Residual Triple Negative Breast Cancer Research Articles

Abstract PO4-03-05: Prognostic value of Ki67 expression in post-treatment tumors of patients with residual triple-negative breast cancer after neoadjuvant chemotherapy

Abstract Introduction Patients with triple-negative breast cancer (TNBC) who do not achieve pathological complete response (pCR) against neoadjuvant chemotherapy (NAC) have a poor prognosis. The prognosis of these patients can be differentiated using various parameters, including the Residual Cancer Burden (RCB) index and tumor-infiltrating lymphocytes. In this study, we took a different angle and aimed to evaluate the prognostic value of post-treatment Ki67 expression, which was examined in tumors following NAC in patients with non-pCR TNBC. Methods A retrospective review of clinical records from February 2008 to December 2021 was conducted of patients from Gangnam Severance Hospital and Asan Medical Center, both in Seoul, South Korea. We included patients with non-metastatic TNBC who underwent NAC including anthracycline and taxane regimens, followed by curative surgery, regardless of adjuvant capecitabine receipt. Ki67 expression and the RCB index were evaluated using residual tumors obtained from surgery. High Ki67 expression was defined as ≥20%. The 5-year recurrence-free survival (RFS) was estimated using Kaplan-Meier analysis, and hazard ratios (HR) were calculated using Cox regression analysis. Results This study included 338 patients with available Ki67 expression data in residual tumors. Among them, 110 patients (30.9%) had low Ki67 expression, while 228 patients (64%) had high Ki67 expression. At a median follow-up of 34 months, those with low Ki67 expression had a 5-year RFS rate of 82.6%, while those with high Ki67 expression had a rate of 58.3%, with a HR of 0.345 (95% CI 0.210-0.565, p< 0.001). When stratified by the RCB index, the 5-year RFS of RCB-I patients was 93%, RCB-II patients 70.2%, and RCB-III patients 40.5%. When assessing survival outcomes based on both Ki67 expression and the RCB index, patients with RCB-I and low Ki67 (n=26) had a 100% 5-year RFS rate. Patients with RCB-I and high Ki67 (n=24) had a rate of 83.3%. Notably, in patients with RCB-III and high Ki67 (n=62), the 5-year RFS rate was 35.5% and there was no significant difference in RFS based on the receipt of adjuvant capecitabine (median RFS: capecitabine - 18 months, observation - 15 months, p-value=0.994). Conclusions Our findings demonstrate the prognostic value of Ki67 expression in residual TNBC after NAC, indicating that cases with low Ki67 expression have a favorable outcome. Combining Ki67 expression with the RCB index allows identification of patients with good residual disease (i.e. low Ki67 expression and RCB-I) who could be potential candidates for de-escalating adjuvant treatments such as capecitabine or pembrolizumab. However, for patients with high Ki67 expression and RCB-III, novel strategies are required to improve survival outcomes beyond the use of capecitabine. Citation Format: Yoonwon Kook, Soo-Young Lee, Seung Ho Baek, Min Ji Kim, Junghyun Kim, Sohyun Moon, Seung Eun Lee, Soong June Bae, Joon Jeong, Sae Byul Lee, Sung Gwe Ahn. Prognostic value of Ki67 expression in post-treatment tumors of patients with residual triple-negative breast cancer after neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-05.

Abstract PO5-19-07: A Single Arm Phase 2 Study of Peri-Operative Immune Checkpoint Inhibition and Cryoablation in Women With Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer

Abstract Background: Triple negative breast cancer (TNBC) is a biologically distinct subtype with a high risk of early relapse. Patients not achieving a pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) have a 3-year event free survival (EFS) of < 60%. Approximately 1/3 of patients receiving NAC with pembrolizumab-mediated immune therapy will not achieve a pCR and of those, approximately 1/3 will experience a recurrence within 3 years. Physical disruption of tumors with local strategies such as cryoablation (cryo) induces inflammation and releases antigens that can activate tumor-specific immune responses. The combination of cryo with immune checkpoint inhibition (ICI) has been shown to induce tumor regression and prevented tumor re-challenge in pre-clinical models. Clinical studies have also demonstrated that the combination of pre-operative cryo with ICI is safe in women with operable, early-stage breast cancer and generates intra-tumoral and systemic immune responses (NCT01502592, NCT02833233). This multi-center, single arm, phase 2 study is currently evaluating the impact of cryo with standard-of-care pembrolizumab (pembro) in women with residual TNBC after taxane-based NAC, a group at high risk of early relapse (NCT03546686). Methods: Eligible women are ≥18y, with ER < 10%, PR < 10%, HER2 negative (per ASCO/CAP definition), ≥ 1.0 cm, residual operable disease after taxane-based NAC. Pts undergo percutaneous, image-guided cryo with concurrent research core biopsy 7-10 days prior to surgery and receive peri-operative pembro per standard-of-care. Adjuvant capecitabine or olaparib is recommended for all patients per local standard-of-care. Patients are stratified by NAC platinum administration, NAC anthracycline administration, and clinical nodal status (positive versus negative). The primary endpoint is 3-year Event Free Survival (EFS). Secondary endpoints include Invasive Disease-Free Survival (IDFS), Distant Disease-Free Survival (DDFS), overall survival (OS) and safety. Exploratory correlative studies will be performed on tumor and serum to characterize the immunologic impact of the intervention and to explore predictors of efficacy and toxicity. Funding sources: Conquer Cancer Foundation, Breast Cancer Research Foundation, Boston Scientific Citation Format: Heather McArthur, Elizabeth Comen, Yolanda Bryce, Stephen Solomon, Sangeetha Reddy, Isaac Chan, Baṣak Dogan, Dawn Klemow, Nisha Unni, Jorge Henrique Santos Leal, Cristal Martinez, Reva Basho, Dorothy Park, Philomena McAndrew, Brigid Larkin, David Page, William Mills, Staci Mellinger, Nicole Fredrich, Nicole Moxon, Lynette Currie, Meredith Carter, Melissa Ramos, Stephanie Rice, Sujata Patil, Margaret Gatti-Mays, Larry Norton. A Single Arm Phase 2 Study of Peri-Operative Immune Checkpoint Inhibition and Cryoablation in Women With Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-19-07.

Abstract PO5-03-09: Concurrent versus sequential use of adjuvant capecitabine and radiation in patients with triple-negative breast cancer with residual disease: A retrospective review

Abstract Background: The CREATE-X trial demonstrated benefit of adjuvant capecitabine for patients with triple-negative breast cancer (TNBC) with residual disease after neoadjuvant chemotherapy and surgery. In clinical practice however, physician discretion determines the sequence of capecitabine relative to radiation therapy (RT), as well as the treatment dose. Therefore, our study aimed to assess the treatment patterns and tolerance of capecitabine and RT in patients with residual TNBC at our institution after publication of the CREATE-X study. Methods: This was a retrospective IRB-approved study that included patients with TNBC who had residual disease following neoadjuvant chemotherapy and surgery and received both adjuvant loco-regional RT and capecitabine at our institution between July 1, 2017 and June 30, 2021. Patient characteristics and treatment regimens were abstracted from medical charts. For this study, we defined optimally-delivered capecitabine to be a starting dose of 1250 mg/m2 twice per day on days 1-14 every 3 weeks as per the CREATE-X trial, and all planned cycles completed without dose reductions or discontinuation. RT was defined as optimally delivered when patients completed the prescribed dose without a treatment break of > 1 week or discontinuation of planned RT. We used descriptive statistics to report our observations. Results: Thirty-four patients met our eligibility criteria. The median age at diagnosis was 56 years (range: 30-77 years) and the median follow up time was 48 months. Of the 27 patients who received sequential RT and capecitabine, the median starting dose of capecitabine was 1000 mg/m2. Of the 7 patients who received concomitant RT and capecitabine, the median starting dose during RT was 800 mg/m2; after completion of RT, patients completed 6 additional cycles of capecitabine at a median dose of 1000 mg/m2. We observed a greater residual breast tumor burden in patients prescribed concomitant RT and capecitabine; 71.4% were ypT2/T3 compared to only 18.5% ypT2/T3 in sequentially treated patients (OR 11.0; 95% CI, 1.64 to 73.97; p=0.05). There was no significant difference in the positive lymph node status between the 2 groups (42.9% and 40.7%, respectively). A median RT dose of 50 Gy in 25 fractions was delivered in both schedules. No patients discontinued RT due to intolerance. In the 27 sequentially treated patients, the majority (73%) received RT before capecitabine. Among these, 14 patients (51.9%) required a dose reduction and 6 patients (22.2%) discontinued capecitabine due to intolerance. Of the 7 patients receiving concomitant RT and capecitabine, 2 patients (28.5%) discontinued capecitabine due to intolerance (one during RT and one following completion of RT). The concomitant RT and capecitabine regimen was not associated with higher odds of prematurely discontinuing capecitabine compared to the sequential schedule (OR 1.15; 95% CI, 0.18 to 7.34). Conclusion: In this study, most patients received a sequential schedule and those with a higher residual disease burden were more likely to be prescribed concomitant RT and capecitabine. The starting dose of capecitabine in both schedules was lower than the starting dose in the CREATE X trial but consistent with the practice standard in the US. Our early experience did not demonstrate any signal to suggest a difference in the tolerance of capecitabine administered sequentially or concurrently. Further studies are needed to evaluate the optimal sequence of RT and capecitabine in the adjuvant setting. Citation Format: Catherine Yu, Alaina Kessler, Theresa Shao, Sarah Cate, Paula Klein, Manjeet Chadha. Concurrent versus sequential use of adjuvant capecitabine and radiation in patients with triple-negative breast cancer with residual disease: A retrospective review [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-03-09.

Abstract PO1-29-01: Single agent and combinatorial efficacy with imipridone ONC206 via inhibition of mitochondrial function in preclinical models of chemorefractory triple negative breast cancer

Abstract Breast cancer remains a major global health concern, with triple-negative breast cancer (TNBC) being one of the most aggressive subtypes associated with limited targeted therapies. Chemotherapy resistance in TNBC patients poses a significant clinical challenge and is associated with poor progression-free and overall survival. Thus, exploring novel approaches to improve chemotherapeutic efficacy is of paramount importance. We previously demonstrated a role for mitochondrial fusion in supporting oxidative phosphorylation (oxphos) activity and cell survival in residual TNBC (PMID: 30996079 and 36813854) cells refractory to chemotherapy treatments. Based on these observations, we sought to inhibit mitochondrial function to improve chemotherapeutic efficacy. We used ONC206, a novel agonist of mitochondrial serine protease, ClpP (Caseinolytic Mitochondrial Matrix Peptidase Proteolytic Subunit) to induce mitochondrial proteotoxic stress. ONC201, a parent molecule of ONC206, has shown efficacy in TNBC as a single agent or when combined with a MEK inhibitor in vitro (PMID: 34680527). We demonstrate treatment of TNBC cell lines with ONC206 results in reduced mitochondrial fusion and OXPHOS. Furthermore, ONC206 co-treatment enhanced chemo-sensitivity in vitro. Based on these promising findings, we tested this in orthotopic patient-derived xenograft (PDX) mouse preclinical trials. Three PDX models of TNBC were tested, BCM-2665, BCM-5471, and BCM-0002. ONC206 as a single agent (twice weekly for 4 weeks, oral gavage, 100mg/kg) significantly decreased tumor growth in all three PDX models. Remarkably, treatment ONC206 achieved nearly complete tumor regression as a single agent or when combined with carboplatin in BCM-2665. Regressed tumors did re-grow, but this was significantly delayed when combined with carboplatin. Treatment with ONC206 in BCM-5471 resulted in a modest but significant reduction in tumor growth rate as a single agent. However, ONC206 did not improve carboplatin (weekly, i.p., 50mg/kg) nor docetaxel (weekly, i.p., 20mg/kg) efficacy in this model. ONC206 treatment of BCM-0002 resulted in prolonged tumor stasis and a slight enhancement of docetaxel and carboplatin efficacy. Interestingly, the efficacy of ONC206 in these PDX models correlates with their relative mRNA expression of ClpP. The mice demonstrated tolerance to ONC206 as a single agent or when combined with chemotherapy during the course of treatment. Our study underscores the potentially crucial role of mitochondria in driving chemotherapy resistance in TNBC and provides novel insights into mitochondria-targeted therapeutic approaches. We report a novel targeting option for TNBC and anticipate that these findings will stimulate further research into innovative combination therapies for TNBC patients, and may lead us to a viable inhibitor. Citation Format: Lily Baek, Lacey Dobrolecki, Stefanie Faucher, Christina Sallas, Nia Griffith, Varun Prabhu, Bora Lim, Michael Lewis, Gloria Echeverria. Single agent and combinatorial efficacy with imipridone ONC206 via inhibition of mitochondrial function in preclinical models of chemorefractory triple negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-29-01.

Abstract PO4-03-11: Discerning the impact of ctDNA detection on patient decisions in early-stage breast cancer

Abstract Background: Detection of circulating tumor DNA (ctDNA) after neoadjuvant therapy for triple negative breast cancer (TNBC) is associated with increased risk of recurrence. Ongoing trials aim to determine whether knowledge of specific genomic mutations in ctDNA can inform targeted adjuvant therapy to improve prognosis. The impact of knowledge of ctDNA status on patient treatment decisions weighing benefit and toxicity is unknown. Methods: 401 women were recruited via the Research Advocacy Network from Young Survivors’ Coalition, Living Beyond Breast Cancer, and Pink-4-Ever Ending Disparities. Participants had to self-report a history of non-metastatic breast cancer and have received chemotherapy in the prior 6 months to 10 years to be eligible. Participants completed a 27 question Qualtrics survey detailing demographics and experience with prior chemotherapy. Based on estimations from prior data, participants were presented with scenarios mimicking residual TNBC and unknown, negative, or positive ctDNA status with corresponding risk of recurrence of 40%, 20%, or 55% respectively. Participants were then presented with 12 scenarios (in random order) combining various degrees of absolute risk reduction (5%, 15%, 35%) with established toxicity profiles of four possible post-neoadjuvant therapies (capecitabine, immunotherapy, PARP inhibitor, and PI3K inhibitor). Participants rated scenarios in terms of acceptability from 0-100. A general linear model with repeated measures (3 × 4) was used to determine the contributions of risk reduction and toxicity to acceptability. Models were also run with the addition of between subject factors: age group (< 40; >40), stage of cancer (Stage 1; Stage 2/3), and previous experience with toxicity (Yes; No), to examine whether any of these factors moderated the effects of risk reduction and toxicity. Effect sizes were determined by partial h2. Results: 286 eligible respondents completed the survey with evaluable responses. Average age was 41.2 (range 27-75). When the hypothetical risk of recurrence decreased from 40% (ctDNA-unknown) to 20% (ctDNA-negative), significantly less participants preferred adjuvant capecitabine vs. no therapy (95.1% versus 63.3%, p< 0.001). Across the 12 scenarios, both benefit (F=448.5, p< 0.001; preference for greater benefit) and toxicity (F=33.64, p< 0.001; preference for lower toxicity) significantly influenced acceptability, but benefit had a much larger effect size than toxicity (h2=0.76 and 0.26, respectively). There was no significant interaction effect, and the pattern of results was not moderated by age, stage of cancer, or prior experience with chemotherapy toxicity. The most preferred scenario (greatest benefit, lowest toxicity) had a mean rating of 87.8/100; however, even when presented with the scenario with the lowest benefit and highest toxicity, the mean rating was still 31.5/100, suggesting that this combination would be acceptable to some individuals. Conclusions: Knowledge of ctDNA-negative status significantly reduced the number of participants preferring adjuvant capecitabine over no further therapy. When faced with ctDNA-positive status, participants preferred maximum risk reduction regardless of toxicity profile. As genomic technology advances, it is imperative that researchers and treating physicians understand its impact on patient decision making. Citation Format: Tarah Ballinger, Gregory Zimet, Elda Railey, Mary Lou Smith, Bryan Schneider. Discerning the impact of ctDNA detection on patient decisions in early-stage breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-11.

Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study

Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints included the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that treatment with immunotherapy containing arms (nivolumab or a combination of nivolumab plus capecitabine) leads to an increase in PIS from baseline to week 6 compared with capecitabine alone, meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) is associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.

Abstract 1149: Spatial transcriptomic analysis of tumor microenvironment in patients with triple negative breast cancer with residual disease after neoadjuvant chemotherapy with immune checkpoint inhibitor

Abstract Recent advance of treatment strategy for triple negative breast cancer (TNBC) including immune checkpoint inhibitor improved survival outcome. Especially, adding pembrolizumab on neoadjuvant chemotherapy (NAC) increased pathologic complete response (pCR) rate at the time of curative surgery. Previous studies suggested that PD-L1 expression in both tumor and immune cells was associated with the response of pembrolizumab in TNBC, but PD-L1 expression state were not associated with pembrolizumab response in NAC setting. In addition, neoadjuvant pembrolizumab increased event-free survival (DFS) rate after NAC even though they had not achieved pCR. However, there were no biomarker for EFS increasement of using pembrolizumab. We designed prospective translational research for evaluating tumor microenvironment (TME) of residual TNBC which had treated with NAC followed by curative surgery. We collected formalin fixed paraffin embedded (FFPE) surgical specimens after NAC with or without pembrolizumab. TNBC samples were used for spatial transcriptomics (ST) analysis, with H&E staining and inspection by an experienced pathologist. Libraries were prepared using Visium Spatial Gene Expression Reagent Kit protocol for FFPE (10x Genomics). Sequencing was conducted on the NovaSeq 6000 System (Illumina). From February 2023 to October 2023, 23 TNBC specimens from 22 patients were collected. Twenty specimens were breast tissues and three were lymph nodes, 18 TNBCs had been treated with NAC with pembrolizumab and four with only NAC, and five had residual cancer burden(RCB) class I, 11 of RCB class II and one of RCB class III. We collected BC and LN samples from BC with class III. Of 23 samples, we performed spatial transcriptomic analysis in 12 samples. In intrinsic subtyping, eight specimens were categorized into normal like, two of basal like and two of luminal A BC subtypes. In TNBC subtyping, mesenchymal stem cell like (MSL) were in six specimens, three of stem cell like (SL), two of luminal androgen receptor (LAR) and one of immunomodulatory (IM). We also performed cell type annotation with unsupervised method and categorized into 11 cell types; three cancer cell types, two macrophages, B and T cells, adipocytes, normal epithelium and perivascular-like and cancer associated fibroblasts. Among these 11 cell types, increasement of immune cells including B cells, T cells and macrophage proportions was associated with pembrolizumab treatment in NAC setting. In our study, we evaluated TME state of TNBC after NAC with or without pembrolizumab. We suggested that MSL or SL TNBC subtypes were associated with residual disease after NAC regardless of pembrolizumab use and pembrolizumab may recruit more immune cells in TME of TNBC. For concreating our suggestion, further analyses would be warranted. Citation Format: Ji-Yeon Kim, Kyunghee Park, Yoon La Choi, Jeong Eon Lee, Byung Joo Chae, Jonghan Yu, Seok Won Kim, Seok Jin Nam, Jin Seok Ahn, Woong-Yang Park, Yeon Hee Park. Spatial transcriptomic analysis of tumor microenvironment in patients with triple negative breast cancer with residual disease after neoadjuvant chemotherapy with immune checkpoint inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1149.

Efficacy of adjuvant capecitabine in residual triple negative breast cancer: a multicenter observational Turkish Oncology Group (TOG) study

ABSTRACT Background Triple negative breast cancer (TNBC) is characterized by high rates of recurrence, especially in patients with residual disease after neoadjuvant chemotherapy (NAC). Capecitabine is being used as standard adjuvant treatment in residual TNBC. We aimed to investigate the real-life data regarding the efficacy of capecitabine in residual TNBC. Design and methods In this retrospective multicenter study, TNBC patients with residual disease were evaluated. Patients, who received standard anthracycline and taxane-based NAC and adjuvant capecitabine were eligible. Overall survival (OS), disease free survival (DFS) and toxicity were analyzed. Results 170 TNBC patients with residual disease were included. Of these, 62.9% were premenopausal. At the time of analysis, the recurrence rate was 30% and death rate was 18%. The 3-year DFS and OS were 66% and 74%, respectively. In patients treated with adjuvant capecitabine, residual node positive disease stood out as an independent predictor of DFS (p = 0.024) and OS (p = 0.032). Undergoing mastectomy and the presence of T2 residual tumor was independent predictors of DFS (p = 0.016) and OS (p = 0.006), respectively. Conclusion The efficacy of capecitabine was found lower compared to previous studies. Selected patients may have further benefit from addition of capecitabine. The toxicity associated with capecitabine was found lower than anticipated.

Abstract B059: Epigenetically defined sub-clonal heterogeneity drives therapy resistance in triple-negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) is a highly aggressive and heterogeneous disease with an average survival of less than 50%. Although immunotherapy is showing promising results, many patients do not respond, and chemotherapy remains the main treatment. High TNBC recurrence rates are in part due to its molecular heterogeneity. Here, we sought to characterise the sub-clonal and spatial diversity of chemotherapy resistant TNBC to identify the epigenetic hallmarks of lethal sub-populations of cells that may induce cell state transition, therapy resistance and ultimately metastatic progression. Methods: Sixteen primary untreated triple-negative breast tumours (eight chemotherapy sensitive (ChemoS) and eight chemotherapy resistant (ChemoR, who died of their disease within three years)) were subjected to cell-matched high-depth multiome single nuclei RNA- and ATAC-sequencing. Four tumours were subject to spatial RNA and ATAC profiling. Fourteen TNBC PDX models generated from patients with residual disease post NAC were subjected to single nuclei sequencing and used for validation. Meta-clustering of epithelial cells from the RNA profiles was used to identify sub-populations of cells harbouring distinct epigenetic and transcriptomic features enriched in ChemoR patients. Findings were validated in the BrighTNess TNBC NAC clinical trial and in chemotherapy treated TNBC patients from the SCAN-B study. Results: Unsupervised meta-clustering (MC) of epithelial cells in G1 phase of the cell cycle identified nine MC’s across the dataset, including a distinct immune-like MC. Two MCs were dominated by cells from ChemoR patients and were defined by hypoxia, EMT, and extra-cellular matrix signalling. Sub-populations of cells in the ChemoR dominant MCs were underpinned by both promoter and distal differential chromatin accessibility, that mapped to H3K27ac enhancer sites, suggesting a role of enhancer regulation of MC transcription. Spatial ATAC and RNA profiling of a subset of tumours identified spatially epigenetically defined regions that showed distinct chromatin profiles, suggesting that the epigenetic regulation of genes that define the MCs are spatially distinct. ChemoR clusters were independently reproduced in a cohort of fourteen residual disease TNBC PDXs. Genes pertaining to the immune-like MC were associated with a good prognosis in independent cohorts of contemporary treated TNBC (SCAN-B) and with response to NAC in the BrighTNess trial. Marker genes from ChemoR dominant MCs were associated with poor prognosis and significant levels of residual disease following NAC. Conclusions: Our multi-modal integrative analysis reveals unprecedented insight into the role of epigenetically defined spatially distinct, sub-clonal populations that pre-exist in treatment naïve TNBC and predict therapy response. This suggests pre-existing populations of cells have already acquired the epigenetic footprints and hence transcriptomic features to allow them to evade therapy. Citation Format: Fatemeh Ahmadimoghari, Yu Zhang, Ioanna Mavrommatis, Shafali Thakur, Chris Starling, Ioannis Roxanis, Syed Haider, Rachael Natrajan. Epigenetically defined sub-clonal heterogeneity drives therapy resistance in triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B059.

Pathologic and immunohistochemical prognostic markers in residual triple-negative breast cancer after neoadjuvant chemotherapy.

The persistence of residual tumour after neoadjuvant chemotherapy (NAC) in localised triple-negative breast cancer (TNBC) is known to have a negative prognostic value. However, different degrees of expression of some immunohistochemical markers may correlate with different prognoses. The expression of biomarkers with a known prognostic value, i.e., cytokeratin 5/6 (CK5/6), androgen receptor (AR), epidermal growth factor receptor (EGFR) proliferation-related nuclear antigen Ki-67, human epidermal growth factor receptor 2 (HER2), protein 53 (p53), forkhead box protein 3 (FOXP3), and cluster differentiation 8 (CD8), was analysed by immunohistochemistry in 111 samples after NAC in non-metastatic TNBC patients addressed to Georges-François Leclerc Cancer Centre Dijon, France. Clinical and pathological variables were retrospectively collected. Cox regression was used to identify immunohistochemical (IHC) and clinicopathological predictors of event-free survival (EFS) (relapse or death). Median age was 50.4 years (range 25.6-88.3), 55.9% (n = 62) were non-menopausal, 70 (63.1%) had stage IIA-IIB disease. NAC was mostly sequential anthracycline-taxanes (72.1%), and surgical intervention was principally conservative (51.3%). We found 65.7% ypT1, 47.2% lymph node involvement (ypN+), and 29.4% lymphovascular invasion (LVI). Most residual tumours were EGFR >110 (H-score) (60.5%, n = 66), AR ≥4% (53.2%, n = 58), p53-positive mutated (52.7%, n = 58), CD8 ≥26 (58.1%, n = 61), FOXP3 ≥7 (51.4%, n = 54), more than half in the stroma, and 52.3% (n = 58) HER2 score 0. After a median follow-up of 80.8 months, 48.6% had relapsed. Median EFS was 62.3 months (95% CI, 37.2-not reached (NR)). Factors independently associated with poor EFS were AR-low (p = 0.002), ypN+ (p < 0.001), and LVI (p = 0.001). Factors associated with lower overall survival (OS) were EGFR-low (p = 0.041), Ki-67 high (p = 0.024), and ypN+ (p < 0.001). Post-NAC residual disease in TNBC showed biomarkers specific to a basal-like subtype and markers of lymphocyte infiltration mostly present in the stroma. Prognostic markers for EFS were AR, LVI, and ypN and warrant further validation in a prognostic model.

Diverging prognostic effects of CD155 and CD73 expressions in locally advanced triple-negative breast cancer.

Immune checkpoint inhibition, combined with novel biomarkers, may provide alternative pathways for treating chemotherapy-resistant triple-negative breast cancer (TNBC). This study investigates the expression of new immune checkpoint receptors, including CD155 and CD73, which play a role in T and natural killer (NK) cell activities, in patients with residual TNBC after neoadjuvant chemotherapy (NAC). The expression of biomarkers was immunohistochemically examined by staining archival tissue from surgical specimens (n = 53) using specific monoclonal antibodies for PD-L1, CD155, and CD73. Of those, 59.2% (29/49) were found to be positive (>1%) for PD-L1 on the tumour and tumour-infiltrating lymphocytes (TILs), while CD155 (30/53, 56.6%) and CD73 (24/53, 45.3%) were detected on tumours. Tumour expressions of CD155 and CD73 significantly correlated with PD-L1 expression on the tumour (p = 0.004 for CD155, p = 0.001 for CD73). Patients with CD155 positivity ≥10% were more likely to have a poor chemotherapy response, as evidenced by higher MDACC Residual Cancer Burden Index scores and Class II/III than those without CD155 expression (100% vs 82.6%, p = 0.03). At a median follow-up time of 80 months (range, 24-239), patients with high CD73 expression showed improved 10-year disease-free survival (DFS) and disease-specific survival (DSS) rates compared to those with low CD73 expression. In contrast, patients with CD155 (≥10%) expression exhibited a decreasing trend in 10-year DFS and DSS compared to cases with lower expression, although statistical significance was not reached. However, patients with coexpression of CD155 (≥10%) and low CD73 were significantly more likely to have decreased 10-year DFS and DSS rates compared to others (p = 0.005). These results demonstrate high expression of CD73 and CD155 in patients with residual tumours following NAC. CD155 expression was associated with a poor response to NAC and poor prognosis in this chemotherapy-resistant TNBC cohort, supporting the use of additional immune checkpoint receptor inhibitor therapy. Interestingly, the interaction between CD155 and CD73 at lower levels resulted in a worse outcome than either marker alone, which calls for further investigation in future studies.

Disease outcomes by race in patients with high-risk triple negative breast cancer with residual disease after neoadjuvant chemotherapy: A post-hoc analysis of the EA1131 randomized clinical trial.

586 Background: Black women with breast cancer have the highest breast cancer mortality (BCM) rates of any racial and ethnic group. The higher burden of triple negative breast cancer (TNBC) in Black women contributes to disparities in BCM, but the extent to which disparate outcomes exist in patients with similar tumor biology is uncertain. The objective of this study was to examine racial differences in disease outcomes and BCM between Black and White patients in a clinical trial population of high-risk TNBC with residual disease after neoadjuvant chemotherapy (NAC). Methods: From 2015-2021, the ECOG-ACRIN EA1131 clinical trial randomized 415 clinical stage II-III TNBC patients with residual disease after NAC to either adjuvant capecitabine or platinum. For this analysis, 366 patients with known self-reported Black or White race and follow-up data were included. The aim of this unplanned exploratory analysis was to examine locoregional recurrence (LRR), distant recurrence (DR), and BCM by race using Kaplan-Meier curves for unadjusted estimates and Cox modeling for adjusted analyses. Results: Racial distribution of the analysis population included 66 (18.0%) Black and 300 (82.0%) White patients. 239 (65.3%) patients presented with clinical stage II and 127 (34.7%) with stage III disease. All patients had residual pathological disease after NAC: 86 (23.5%) stage I, 176 (48.1%) stage II, and 102 (27.9%) stage III (n=2 unknown). Median age was 49 years in Black and 54 years in White patients, p=0.003. Disease presentation, response to chemotherapy, and treatment arm were similar by race. Median follow up was 20 months. 2-year estimated LRR occurred in 31.6% of Black and 18.6% of White patients although this was not statistically significant (p=0.387), and 2-year estimated DR and BCM were similar by race. Estimated 2-year outcomes are outlined. Models adjusted for race, age, stage, grade, treatment arm, and locoregional therapy did not identify race as an independent predictor of LRR, DR, or BCM. Higher pathologic stage was the only consistent independent predictor of recurrent disease or BCM (stage III with HR 6.14 for LRR; HR 5.16 for DR; HR 6.84 for BCM; all p&lt;0.001). Conclusions: In this population of high-risk patients with residual TNBC after NAC with similar tumor biology treated on a clinical trial, there was a trend towards increased LRR in Black patients and similar DR and BCM between Black and White patients at 2 years of follow-up. This suggests that differences in BCM in other breast cancer populations may be at least partially driven by differences in tumor biology. Clinical trial information: NCT02445391 . [Table: see text]

A single-arm phase 2 study of peri-operative immune checkpoint inhibition and cryoablation in women with hormone receptor-negative, HER2-negative, early-stage/resectable breast cancer.

TPS635 Background: Local tumor destruction with cryoablation (cryo) induces inflammation and releases antigens that can activate tumor-specific immune responses. Pre-clinically, cryo with immune checkpoint inhibition (ICI) augmented tumor-specific immune responses and prevented recurrence. Clinically, we established that peri-operative (peri-op) cryo with ICI [ipilimumab (ipi) +/- nivolumab (nivo)] was safe in patients (pts) with operable, early stage breast cancer (ESBC) and generated robust intra-tumoral and systemic immune responses. In this phase 2 study, we evaluate the disease specific impact of peri-op ICI in women with residual triple negative breast cancer (TNBC) after neoadjuvant chemotherapy (NAC), a subset at high risk of early relapse. Methods: Eligible women are ≥18y, with ER &lt;10%, PR &lt;10%, HER2 negative (per ASCO/CAP definition), ≥ 1.0 cm, residual operable disease after taxane-based NAC. As of 2/14/21, 16/80 pts have been enrolled and treated with ipi/nivo/cryo followed by breast surgery and adjuvant nivo. Pts undergo percutaneous, image-guided cryo with concurrent research core biopsy 7-10 days prior to surgery and received ipi (1mg/kg IV) with nivo (240mg IV) 1 to 5 days prior to cryo. After surgery, pts received 3 additional doses of nivo at 240mg IV Q2 weeks. To reflect the US FDA approval of curative-intent pembrolizumab (pembro) in 2021, the protocol was recently amended to allow standard-of-care pembro as an alternative ICI option. Adjuvant capecitabine or olaparib is recommended for all patients per local standard-of-care. Patients will be stratified by NAC platinum administration, NAC anthracycline administration, and clinical nodal status (positive versus negative). The primary endpoint is 3-year Event Free Survival (EFS). Secondary endpoints include Invasive Disease-Free Survival (IDFS), Distant Disease-Free Survival (DDFS), overall survival (OS) and safety. Exploratory correlative studies will be performed on tumor and serum to characterize the immunologic impact of the intervention and to explore predictors of efficacy and toxicity. Clinical trial information: NCT03546686 .

IKKα inhibition re-sensitizes acquired adriamycin-resistant triple negative breast cancer cells to chemotherapy-induced apoptosis

IKKα has been shown to be responsible of multiple pro-tumorigenic functions and therapy resistance independent of canonical NF-κB, but its role in acquired chemotherapy resistance in breast cancer remains unclarified. In this study, we obtained pre-treatment biopsy and post-treatment mastectomy specimens from a retrospective cohort of triple-negative breast cancer (TNBC) patients treated with neoadjuvant chemotherapy(NAC) (n = 43). Immunohistochemical methods were used to detect the expression of IKKα before and after NAC, and the relationship between IKKα and the pathologic response to NAC was examined. In addition, we developed a new ADR-resistant MDA-MB-231 cell line(MDA-MB-231/ADR) and analyzed these cells for changes in IKKα expression, the role and mechanisms of the increased IKKα in promoting drug resistance were determined in vitro and in vivo. We demonstrated that the expression of IKKα in residual TNBC tissues after chemotherapy was significantly higher than that before chemotherapy, and was positively correlated with lower pathological reaction. IKKα expression was significantly higher in ADR-resistant TNBC cells than in ADR-sensitive cells, IKKα knockdown results in apoptotic cell death of chemoresistant cells upon drug treatment. Moreover, IKKα knockdown promotes chemotherapeutic drug-induced tumor cell death in an transplanted tumor mouse model. Functionally, we demonstrated that IKKα knockdown significantly upregulated the expression of cleaved caspase 3 and Bax and inhibited the expression of Bcl-2 upon ADR treatment. Our findings highlighted that IKKα exerts an important and previously unknown role in promoting chemoresistance in TNBC, combining IKKα inhibition with chemotherapy may be an effective strategy to improve treatment outcome in chemoresistant TNBC patients.

Abstract P6-11-14: Mitochondrial structure and function adaptation in residual triple negative breast cancer cells surviving chemotherapy treatment

Abstract Background: Neoadjuvant chemotherapy (NACT) used for triple-negative breast cancer (TNBC) eradicates tumors in only 45% of patients. TNBC patients with substantial residual cancer burden have poor metastasis-free and overall survival rates. Our previous studies demonstrated mitochondrial oxidative phosphorylation (OXPHOS) was elevated, suggesting a unique therapeutic dependency of residual tumor cells that survived after NACT. However, mechanisms underlying this enhanced reliance on OXPHOS are yet unknown. Mitochondria are morphologically plastic organelles that cycle between fission and fusion to maintain mitochondrial integrity and metabolic homeostasis. Methods: We modeled residual disease in human TNBC cells by treating with chemotherapeutic agents at the IC50 of cell killing, then evaluating surviving cells after 48 hours of treatment. We modeled residual TNBC in orthotopic patient-derived xenograft (PDX) model (PIM001p) by treating with standard front-line NACT (Adriamycin + cyclophosphamide; AC), then longitudinally harvesting tumors prior to treatment, residual, and upon regrowth. We analyzed mitochondrial morphology, mtDNA content and integrity, mitochondrial oxygen consumption rate, and metabolomic flux. We developed a U-Net based deep learning model that automatically detects and quantifies mitochondrial features in transmission electron micrographs. To test the functional dependency of mitochondrial structure in TNBC, we perturbed mitochondrial fusion genetically (by knocking down the fusion-driving protein Optic Atrophy 1, OPA1) and pharmacologically (using the first-in-class small molecule OPA1 inhibitor, MYLS22). Results: Pharmacologic or genetic disruption of mitochondrial fusion and fission resulted in decreased or increased OXPHOS rate, respectively, in TNBC cells, revealing for the first time that mitochondria morphology regulates OXPHOS in TNBC. Upon comparing mitochondrial effects of conventional chemotherapies, we found that DNA-damaging agents (adriamycin, carboplatin) increased mitochondrial elongation, mitochondrial content, flux of glucose through the TCA cycle, and OXPHOS, whereas taxanes (paclitaxel, docetaxel) instead decreased mitochondrial elongation and OXPHOS rate. Increased levels of the short protein isoform of OPA1 were observed in residual cells that not killed by DNA-damaging chemotherapy treatment. Treatment of cells with adriamycin followed by MYLS22 or given concurrently with MYLS22 drastically decreased cell growth. Conversely, cells treated with adriamycin, inducing fusion, followed by the DRP1 inhibitor Mdivi-1, further inducing fusion, were less sensitive to adriamycin than were vehicle-treated cells. Further, we observed heightened OXPHOS, OPA1 protein levels, and mitochondrial elongation in residual tumors of the PDX model following AC treatment. We found that sequential treatment first with AC, thus inducing mitochondrial fusion and OXPHOS, followed by MYLS22 to inhibit OPA1 in residual tumors, was able to suppress mitochondrial fusion and OXPHOS and significantly inhibited residual tumor regrowth. Our deep-learning algorithm identified distinct changes in mitochondrial phenotypes in residual tumors of multiple PDX models. Treatment of non-chemotherapy-treated mice with the OPA1 inhibitor MYLS22 as a single agent had no effect on tumor growth, revealing that post-AC residual tumors have an enhanced dependency on mitochondrial fusion compared to treatment-naïve tumors. Taken together, our findings establish a functional role for mitochondrial structure in chemotherapeutic response and metabolic reprogramming, which may confer survival advantage to TNBC cells. These results suggest that pharmacologic perturbation of mitochondrial structure can overcome chemoresistance in TNBC cells when administered rationally based on our understanding of chemotherapy-induced mitochondrial adaptations. Citation Format: Lily Baek, Junegoo Lee, Katherine E. Pendleton, Mariah J. Berner, Emily Goff, Lin Tan, Sara Martinez, Iqbal Mahmud, Argenis Arriojas, Alexander Zhurkevich, Tao Wang, Matthew Meyer, Bora Lim, James P. Barrish, Weston Porter, Kourosh Zarringhalam, Philip L. Lorenzi, Gloria V. Echeverria. Mitochondrial structure and function adaptation in residual triple negative breast cancer cells surviving chemotherapy treatment [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 P6-11-14.

Abstract P6-11-15: Lipid accumulation in residual triple negative breast cancer cells surviving chemotherapy treatment

Abstract Background: Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype for which limited targeted therapies are available. Therefore, conventional chemotherapy remains the backbone of standard neoadjuvant treatment (NACT) for TNBC patients. Unfortunately, ~45% of patients will have substantial residual tumor burden post neoadjuvant chemotherapy, leading to poor prognoses (PMID: 28135148). Recently, it has been demonstrated that mitochondrial oxidative phosphorylation (oxphos) is upregulated and is a therapeutic vulnerability in chemoresistant TNBC (PMID: 30996079; Baek et al., BioRxiv doi.org/10.1101/2022.02.25.481996). However, mechanisms driving increased oxphos in chemoresistant TNBC are not understood. Upregulated fatty acid (FA) metabolism is a common adaptation in tumors, providing an energy source through fatty acid β-oxidation (FAO), and promoting lipid accumulation after fatty acid synthesis (FAS) when energy needs are met. Chemotherapy can induce oxidative stress through the generation of reactive oxygen species. Cancer cells adapt to these damaging molecules by increasing de novo lipogenesis, resulting in the accumulation of lipid droplets (LDs) in the cytosol (PMID: 32782526, 20876798). We hypothesize that TNBC cells metabolically adapt to the stress of NACT by upregulating lipid metabolic pathways, providing highly energetic molecules that can be utilized to drive oxphos in chemoresistant TNBC. Methods: Using orthotopic patient-derived xenograft (PDX) models of TNBC (PIM001-P, PMID: 30996079, HCI-010, PMID: 22019887; WHIM14, PMID:24055055), we are measuring protein levels of fatty acid synthase (FASN) in vehicle tumors vs residual tumors surviving treatment with the standard front-line neoadjuvant chemotherapy regimens (Adriamycin plus cyclophosphamide (AC), docetaxel, carboplatin, or docetaxel+carboplatin) using immunohistochemistry (IHC). Vectra 3 microscopy (Akoya) is being used to quantify tumor cell-specific staining. We complemented our IHC analysis with reverse-phase protein array (RPPA). To assess LD accumulation in residual PDX tumors, we conducted transmission electron microscopy (TEM). To complement these PDX studies, we modeled the residual tumor metabolic state in cultured human TNBC cells. Following treatment with the IC50 of standard chemotherapeutic agents (AC, carboplatin, paclitaxel, docetaxel), we assessed oxphos by measuring oxygen consumption rate (OCR) using a Seahorse Bioanalyzer (Agilent). Further, we tested LD accumulation using LipidTOX staining. In ongoing studies, we are measuring incorporation of 13C palmitate into the tricarboxylic acid cycle (TCA) prior to and following chemotherapy treatments to assess if lipids fuel mitochondrial metabolism in residual TNBC cells. Results/Discussion: IHC in the PIM001-P PDX model after in vivo AC treatment revealed increased levels of FASN in post-AC residual tumors compared to the treatment-naive tumors. Further, key proteins involved in fatty acid synthesis, FASN and Acetyl-CoA carboxylase, were significantly increased in residual PIM001-P cells that survived AC compared to vehicle by RPPA. TEM analysis of the HCI-010 PDX revealed significantly more LDs in carboplatin-treated tumors compared to vehicle. This finding was supported by increased LDs observed in TNBC cell lines treated with NACT compared to vehicle in our LipidTOX analyses. Taken together, these data indicate that NACT induces increased expression of key lipid metabolism proteins and accumulation of cytosolic LDs. Our future experiments will reveal if chemoresistant TNBC cells preferentially utilize and incorporate lipids into the tricarboxylic acid cycle, in turn driving oxphos. These data have the potential to provide rationale for the incorporation of FAO/LD inhibitors in sequential combinations with conventional chemotherapies to more effectively kill TNBC cells that are chemo-refractory. Citation Format: Katherine E. Pendleton, Mokryun L. Baek, Junegoo Lee, Lin Tan, Hannah L. Johnson, Lacey E. Dobrolecki, James P. Barrish, Michael T. Lewis, Philip L. Lorenzi, Fabio Stossi, Gloria V. Echeverria. Lipid accumulation in residual triple negative breast cancer cells surviving chemotherapy treatment [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 P6-11-15.

Abstract OT1-19-01: A Single Arm Phase 2 Study of Peri-Operative Checkpoint-Mediated Immune Therapy and Cryoablation in Women with Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer

Abstract Background: Local tumor destruction with cryoablation (cryo) induces inflammation and releases antigens that can activate tumor-specific immune responses. Pre-clinically, cryo with immune checkpoint inhibition (ICI)-augmented tumor-specific immune responses and prevented recurrence. Clinically, we established that peri-operative (peri-op) cryo with ipilimumab (ipi) +/- nivolumab (nivo) was not only safe in patients (pts) with operable, early stage breast cancer (ESBC) but also generated robust intra-tumoral and systemic immune responses. In this phase 2 study, we evaluate the disease specific impact of peri-op ICI in women with residual triple negative breast cancer (TNBC) after neoadjuvant chemotherapy (NAC), a subset at high risk of early relapse. Methods: Eligible pts are ≥18y, with ER &amp;lt; 10%, PR &amp;lt; 10%, HER2 negative (per ASCO/CAP definition), ≥ 1.0 cm, residual operable disease after taxane-based NAC. Approximately 80 pts will be enrolled and treated with ipi/nivo/cryo followed by breast surgery and adjuvant nivo across multiple institutions. Pts undergo percutaneous, image-guided cryo with concurrent research core biopsy 7-10 days prior to surgery and will receive ipi (1mg/kg IV) with nivo (240mg IV) 1 to 5 days prior to cryo. After surgery, pts will receive 3 additional doses of nivo at 240mg IV Q2 weeks. Adjuvant capecitabine is recommended for all patients per local standard-of-care. Patients will be stratified by NAC platinum administration, NAC anthracycline administration, and clinical nodal status (positive versus negative). The primary endpoint is 3-year Event Free Survival (EFS). Secondary endpoints include Invasive Disease-Free Survival (IDFS), Distant Disease-Free Survival (DDFS), overall survival (OS) and safety. Exploratory correlative studies will be performed on tumor and serum to characterize the immunologic impact of the intervention and to explore predictors of efficacy and toxicity. Funding sources: Susan G. Komen, ASCO Conquer Cancer Foundation, Breast Cancer Research Foundation, Bristol-Myers Squibb, BTG International Ltd. NCT03546686 Citation Format: Heather McArthur, Elizabeth Comen, Yolanda Bryce, Stephen Solomon, Jorge Henrique Santos Leal, Christina DiLauro Abaya, Cristal Martinez, Reva Basho, Dorothy Park, Philomena McAndrew, Brigid Larkin, William Mills, David B. Page, Staci Mellinger, Nicole Fredrich, Nicole Moxon, Sangeetha Reddy, Meredith Carter, Sujata Patil, Larry Norton. A Single Arm Phase 2 Study of Peri-Operative Checkpoint-Mediated Immune Therapy and Cryoablation in Women with Hormone Receptor-Negative, HER2-Negative Early Stage/Resectable Breast Cancer [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 OT1-19-01.

Abstract P6-11-10: Investigating the role of mitochondrial protein translation in the metabolic adaptation of chemoresistant triple negative breast cancer

Abstract BACKGROUND: Nearly 50% of patients with triple negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NACT) retain residual tumors resulting in high rates of metastatic relapse and poor overall survival. Residual tumors surviving NACT (Adriamycin plus cyclophosphamide; AC) were found to undergo a metabolic transition to heightened mitochondrial oxidative phosphorylation (oxphos; PMID: 30996079). Pharmacologic inhibition of mitochondrial electron transport chain (ETC) complex I with IACS-010759 (PMID: 29892070) had enhanced efficacy in residual, rather than treatment-naïve, tumors of orthotopic patient-derived xenograft (PDX) models. Our analyses of mitochondrial structure and function in human TNBC cell lines revealed differing adaptations in residual cells surviving treatment with conventional NACT agents. While DNA-damaging chemotherapies (e.g.Adriamycin, carboplatin) induced mitochondrial fusion and oxphos, taxanes (e.g.paclitaxel, docetaxel) induced mitochondrial fragmentation and reduced oxphos (Baek et al., Biorxiv Doi 10.1101/2022.02.25.481996). The mechanistic basis of these mitochondrial adaptations is not yet understood. The mitochondrial ETC consists of 92 proteins, 13 of which are encoded in the mitochondrial genome (mtDNA) and translated by the mitoribosome, while the remaining are encoded by the nuclear genome (nDNA), translated by the cytoribosome, and inserted into the inner mitochondrial membrane by accessory proteins, namely Oxidase (Cytochrome C) Assembly 1-Like (OXA1L). Disruption of OXA1L in mammalian cells has been shown to affect the levels and activity of ETC complexes I, III, IV, and V, and thus diminish oxphos. We aim to determine whether mitochondrial translation and OXA1L activity represent therapeutic vulnerabilities to overcome pro-survival metabolic adaptations in chemoresistant TNBC thereby augmenting treatment response. METHODS: Weare evaluating the effects of conventional TNBC chemotherapies singly, and in standard combinations, on mitochondrial translation and ETC formation in human TNBC cells and PDX models(PIM001-P, WHIM14, BCM15116) using metabolomic and proteomic profiling. To perturb these processes genetically, we knocked down (KD) OXA1Lwith siRNA. We are complementing these studies pharmacologically using conventional antibiotics, such as tigecycline, as previous studies showed they inhibit mitochondrial translation in breast and other cancers (PMID: 25625193). These studies will reveal whether OXA1L and mitochondrial translation are required for metabolic adaption and chemotherapy resistance of residual TNBC cells. PDX preclinical trials based on our published residual tumor testing schema (PMID: 30996079), will reveal whether the sequential combination of NACT followed by tigecycline can effectively perturb residual tumor relapse. RESULTS: Proteomic profiling of longitudinally harvested PDX tumors demonstrates substantial disruption of mitochondria-and nuclear-encoded ETC components in residual vs. treatment-naïve tumors. Interestingly, these patterns are distinct between different chemotherapy treatments, with an increase of ETC components in carboplatin-treated residual tumors compared to a decrease in docetaxel-treated residual tumors. Western blot analyses of human cell lines show OXA1LKD perturbs levels of both nuclear-and mitochondria-encoded ETC components. Preliminary findings suggest OXA1LKD increases sensitivity to chemotherapies in human TNBC cell lines. Finally, tigecycline effectively inhibits TNBC cell growth. We next will evaluate whether residual cells not killed by conventional chemotherapies have enhanced tigecycline susceptibility. CONCLUSION: These data suggest targeting mitochondrial translation may be a promising approach to overcome pro-survival metabolic adaptations in residual TNBC cells not killed by conventional chemotherapies. Citation Format: Mariah J. Berner, Lily Baek, Junegoo Lee, Philip L. Lorenzi, Mei Leng, Alexander B. Saltzman, Anna Malovannaya, Lacey E. Dobrolecki, Christina Sallas, Michael T. Lewis, Gloria V. Echeverria. Investigating the role of mitochondrial protein translation in the metabolic adaptation of chemoresistant triple negative breast cancer [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 P6-11-10.

Mitochondrial structure and function adaptation in residual triple negative breast cancer cells surviving chemotherapy treatment.

Neoadjuvant chemotherapy (NACT) used for triple negative breast cancer (TNBC) eradicates tumors in ~45% of patients. Unfortunately, TNBC patients with substantial residual cancer burden have poor metastasis free and overall survival rates. We previously demonstrated mitochondrial oxidative phosphorylation (OXPHOS) was elevated and was a unique therapeutic dependency of residual TNBC cells surviving NACT. We sought to investigate the mechanism underlying this enhanced reliance on mitochondrial metabolism. Mitochondria are morphologically plastic organelles that cycle between fission and fusion to maintain mitochondrial integrity and metabolic homeostasis. The functional impact of mitochondrial structure on metabolic output is highly context dependent. Several chemotherapy agents are conventionally used for neoadjuvant treatment of TNBC patients. Upon comparing mitochondrial effects of conventional chemotherapies, we found that DNA-damaging agents increased mitochondrial elongation, mitochondrial content, flux of glucose through the TCA cycle, and OXPHOS, whereas taxanes instead decreased mitochondrial elongation and OXPHOS. The mitochondrial effects of DNA-damaging chemotherapies were dependent on the mitochondrial inner membrane fusion protein optic atrophy 1 (OPA1). Further, we observed heightened OXPHOS, OPA1 protein levels, and mitochondrial elongation in an orthotopic patient-derived xenograft (PDX) model of residual TNBC. Pharmacologic or genetic disruption of mitochondrial fusion and fission resulted in decreased or increased OXPHOS, respectively, revealing longer mitochondria favor oxphos in TNBC cells. Using TNBC cell lines and an in vivo PDX model of residual TNBC, we found that sequential treatment with DNA-damaging chemotherapy, thus inducing mitochondrial fusion and OXPHOS, followed by MYLS22, a specific inhibitor of OPA1, was able to suppress mitochondrial fusion and OXPHOS and significantly inhibit regrowth of residual tumor cells. Our data suggest that TNBC mitochondria can optimize OXPHOS through OPA1-mediated mitochondrial fusion. These findings may provide an opportunity to overcome mitochondrial adaptations of chemoresistant TNBC.

Is the benefit of using adjuvant capecitabine in patients with residual triple-negative breast cancer related to pathological response to neoadjuvant chemotherapy?

Background Triple-negative-breast-cancer (TNBC) has a poor prognosis if pathologic complete response (pCR) cannot be achieved after receiving neoadjuvant chemotherapy (NAC). The group of patients that benefit most from adjuvant capecitabine remains unclear. Materials and Methods We collected data from 218 consecutive patients who had previously received NAC and operated for TNBC from eight cancer centers. Data of 160 patients without PCR was included in the statistical analysis. Pathologic response to NAC was defined into two groups as having good-pathologic response (MillerPayneGrading (MPG) IV-III) or poor-pathologic response (MPG I-II). The histopathological characteristics of patients were compared in regard to adjuvant capecitabine usage. Results Univariate-analysis revealed that age, histological subtype, clinical stage, size of tumor, number of lymph-nodes, menopausal status, pathological T and N stage, were significantly different between two groups. In multivariate-analysis, menopausal status (p=0.043) and residual tumor size (p<0.001) were found to be independent prognostic factors for pathological response. The hazard ratio for disease recurrence and death in the poor responsive group with adjuvant capecitabin was 2.94 (95% confidence interval (CI), 1.21 to 7.10; p=0.016) and 4.080 (95% CI, 1.22 to 13.64; p=0.022) respectively. DFS (p=0.58) and OS (p=0.89) improvements with adjuvant capecitabine were not demonstrated in good response groups. Conclusion This multicenter study suggested that only the poor responsive group to NAC achieved benefit from adjuvant capecitabine. Postmenopausal status and residual tumor size were related to poor prognosis.