included pCR in all surgery patients, change in FASN expression, enzyme activity, and downstream protein expression after OMP monotherapy; safety, and limited OMP pharmacokinetics.

RESULTS

Forty-two patients were recruited with a median age of 51y (28-72). Most patients had {greater than or equal to}cT2 (33, 79%) and {greater than or equal to}N1 (22, 52%) disease. FASN overexpression prior to AC-T was identified in 29/34 (85%) evaluable samples. The pCR rate was 72.4% (95% CI 52.8, 87.3) in FASN+ patients and 74.4% (95% CI 57.9, 87.0) in all surgery patients. Peak OMP concentration was significantly higher than the IC₅₀ for FASN inhibition observed in preclinical testing; FASN expression decreased with OMP monotherapy (mean change 0.12 (SD 0.25) ; p = 0.02). OMP was well tolerated with no {greater than or equal to} grade 3 toxicities.

CONCLUSIONS

FASN is commonly expressed in early TNBC. OMP can be safely administered in doses that inhibit FASN. The addition of OMP to neoadjuvant AC-T yields a promising pCR rate that needs further confirmation in randomized studies.

Identification of germline cancer predisposition variants during clinical ctDNA testing

Next-generation sequencing of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or somatic. We report on the fidelity of VAF in ctDNA as a predictor for germline variant carriage. Two patient cohorts were studied. Cohort 1 included patients with known germline variants. Cohort 2 included patients with any variant detected by the ctDNA assay with VAF of 40-60%. In cohort 1, 36 of 91 (40%) known germline variants were identified through ctDNA analysis with a VAF of 39-87.6%. In cohort 2, 111 of 160 (69%) variants identified by ctDNA analysis with a VAF between 40 and 60% were found to be germline. Therefore, variants with a VAF between 40 and 60% should induce suspicion for germline status but should not be used as a replacement for germline testing.

Chemotherapy-related amenorrhea (CRA) after adjuvant ado-trastuzumab emtansine (T-DM1) compared to paclitaxel in combination with trastuzumab (TH) (TBCRC033: ATEMPT Trial)

PURPOSE

Chemotherapy-related amenorrhea (CRA) is a surrogate for ovarian toxicity and associated risk of infertility and premature menopause. Here, we compare CRA rate with paclitaxel (T)-trastuzumab (H) to that with ado-trastuzumab emtansine (T-DM1).

METHODS

Patients with T1N0 HER2 + early-stage breast cancer (eBC) enrolled on the ATEMPT trial and were randomized 3:1 to T-DM1 3.6 mg/kg IV every (q) 3 weeks (w) × 17 vs. T 80 mg/m² with H IV qw × 12 (4 mg/kg load → 2 mg/kg), followed by H (6 mg/kg IV q3w × 13). Enrollees who self-reported as premenopausal were asked to complete menstrual surveys at baseline and every 6-12 months for 60 months. 18-month CRA (no periods reported during prior 6 months on 18-month survey) was the primary endpoint of this analysis.

RESULTS

Of 512 ATEMPT enrollees, 123 who began protocol therapy and answered baseline and at least one follow-up menstrual survey were premenopausal at enrollment. 76 had menstrual data available at 18 months without having received a gonadotropin-releasing hormone agonist or undergone hysterectomy and/or oophorectomy. Median age was 45 (range 23-53) among 18 who had received TH and 46 (range 34-54) among 58 who had received T-DM1. The 18-month rate of CRA was 50% after TH and 24% after T-DM1 (p = 0.045).

CONCLUSION

Amenorrhea at 18 months was less likely in recipients of adjuvant T-DM1 than TH. Future studies are needed to understand how T-DM1 impacts risk of infertility and permanent menopause, and to assess amenorrhea rates when T-DM1 is administered after standard HER2-directed chemotherapy regimens.

Transcriptome-wide association study uncovers the role of essential genes in anthracycline-induced cardiotoxicity

Anthracyclines are highly effective chemotherapeutic agents; however, their clinical utility is limited by severe anthracycline-induced cardiotoxicity (ACT). Genome-wide association studies (GWAS) have uncovered several genetic variants associated with ACT, but the impact of these findings requires further elucidation. We conducted a transcriptome-wide association study (TWAS) using our previous GWAS summary statistics (n = 280 patients) to identify gene expression-related associations with ACT. We identified a genetic association between decreased expression of GDF5 and ACT (Z-score = -4.30, P = 1.70 × 10^-5), which was replicated in an independent cohort (n = 845 patients, P = 3.54 × 10^-3). Additionally, cell viability of GDF5-silenced human cardiac myocytes was significantly decreased in response to anthracycline treatment. Subsequent gene set enrichment and pathway analyses of the TWAS data revealed that genes essential for survival, cardioprotection and response to anthracyclines, as well as genes involved in ribosomal, spliceosomal and cardiomyopathy pathways are important for the development of ACT.

Social determinants of health, genetic ancestry, and mortality in ECOG-ACRIN E5103

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Background: Social determinants of health (SDH) and genetic ancestry have been independently implicated in breast cancer presentation, treatment and mortality. However, little is known about the relationship between SDH and genetic ancestry on clinical trial outcomes. The objective of this study is to assess the association between SDH, genetic ancestry and clinical outcomes in patients enrolled in an adjuvant breast cancer clinical trial. Methods: ECOG-ACRIN (EA) 5103 randomized patients to receive AC + taxane + bevacizumab or placebo. SDH were operationalized as insurance status at trial registration (individual SES) and neighborhood socioeconomic status (nSES). Insurance categories included: (1) Private, 2) Medicare including private/Medicare, military, 3) Medicaid including Medicaid/Medicare, uninsured, 4) self-pay). The nSES index was calculated using zip codes linked to county level data on occupation, income, poverty, wealth, education and crowding. Genome-wide single-nucleotide polymorphism arrays were used to define African ancestry (AA), European ancestry (EA) and other (OA). Multivariable regression and Cox-Proportional Hazard models (odds ratios (OR) and hazard ratios (HR) with corresponding 95% confidence intervals (CI)) were used to assess associations with chemotherapy completion and overall mortality. Estimates were adjusted for the following clinical covariates: age, tumor size, nodal status, hormone receptor status, and primary surgery at randomization. Results: The study cohort included 2453 EA (79.2%), 381 AA (12.2%) and 265 OA (8.6%). Medicaid patients (OR 0.76(0.59-0.99); ref private) and those with AA (OR 0.62(0.49-0.78); ref EA) were less likely to complete chemotherapy. Regarding overall mortality, Medicaid insurance (HR 1.42(1.05-1.92) was associated with a higher mortality than private insurance. Conversely, there was no significant difference in mortality by ancestry (AA HR 1.27 (0.97-1.66); OA HR 0.90 (0.63-1.29): ref EA). Neighborhood socioeconomic status did not appear to be associated with chemotherapy completion or mortality. Conclusions: SDH reflective of individual SES, such as insurance, appear to be stronger drivers of trial completion and mortality compared to nSES among patients enrolled in E5103. Moreover, study results suggest an interplay between ancestry and individual proxies for SDH in trial completion. Nevertheless, the relationship between ancestry and lower rates of chemotherapy completion do not appear to translate into higher mortality rates among patients of AA.

Clinicogenomic characterization of metastatic thymic epithelial tumors

8579

Background: Thymic epithelial tumors (TET) are one of the rarest adult malignancies. Overall, patients have favorable survival outcomes, however a small subset develop metastatic disease. Genomic characterization of this very rare, clinically aggressive TET subset is lacking. Herein, we evaluated the clinical and genomic characteristics of metastatic TET (mTET) compared to a large cohort (n = 117) of primary TET (pTET) from The Cancer Genome Atlas (TCGA). Methods: From 2015 to 2020, 52 pts with mTET underwent clinical CLIA-based sequencing using either whole-exome (n = 35), panel-based testing (n = 13) and/or liquid biopsy (n = 22). The specimen was taken from a metastatic organ (n = 34) or relapsed primary mediastinal mass (n = 14); 4 pts had liquid bx only. Data on pTET was derived from the TCGA. Kaplan-Meier and log-rank test was used for assessment of PFS, OS. Results: The median age was 56 yrs in mTET (range 32-74) vs. 60 yrs (range 17-84) in TCGA data. The M/F (%) was 40/60 in mTET and 48/52 in TCGA, respectively. Of note, 13 mTET pts had other types of cancer prior or concurrent with TET diagnosis (4-breast, 2-bladder, 5-other) in which radiotherapy (n = 4) and/or chemotherapy (n = 3) was administered prior to TET diagnosis. In our cohort, 19 pts had stage IVA and 33 pts had stage IVB (most common metastatic site was liver in 17 pts). WHO histologic classification was: A = 1, A/B = 3, B1 = 4, B2 = 10, B3 = 12, TC = 18, TC with neuroendocrine feature = 3, and lymphoepithelial carcinoma = 1. WHO B3 and TC histologies were more common in our cohort of mTET than in the TCGA cohort (63% (33/52) vs. 17% (20/117), respectively). Pts with TC had worse mOS compare to thymoma (109m vs. 163m, HR = 2.78, P = 0.04). The most common genomic alteration in mTET was TP53 (n = 17, 33%) compared to 3% in TCGA. This was followed by CDKN2A (n = 5, 10%), PIK3CA (n = 4, 8%), CDKN2B (n = 3, 6%) and NF1 (n = 3, 6%). All TP53 missense mut functionality was analyzed with polyphen-2 software and 91.6% (22/24) had 98-100% damaging probability. 70% of pts that harbored TP53 muts were TC (41%) or B3 (29%) histology. Clinically actionable genomic alterations targetable with available or investigational agents (e.g. high TMB; gain-of-function mutations in PIK3CA, CDK4, and mTOR; loss-of-function mutations in NF1) were seen in 23% (12/52) of pts. Conclusions: Patients with mTET are associated with more aggressive WHO histology (B3 and TC). Greater frequency of TP53 mutations are observed in mTET compared to pTET. Clinically actionable genomic alterations are frequently seen in mTET suggesting value in the routine sequencing of these patients.

Impact of African ancestry on the relationship between BMI and survival in early stage breast cancer: Retrospective analysis from E5103

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Background: Both Black race and obesity are associated with worse survival in early stage breast cancer. Obesity disproportionately affects Black women; however, the degree this contributes to racial disparities in breast cancer remains unclear. Prior work evaluated heterogeneous populations or used self- reported race, rather than genetic ancestry. African ancestry is associated with higher BMI and worse survival in breast cancer; however, the intersection between genetic ancestry and obesity on survival outcomes remains unknown. Methods: We analyzed data from the adjuvant trial E5103. Patients with high risk, HER2 negative breast cancer received doxorubicin/cyclophosphamide x 4, followed by weekly paclitaxel x 12, with or without bevacizumab. Genetic ancestry was determined on the 2,854 patients with available germline DNA, BMI, and outcome data using principal components from a genome-wide array. The primary objective assessed impact of BMI on DFS and OS by ancestry. Multivariate Cox proportional hazard models evaluated correlation between continuous or binary BMI and survival in African (AA) and European (EA) Americans. Results: 13.4% of patients were genetically classified as AA and 86.6% as EA. Higher continuous BMI was significantly associated with worse DFS and OS only in AAs (DFS: HR = 1.25 95% CI 1.07-1.46, p = 0.004; OS: HR = 1.38 95% CI 1.10-1.73, p = 0.005); not in EAs (DFS HR = 0.97 95% CI 0.90-1.05, p = 0.50; OS HR = 1.03 95% CI 0.93-1.14, p = 0.52). By disease subtype, BMI was associated with worse outcomes only in AAs with ER+, and not TNBC. By categorical BMI, WHO class III obesity (³ 40) significantly associated with worse DFS and OS only in AAs (DFS HR = 1.98, p = 0.010; OS HR = 2.07, p = 0.064), not in EAs (DFS HR = 0.97, p = 0.86; OS HR = 1.28, p = 0.30). Proportion of African ancestry (proAA) was associated with higher BMI and worse outcomes in the total population; however, within AAs there was no significant interaction between proAA and BMI on DFS (HR = 0.36, p = 0.06) or OS (HR = 0.38, p = 0.24). In AAs, BMI remained associated with DFS (HR = 2.78, p = 0.019), suggesting higher BMI is associated with worse DFS regardless of proAA. Coefficients for the interaction term indicate that as proAA increases the impact of BMI on outcome is lessened. Conclusions: Higher BMI is significantly associated with worse breast cancer outcomes in women of African ancestry in E5103, but not in those of European ancestry. Categorically, this association was significant only for severe obesity, indicating the relationship may depend on the degree of obesity. As proAA increased in AAs, the impact of BMI on outcome was lessened, suggesting other host factors may contribute more to obesity’s influence on outcome than genetics. Determination of the optimal populations for weight loss interventions will advance precision medicine efforts to impact racial disparities and outcomes in early stage breast cancer.

Abstract PD15-06: Circulating TP53 mutations in TNBC after neoadjuvant chemotherapy is associated with rapid disease recurrence: Correlative analysis from clinical trial BRE12-158

Background: Neoadjuvant chemotherapy (NAC) is a standard approach for many patients with triple negative breast cancer (TNBC). Our group, and others, have previously reported that the detection of circulating tumor DNA (ctDNA) after NAC and surgery is a surrogate for the presence of minimal residual disease (MRD) leading to inferior survival outcomes. Further, our group has also reported that the emergence of somatic TP53 mutations in tissue samples post-NAC was associated with inferior survival outcomes. In this study, we sought to determine whether TP53 mutations detected in the plasma of patients with ctDNA-positivity after NAC was associated with inferior outcomes compared to non-TP53 mutated patients.

Methods:BRE12-158 was a phase II clinical trial which randomized early-stage TNBC patients with residual disease after NAC to post-neoadjuvant genomically-directed therapy vs treatment of physician choice. 196 patients were enrolled. Patients had blood samples collected for ctDNA at the time of post-neoadjuvant treatment assignment. ctDNA was successfully sequenced using the FoundationACT or FoundationOneLiquid Assay in 142 patients. Patients who were ctDNA positive after NAC (N=90, 63%), were selected for this comparison. Median clinical follow-up was 22.9 months. A multivariate cox proportional-hazards model was used to compare DDFS, DFS, and OS of ctDNA-positive patients with and without TP53 mutations found in the ctDNA.

Results: 90 patients in BRE12-158 were ctDNA-positive after NAC and surgery. 36/90 (40%) of those patients had TP53 mutations detected in their plasma. Patients with TP53-mutated ctDNA had significantly inferior outcomes and a significantly shorter time to recurrence when compared to those without TP53 mutations. Detection of TP53-mutated ctDNA was significantly associated with an inferior DDFS (median DDFS: 6.99 months vs. 48.69 months; HR=2.78, 95%CI: 1.41-5.49; p=0.0033). At 24 months, the DDFS probability was 36% in TP53-mutated patients as compared to 72% in non-mutated patients. Similarly, detection of TP53-mutated ctDNA was significantly associated with an inferior DFS (median DFS: 4.83 months vs. 48.69 months; HR=3.63, 95%CI: 1.76-7.48; p=0.00047). At 24 months, the DFS probability was 30% in TP53-mutated patients as compared to 72% in non-mutated patients. Lastly, detection of TP53-mutated ctDNA was significantly associated with an inferior OS (median OS: 17.8 months vs. Not Reached; HR=3.48, 95%CI: 1.51-8.01; p=0.0034). At 24 months, the OS probability was 42% in TP53-mutated patients as compared to 80% in non-mutated patients.

Conclusion: In patients with ctDNA-positivity after NAC, the presence of TP53 mutations was associated with rapid disease relapse. These data suggest that TP53 mutation status may stratify outcomes among this high-risk group of patients with ctDNA positivity in the post-neoadjuvant setting.

Citation Format: Milan Radovich, Nawal Kassem, Guanglong Jiang, Bradley A. Hancock, Bryan P. Schneider. Circulating TP53 mutations in TNBC after neoadjuvant chemotherapy is associated with rapid disease recurrence: Correlative analysis from clinical trial BRE12-158 [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 PD15-06.

Abstract PS10-26: An initial safety study of gedatolisib plus cofetuzumab pelidotin for metastatic triple-negative breast cancer

Background: The PI3K pathway is dysregulated in the majority of triple-negative breast cancer (TNBCs), yet single agent inhibition of PI3K in TNBC has minimal clinical activity. We previously reported that PI3K inhibition leads to an immediate compensatory up-regulation of the Wnt pathway. Dual targeting of both pathways is highly synergistic against TNBC models in vitro and in vivo. We initiated a Phase I clinical trial of gedatolisib, a pan-class I isoform PI3K/mTOR inhibitor, and cofetuzumab pelidotin, an antibody-drug conjugate against the cell-surface PTK7 protein (Wnt pathway co-receptor) with an auristatin payload. PTK7 is up-regulated after PI3K inhibition and auristatin is in itself synergistic with gedatolisib providing the potential for a dual mechanism of synergy.

Methods: Dose escalation proceeded using a traditional 3+3 schema with a small expansion cohort at the final dose level to better characterize safety. Participants had metastatic TNBC or ER low (ER and PgR &lt;5%, HER2 negative) breast cancer, and had received at least one prior line of chemotherapy. The primary objective was safety. Secondary endpoints included objective response (ORR), clinical benefit at 18 weeks (CB18), and progression-free survival (PFS). Exploratory analyses probed the association of tumor DNA, RNA, and IHC with clinical efficacy to identify putative biomarkers.

Results: Between January 2018 and January 2020, 18 patients were enrolled in 3 dose cohorts: gedatolisib (qw) & cofetuzumab pelidotin (q3w) 110mg+1.4mg/kg (n=4), 180mg+1.4mg/kg (n=3), and 180mg+2.8mg/kg dose levels (n=11). The median age was 53 years (32-77). Nausea (n=16), anorexia (n=13), fatigue (n=12), and mucositis (n=12) were common but rarely reached &gt;Grade 3 severity (nausea, n=1; fatigue, n=2). Myelosuppression was uncommon (Grade &gt;3 neutropenia, n=2). 16 participants were evaluable for response. 3 achieved a confirmed partial response (PR), and 3 had stable disease (SD). ORR=18.8%. All 3 PRs lasted &gt; 6 months. CB18=31.3%. Median PFS was 2.0 months (95% CI for PFS:1.2-6.2); median OS was 9.5 months (95% CI for OS:4.3-not reached). Correlative analyses of genomic, transcriptomic, and protein biomarkers with response are currently ongoing.

Conclusions: The combination of gedatolisib + cofetuzumab pelidotin for the treatment of metastatic TNBC was found to be well tolerated and demonstrated promising clinical activity. Further investigation of this drug combination in metastatic TNBC is warranted.

Trial Registration: NCT03243331

Citation Format: Milan Radovich, Jeffrey P. Solzak, Bradley A. Hancock, Sunil Badve, Anna Maria V. Storniolo, Tarah J. Ballinger, Bryan P. Schneider, Kathy D. Miller. An initial safety study of gedatolisib plus cofetuzumab pelidotin for metastatic triple-negative 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 PS10-26.

Abstract PS13-22: Shedding light on the dark side of chemo: Post-GWAS functional studies of rs28714259 in anthracycline-induced cardiotoxicity

Anthracyclines are commonly used chemotherapies for breast cancer treatment, but can cause dose-related cardiotoxicities and lead to congestive heart failure (CHF) in 2% of patients. Several mechanisms of anthracycline’s cardiotoxic effect have been proposed, but the molecular pathogenesis is not fully understood. In addition, there are no clinically available biomarkers to predict cardiotoxicity. Previously we have identified and validated the association of a single nucleotide polymorphism (SNP), rs28714259 (G/A), with risk of anthracycline-induced CHF through genome-wide association study (GWAS) across three large phase III adjuvant breast cancer trials. rs28714259 (G/A) locates in a putative glucocorticoid receptor (GR) response element and the risk allele (A) is predicted to disrupt GR binding. The activation of GR signaling pathway by dexamethasone is known to protect cardiomyocytes from doxorubicin-induced apoptosis in rats. To investigate the role of rs28714259 in CHF post-GWAS, we set out to determine whether rs28714259 modulates GR signaling pathway through allele-specific GR enhancer activity. We cloned a 1kb DNA sequence on both sides of rs28714259, containing either the wildtype (G) or risk allele (A), into a luciferase reporter plasmid. Luciferase assay in iPSC-derived cardiomyocytes (iPSC-CMs) with GR activation by 100nM dexamethasone showed that cardiomyocytes transfected with wildtype construct had 60% increased activity compared to control vector with no enhancer. iPSC-CMs transfected with risk allele constructs did not show increased luciferase activity, suggesting that the A-allele disrupts GR-mediated transcriptional activation. Using electrophoretic mobility shift assay (EMSA) with nuclear extract from iPSC-CMs treated with dexamethasone, we observed a prominent band shift with either G- or A-allele probes. Furthermore, a supershift band was observed with GR antibody, confirming that GR indeed binds to the rs28714259 region. Notably, the band intensity of risk allele probes decreased by 50% compared to wildtype, suggesting weaker GR binding affinity to risk allele probes, consistent with reduced transcriptional activation. Finally, to identify genes differentially regulated by rs28714259 with anthracycline exposure, we performed RNA-Seq analysis on iPSC-CMs of each genotype. RNA-Seq data revealed that the top differentially regulated network was the death receptor pathway including: FADD, FAS, and Caspase-8; these effectors are known to induce apoptosis in response to doxorubicin. Moreover, 11 genes in the GR signaling pathway were also differentially regulated by rs28714259. Taken together, these findings suggest that the rs28714259 variant may possess allele-specific GR enhancer activity and differentially regulates genes involved in doxorubicin-induced apoptosis.

Citation Format: Xi Wu, Gloria Xue, Fei Shen, Guanglong Jiang, Santosh Philips, Geneva Cunningham, Erica Cantor, Bryan P Schneider. Shedding light on the dark side of chemo: Post-GWAS functional studies of rs28714259 in anthracycline-induced cardiotoxicity [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 PS13-22.

Impact of Body Mass Index on Presence of ctDNA and Disease Recurrence after Neoadjuvant Chemotherapy for Triple-Negative Breast Cancer: Analysis from BRE12-158

PURPOSE

This retrospective analysis aimed to determine the relationship between body mass index (BMI) and circulating tumor DNA (ctDNA) in triple-negative breast cancer (TNBC), and to evaluate the impact of BMI on disease recurrence and survival in the homogeneous, high-risk population of patients with residual TNBC after neoadjuvant chemotherapy.

EXPERIMENTAL DESIGN

BRE12-158 was a phase II trial of genomically directed therapy versus physician's choice in residual TNBC after chemotherapy. ctDNA was isolated from plasma samples, and categorized as positive or negative. BMI (kg/m²) after surgery was analyzed as both a continuous and categorical variable: normal weight, <25; overweight, 25-30; and obese, ≥30. We compared ctDNA category and BMI, and estimated probability of disease-free survival (DFS), distant DFS (DDFS), and overall survival (OS) by BMI.

RESULTS

Of 177 patients in BRE12-158, 172 had BMI and 140 had ctDNA data. There was no difference in mean BMI between those with ctDNA positivity versus negativity (P = 0.48). There was no relationship between BMI category and presence of ctDNA (P = 0.31). In multivariate analysis, continuous BMI was not prognostic of DDFS (P = 0.996), DFS (P = 0.41), or OS (P = 0.98). There was no association between BMI categories and survival (P = 0.92, 0.74, and 0.97 for DDFS, DFS, and OS, respectively).

CONCLUSIONS

In patients with residual TNBC after neoadjuvant chemotherapy, BMI was not prognostic of DDFS, DFS, or OS. There was no signal of a relationship between BMI and presence of ctDNA. This suggests inherent aggressive tumor biology, in which host phenotype may have less influence and impact of weight loss interventions may be diminished.

Targeted immunotherapy for HER2-low breast cancer with 17p loss

The clinical challenge for treating HER2 (human epidermal growth factor receptor 2)-low breast cancer is the paucity of actionable drug targets. HER2-targeted therapy often has poor clinical efficacy for this disease due to the low level of HER2 protein on the cancer cell surface. We analyzed breast cancer genomics in the search for potential drug targets. Heterozygous loss of chromosome 17p is one of the most frequent genomic events in breast cancer, and 17p loss involves a massive deletion of genes including the tumor suppressor TP53 Our analyses revealed that 17p loss leads to global gene expression changes and reduced tumor infiltration and cytotoxicity of T cells, resulting in immune evasion during breast tumor progression. The 17p deletion region also includes POLR2A, a gene encoding the catalytic subunit of RNA polymerase II that is essential for cell survival. Therefore, breast cancer cells with heterozygous loss of 17p are extremely sensitive to the inhibition of POLR2A via a specific small-molecule inhibitor, α-amanitin. Here, we demonstrate that α-amanitin-conjugated trastuzumab (T-Ama) potentiated the HER2-targeted therapy and exhibited superior efficacy in treating HER2-low breast cancer with 17p loss. Moreover, treatment with T-Ama induced immunogenic cell death in breast cancer cells and, thereby, delivered greater efficacy in combination with immune checkpoint blockade therapy in preclinical HER2-low breast cancer models. Collectively, 17p loss not only drives breast tumorigenesis but also confers therapeutic vulnerabilities that may be used to develop targeted precision immunotherapy.

Association of Circulating Tumor DNA and Circulating Tumor Cells After Neoadjuvant Chemotherapy With Disease Recurrence in Patients With Triple-Negative Breast Cancer: Preplanned Secondary Analysis of the BRE12-158 Randomized Clinical Trial

Importance

A significant proportion of patients with early-stage triple-negative breast cancer (TNBC) are treated with neoadjuvant chemotherapy. Sequencing of circulating tumor DNA (ctDNA) after surgery, along with enumeration of circulating tumor cells (CTCs), may be used to detect minimal residual disease and assess which patients may experience disease recurrence.

Objective

To determine whether the presence of ctDNA and CTCs after neoadjuvant chemotherapy in patients with early-stage TNBC is independently associated with recurrence and clinical outcomes.

Design, Setting, and Participants

A preplanned secondary analysis was conducted from March 26, 2014, to December 18, 2018, using data from 196 female patients in BRE12-158, a phase 2 multicenter randomized clinical trial that randomized patients with early-stage TNBC who had residual disease after neoadjuvant chemotherapy to receive postneoadjuvant genomically directed therapy vs treatment of physician choice. Patients had blood samples collected for ctDNA and CTCs at time of treatment assignment; ctDNA analysis with survival was performed for 142 patients, and CTC analysis with survival was performed for 123 patients. Median clinical follow-up was 17.2 months (range, 0.3-58.3 months).

Interventions

Circulating tumor DNA was sequenced using the FoundationACT or FoundationOneLiquid Assay, and CTCs were enumerated using an epithelial cell adhesion molecule-based, positive-selection microfluidic device.

Main Outcomes and Measures

Primary outcomes were distant disease-free survival (DDFS), disease-free survival (DFS), and overall survival (OS).

Results

Among 196 female patients (mean [SD] age, 49.6 [11.1] years), detection of ctDNA was significantly associated with inferior DDFS (median DDFS, 32.5 months vs not reached; hazard ratio [HR], 2.99; 95% CI, 1.38-6.48; P = .006). At 24 months, DDFS probability was 56% for ctDNA-positive patients compared with 81% for ctDNA-negative patients. Detection of ctDNA was similarly associated with inferior DFS (HR, 2.67; 95% CI, 1.28-5.57; P = .009) and inferior OS (HR, 4.16; 95% CI,1.66-10.42; P = .002). The combination of ctDNA and CTCs provided additional information for increased sensitivity and discriminatory capacity. Patients who were ctDNA positive and CTC positive had significantly inferior DDFS compared with those who were ctDNA negative and CTC negative (median DDFS, 32.5 months vs not reached; HR, 5.29; 95% CI, 1.50-18.62; P = .009). At 24 months, DDFS probability was 52% for patients who were ctDNA positive and CTC positive compared with 89% for those who were ctDNA negative and CTC negative. Similar trends were observed for DFS (HR, 3.15; 95% CI, 1.07-9.27; P = .04) and OS (HR, 8.60; 95% CI, 1.78-41.47; P = .007).

Conclusions and Relevance

In this preplanned secondary analysis of a randomized clinical trial, detection of ctDNA and CTCs in patients with early-stage TNBC after neoadjuvant chemotherapy was independently associated with disease recurrence, which represents an important stratification factor for future postneoadjuvant trials.

Trial Registration

ClinicalTrials.gov Identifier: NCT02101385.

MAL2 drives immune evasion in breast cancer by suppressing tumor antigen presentation

Immune evasion is a pivotal event in tumor progression. To eliminate human cancer cells, current immune checkpoint therapy is set to boost CD8+ T cell-mediated cytotoxicity. However, this action is eventually dependent on the efficient recognition of tumor-specific antigens via T cell receptors. One primary mechanism by which tumor cells evade immune surveillance is to downregulate their antigen presentation. Little progress has been made toward harnessing potential therapeutic targets for enhancing antigen presentation on the tumor cell. Here, we identified MAL2 as a key player that determines the turnover of the antigen-loaded MHC-I complex and reduces the antigen presentation on tumor cells. MAL2 promotes the endocytosis of tumor antigens via direct interaction with the MHC-I complex and endosome-associated RAB proteins. In preclinical models, depletion of MAL2 in breast tumor cells profoundly enhanced the cytotoxicity of tumor-infiltrating CD8+ T cells and suppressed breast tumor growth, suggesting that MAL2 is a potential therapeutic target for breast cancer immunotherapy.

Abstract PO-172: Impact of African ancestry on the relationship between body mass index (BMI) and survival in early stage breast cancer: Retrospective analysis from E5103

Purpose: Both African American (AA) race and obesity are associated with worse survival in early stage breast cancer. Obesity disproportionately affects AA women, and may further racial disparities in breast cancer. Prior work investigating the intersection of race, BMI, and outcome in the large adjuvant trial E1199 found obesity to be prognostic of worse survival in White patients, with no significant impact on the disparately inferior survival outcomes seen in Black patients. However, this analysis was based on self-reported race, which neglects underlying genetic ancestry that may drive biologic differences. Here, we investigate the impact of BMI on outcomes in patients of African or European ancestry in the phase III adjuvant breast cancer trial E5103. Methods: E5103 enrolled patients with high risk, HER2 negative, early stage breast cancer to receive adjuvant doxorubicin and cyclophosphamide for 4 cycles, followed by 12 weeks of weekly paclitaxel, with or without bevacizumab. Genetic ancestry was determined on the 3,373 patients with available germline DNA, BMI, and outcome data using principal components from a genome-wide array. The primary objective was to assess the impact of BMI on disease free survival (DFS) and overall survival (OS) by ancestry. A univariate Cox proportional hazard model was used to evaluate the correlation between continuous or binary BMI and survival in AA or European Americans (EA). Results: 11.6% (n=390) of patients were genetically classified as AA and 74.6% (n=2517) as EA. Higher BMI (increment of every 5 kg/m2) was significantly associated with worse DFS (HR=1.24, p=0.006) and OS (HR=1.38, p=0.005) only in AAs, but not in EAs (DFS p=0.76, OS p=0.35). Exploring BMI categories in AAs, survival differences were most significant between patients who had morbid obesity (BMI ≥40) and those who did not (DFS HR= 2.01, p=0.009; OS HR=2.19, p=0.045). However, in EAs, even morbid obesity was not associated with survival (DFS p=0.89, OS p=0.31). In the ER+ sub-population, BMI was associated with both DFS (HR=1.29, p=0.032) and OS (HR=1.60, p=0.017) in AAs, but only with OS in EAs (HR=1.15, p=0.049). In the triple negative sub-population, there was a trend toward worse survival with increasing BMI in AAs (p=0.098), but not in EAs (p=0.62). Conclusion: In contrast to prior work based on self-reported race, we found BMI to be significantly associated with worse survival in women of African ancestry in E5103, a large adjuvant trial that reflects our current approach to curative systemic therapy in breast cancer. Categorically, this association was significant only for morbid obesity, suggesting the relationship between BMI, race, and outcome may depend on the degree of obesity. Genetic ancestry may explain biologic differences driving both higher BMI and worse outcomes resulting in racial disparities in breast cancer.

Citation Format: Tarah J. Ballinger, Guanglong Jiang, Fei Shen, Kathy D. Miller, Bryan P. Schneider. Impact of African ancestry on the relationship between body mass index (BMI) and survival in early stage breast cancer: Retrospective analysis from E5103 [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-172.

Phase II trial of carboplatin and bevacizumab in patients with breast cancer brain metastases

BACKGROUND

We aimed to examine the safety and efficacy of bevacizumab and carboplatin in patients with breast cancer brain metastases.

METHODS

We enrolled patients with breast cancer and > 1 measurable new or progressive brain metastasis. Patients received bevacizumab 15 mg/kg intravenously (IV) on cycle 1 day 1 and carboplatin IV AUC = 5 on cycle 1 day 8. Patients with HER2-positive disease also received trastuzumab. In subsequent cycles, all drugs were administered on day 1 of each cycle. Contrast-enhanced brain MRI was performed at baseline, 24-96 h after the first bevacizumab dose (day + 1), and every 2 cycles. The primary endpoint was objective response rate in the central nervous system (CNS ORR) by composite criteria. Associations between germline VEGF single nucleotide polymorphisms (rs699947, rs2019063, rs1570360, rs833061) and progression-free survival (PFS) and overall survival (OS) were explored, as were associations between early (day + 1) MRI changes and outcomes.

RESULTS

Thirty-eight patients were enrolled (29 HER2-positive, 9 HER2-negative); all were evaluable for response. The CNS ORR was 63% (95% CI, 46-78). Median PFS was 5.62 months and median OS was 14.10 months. As compared with an Eastern Cooperative Oncology Group performance status (ECOG PS) of 0, patients with ECOG PS 1-2 had significantly worse PFS and OS (all P < 0.01). No significant associations between VEGF genotypes or early MRI changes and clinical outcomes were observed.

CONCLUSIONS

The combination of bevacizumab and carboplatin results in a high rate of durable objective response in patients with brain metastases from breast cancer. This regimen warrants further investigation.

TRIAL REGISTRATION

NCT01004172 . Registered 28 October 2009.

Implications of Incidental Germline Findings Identified In the Context of Clinical Whole Exome Sequencing for Guiding Cancer Therapy

PURPOSE

Identification of incidental germline mutations in the context of next-generation sequencing is an unintended consequence of advancing technologies. These data are critical for family members to understand disease risks and take action.

PATIENTS AND METHODS

A retrospective cohort analysis was conducted of 1,028 adult patients with metastatic cancer who were sequenced with tumor and germline whole exome sequencing (WES). Germline variant call files were mined for pathogenic/likely pathogenic (P/LP) variants using the ClinVar database and narrowed to high-quality submitters.

RESULTS

Median age was 59 years, with 16% of patients ≤ 45 years old. The most common tumor types were breast cancer (12.5%), colorectal cancer (11.5%), sarcoma (9.3%), prostate cancer (8.4%), and lung cancer (6.6%). We identified 3,427 P/LP variants in 471 genes, and 84% of patients harbored one or more variant. One hundred thirty-two patients (12.8%) carried a P/LP variant in a cancer predisposition gene, with BRCA2 being the most common (1.6%). Patients with breast cancer were most likely to carry a P/LP variant (19.2%). One hundred ten patients (10.7%) carried a P/LP variant in a gene that would be recommended by the American College of Medical Genetics and Genomics to be reported as a result of clinical actionability, with the most common being ATP7B (2.7%), BRCA2 (1.6%), MUTYH (1.4%), and BRCA1 (1%). Of patients who carried a P/LP variant in a cancer predisposition gene, only 53% would have been offered correct testing based on current clinical practice guidelines. Of 471 mutated genes, 231 genes had a P/LP variant identified in one patient, demonstrating significant genetic heterogeneity.

CONCLUSION

The majority of patients undergoing clinical cancer WES harbor a pathogenic germline variation. Identification of clinically actionable germline findings will create additional burden on oncology clinics as broader WES becomes common.

Protocol of a randomized trial of acceptance and commitment therapy for fatigue interference in metastatic breast cancer

Fatigue interference with activities, mood, and cognition is one of the most prevalent and distressing concerns of metastatic breast cancer patients. To date, there are no evidence-based interventions for reducing fatigue interference in metastatic breast cancer and other advanced cancer populations. In pilot studies, Acceptance and Commitment Therapy (ACT) has shown potential for reducing symptom-related suffering in cancer patients. The current Phase II trial seeks to more definitively examine the efficacy of telephone-based ACT for women with metastatic breast cancer who are experiencing fatigue interference. In this trial, 250 women are randomly assigned to either the ACT intervention or an education/support control condition. Women in both conditions attend six weekly 50-min telephone sessions. The primary aim of this study is to test the effect of telephone-based ACT on fatigue interference. Secondary outcomes include sleep interference, engagement in daily activities, and quality of life. Outcomes are assessed at baseline, 2 weeks post-intervention, and 3 and 6 months post-intervention. This trial also examines whether increases in psychological flexibility, defined as full awareness of the present moment while persisting in behaviors aligned with personal values, account for the beneficial effect of ACT on fatigue interference. After demonstrating ACT's efficacy, the intervention can be widely disseminated to clinicians who care for metastatic breast cancer patients. Our findings will also inform future ACT trials with various cancer populations and functional outcomes.