Biology Of Triple-negative Breast Cancer Research Articles

Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies

Triple-negative breast cancer (TNBC) poses significant challenges in oncology due to its aggressive nature, limited treatment options, and poorer prognosis compared to other breast cancer subtypes. This comprehensive review examines the therapeutic and diagnostic landscape of TNBC, highlighting current strategies, emerging therapies, and future directions. Targeted therapies, including PARP inhibitors, immune checkpoint inhibitors, and EGFR inhibitors, hold promise for personalized treatment approaches. Challenges in identifying novel targets, exploring combination therapies, and developing predictive biomarkers must be addressed to optimize targeted therapy in TNBC. Immunotherapy represents a transformative approach in TNBC treatment, yet challenges in biomarker identification, combination strategies, and overcoming resistance persist. Precision medicine approaches offer opportunities for tailored treatment based on tumor biology, but integration of multi-omics data and clinical implementation present challenges requiring innovative solutions. Despite these challenges, ongoing research efforts and collaborative initiatives offer hope for improving outcomes and advancing treatment strategies in TNBC. By addressing the complexities of TNBC biology and developing effective therapeutic approaches, personalized treatments can be realized, ultimately enhancing the lives of TNBC patients. Continued research, clinical trials, and interdisciplinary collaborations are essential for realizing this vision and making meaningful progress in TNBC management.

Abstract PO1-03-08: Association of patient-reported triple-negative breast cancer (TNBC) knowledge with clinical trial participation

Abstract Background: Patients with TNBC are highly encouraged to participate in clinical trials given the lack of targeted treatment options for this breast cancer subtype. Yet little is known regarding barriers to trial participation in this population, including the impact of patients’ understanding about TNBC biology. We examined whether disease knowledge and other patient-level factors were associated with TNBC patients’ participation in trials. Methods: From a multicenter, prospective cohort study of patients enrolled from 2019-present with newly diagnosed TNBC (ER/PR ≤10% also eligible), we identified those with stage I-III tumors who completed at least one survey. Surveys assessed demographics, TNBC knowledge, risk perceptions, and participation in clinical trials. Patients were assigned to Cohort A if surgery was the first intervention and Cohort B if neoadjuvant therapy was given. Medical records were reviewed to verify the accuracy of tumor characteristics reported by patients. Data was summarized with descriptive statistics and logistic regression was used to identify factors associated with trial participation. Results: Of the 137 patients included, median age was 56 years (IQR 46-63), 104 (82%) were non-Hispanic White, 10 (8%) Black, 5 (4%) Hispanic. and 110 (86%) had at least some college education. Overall, 55 (41%) had stage I tumors, 65 (48%) stage II, and 14 (10%) stage III. Among 116 patients with available clinical trial participation data, 55 (47%) reported trial participation, 59 (51%) reported no trial participation, and 2 (2%) were unsure. The majority (36/55, 65%) of trial participants were in Cohort B. Among 129 patients with TNBC knowledge data, 82 (64%) and 73 (57%) correctly reported their tumor stage and grade, respectively. Most (104/129, 81%) knew TNBC was defined as ER/PR/HER2-negative, but only 16% (21/128) knew the ER/PR-negative cut off was ≤1%. Of 98 patients with risk perception data, 30 (31%) estimated their likelihood of recurrence within the next 5 years as 0%, 60 (61%) between 10-50%, and 8 (8%) between 60-100%. When asked if TNBC patients who remain cancer-free after 3 years will most likely not experience recurrence, 44 (45%) said “True,” 13 (13%) said “False,” and 40 (41%) were unsure. On univariate analysis, trial participation was less likely in Cohort A patients (OR 0.42, 95% CI 0.20 – 0.89, P=0.02) and more likely in stage II patients (vs. stage I, OR 2.43, 95% CI 1.09 – 5.39, P=0.03). On multivariable analysis, patients with at least some college education had higher odds of trial participation compared to patients with a college degree or higher (OR 3.21, 95% CI 1.11 – 9.28, P=0.03). No associations were found for other factors, including TNBC knowledge. Conclusions: About half of TNBC patients surveyed reported participating in clinical trials. Most of these patients were undergoing neoadjuvant therapy, likely reflective of greater study availability in this setting. While TNBC knowledge was not significantly associated with trial participation in this small sample, a considerable number of patients reported their tumor characteristics incorrectly and/or appeared to underestimate their recurrence risks. This highlights the need for enhanced informational support for TNBC patients during treatment decision-making. More research is needed to understand barriers to trial participation in this population to leverage patient engagement and accelerate progress towards more effective treatments for TNBC. Citation Format: Megan Tesch, Noah Graham, Sean Ryan, Melissa Hughes, Eileen Wrabel, Nadine Tung, Steve Lo, Thomas Fynan, Meredith Faggen, Natalie Sinclair, Maria Constantinou, Sarah Sinclair, Nabihah Tayob, Nancy Lin, Ann Partridge, Eric Winer, Sara Tolaney, Ana Garrido-Castro. Association of patient-reported triple-negative breast cancer (TNBC) knowledge with clinical trial participation [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 PO1-03-08.

Abstract PO2-03-07: Immune Landscape in PD-L1-positive and TROP2-positive Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) tends to be more aggressive, and more likely to recur than other subtypes of breast cancer, and patients with metastatic TNBC have a poor prognosis. The recent approvals and data of pembrolizumab (anti-PD-1 inhibitor) in combination with chemotherapy in advanced-metastatic and early high-risk TNBC, and sacituzumab govitecan (an ADC that targets the tumor cell surface antigen TROP2 coupled with the irinotecan metabolite SN-38) in metastatic TNBC, has shed light on some of the immune and cancer signaling associated with TNBC. Although exciting progress has been made in the treatment of TNBC, there are still important gaps to fill to understand the biology of TNBC and identify additional therapies. Materials and Methods: We identified a total of 1500 patients whose tumors were negative for the expression of ER and HER2 receptors by gene array. PD-L1 and TROP2 expression data were available for 802 early TNBC patients, of whom 657 were treated with adjuvant chemotherapy. A comprehensive identification and analysis of immune-related genes (n= 1169) was conducted. Mann-Whitney test comparing the gene expression for all immune related-genes was evaluated in patients expressing PD-L1 and TROP2 at low and high expression levels. Immune gene modules resembling key immune gene signaling were analyzed in all subgroups identified. Fold changes and Mann-Whitney P values were calculated in each subgroup. Results: Patients were stratified based on high and low expression levels of PD-L1 and TROP-2 mRNA. PD-L1 highly expressing (PD-L1+) tumors showed a marked difference in immune-related genes as compared to PD-L1 low-level tumors (PD-L1-) with PD-L1+ tumors demonstrating a significantly higher proportion of correlated immune genes (CXCL9/10/11, IFN-γ, CCL5 and STAT1). TROP2 highly and low expressing tumors (TROP2+ and TROP2-, respectively) showed a relatively limited difference in terms of immune-related gene expression with key immune-related genes having statistical differential expression in the two subgroups. TROP2+ tumors showed a high presence of several Mucin family gene members (MUC1, -5AC, -4). In addition, CLDN 4, VTCN1, and MET were among the key immune genes significantly expressed in TROP2+ tumors (P = 5.73E-20; P = 6.2E-13, P = 2.1E-11). Overall, PD-L1+ tumors and TROP2+ tumors showed an immune suppressive genomic landscape but were potentially regulated by different signaling. Of note, tumors with very high expression of PD-L1 showed an inverse correlation with VTCN1 gene expression. Conclusions: This preliminary analysis confirmed that only a limited number of early TNBC highly expressed PD-L1 and that a different immune suppressive landscape for PD-L1± and TROP2± tumors exists. In addition, our data suggest that early TNBC cases lacking PD-L1 might escape immune surveillance by virtue of the upregulation of key alternate signaling. Ongoing efforts investigating the expression of such markers on stroma/epithelial tumor components will help to clarify their biological, clinical, and potential therapeutic role in TNBC. Citation Format: Balazs Gyorffy, Libero Santarpia. Immune Landscape in PD-L1-positive and TROP2-positive 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 PO2-03-07.

Abstract PO3-03-10: Race and neoadjuvant treatment of triple negative breast cancer (TNBC) in the US community oncology setting

Abstract Background: TNBC is an aggressive subtype of breast cancer with limited targeted therapies. Black women have twice the incidence of TNBC compared to White women and within TNBC, Black women have worse outcomes than White women. Differences in both tumor biology of TNBC and social determinants of health (SDOH) play a role in observed disparities. The focus of this study is to evaluate SDOH factors associated to differences in the use of neoadjuvant chemotherapy (NC) in Black and White women in the US community oncology setting. Methods: This study was a retrospective, observational, cross-sectional design and used iKnowMed SM EHR data from the The US Oncology Network. Patients diagnosed with TNBC between 03/31/2017 and 09/30/2021 with stages II-III disease of tumor size ≥ 2cm (T2 or higher) were included. The index date was date of TNBC diagnosis and records were assessed from 6 months pre- to 6 months post-diagnosis for NC initiation. Univariable and multivariable logistic regression was conducted to evaluate impact of self-reported race on NC. Age, stage, BMI, insurance, area deprivation index (ADI), size of practice represented by physician count and geographical region, were studied in their mediating and moderating effects1 on the relationship between race and NC treatment. Results: Of the 3321 patients with TNBC identified in this study, 1969 self-reported white and 494 self-reported black (80% and 20% respectively). In multivariable regression accounting for all variables, Black race (OR = 1.57, 95% CI [ 1.02, 2.44], p=0.04), younger age, more advanced stage, obesity, non-Medicaid insurance, and West region, were all found to be positively associated with use of NC. Higher physician count was nominally associated, (p = 0.07). ADI was not found to be associated to NC. Mediator and moderator analysis for the relationship between race and NC showed that only stage and ADI variable inclusion in the model are required for the positive association between black race and NC. This is driven by a significant interaction between ADI and stage (p = 0.027) which differed for Black and White women. Mainly, for Black women ADI is positively associated to NC treatment in stage IIA, but negatively associated in all other stages (interaction term, p = 0.033). For White women, ADI is negatively associated to NC treatment in all stages. Only Black women with stage IIA tend to be treated more instead of less with NC in areas of greater deprivation (greater ADI). BMI presents nominal interactions with both race and stage, where obesity was more strongly associated with NC treatment in Black women (p = 0.088) and in stage IIA (p = 0.086). All other variables presented association to NC treatment without mediation or moderation of the race effect and without detectable differences across stages. Conclusions: Black women with stage IIA appear to be a special subgroup of TNBC patients for whom treatment with NC increases with ADI. Increased ADI generally results in less standard of care treatment; this is observed in this study for White women overall and for Black women in stages > IIA. Black women in areas of greater deprivation with stage IIA disease, may be perceived to be presenting with more aggressive disease and thus offered NC preferentially. This result lends support to the hypothesis that young black women present with a distinct, more aggressive subtype of TNBC in the early stages. Mediator and moderator analyses are important tools in elucidating the relationships between factors underlying racial disparities in both care and outcomes. 1. Hayes AF, Rockwood NJ. Regression-based statistical mediation and moderation analysis in clinical research: Observations, recommendations, and implementation. Behav Res Ther. 2017 Nov;98:39-57. Odds ratios for multivariable analysis –insert figure image– Race, stage and ADI –insert figure image– Race and BMI in stage IIA –insert figure image– Citation Format: Paola Raska, Joseph Dye, Nicholas J Robert, Angel Kidd, Michael Danso. Race and neoadjuvant treatment of triple negative breast cancer (TNBC) in the US community oncology setting [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 PO3-03-10.

Abstract PO4-24-01: Comprehensive Molecular and Immunological Characterization of Invasive Ductal Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease and characterized by poor outcomes with a lack of targeted therapies. A comprehensive analysis of the molecular and immune landscape of invasive ductal TNBC can help improve our understanding of TNBC biology and identify novel targets and/or pathways for better management of this disease. Here, we characterized the molecular and immune signature of invasive ductal (ID) TNBC. Methods: 13,036 BC samples (ID TNBC, n=392; ID non-TNBC, n=927) were analyzed by NGS (592, NextSeq; WES, NovaSeq), WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). A total of 10 pro-apoptotic (BAX, BAK1, BID, BAD, BIK, BCL2L11, BMF, HRK, PMAIP1, BBC3) and 6 anti-apoptotic (BCL2, BCL2L1, BCL2L2, MCL1, BCL2A1, BCL2L10) BCL2 family genes were analyzed. Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Real world overall survival (OS) and treatment-associated survival was extracted from insurance claims and calculated from tissue collection or treatment start to last contact using Kaplan-Meier estimates. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: ID TNBC had a higher frequency of TP53, RB1, NF1, PIK3R1, NOTCH1, CREBBP, BRCA1, FANCI, and HRAS mutations (Table 1), NOTCH2 (4.3% vs 0.47%), EGFR (3.4% vs 0%), NFIB (4% vs 0.6%), MYB (3.5% vs 0.5%), CCNE1 (4.4% vs 1.1%) and AKT2 (2.4% vs 0.3%) copy number alterations, and NOTCH2 (1.6% VS 0.2%) fusion (all p < 0.05) compared to invasive ductal non-TNBC. Analysis of inferred immune cell infiltrates showed that ID TNBC had increased infiltration of Tregs (2% vs 1.7%), DC (3.2% vs 2.4%), CD8 T cells (0.5% vs 0.1%), and M1 macrophages (M) (3.4% vs 2.9%), but decreased infiltration of B cells (4.5% vs 6%) and M2M (2.9% vs 4.5%) (all p < 0.05). ID TNBC had increased T cell inflamed score (23 vs -9, p < 0.05), IFNy score (-0.24 vs -0.34, p < 0.05), MHC class I genes (HLA-A, HLA-B, TAP1, TAP2, FC: 1.1-1.5, all p < 0.05), immune checkpoint genes (CD274, PDCD1, CTLA4, PD-L2, FOXP3, IDO, FC: 1.1-2, all p < 0.05) and PD-L1 protein expression (SP142: 49.8% vs. 28.4%; 22c3: 41.7% vs. 16.8%, all p < 0.05). ID TNBC had differential expression of BCL2 family genes (upregulation: BAK1, BID, MCL1, BCL2A1, BCL2L10, FC: 1.1-2.0; downregulation: BAD, BIK, BBC3, BCL2, BCL2L1, BCL2L2, FC: 1.2-2.8, all p < 0.05) compared to invasive ductal non-TNBC. ID TNBC was associated with worse OS compared to ID non-TNBC (mOS: 24.5 vs 54.6 months; HR: 0.5, 95% CI 0.47-0.57; p < 0.00001) but trend towards better survival with pembrolizumab (mOS: 29.4 vs 8.8 month; HR: 0.67, 95% CI 0.28-1.5; p=0.3) treatment. No significant OS difference was noted for by high vs. low pro and anti-apoptotic BCL2 genes except for anti-apoptotic BCL2A1 (higher expression associated with better OS (mOS: 5.7 months, HR: 0.78, 95% CI 0.6-0.99; p=0.047). Conclusion: These data indicate that ID TNBC is associated with distinct mutational profile compared to non-TNBC, has increased T cell inflamed score, IFNy score, MHC class I and immune checkpoint gene expression, and differential immune cell infiltration. Interestingly, TNBC was associated with increased M1 and decreased M2M. There is evidence to suggest that transcriptomically defined M1 high tumors are clinically aggressive and have worse OS in TNBC. BCL2 family genes are not prognostic for TNBC outcomes except BCL2A1, which needs further prospective validation. Table 1: Mutation frequency in invasive ductal TNBC and invasive ductal non-TNBC Citation Format: Pooja Advani, Sachin Deshmukh, Sharon Wu, Jacob Andring, Joanne Xiu, Alex Farrell, Jose Leone, Priya Jayachandran, Stephanie Graff, Matthew Oberley, George Sledge Jr, Asher Chanan-Khan. Comprehensive Molecular and Immunological Characterization of Invasive Ductal 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 PO4-24-01.

PYCR3 modulates mtDNA copy number to drive proliferation and doxorubicin resistance in triple-negative breast cancer

Triple-negative breast cancer (TNBC) poses significant challenges in treatment due to its aggressive nature and limited therapeutic targets. Understanding the underlying molecular mechanisms driving TNBC progression and chemotherapy resistance is imperative for developing effective therapeutic strategies. Thus, in this study, we aimed to elucidate the role of pyrroline-5-carboxylate reductase 3 (PYCR3) in TNBC pathogenesis and therapeutic response. We observed that PYCR3 is significantly upregulated in TNBC specimens compared to normal breast tissues, correlating with a poorer prognosis in TNBC patients. Knockdown of PYCR3 not only suppresses TNBC cell proliferation but also reverses acquired resistance of TNBC cells to doxorubicin, a commonly used chemotherapeutic agent. Mechanistically, we identified the mitochondrial localization of PYCR3 in TNBC cells and demonstrated its impact on TNBC cell proliferation and sensitivity to doxorubicin through the regulation of mtDNA copy number and mitochondrial respiration. Importantly, Selective reduction of mtDNA copy number using the mtDNA replication inhibitor 2′, 3′-dideoxycytidine effectively recapitulates the phenotypic effects observed in PYCR3 knockout, resulting in decreased TNBC cell proliferation and the reversal of doxorubicin resistance through apoptosis induction. Thus, our study underscores the clinical relevance of PYCR3 and highlight its potential as a therapeutic target in TNBC management. By elucidating the functional significance of PYCR3 in TNBC, our findings contribute to a deeper understanding of TNBC biology and provide a foundation for developing novel therapeutic strategies aimed at improving patient outcomes.

Abstract A060: Organoid Culture as a Unique Resource for Studying Aggressive Triple Negative Breast Cancer in African American

Abstract Introduction Triple negative breast cancer (TNBC) among women with African ancestry has been shown to be more aggressive than in women of European ancestry. However, the root cause for this disparity is not fully understood. In our previous studies, we show that the gene expression in the breast cancer stem cells of TNBC tumors was differential based on Western sub-Saharan ancestry. To study the role of African ancestry in the biology of TNBC, we have developed patient-derived organoids (PDO) from African (Ghanaian) and African American tumors that will be available for research. Organoid culture has the capacity to mimic the physiological tissue organization and functionality and has been used as an invaluable tool for disease modeling and drug discovery. Objective The objective is to develop and characterize PDOs based on African TNBC that will serve as a renewable source of African tumors for breast cancer research. Methods Through our international collaboration called Precision Medicine for Aggressive Breast Cancers (PMABC), we obtained fresh patient tumors from continental Africa (Ghana) and African American tumors from Henry Ford Health. PDOs were developed form both primary tumors and patient-derived xenografts (PDX). Tissues were processed using the Miltenyi Gentle Mac. The cells were seeded in a 12-well plate coated with Matrigel. Developed organoids are characterized using single cell RNA sequencing as well as 10X spatial sequencing Results We have successfully developed organoids using frozen tissues from both West African and African American breast patients. We have successfully established four (4) organoid lines from individual primary breast cancer tissues and one PDX. The organoids are passaged after every 7-14 days, and the highest passage so far is passage number 12 for the organoids from primary tissues and passage number 15 for the PDXs. We are in the process of characterizing the developed organoids using single-cell assay in comparisons to their primary tumor of origin. Conclusion Establishment of organoids has helped us have a renewable source of tumor for studying the aggressive TNBC among Women with African ancestry. We aim to use the organoids to identify tumor biomarkers for treating aggressive TNBC that disproportionately affects women of western sub Saharan ancestry. Citation Format: Moses Kamita, Kurt Fernando, Sylvester Antwi, Forster Amponsah-Manu, Josephine Nsaful, Kafui Akakpo, Jessica Bensenhaver, Kwabena Agbedinu, Michael Nortey, Nelson Affram, Mohammed Sheriff, Cassandra Mills, Alex Mremi, Jieoma Aja, Moses Dokurugu, Haythem Ali, Eleanor Walker, Max Wicha, Evelyn Jiagge. Organoid Culture as a Unique Resource for Studying Aggressive Triple Negative Breast Cancer in African American [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 A060.

Schlafen Family Intra-Regulation by IFN-α2 in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) has a poor prognosis and no targeted therapy for treatment. The Schlafen gene family, particularly SLFN12, critically mediates TNBC biology. Higher expression of SLFN12 correlates with decreased TNBC viability and increased chemosensitivity and patient survival, yet no treatment is known to upregulate SLFN12 in TNBC. We hypothesized that Interferon-α (IFN-α2) upregulates SLFN12 in TNBC, subsequently reducing cell viability. We utilized short hairpin adenovirus to knockout SLFN12 (AdvShSLFN12) in MDA-MB-231, Hs-578T, and BT-549 TNBC cells. Cells were treated with AdvShSLFN12 and IFN-α2. After treatment, TNBC cell viability, SLFN family mRNA, and protein expression were analyzed. Treating TNBC cells with IFN-α2 increased SLFN12 expression and reduced cell viability. However, when AdvShSLFN12 knocked down SLFN12 during IFN-α2 treatment, TNBC cell viability was still reduced. We, therefore, investigated the potential involvement of other SLFN members IFN-α2 effects on cell viability. IFN-α2 increased SLFN5, SLFN12-Like, and SLFN14 but not SLFN11 or SLFN13. During AdvShSLFN12 + IFN-α2 treatment, the expressions of SLFN5, SLFN12-Like, and SLFN14 further increased. However, when siRNA knocked down SLFN5, SLFN12-Like, and SLFN14, the IFN-α2 reduction in viability was blunted. Although the interpretation of these results may be limited by the potential interactions between different siRNAs, these data suggest a complex regulatory signaling cascade among SLFN family members. Targeting this cascade to manipulate SLFN levels may, in the future, offer the potential to manipulate the chemosensitivity of TNBC tumors.

THU489 The Role Of Noncoding Genes With The Bidirectional Promoter In Triple-negative Breast Cancer

Abstract Disclosure: B. Yang: None. M. Sedano: None. M.V. Jimenez: None. E.I. Ramos: None. S. Gadad: None. Breast cancer is the second leading cause of cancer mortality in women after lung cancer. Breast cancer is grouped into different molecular subtypes; triple-negative breast cancer (TNBC) accounts for 20%. TNBC is a highly aggressive histologic subtype; the lack of unique therapeutic targets makes it harder to treat. Recent studies have implicated genes involved in cancers that are transcribed using a process known as divergent transcription. The expression of these genes is tightly regulated; however, many escape regulation and become aberrantly expressed in tumors. Interestingly, our genomic analysis suggests that several of these genes encode noncoding transcripts. Analysis of transcriptome from different tissue types, including cancer and normal, revealed that many are upregulated in various cancers. Selected divergent transcript, such as lncRNA67, has been completely characterized (transcription start and stop site, 5’ cap, polyA tail, and exon/intron structure) and cloned. In functional assays, overexpression of lncRNA67 regulates gene expression, cell proliferation, and tumor growth. Our molecular analyses indicate that lncRNA67 plays a vital role in triple-negative breast cancer biology. Collectively, our results suggest that divergent transcripts are an integral component of cancer biology and present a new repertoire of diagnostic and potential therapeutic targets. Presentation: Thursday, June 15, 2023

MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. This Myc;Ptenfl model develops heterogeneous triple-negative mammary tumors that display histological and molecular features commonly found in human TNBC. Our research involves deep molecular and spatial analyses on Myc;Ptenfl tumors including bulk and single-cell RNA-sequencing, and multiplex tissue-imaging. Through comparison with human TNBC, we demonstrate that this genetic mouse model develops mammary tumors with differential survival and therapeutic responses that closely resemble the inter- and intra-tumoral and microenvironmental heterogeneity of human TNBC, providing a pre-clinical tool for assessing the spectrum of patient TNBC biology and drug response.

Abstract 2147: Decoding the natural biology of triple-negative breast cancer and response to chemotherapy by single-cell transcriptomics

Abstract Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that lacks the expression of estrogen receptor (ER), progesterone receptor (PR) and HER2 and therefore have limited hormonal treatment options. Neoadjuvant chemotherapy (NAC) is backbone of treatment for TNBC, and about 50% of patients respond well leading to pathological complete response (pCR). However, the remaining patients develop resistance to NAC and progress to metastatic disease and poor survival in 1-2 years after the initial treatment. Previous studies have performed bulk RNA expression profiling of TNBC patients and identified 5-6 subgroups of patients, however these studies could not resolve expression programs at single cell resolution to distinguish between the tumor cells and different components of the tumor microenvironment (TME). Here we performed scRNA-seq of pre-treatment fresh core biopsy tissue samples from TNBC patients in the ARTEMIS clinical trial and compared these data between pCR and non-pCR patients to identify programs associated with response to NAC. We also compared these data to scRNA-seq data from patients with disease-free breast tissue to understand the basic biology of TNBC and identify cell types that are reprogrammed in malignant disease. Using the single cell tumor cell data, we identified 4 archetypes of TNBC which represent patient-level intertumor expression programs: luminal secretory-like (LS), basal/luminal-like (BL), immunoregulatory (IM), and luminal androgen receptor (LAR). Notably, the archetype BL was associated with non-pCR, while IM was associated with pCR. We further identified 13 metatraits, which are unique intratumoral expression programs that are shared across patients. Across the cancer cells, we identified 13 metatraits such as cell cycling, stress, hypoxia, interferon response, HLA, partial epithelial-mesenchymal transition, and endoplasmic reticulum stress, many of which corresponded to NAC response. In the immune compartment, we found 15 myeloid cell states, 14 T/NK cell states, and 6 B cell states, several of which corresponded to pCR/non-pCR. Similarly, in the stromal compartment, there were 4 fibroblast cell states, 4 pericyte cell states, and 7 endothelial cell subtypes, of which several cell states were associated with NAC response. Overall, these data report the natural biology of TNBC patients and malignant cell states that are reprogrammed in malignant disease, as well as their correspondence to NAC response, providing new data to predict which TNBC patients are likely to respond to chemotherapy. Citation Format: Tapsi Kumar, Yiyun Lin, Yun Yan, Shanshan Bai, Jianzhuo Li, Tuan Tran, Min Hu, Elizabeth Ravenberg, Maia Rauch, Alyson Clayborn, Alastair Thompson, Lei Huo, Stacy Moulder, Clinton Yam, Nicholas Navin. Decoding the natural biology of triple-negative breast cancer and response to chemotherapy by single-cell transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2147.

Abstract P1-08-04: Therapeutic Advances in Metastatic Triple-Negative Breast Cancer: Identifying and Reducing Clinician Knowledge Gaps

Abstract Background: Characterization of the aggressive biology of triple-negative breast cancer (TNBC), defined by its lack of estrogen receptor, progesterone receptor, and human epidermal growth factor 2 (HER2) expression, has led to the development of more effective treatments for patients, but research indicates that clinicians face challenges in maintaining a working knowledge of evolving data. This study was conducted to determine what learning gaps exist in the area of therapeutic advances in TNBC and to investigate whether an online, case-based continuing medical education (CME)/nursing continuing professional development (NCPD)–approved activity could address gaps in clinicians’ knowledge regarding the personalized care of patients with metastatic TNBC. Methods: The CME/NCPD-approved live webinar series titled Metastatic Triple-Negative Breast Cancer: Applying Treatment Advances to Personalized Care was presented by Sara A. Hurvitz, MD, FACP, on July 13 and July 15, 2021, and was made accessible as a CME/NCPD-approved enduring webinar archive starting on July 23, 2021. Learners participated in a 1-hour activity that highlighted emerging therapeutic targets in TNBC, with an emphasis on current challenges and new opportunities in the management of metastatic disease. Learners completed a repeated-pairs pre- and post-activity assessment consisting of case-based questions that gauged their ability to apply emerging data to clinical decision making. Baseline knowledge gaps and subsequent learning gains were calculated based on percentages of learners obtaining correct responses on the pre- and post-activity assessments. Significance was assessed using a chi-squared test. In addition, learners reported self-perceived gains in confidence and competence using 5-point Likert scale questions. Results: As of June 28, 2022, 811 clinicians had completed the activity for credit; 62 learners participated in the live webinar, while 749 participated in the online enduring activity. Baseline assessment data revealed gaps in knowledge regarding emerging actionable targets and management of treatment-related adverse events (Table 1). Learners participating in the enduring activity scored an average of 43% on pretest topics; after completing the activity, the posttest average rose to 92%. The activity resulted in significant gains in knowledge and competence related to these topics, with P < 0.0001 for all learning gains. Upon completion of the activity, 86% of learners self-reported that knowledge acquired from this activity would be utilized to improve the outcomes of their patients, and 86% of learners self-reported that based on the information learned during the activity, they felt more confident in treating patients with metastatic TNBC. Conclusions: These data indicate that a substantial knowledge gap exists regarding the latest developments in the treatment of metastatic TNBC. They also demonstrate that online, case-based CME/NCPD-approved activities can result in statistically significant improvements in clinicians’ knowledge of therapeutic advances and management of treatment-related adverse events for patients with metastatic TNBC. Acknowledgements: This activity was supported by an independent educational grant from Merck. Table 1. Baseline Knowledge Gaps and Post-Activity Learning Gains. Citation Format: Elizabeth J. Heller, Keira Smith, Sarah L. Williams. Therapeutic Advances in Metastatic Triple-Negative Breast Cancer: Identifying and Reducing Clinician Knowledge Gaps [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 P1-08-04.

Disruption of estrogen receptor beta's DNA binding domain impairs its tumor suppressive effects in triple negative breast cancer.

Triple negative breast cancer (TNBC) is an aggressive sub-type of the disease which accounts for a disproportionately high percentage of breast cancer morbidities and mortalities. For these reasons, a better understanding of TNBC biology is required and the development of novel therapeutic approaches are critically needed. Estrogen receptor beta (ERβ) is a reported tumor suppressor that is expressed in approximately 20% of primary TNBC tumors, where it is associated with favorable prognostic features and patient outcomes. Previous studies have shown that ERβ mediates the assembly of co-repressor complexes on DNA to inhibit the expression of multiple growth promoting genes and to suppress the ability of oncogenic transcription factors to drive cancer progression. To further elucidate the molecular mechanisms by which ERβ elicits its anti-cancer effects, we developed MDA-MB-231 cells that inducibly express a mutant form of ERβ incapable of directly binding DNA. We demonstrate that disruption of ERβ's direct interaction with DNA abolishes its ability to regulate the expression of well characterized immediate response genes and renders it unable to suppress TNBC cell proliferation. Loss of DNA binding also diminishes the ability of ERβ to suppress oncogenic NFκB signaling even though it still physically associates with NFκB and other critical co-factors. These findings enhance our understanding of how ERβ functions in this disease and provide a model system that can be utilized to further investigate the mechanistic processes by which ERβ elicits its anti-cancer effects.

Abstract C051: Unraveling the biology of TNBC in African American women through the WHITNEY study

Abstract Cancer disparities arise from structural racism in the United States, which affects overall standard of living due to unequal access to crucial resources. Barriers in access to clinical care among under-served populations in combination with a vast underrepresentation at a scientific research level further perpetuate inequalities in cancer treatment. Specifically, Black women in the US are approximately twice as likely as Caucasian women to die of Triple-Negative Breast Cancer (TNBC), a particularly aggressive breast cancer subset, lacking expression of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor-2. Our previous work and that of others has shown racial differences in TNBC tumor biology, with preference of basal-like subtypes in African American (AA) women. Herein, we present the Women’s Health Initiative for Triple-Negative Breast Cancer Equity (WHITNEY) study, a first of its kind, coordinated effort between Massachusetts General Hospital, and Boston Medical Center, the largest safety-net hospital in New England. The WHITNEY study seeks to understand factors contributing to biological differences and outcome of TNBC diagnoses in AA women. Response to neoadjuvant chemotherapy (NACT) response is a strong predictor of TNBC outcomes and failure to achieve a pathological complete response (pCR) in the breast following NACT is associated with a high probability of metastatic relapse. As Black women with TNBC have lower pCR rates, WHITNEY has collected pre-treatment biopsies from AA and other TNBC patients undergoing NACT to understand actionable insights into the biological differences in TNBC. Our prior published work has suggested that intratumoral heterogeneity is greater in TNBCs among AA patients than others, and that epigenetic silencing of key tumor suppressors is selectively increased in these TNBCs. Core needle baseline biopsies were obtained from consented patients diagnosed with TNBC at either MGH or BMC. We utilized single-cell RNA sequencing, spatial transcriptomics, genomic and epigenetic profiling to characterize minor cell subpopulations that drive poor outcomes among African American TNBC patients. Here, we outline our preliminary tissue collection, processing and analysis methods used in the WHITNEY study to better understand the biology of TNBC in African American women. Citation Format: Malalage N. Peiris, Emma Kelly, Christina Ennis, Kiana Mahdaviani, Aylin Dedeoglu, Adrian Ilinski, Esther Rheinbay, Ruben Dries, Naomi Ko, Leif Ellisen. Unraveling the biology of TNBC in African American women through the WHITNEY study [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C051.

Abstract C054: Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines

Abstract African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remain underexplored. Using ATAC-sequencing, we characterized differences in chromatin accessibility between EA-derived versus AA-derived breast cancer cell lines across a range of breast cancer subtypes. Interestingly, our principal component analysis of the top 50,000 peaks with the most variance revealed separation of chromatin profiles by genetic ancestry specifically in TNBC cell lines (N=10). Digital footprinting analysis of differentially open chromatin regions using TOBIAS revealed significant differences in transcription factor (TF) binding by ancestry (61 TFs with a differential binding score > 0.25 or < -0.25 and FDR < 0.01). AA TNBC cell lines exhibited increased binding of transcription factors associated with epithelial-to-mesenchymal transition (ZEB1, SNAI1, GRHL2), cancer stemness and chemotherapeutic resistance (TFAP2C, NRF1), and others such as KAISO, whose aberrant expression has been previously linked to a distinct biology and poor outcomes in AA breast and prostate cancer patients. Pathway analysis of genes located within promoters of differentially open chromatin regions reveals enrichment of the following KEGG pathways in AA TNBC cells: inflammatory mediator regulation of TRP channels (p-adj = 0.009), Hippo signaling (p-adj = 0.006), Wnt signaling (p-adj = 0.031), and Rap-1 signaling (p-adj = 0.046). Together, these data reveal a differential chromatin landscape associated with the aberrant activity of critical TFs and downstream gene expression changes that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. Citation Format: Alexandra R. Harris, Vishal Koparde, Gatikrushna Panigrahi, Maeve Bailey-Whyte, Tiffany Dorsey, Stefan Ambs. Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C054.

A novel ribociclib derivative WXJ-103 exerts anti-breast cancer effect through CDK4/6.

The triple-negative breast cancer (TNBC) subtype is the most aggressive type of breast cancer with a low survival prognosis and high recurrence rate. There is currently no effective treatment to improve it. In this work, we explored the effect of a synthetic compound named WXJ-103 on several aspects of TNBC biology. The human breast cancer cell lines MDA-MB-231 and MCF-7 were used in the experiments, and the cell viability was detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method, and the cell migration and invasion abilities were detected by wound healing assay and Transwell invasion assay. Cell cycle and apoptosis experiments were analyzed by flow cytometry, and protein levels related to cyclin-dependent kinase (CDK) 4/6-cyclin D-Rb-E2F pathway were analyzed by western blotting. Then, in-vivo experiments were performed to determine the clinical significance and functional role of WXJ-103. The results show that WXJ-103 can inhibit the adhesion, proliferation, migration, and invasion of TNBC cells, and can arrest the cell cycle in G1 phase. The levels of CDK4/6-cyclin D-Rb-E2F pathway-related proteins such as CDK6 and pRb decreased in a dose-dependent manner. Therefore, the antitumor activity of WXJ-103 may depend on the inhibition of CDK4/6-cyclin D1-Rb-E2F pathway. This research shows that WXJ-103 may be a new promising antitumor drug, which can play an antitumor effect on TNBC and provide new ideas for the treatment of TNBC.

Myricetin-induced apoptosis in triple-negative breast cancer cells through inhibition of the PI3K/Akt/mTOR pathway

Breast cancer is still a severe origin of malignant demise in females, and its prevalence is rising worldwide. Triple-negative breast cancer (TNBC) is a diversified aggressive breast tumor distinguished by inadequate prognosis, early recurrence, high invasion, and extremely metastasized disease. Chemotherapy is being used to treat it; however, it has low efficacy. On the other hand, with the growing number of corroborations on subtypes of TNBC and molecular biology of tumors, significant advancement in TNBC targeted treatment has been made. Myricetin (MYR), a polyhydroxyflavonol compound widely found in nature, has been shown to possess anticancer effects in various cancers. Though, the mechanisms and impacts of MYR on metastasis of TNBC remain unclear. Early and late apoptotic cell death and cell proliferation inhibition were observed in MYR-treated TNBC cells. MYR modulated cell cycle, pro-angiogenic, and invasion effects via the mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)/Protein kinase B (PKB/also known as AKT) signaling pathways. Moreover, it regulates the expression of MAPK, PI3K/AKT/mTOR, IκB/NF-κB, Hippo, STAT3, GSK-3β, Nrf2/HO-1, TLR, eNOS / NO, ACE, and AChE. Here, we review the anticancer effects of MYR for TNBC and target the PI3K/AKT/mTOR pathway as a therapeutic target for the fruitful treatment of TNBC to summarize MYR's therapeutic potential.

African Ancestry-Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent.

Our comprehensive ancestry quantification process revealed that ancestry-associated gene expression profiles in TNBC include population-level distinctions in immunologic landscapes. These differences may explain some differences in race-group clinical outcomes. This study shows the first definitive link between African ancestry and the TNBC immunologic landscape, from an African-enriched international multiethnic cohort. See related commentary by Hamilton et al., p. 2496. This article is highlighted in the In This Issue feature, p. 2483.

Triple-Negative Breast Cancer: A Review of Current Curative Intent Therapies.

Breast cancer is the most commonly diagnosed malignancy in women, with triple-negative breast cancer (TNBC) accounting for 10–20% of cases. Historically, fewer treatment options have existed for this subtype of breast cancer, with cytotoxic chemotherapy playing a predominant role. This article aims to review the current treatment paradigm for curative-intent TNBC, while also reviewing potential future developments in this landscape. In addition to chemotherapy, recent advances in the understanding of the molecular biology of TNBC have led to promising new studies of targeted and immune checkpoint inhibitor therapies in the curative-intent setting. The appropriate selection of TNBC patient subgroups with a higher likelihood of benefit from treatment is critical to identify the best treatment approach.

LncRNA-Based Classification of Triple Negative Breast Cancer Revealed Inherent Tumor Heterogeneity and Vulnerabilities.

Triple negative breast cancer (TNBC) represents a diverse group of cancers based on their gene expression profiles. While the current mRNA-based classification of TNBC has contributed to our understanding of the heterogeneity of this disease, whether such heterogeneity can be resolved employing a long noncoding RNA (lncRNA) transcriptome has not been established thus far. Herein, we used iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP) dimensionality reduction analysis on a large cohort of TNBC transcriptomic data (TNBC = 360, normal = 88) and classified TNBC into four main clusters: LINC00511-enriched, LINC00393-enriched, FIRRE-enriched, and normal tissue-like. Delving into associated gene expression profiles revealed remarkable differences in canonical, casual, upstream, and functional categories among different lncRNA-derived TNBC clusters, suggesting functional consequences for altered lncRNA expression. Correlation and survival analysis comparing mRNA- and lncRNA-based clustering revealed similarities and differences between the two classification approaches. To provide insight into the potential role of the identified lncRNAs in TNBC biology, CRISPR-Cas9 mediated LINC00511 promoter deletion reduced colony formation and enhanced the sensitivity of TNBC cells to paclitaxel, suggesting a role for LINC00511 in conferring tumorigenicity and resistance to therapy. Our data revealed a novel lncRNA-based classification of TNBC and suggested their potential utilization as disease biomarkers and therapeutic targets.