The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers

Micro-RNAs targeting the estrogen receptor alpha involved in endocrine therapy resistance in breast cancer

Endocrine therapy resistance (ETR) in breast cancer (BC) is a multicausal phenomenon with diverse alterations in the tumor cell interactome. Within these alterations, non-coding RNAs (ncRNAs) such as micro-RNAs (miRNAs) modulate the expression of tumor suppressor genes and proto-oncogenes, such as the ESR1 gene encoding estrogen receptor alpha (ERα). This work aims to review the effects of miRNAs targeting ERα mRNA and their mechanisms related to ETR in BC. A thorough review of the literature and an in silico study were carried out to elucidate the involvement of each miRNA, thus contributing to the understanding of ETR in BC.

Selective degradation of FGFR1/2 overcomes antiestrogen resistance in ER+ breast cancer with FGFR1/2 alterations

FGFR1 amplification and FGFR1/2 activating mutations have been associated with antiestrogen resistance in estrogen receptor-positive (ER+) breast cancer. However, there are no approved FGFR1-targeted therapies for breast cancers harboring these alterations. In this study, we investigated the selective degradation of FGFR1/2 using the proteolysis-targeting chimera (PROTAC) DGY-09-192 as a novel therapeutic strategy in ER + breast cancers harboring FGFR1/2 somatic alterations. Treatment of ER+/FGFR1-amplified breast cancer cells and patient-derived xenografts with DGY-09-192 resulted in sustained degradation of FGFR1 in a proteasome-dependent manner and suppressed downstream signal transduction. The combination of DGY-09-192 and the ERα degrader fulvestrant resulted in complete cell growth arrest and tumor regression of ER+/FGFR1-amplified patients-derived xenografts. In addition, we tested the effect of DGY-09-192 on breast cancer cells expressing FGFR1N546K and FGFR2K659E hotspot kinase domain mutations as well as ER-negative breast cancer cells harboring FGFR2 gene amplification. Treatment with DGY-09-192 resulted in the degradation of mutant FGFR1/2 and blocked mutant receptor-induced signal transduction and antiestrogen resistance. Collectively, our study suggests that degradation of FGFR1/2, in combination with antiestrogens, can be leveraged as a therapeutic strategy in ER + breast cancers harboring FGFR1/2 driver alterations.

Primary cilia and cancer: a tale of many faces

Cilia are microtubule-based sensory organelles which project from the cell surface, enabling detection of mechanical and chemical stimuli from the extracellular environment. It has been shown that cilia are lost in some cancers, while others depend on cilia or ciliary signaling. Several oncogenic molecules, including tyrosine kinases, G-protein coupled receptors, cytosolic kinases, and their downstream effectors localize to cilia. The Hedgehog pathway, one of the most studied ciliary-signaling pathways, is regulated at the cilium via an interplay between Smoothened (an oncogene) and Patched (a tumor suppressor), resulting in the activation of pro-survival programs. Interestingly, cilia loss can result in resistance to Smoothened-targeting drugs and increased cancer cell survival. On the other hand, kinase inhibitor-resistant and chemoresistant cancers have increased cilia and increased Hedgehog pathway activation, and suppressing cilia can overcome this resistance. How cilia regulate cancer is therefore context dependent. Defining the signaling output of cilia-localized oncogenic pathways could identify specific targets for cancer therapy, including the cilium itself. Increasing evidence implicates cilia in supporting several hallmarks of cancer, including migration, invasion, and metabolic rewiring. While cell cycle cues regulate the biogenesis of cilia, the absence of cilia has not been conclusively shown to affect the cell cycle. Thus, a complex interplay between molecular signals, phosphorylation events and spatial regulation renders this fascinating organelle an important new player in cancer through roles that we are only starting to uncover. In this review, we discuss recent advances in our understanding of cilia as signaling platforms in cancer and the influence this plays in tumor development.

CDK4/6 inhibition in early and advanced hormone receptor-positive, HER2-negative breast cancer

INTRODUCTION

Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibition in combination with endocrine therapy is the mainstay of treatment for hormone receptor-positive, HER2-negative (HR  +  /HER2-) advanced breast cancer; the CDK4/6 inhibitors abemaciclib and ribociclib are also approved for high-risk, early-stage, HR  +  /HER2- breast cancer. Numerous studies exploring CDK4/6 inhibitors in the early-stage setting are ongoing, as well as many more exploring novel combinations in the metastatic setting.

AREAS COVERED

Here, we review the basis of CDK4/6 inhibition for HR  +/HER2- breast cancer, the pivotal clinical trials which led to regulatory approval, and ongoing trials evaluating novel combinations to further improve outcomes for those with both early and advanced HR+/HER2- breast cancer. Current literature was reviewed by a comprehensive search of PubMed MEDLINE (1/1/2000-12/31/2024).

EXPERT OPINION

CDK4/6 inhibitors are integral in the management of both advanced and high-risk, early-stage HR  +  /HER2- breast cancer. Biomarkers predictive of CDK 4/6 inhibitor (CDK4/6i) benefit remain elusive, and clinical and pathological features remain key to identifying those who are candidates for CDK4/6 inhibition in the early-stage setting. Numerous trials evaluating the role of a CDK4/6i with novel endocrine therapy partners and other targeted agents are ongoing, with the goal of improving outcomes for those with HR  +  /HER2- disease.

Comprehensive Analysis of Oncogenic Somatic Alterations of Mismatch Repair Gene in Breast Cancer Patients

Recent clinical trials have suggested that solid cancers with mismatch repair (MMR) deficiency are highly responsive to immunotherapy, regardless of cancer types. Previous MMR-related studies on breast cancer have predominantly focused on germline variants. However, the somatic MMR alterations have not been comprehensively characterized in breast cancer. In this study, we integrated genomic, transcriptomic, and clinical data from over 3000 breast cancer cases across six public cohorts. Our findings revealed that 1.2% of breast cancers harbored oncogenic somatic MMR alterations, with triple-negative breast cancer (TNBC) demonstrating the highest mutation rate at 3.1%. Additionally, somatic MMR alterations were significantly associated with microsatellite instability-high (MSI-H) and MMR-related mutational signatures, indicating that somatic MMR alterations led to impaired function of the MMR system. Biallelic inactivation of MMR genes resulted in a more pronounced loss of MMR function compared to monoallelic inactivation. Importantly, these MMR alterations significantly increased the tumor mutational burden (TMB) and neoantigen load in breast cancer, regardless of MSI-H status. These findings indicate that the frequency of MMR alterations is highest in TNBC and that MMR alterations in breast cancer can lead to MMR functional deficiencies, suggesting that some patients harboring such alterations may benefit from immunotherapy.

Molecular Mechanisms and Therapeutic Strategies to Overcome Resistance to Endocrine Therapy and CDK4/6 Inhibitors in Advanced ER+/HER2- Breast Cancer

Approximately 70-80% of breast cancers are estrogen receptor-positive (ER+), with 65% of these cases also being progesterone receptor-positive (ER+PR+). In most cases of ER+ advanced breast cancer, endocrine therapy (ET) serves as the first-line treatment, utilizing various drugs that inhibit ER signaling. These include tamoxifen, a selective estrogen receptor modulator (SERM); fulvestrant, a selective estrogen receptor degrader (SERD); and aromatase inhibitors (AIs), which block estrogen synthesis. However, intrinsic or acquired hormone resistance eventually develops, leading to disease progression. The combination of ET with cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6is) has been shown to significantly increase progression-free survival (PFS) and, in some cases, overall survival (OS). CDK4/6is works by arresting the cell cycle in the G1 phase, preventing DNA synthesis, and enhancing the efficacy of ET. This review highlights the key mechanisms of resistance to ET, whether used alone or in combination with biological agents, as well as emerging therapeutic strategies aimed at overcoming resistance. Addressing ET resistance remains a work in progress, and in the near future, better patient selection for different therapeutic approaches is expected through the identification of more precise biological and genetic markers. In particular, liquid biopsy may provide a real-time portrait of the disease, offering insights into mechanisms driving ET resistance and cancer progression.

Native top-down proteomics enables discovery in endocrine-resistant breast cancer

Oligomerization of proteoforms produces functional protein complexes. Characterization of these assemblies within cells is critical to understanding the molecular mechanisms involved in disease and to designing effective drugs. Here we present a native top-down proteomics (nTDP) strategy to identify protein assemblies (≤70 kDa) in breast cancer cells and in cells that overexpress epidermal growth factor receptor (EGFR), which serves as a resistance model of estrogen receptor-alpha (ER)-targeted therapies. This nTDP approach identified ~104 complexoforms from 17 protein complexes, which revealed several molecular features of the breast cancer proteome, including EGFR-induced dissociation of nuclear transport factor 2 (NUTF2) assemblies that modulate ER activity. We found that the K4 and K55 post-translational modification sites discovered with nTDP differentially impact the effects of NUTF2 on the inhibition of the ER signaling pathway. The characterization of endogenous proteoform-proteoform/ligand interactions revealed the molecular diversity of complexoforms and their role in breast cancer growth.

Bone-Induced HER2 Promotes Secondary Metastasis in HR+/HER2- Breast Cancer

SIGNIFICANCE

Given the urgent need for alternative strategies to block metastasis progression, we demonstrate that blocking HER2-mediated secondary metastasis improves clinical outcome and establish HER2 as a biomarker for bone metastasis in patients with initial HR+/HER2- breast cancer, which represents ∼70% of all cases.

Serial Circulating Tumor DNA Sequencing to Monitor Response and Define Acquired Resistance to Letrozole/Abemaciclib in Endometrial Cancer

PURPOSE

In a phase II study, letrozole/abemaciclib demonstrated an objective response rate of 30% and a median progression-free survival (PFS) of 9.1 months in recurrent estrogen receptor-positive endometrial cancer (EC). While tissue-based tumor profiling revealed several mechanistically relevant candidate baseline genomic predictors of response, circulating tumor DNA (ctDNA) is a less invasive alternative to monitor therapeutic efficacy and define acquired resistance.

METHODS

Serial plasma specimens were obtained at baseline, C2D1, C3D1, C8D1, the time of objective response, and the time of progression. Samples were analyzed using the Guardant Reveal assay to assess methylation-based tumor fraction (TF), with the Guardant360 assay providing genotyping of >700 genes in samples with detectable ctDNA. Treatment response was assessed using a measure of the relative change in TF pre- versus on-treatment.

RESULTS

A total of 99 of 102 (97%) samples from 28 patients were successfully analyzed. Patients with above median baseline TF exhibited worse median PFS (2.0 months v 16.5 months, P < .005, hazard ratio [HR], 24.1) and worse overall survival (OS) (10.7 months v not yet reached, P < .005, HR, 14.8). Patients with molecular response (MR) after the first or second cycle of letrozole/abemaciclib therapy had significantly better median PFS and OS regardless of the cutoff used for definition of MR. ctDNA analysis of postprogression specimens identified several acquired genomic alterations associated with resistance to letrozole/abemaciclib therapy in more than half of the patients, including PI3K pathway, receptor tyrosine kinase (FGFR1,2 and ERBB2 alterations), cell cycle pathway (RB1 and CCNE1 alterations), and ESR1 and MAPK pathway alterations. Two of the three patients with mismatch repair-deficient ECs acquired ESR1 mutations at the time of progression.

CONCLUSION

Baseline and on-treatment ctDNA dynamics may provide an early indication of benefit from letrozole/abemaciclib in EC. ctDNA at the time of progression may identify resistance alterations that may inform subsequent therapy.

Personalized multifactorial risk assessment in neoadjuvant-treated breast carcinoma

PURPOSE

Due to biological heterogeneity of breast carcinoma, predicting the individual response to neoadjuvant treatment (NAT) is complex. Consequently, there are no comprehensive, generally accepted practices to guide post-treatment follow-up. We present clinical and histopathological criteria to advance the prediction of disease outcome in NA-treated breast cancer.

METHODS

A retrospective consecutive cohort of 257 NA-treated Finnish breast cancer patients with up to 13-year follow-up and the corresponding tissue samples of pre- and post-NAT breast and metastatic specimen were evaluated for prognostic impacts. All relevant clinical and biomarker characteristics potentially correlated with tumor response to NAT, course of disease, or outcome of breast cancer were included in the statistical analyses.

RESULTS

The results highlight the intensified characterization of distinguished prognostic factors and previously overlooked histological features, e.g., mitotic and apoptotic activity. Particularly, decreased PR indicated 3.8-fold (CI 1.9-7.4, p = 0.0001) mortality risk, and a > 10.5-year shorter survival for the majority, > 75% of patients (Q1). Clinically applicable prognostic factors both preceding and following NAT were identified and compiled into heat maps to quantify mortality and recurrence risks. Combinations of risk factors for aggressive disease were exemplified as an interactive tool (bcnatreccalc.utu.fi) to illustrate the spectrum of disease outcomes.

CONCLUSION

The results emphasize the value of comprehensive evaluation of conventional patient and biomarker characteristics, especially concerning re-assessment of biomarkers, risk-adapted surveillance, and personalized treatment strategies. Future personalized NA-treatment strategies might benefit from models combining risk-adapted surveillance data and post-NAT re-assessed biomarkers.

Novel Estrogen Receptor - Targeted Therapies in Hormone-Receptor Positive Breast Cancer

OPINION STATEMENT

Endocrine therapy is the backbone of treatment for HR + /HER2- MBC. The introduction of novel endocrine-based therapies has changed the landscape of metastatic breast cancer care, with even more promising agents on the horizon. Given the consistent success in prolonging PFS and OS, CDK4/6 inhibitors should be used as first-line treatment. Once secondary resistance eventually develops after use of a CDK4/6 inhibitor, use of monotherapy with either AI or fulvestrant has shown poor outcome. For example, in the control group of the EMERALD trial, in which all the patients were required to have previously received a CDK4/6 inhibitor, median progression-free survival with endocrine therapy was only 1.9 months. Based on the emerging evidence, molecular profiling of tissue or liquid biopsy at progression of disease is crucial to select future therapy. For patients whose tumors harbor ESR1 mutations, oral SERDs are the preferred option. For those with PIK3CA or AKT1 mutation or PTEN inactivation, combination therapy with the AKT pathway inhibitor capivasertib is recommended. Alpelisib, the first AKT1 inhibitor approved in combination therapy with fulvestrant in PIK3CA mutated tumors only, is now less in favor given its challenging side effect profile. When mutations are not present, options include combination therapy with the mTOR inhibitor everolimus or changing endocrine therapy and continuing a CDK 4/6 inhibitor. In patients with short response to CDK4/6 inhibitors suggesting endocrine resistant disease, chemotherapy or antibody-drug conjugates should be considered. With better understanding of the mechanisms of resistance to CDK4/6 inhibitors, additional mutations could be identified and potentially targeted in order to provide individualized treatment options. Optimal sequencing of treatment options depends on several factors: (1) the presence of specific molecular aberrations; (2) previous treatment history, duration of response and patient's performance status; (3) balance between maximizing survival benefits with quality of life/toxicities; (4) disease burden. In the upcoming years, we anticipate FDA approvals for more of the SERD molecules both in monotherapy and in combination therapy which will continue to expand the options available for HR + /HER2- MBC patients.

Elacestrant in Women with Estrogen Receptor-Positive and HER2-Negative Early Breast Cancer: Results from the Preoperative Window-of-Opportunity ELIPSE Trial

PURPOSE

Elacestrant has shown significantly prolonged progression-free survival compared with standard-of-care endocrine therapy in estrogen receptor-positive (ER-positive), HER2-negative metastatic breast cancer, whereas potential benefit in early-stage disease requires further exploration. The SOLTI-ELIPSE window-of-opportunity trial investigated the biological changes induced by a short course of preoperative elacestrant in postmenopausal women with early breast cancer.

PATIENTS AND METHODS

Eligible patients with untreated T1c (≥1.5 cm)-T3, N0, ER-positive/HER2-negative breast cancer with locally assessed Ki67 ≥10% received elacestrant at a daily dose of 345 mg for 4 weeks. The primary efficacy endpoint was complete cell cycle arrest, defined as Ki67 ≤2.7%, on day 28.

RESULTS

Overall, 22 patients were evaluable for the primary endpoint. Elacestrant was associated with a complete cell cycle arrest rate of 27.3% and a statistically significant Ki67 geometric mean change of -52.9% (P = 0.007; 95% confidence interval, -67.4 to -32.1). Notably, the treatment with elacestrant led to a shift toward a more endocrine-sensitive and less proliferative tumor phenotype based on PAM50-based gene signatures. Elacestrant increased the expression of immune-response genes (GZMB, CD4, and CD8A) and suppressed proliferation and estrogen-signaling genes (MKI67, ESR1, and AR). These biological changes were independent of the levels of Ki67 suppression on day 28. The most common adverse events were grade 1 anemia (21.7%), hot flushes (8.7%), constipation (8.7%), and abdominal pain (8.7%). One patient experienced a grade 3 cutaneous rash, leading to treatment discontinuation. No other serious adverse events were reported.

CONCLUSIONS

Preoperative treatment with elacestrant in early breast cancer demonstrated relevant biological and molecular responses and exhibited a manageable safety profile. These findings support further investigation of elacestrant in the early setting.

A Novel Multiple Endocrine Neoplasia Type 1 Gene Variant Found in Scalp Pulmonary Neuroendocrine Tumor Metastasis

Multiple endocrine neoplasia type 1 (MEN1) is a genetic disorder usually diagnosed following hyperparathyroidism or pancreatic and gastrointestinal neuroendocrine neoplasm (NEN). We report here a case of MEN1 that was diagnosed following cancer multigene panel testing of a scalp metastasis of small cell lung carcinoma (SCLC). A 45-year-old male had noticed weight loss 20 months before admission to our department. He was identified with multiple nodules in the lungs, and bronchoscopy permitted diagnosis of SCLC at another hospital. He was then relocated to our hospital, where he began receiving chemotherapy and radiation therapy. A metastatic lesion had appeared on his scalp 3 months before admission, which had been diagnosed as a neuroendocrine tumor (NET, corresponding to grade 2) based on histopathological examination. Cancer multigene panel testing was performed and a MEN1 variant (c.266T > G; p.Leu89Arg) was discovered; the patient was then referred to our department. Germline genetic testing revealed the same, novel germline variant in MEN1, leading to his diagnosis of MEN1 and lung NEN metastases. In this case, the stage of NENs can vary between the primary tumor (SCLC) and its metastases (NET), potentially involving second-hit mutations or tumor suppressor genes.

Hotspot mutations in HER2 interfaces destabilize structure, causing breast cancer treatment failure

Many HER2-positive breast cancer (BC) patients relapse within a year of trastuzumab or neratinib treatment. We identified specific pathogenic mutations in the dimerization domains II and IV of the HER2 receptor that contribute to treatment resistance. Mutations G309A, S310Y, and P523S induce significant structural alterations, disrupting crucial HER2:HER2 binding pockets. HER3-preferring mutants exhibited increased HER2:HER3 interactions, as confirmed by proximity ligation assay in HER2-low and HER2-high cell lines. G309A, S310Y, and P523S mutations induced a receptor switch, altering downstream signaling from ERK to AKT activation, leading to high insensitivity to trastuzumab or neratinib in cell survival and migration assays, which was further confirmed by bioluminescence imaging of orthotopic tumors expressing the P523S mutation. This study identifies new hotspot mutations in HER2 domains II and IV causing trastuzumab resistance. Notably, cells with either wild-type or the examined dimerization domain mutations retained sensitivity to the FDA-approved HER2 kinase inhibitor, tucatinib.

The evolving landscape of genetic biomarkers for immunotherapy in primary and metastatic breast cancer

Background

Major advances have been achieved in the characterization of primary breast cancer genomic profiles. Limited information is available on the genomic profile of tumors originating from different metastatic locations in recurrent/metastatic (R/M) breast cancer, especially in Asian patients. This study aims to decipher the mutational profiles of primary and R/M breast cancer in Chinese patients using next-generation sequencing.

Methods

A total of 563 breast cancer patients were enrolled, and 590 tumor tissues and matched peripheral blood samples were collected and subjected to targeted sequencing with a panel of 1,021 cancer-related genes. The mutation spectrum, DNA damage response (DDR) genes, commonly altered signal pathways, and immunotherapy-related markers were compared between primary and R/M breast cancer. The molecular differences between our cohort and the Memorial Sloan Kettering Cancer Center (MSKCC) dataset were also explored.

Results

A total of 361 samples from primary and 229 samples from R/M breast cancer were analyzed. BRCA2, ATRX, and ATM were more frequently observed in R/M lesions among the 36 DDR genes. An ESR1 mutation and PD-L1 and PD-L2 amplification were enriched in R/M breast cancer (all p<0.05). Compared with the MSKCC dataset, we recruited more patients diagnosed at age 50 or younger and more patients with triple-negative breast cancer (TNBC) subtypes. The TNBC patients in our dataset had a higher percentage of PD-L1 amplification in metastasis tumors (p<0.05).

Conclusions

This study revealed the distinctive mutational features of primary and R/M tumors in Chinese breast cancer patients, which are different from those from Western countries. The enrichment of PD-L1 amplification in metastatic TNBC indicates the necessity to re-biopsy metastatic tumors for immunotherapy.

Triple-positive breast cancer: navigating heterogeneity and advancing multimodal therapies for improving patient outcomes

Triple-positive breast cancer (TPBC), a unique subtype of luminal breast cancer, is characterized by concurrent positivity for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Owing to the crosstalk between the ER and HER2 signaling pathways, the standard of care and drug resistance of this particular subtype are difficult challenges. Recent research and clinical trials have indicated a shift in the treatment paradigm for TPBC from single-target therapies to multi-pathway, multitarget strategies aiming to comprehensively modulate intricate signaling networks, thereby overcoming resistance and enhancing therapeutic outcomes. Among multiple strategies, triple-drug therapy has emerged as a promising treatment modality, demonstrating potential efficacy in patients with TPBC. Moving forward, there is a critical need to perform in-depth analyses of specific mechanisms of cancer pathogenesis and metastasis, decipher the complex interactions between different genes or proteins, and identify concrete molecular targets, thus paving the way for the development of tailored therapeutic strategies to combat TPBC effectively.

Kinase Plasticity in Response to Vandetanib Enhances Sensitivity to Tamoxifen in Estrogen Receptor Positive Breast Cancer

Resistance to endocrine therapy (ET) is common in estrogen receptor (ER) positive breast cancer. Multiple studies have demonstrated that upregulation of MAPK signaling pathways contributes to ET resistance. Herein we show that vandetanib treatment enhances sensitivity to ET in ET-sensitive and -resistant ER+ breast cancer models. Vandetanib treatment alters the gene expression program of ER+ breast cancer cells resulting in a less proliferative and more estrogen responsive Luminal-A like character. Tyrosine kinase network reprogramming was assessed using multiplexed kinase inhibitor beads-mass spectrometry (MIB/MS) assay to identify adaptive resistance mechanisms to vandetanib treatment, including upregulation of HER2 activity. Co-treatment to inhibit HER2 with lapatinib enhanced sensitivity to vandetanib, demonstrating biologic activity of HER2 upregulation. Using a CRISPR knockout model, we demonstrate that vandetanib effects are partially mediated by RET receptor tyrosine kinase. Finally, we use our operating room-to-laboratory assay that measures drug response in individual primary tumor cells in short term cultures to demonstrate conserved gene expression changes, including increased HER2 activity signatures, in vandetanib treated cells, and identify features associated with vandetanib response. These results support future investigation of RET targeting strategies considering reprogrammed networks, such as activated HER2, in patients with ET resistant ER+ breast cancer.

Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients: mutation frequencies, testing intention, and clinical impact

Background

Circulating cell-free tumor DNA (ctDNA) provides a non-invasive approach for assessing somatic alterations. The German PRAEGNANT registry study aims to explore molecular biomarkers and investigate their integration into clinical practice. In this context, ctDNA testing was included to understand the motivations of clinicians to initiate testing, to identify somatic alterations, and to assess the clinical impact of the results obtained.

Methods

Patients with advanced/metastatic breast cancer were prospectively enrolled in the Prospective Academic Translational Research Network for the Optimization of Oncological Health Care Quality in the Adjuvant and Advanced/Metastatic Setting (PRAEGNANT study; NCT02338167). The FDA-approved and CE-marked GUARDANT360 CDx test was used to assess somatic alterations. A ctDNA-analysis report was provided to the treating physician along with a questionnaire about the intent for testing and the clinical implications of test results.

Results

ctDNA from 49 patients was analyzed prospectively: 37 (76%) had at least one somatic alteration in the analyzed geneset; 14 patients (29%) harbored alterations in TP53, 12 (24%) in PIK3CA, and 6 (12%) in ESR1. Somatic mutations in BRCA1 or BRCA2 were detected in 3 (6%) and 4 (8%) patients, respectively, and 59% of patients had hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. Questionnaires regarding test intentions and clinical impact were completed for 48 (98%) patients. These showed that ctDNA testing influenced treatment decisions for 35% of patients.

Discussion

The high prevalence of somatic alterations in TP53, PIK3CA, ESR1, and BRCA1/2 genes, identified by ctDNA genotyping, highlights their potential as biomarkers for targeted therapies. Detection of specific mutations affected treatment decisions, such as eligibility for alpelisib, and might further facilitate treatment with e.g. elacestrant or capiversatib in future treatment lines.

ctDNA-based liquid biopsy reveals wider mutational profile with therapy resistance and metastasis susceptibility signatures in early-stage breast cancer patients

A minimally invasive analysis of plasma cell-free DNA (cfDNA) offers a genomic profiling of early-stage breast cancer (EBC), potentially identifying mutational signatures linked to metastasis and therapy resistance. In this study, paired plasma and tissue samples from 40 hormone receptor-positive (HR+) EBC patients were sequenced using a custom-designed comprehensive gene panel, OncoIndx. The genomic landscape of circulating tumor DNA (ctDNA) showed a broader mutation spectrum compared to tumor tissue DNA (tDNA), and provided reliable assessments of microsatellite instability (MSI), tumor mutation burden (TMB), homologous recombination deficiency (HRD), and loss of heterogeneity (LOH), all indicating high genomic instability. Importantly, early detection of estrogen receptor α (ESR1) mutations in ctDNA was achieved, highlighting its potential to identify patients at risk for endocrine resistance, a standard of care for HR + breast tumors. Mutations, particularly in DNA damage response (DDR) and proliferative signaling pathways (phosphatidyl inositol-4,5-bisphosphate 3-kinase; PIK3CA) suggest an increased risk of therapy resistance, pointing to opportunities for risk stratification and tailored treatment strategies in EBC. ctDNA-based liquid biopsy may provide minimally invasive comprehensive genomic analysis of EBC for identifying actionable targets and risk prediction for better disease management.

Ipsilateral Breast Carcinoma Recurrence: True Recurrence or New Primary? A Clinicopathologic and Molecular Study

Determining whether an ipsilateral breast carcinoma recurrence is a true recurrence or a new primary remains challenging based solely on clinicopathologic features. Algorithms based on these features have estimated that up to 68% of recurrences might be new primaries. However, few studies have analyzed the clonal relationship between primary and secondary carcinomas to establish the true nature of recurrences. This study analyzed 70 breast carcinomas from 33 patients using immunohistochemistry, FISH, and massive parallel sequencing. We compared 35 primary carcinomas with the associated recurrences, identifying 24 (68.6%) as true recurrences, 7 (20%) as new primaries, and 4 (11%) as undetermined. Twenty-eight primary carcinomas were invasive carcinomas (22 of no special type, 5 invasive lobular, and 1 invasive micropapillary carcinoma), and 7 were in situ (6 ductal and 1 lobular). Time to recurrence was longer for new primaries (median 12.8 y) than for true recurrences (median 6.8 y). Among the new primary cases, 6 of 7 (85%) patients had undergone mastectomy as their initial treatment. Clinicopathologic classifications of invasive carcinomas overestimated the number of new primaries (41.6% to 68.6%), partially due to phenotype conversion in 14% of true recurrences. Although 41.7% of recurrences showed private mutations or amplifications relevant to tumor progression, such as PIK3CA, PIK3R1, MAP3K1, AKT1, GATA3, CCND1, MDM4 , or T P 5 3 ; a common mutational progression pattern was not identified. Further studies, including larger series, are necessary to evaluate the prognostic significance of the molecular classification of recurrences.

Decoding mutational signatures in breast cancer: Insights from a multi-cohort study

PURPOSE

Diagnosis and treatment decisions of hormonal breast cancers (BC) are now guided by genomic mutations determination, combined into mutational signatures, and provide insight into the patients' genomic landscape. This work aims to compare genomic data and signatures extracted from tissue samples collected in the CICLADES study to existing cohorts. Ultimately, the goal is to prove the accuracy of smaller cohorts and provide new relevant data.

MATERIALS AND METHODS

DNA from patients of the CICLADES cohort was extracted, sequenced, and custom filtering was applied to the resulting files. Genomic data was pulled from 6 BC cohorts available on cBioPortal.com. In total, 2303 samples were analyzed. Mutational signatures were extracted and matched to known signatures of the Catalogue of Somatic Mutations in Cancer (COSMIC). Tumor Mutation Burden (TMB) and hypermutation were estimated and compared between samples.

RESULTS

PIK3CA and TP53 represented the two genes highly mutated across all cohorts. TMB was similar between the CICLADES and CBSM groups, however the MSKCC population showed a significantly higher TMB than both. Nine signatures were extracted, with recurring Single Base Substitutions (SBS) signatures like SBS1, SBS2 and SBS5. The presence of APOBEC-specific signatures was concordant with cohorts presenting APOBEC enrichment. The mean number of mutations was significantly higher in enriched samples for each analyzed cohort.

CONCLUSION

The use of comprehensive genomic profiling provided accurate evaluation of the TMB and extraction of signatures consistent with published literature. The genomic analysis of the tissue samples of the CICLADES cohort brings new and relevant data, comparable to results found in bigger cohorts.

Molecular mechanisms altering cell identity in cancer

Intrinsic and extrinsic factors influence cancer cell identity throughout its lifespan. During tumor progression and metastasis formation, cancer cells are exposed to different environmental stimuli, resulting in a stepwise cellular reprogramming. Similar stepwise changes of cell identity have been shown as a major consequence of cancer treatment, as cells are exposed to extracellular stress that can result in the establishment of subpopulations exhibiting different epigenetic and transcriptional patterns, indicating a rapid adaptation mechanism of cellular identity by extrinsic stress factors. Both mechanisms, tumor progression-mediated changes and therapy response, rely on signaling pathways affecting the epigenetic and subsequent transcriptional landscape, which equip the cells with mechanisms for survival and tumor progression. These non-genetic alterations are propagated to the daughter cells, indicating a need for successful information propagation and transfer to the daughter generations, thereby allowing for a stepwise adaptation to environmental cues. However, the exact mechanisms how these cell identity changes are occurring, which context-specific mechanisms are behind and how this can be exploited for future therapeutic interventions is not yet fully understood and exploited. In this review, we discuss the current knowledge on cell identity maintenance mechanisms intra- and intergenerational in development and disease and how these mechanisms are altered in cancer. We will as well address how cancer treatment might target these properties.

Radiogenomic Landscape of Metastatic Endocrine-Positive Breast Cancer Resistant to Aromatase Inhibitors

Breast cancer poses a significant global health challenge and includes various subtypes, such as endocrine-positive, HER2-positive, and triple-negative. Endocrine-positive breast cancer, characterized by estrogen and progesterone receptors, is commonly treated with aromatase inhibitors. However, resistance to these inhibitors can hinder patient outcomes due to genetic and epigenetic alterations, mutations in the estrogen receptor 1 gene, and changes in signaling pathways. Radiogenomics combines imaging techniques like MRI and CT scans with genomic profiling methods to identify radiographic biomarkers associated with resistance. This approach enhances our understanding of resistance mechanisms and metastasis patterns, linking them to specific genomic profiles and common metastasis sites like the bone and brain. By integrating radiogenomic data, personalized treatment strategies can be developed, improving predictive and prognostic capabilities. Advancements in imaging and genomic technologies offer promising avenues for enhancing radiogenomic research. A thorough understanding of resistance mechanisms is crucial for developing effective treatment strategies, making radiogenomics a valuable integrative approach in personalized medicine that aims to improve clinical outcomes for patients with metastatic endocrine-positive breast cancer.

Mismatch repair (MMR) and microsatellite instability (MSI) phenotypes across solid tumors: A comprehensive cBioPortal study on prevalence and prognostic impact

Mismatch repair deficiency (MMR-d) and microsatellite instability (MSI) are prognostic and predictive biomarkers in oncology. Current testing for MMR/MSI relies on immunohistochemistry (IHC) for MMR proteins and molecular assays for MSI detection. This combined diagnostic strategy, however, lacks tumor specificity and does not account for gene variants. This study provides an in-depth analysis of MMR mutations frequency, spectrum, and distribution in solid tumors. Data from 23,893 patients across 11 tumor types, using 66 publicly available studies, were analyzed. MMR-mutated (MMR-m) status was defined by alterations in MLH1, PMS2, MSH2, and/or MSH6; MSI was assessed by MSIsensor. Cases with indeterminate labelling were excluded. Survival was analyzed using the Kaplan-Meier method. Among 19,353 tumors, 949 MMR variants were identified, comprising 432 pathogenic and 517 variants of unknown significance (VUS), as defined by OncoKB. MSH6 mutations were the most frequent (n = 279, 29.4 %), followed by MSH2 (n = 198, 20.9 %), MLH1 (n = 187, 19.7 %), and PMS2 (n = 161, 16.9 %). MMR-m cases were more frequent in endometrial (EC, 20.5 %), colorectal (CRC, 8.2 %), bladder (BLCA, 8.7 %), and gastroesophageal cancers (GEC, 5.4 %). Pathogenic mutations were more common than non-pathogenic in EC, CRC, and GEC (p < 0.001, p = 0.01, p = 0.32, respectively). MMR-m status was not associated with MSI in 247 (48.9 %) cases, including 67 (13.2 %) with pathogenic mutations. The highest concordance between MMR-m and MSI was observed in CRC (65.7 %), EC (91.2 %), and GEC (69.6 %), while the lowest in pancreatic (0.2 %) and lung cancers (0.1 %). MMR-m GECs showed improved overall survival compared to MMR-wt (p = 0.009), a relationship not observed in other tumor types. This study demonstrates that the MMR spectrum is extremely hetoerogeneous in solid tumors, highliting the need for comprehensive and tumor-specific testing strategies.

Genomic hallmarks of endocrine therapy resistance in ER/PR+HER2- breast tumours

ER/PR+HER2- breast tumours are the most predominant subtype of breast cancer worldwide, including India. Unlike TNBCs, these tumours can be treated with anti-estrogens or aromatase inhibitors. Despite the success of endocrine therapy, a fraction of patients with ER/PR+ breast tumours do not respond to hormone-receptor-specific treatment and encounter disease recurrence contributing to their poor survival. The genomic underpinnings of therapy resistance in ER/PR+HER2- breast tumours are incompletely understood. We have performed whole genome sequencing (WGS) from tumour and normal tissue samples from endocrine-therapy resistant ER/PR+HER2- breast cancer patients who have relapsed on endocrine therapy and have conducted a comparative analysis of WGS data generated from tissues of endocrine therapy sensitive patients who remained free of disease during a minimum 5-year follow-up. Our analysis shows (a) a three-gene (PIK3CA-ESR1-TP53) resistance signature, and (b) impaired DNA double-strand break repair and homologous recombination pathways, were significantly associated with endocrine-therapy resistance and disease recurrence in ER/PR+HER2- tumours. Genome instability, contributing to high burden of copy-number, structural alterations and telomere-shortening identified as major markers of endocrine treatment resistance. Early prediction of endocrine-therapy resistance from the genomic landscape of breast tumours will aid therapeutics. Our finding also opens up the possibility of repurposing PARP inhibitors in treating endocrine therapy-resistant breast cancer patients.

Racial Differences in ctDNA Profiles, Targeted Therapy Use, and Outcomes in Metastatic Breast Cancer

Importance

Black patients with metastatic breast cancer (mBC) have higher mortality rates than White patients despite advances in treatment.

Objectives

To examine whether Black patients with metastatic breast cancer have different genomic profiles compared with White patients and whether there are inequities in targeted treatment use between these groups.

Design, Setting, and Participants

This retrospective, population-based cohort study assessed adult patients with mBC who underwent genomic profiling at academic institutions in the US between January 1, 2015, and December 31, 2023. Data analysis was performed between July 2023 and July 2024. A validation cohort was also included.

Exposures

Targeted treatment use.

Main Outcomes and Measures

The main outcomes were differences in circulating tumor DNA profiles and use of phosphoinositide 3-kinase (PI3K), mammalian target of rapamycin (mTOR), and cyclin-dependent kinase 4/6 (CDK4/6) inhibitors between Black and White patients with metastatic breast cancer.

Results

The study sample included 1327 women with mBC (mean [SD] age, 58.0 [12.8] years; 140 Black and 1057 White). Black patients had a significantly higher rate of GATA3 single-nucleotide variants (odds ratio, 2.31; 95% CI, 1.17-4.54; P = .02) and CCND2 copy number variants (odds ratio, 4.63; 95% CI, 1.79-11.97; P = .002) on multivariate analysis. These differences were validated in a population-based evidence cohort of 27 224 patients. Black patients with PIK3CA single-nucleotide variants were significantly less likely to receive PI3K inhibitors than White patients (1 of 17 [5.9%] vs 45 of 156 [28.8%]; P = .04), whereas there was no difference in use of CDK4/6 and mTOR inhibitors, which do not require a targetable alteration. Black patients had a shorter overall survival from the time of circulating tumor DNA testing compared with White patients.

Conclusions and Relevance

This cohort study of patients with mBC found somatic differences, shorter overall survival, and targeted treatment disparities in PI3K inhibitor use in Black compared with White patients despite equal incidence of PIK3CA alterations. Researchers should consider these differences when designing future research and interventions to address the striking and persistent outcomes gap between Black and White patients with mBC.

Stromal Tumor-Infiltrating Lymphocytes in Hormone Receptor-Positive/HER2 Negative Metastatic Breast Cancer

The immune landscape of hormone receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer (HR+/HER2- mBC), the most common subtype of BC, remains understudied. This is mainly because of reduced sample acquisition opportunities from metastases as compared with primary tumors. In this study, we explored stromal tumor-infiltrating lymphocytes (sTIL) in metastatic samples collected through our post-mortem tissue donation program UZ/KU Leuven Post-mortem Tissue Donation program to Enhance Research (NCT04531696). sTIL were scored as a continuous parameter according to the international guidelines on 427 metastases and 38 primary untreated tumors acquired from 20 patients with HR+/HER2- mBC. Estrogen receptor (ER) status was evaluated on 362 metastases with a cutoff value for positivity set at 1% according to the American Society of Clinical Oncology/College of American Pathologists guidelines. Our analyses show that 54% and 15% of metastases had sTIL levels of ≥1% and ≥5%, respectively. sTIL levels tended to be lower in metastases as compared with their respective primary tumors (estimate, -2.83; 95% CI, -5.77 to 0.11; P = .07). sTIL levels were lower in metastases from invasive lobular carcinoma than in metastases from invasive breast carcinoma of no special type (estimate, -1.67; 95% CI, -2.35 to -0.98; P < .001). A loss of ER expression was observed in 14% of all metastases, yet a negative ER status was not significantly associated with increased sTIL levels. Finally, sTIL levels were significantly higher in lung and axillary lymph node metastases compared with all metastases. Although these analyses were conducted on multiple metastases obtained at the end of life after several lines of treatment, the data provide novel and valuable insights into the state of immune infiltration in patients with HR+/HER2- mBC.

An update on promising and emerging protein kinase B/AKT inhibitors for breast cancer

INTRODUCTION

The PI3K pathway is crucial in breast cancer (BC), influencing cell survival, growth, and metabolism, with AKT playing a central role in treatment resistance. This pathway's involvement in breast carcinogenesis and its link to treatment resistance underscores the significance of targeting it in BC therapy. PI3K-pathway inhibitors offer new therapeutic avenues but bring challenges, especially due to toxicity issues that hinder their development.

AREAS COVERED

This review discusses the PI3K-pathway inhibitors used in BC, highlighting emerging, innovative strategies.

EXPERT OPINION

The introduction of mTOR inhibitors marked a key step in tackling hormone receptor-positive (HR+) BC, targeting endocrine resistance. However, toxicity concerns remain, especially with PIK3CA and AKT inhibitors. Selective PI3K-targeted agents aim to reduce off-target toxicity, enhancing patient adherence and control over the disease. New compounds employing allosteric mechanisms may further limit adverse effects and allow safer combination therapies, previously limited by toxicity. Advancements in dosing strategies focus on patient-centered outcomes, and synergistic agents are essential in advancing AKT-pathway inhibition, paving the way for a new phase in HR+ BC treatment.

Targeting CDK4/6 in breast cancer

Dysregulation of the cell cycle machinery, particularly the overactivation of cyclin-dependent kinases 4 and 6 (CDK4/6), is a hallmark of breast cancer pathogenesis. The introduction of CDK4/6 inhibitors has transformed the treatment landscape for hormone receptor-positive breast cancer by effectively targeting abnormal cell cycle progression. However, despite their initial clinical success, drug resistance remains a significant challenge, with no reliable biomarkers available to predict treatment response or guide strategies for managing resistant populations. Consequently, numerous studies have sought to investigate the mechanisms driving resistance to optimize the therapeutic use of CDK4/6 inhibitors and improve patient outcomes. Here we examine the molecular mechanisms regulating the cell cycle, current clinical applications of CDK4/6 inhibitors in breast cancer, and key mechanisms contributing to drug resistance. Furthermore, we discuss emerging predictive biomarkers and highlight potential directions for overcoming resistance and enhancing therapeutic efficacy.

Non-Hotspot PIK3CA Variants Have Higher Variant Allele Frequency and are More Common in Syndromic Vascular Malformations

PIK3CA variants are known to cause vascular malformations. We were interested in studying the phenotypic spectrum, the location within the PIK3CA gene, and the variant allele frequency (VAF) of somatic PI3KCA variants in vascular malformations. Clinical data of consecutive patients with extracranial/extraspinal vascular malformations were collected in the context of the VASCOM cohort (2008-2022, n = 558). Starting October 2020, biopsy samples were tested with the TSO500 gene panel (Illumina). All consenting patients with PIK3CA variants were included in this study. Eighty-nine patients had available genetic results by June 2022. PIK3CA variants (n = 25) were found in 16 simple/combined (nonsyndromic) vascular malformations and in nine vascular malformations associated with other anomalies (syndromic). Four hotspot variants in exons 9 and 20 (c.1624G>A, c.1633G>A, c.3140A>G, c.3140A>T) were identified in 16/25 patients (VAF 0.9%-9.7%). Six non-hotspot variants (c.328_330del, c.323_337del, c.353G>A, c.1258T>C, c.3132T>A, c.3195_3203delinsT) were detected in nine patients (VAF 3.6%-31.7%). Non-hotspot variants were more frequent in syndromic than nonsyndromic vascular malformations (p = 0.0034) and exhibited a higher VAF than hotspot variants (p = 0.0253). Our study contributes to the growing body of knowledge of the genetic background in vascular malformations. Further studies will enrich the ever-growing list of pathogenic PIK3CA variants associated with vascular malformations.

Beyond Hormone Receptors: liquid biopsy tools to unveil new clinical meanings and empower therapeutic decision-making in Luminal-like metastatic breast cancer

Immunohistochemical (IHC) tissue profiling is a standard practice in the management of metastatic breast cancer (mBC), that enables the identification of distinct biological phenotypes based on hormone receptors' expression. Luminal-like tumors primarily benefit from a first line treatment strategy combining endocrine therapy and cyclin-dependent kinase 4/6 inhibitors. However, IHC analyses necessitate invasive procedures and may encounter technical and interpretational challenges. In the current era of precision medicine, liquid biopsy holds potential to provide clinicians with additional insights into disease biology, including mechanisms underlying endocrine resistance and disease progression. Several liquid-based biomarkers are entering clinical practice and hold prognostic and predictive values in Luminal-like mBC, while many others are currently being investigated. The present work aims to summarize the current evidence regarding the clinical meanings of hormone receptors and their downstream molecular pathways, alongside their implications for therapeutic decision-making in Luminal-like mBC.

Clinicopathological and molecular features of HR + /HER2 - breast cancer patients with distinct endocrine resistance patterns

Objective

Recurrence continues to be a pivotal challenge among hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) breast cancers. In the international consensus guidelines, HR+/HER2- breast cancer relapse patterns are divided into three distinct types: primary resistant, secondary resistant, and endocrine sensitive. However, owing to the lack of cohorts with treatment and follow-up data, the heterogeneity among different recurrence patterns remains uncharted. Current treatments still lack precision.

Methods

This analysis included data from a large-scale multiomics study of a HR+/HER2- breast cancer cohort (n=314). Through the analysis of transcriptomics (n=312), proteomics (n=124), whole-exome sequencing (n=290), metabolomics (n=217), and digital pathology (n=228) data, we explored distinctive molecular features and identified putative therapeutic targets for patients experiencing recurrence.

Results

We explored distinct clinicopathological characteristics, biological heterogeneity, and potential therapeutic strategies for recurrence. Based on a shared relapse signature, we stratified patients into high- and low-recurrence-risk groups. Patients with different relapse patterns presented unique molecular features in primary tumors. Specifically, receptor tyrosine kinase (RTK) pathway activation in the primary resistant group suggested the utility of RTK inhibitors, whereas mammalian target of rapamycin (mTOR) and cell cycle pathway activation in the secondary resistant group highlighted the potential of mTOR and CDK4/6 inhibitors. Interestingly, the endocrine-sensitive group displayed a quiescent state and high genomic instability, suggesting that targeting quiescent cells and using poly-ADP-ribose polymerase (PARP) inhibitors could be effective strategies.

Conclusions

These findings illuminate the clinicopathological and molecular landscape of HR+/HER2- breast cancer patients with distinct recurrence patterns, highlighting potential targeted therapies.

Pre-Clinical Rationale for Amcenestrant Combinations in HER2+/ER+ Breast Cancer

HER2-positive/oestrogen receptor-positive (HER2+/ER+) represents a unique breast cancer subtype. The use of individual HER2- or ER-targeting agents can lead to the acquisition of therapeutic resistance due to compensatory receptor crosstalk. New drug combinations targeting HER2 and ER could improve outcomes for patients with HER2+/ER+ breast cancer. In this study, the pre-clinical rationale is explored for combining amcenestrant (Amc), a selective oestrogen receptor degrader (SERD), with HER2-targeted therapies including trastuzumab, trastuzumab-emtansine (T-DM1) and tyrosine kinase inhibitors (TKIs). The combination of Amc and anti-HER2 therapies was investigated in a panel of four HER2+/ER+ cell lines: BT-474, MDA-MB-361, EFM-192a and a trastuzumab-resistant variant BT-474-T. Proliferation (IC50 and matrix combination assays) was determined using acid phosphatase assays. HER2/ER and intracellular signalling pathway protein levels/activity were investigated by western blot. Apoptosis was assessed using caspase 3/7 assays. Additivity and synergy were observed between Amc and the TKIs neratinib, lapatinib and tucatinib in all cell lines. Amc increased the anti-proliferative effect of trastuzumab in MDA-MB-361 and BT-474-T. Addition of Amc also increased anti-proliferative efficacy of T-DM1 in BT-474-T. TKI/Amc combinations reduced p-HER2 and ER levels and resulted in increased apoptosis. Higher ER expression in MDA-MB-361 and BT-474-T was associated with greater potential for synergy. In conclusion, the combination of Amc- and HER2-targeted treatments has potential as a therapeutic strategy for the treatment of HER2+/ER+ breast cancer and warrants further clinical investigation to validate safety and efficacy in patients.

New Promising Steroidal Aromatase Inhibitors with Multi-Target Action on Estrogen and Androgen Receptors for Breast Cancer Treatment

Background/Objectives: Endocrine therapies that comprise anti-estrogens and aromatase inhibitors (AIs) are the standard treatment for estrogen receptor-positive (ER+) (Luminal A) breast cancer-the most prevalent subtype. However, the emergence of resistance restricts their success by causing tumor relapse and re-growth, which demands a switch towards other therapeutic approaches in order to minimize or overcome resistance. Indeed, this clinical limitation highlights the search for new molecules to improve cancer treatment. Recently, strategies that address multiple targets have been emerging, and multi-target drugs have the potential to become the future anti-cancer molecules. Our group has been searching for new multi-target compounds, and as part of this, our study aims to understand the anti-cancer and multi-target potential of three new steroidal aromatase inhibitors (AIs): 7α-methylandrost-4-en-17-one (6), 7α-methylandrost-4-ene-3,17-dione (10a) and androsta-4,9(11)-diene-3,17-dione (13). Methods: Their in vitro actions and molecular mechanisms were elucidated in a sensitive ER+ aromatase-overexpressing breast cancer cell line, MCF-7aro cells, as well as in an AI-resistant ER+ breast cancer cell line, LTEDaro cells. Results: All the new AIs (10 µM) prevented the proliferation of MCF-7aro cells by arresting cell cycle progression. Interestingly, all AIs (10 µM) act as androgen receptor (AR) agonists and modulate ER levels, synthesis and signaling to induce the apoptosis of ER+ breast cancer cells. Additionally, these new AIs (10 µM) also re-sensitize resistant cells by promoting apoptosis, offering a therapeutic benefit. Conclusions: Overall, new steroidal polypharmacological compounds have been discovered that, by acting as AIs, ER modulators and AR agonists, impair ER+ breast cancer cell growth. Overall, this study is a breakthrough on drug discovery as it presents new molecules with appealing anti-cancer properties and multi-target action for the treatment of ER+ breast cancer.

Molecular Basis of Breast Tumor Heterogeneity

Breast cancer (BC) is a profoundly heterogenous disease, with diverse molecular, histological, and clinical variations. The intricate molecular landscape of BC is evident even at early stages, illustrated by the complexity of the evolution from precursor lesions to invasive carcinoma. The key for therapeutic decision-making is the dynamic assessment of BC receptor status and clinical subtyping. Hereditary BC adds an additional layer of complexity to the disease, given that different cancer susceptibility genes contribute to distinct phenotypes and genomic features. Furthermore, the various BC subtypes display distinct metabolic demands and immune microenvironments. Finally, genotypic-phenotypic correlations in special histologic subtypes of BC inform diagnostic and therapeutic approaches, highlighting the significance of thoroughly comprehending BC heterogeneity.

Hormone Signaling in Breast Development and Cancer

Hormones control normal breast development and function. They also impinge on breast cancer (BC) development and disease progression in direct and indirect ways. The major ovarian hormones, estrogens and progesterone, have long been established as key regulators of mammary gland development in rodents and linked to human disease. However, their roles have been difficult to disentangle because they act on multiple tissues and can act directly and indirectly on different cell types in the breast, and their receptors interact at different levels within the target cell. Estrogens are well-recognized drivers of estrogen receptor-positive (ER+) breast cancers, and the ER is successfully targeted in ER+ disease. The role of progesterone receptor (PR) as a potential target to be activated or inhibited is debated, and androgen receptor (AR) signaling has emerged as a potentially interesting pathway to target on the stage.In this chapter, we discuss hormone signaling in normal breast development and in cancer, with a specific focus on the key sex hormones: estrogen, progesterone, and testosterone. We will highlight the complexities of endocrine control mechanisms at the organismal, tissue, cellular, and molecular levels. As we delve into the mechanisms of action of hormone receptors, their interplay and their context-dependent roles in breast cancer will be discussed. Drawing insights from new preclinical models, we will describe the lessons learned and the current challenges in understanding hormone action in breast cancer.

A Review on Integrating Breast Cancer Clinical Data: A Unified Platform Perspective

OPINION STATEMENT

Integrating clinical datasets in breast cancer research emerges as a necessary tool for advancing our knowledge of the disease and enhancing patient outcomes. Synthesizing diverse datasets offers advantages, from facilitating evidence-based insights to enabling predictive analytics and precision medicine strategies. Crucially, effective integration of clinical datasets necessitates collaborative efforts, policy interventions, and technological advancements to elevate global standards of breast cancer care. This narrative review underscores the imperative and substantial benefits of dataset integration in advancing breast cancer research and optimizing patient management. First, integrating diverse datasets-encompassing patient demographics, tumor characteristics, treatment modalities, and clinical outcomes-can significantly enhance our understanding of the disease's complexities and treatment responses across diverse patient populations. Second, we suggest that regulatory approval processes should allow new treatments to be conditionally approved for patients who were not part of the initial trials. This approval would depend on evaluating how well these treatments perform in real-world situations before full approval is granted. Third, we emphasize the importance of incorporating high-quality real-world evidence into treatment guidelines to better inform patient counselling and optimize personalized treatment strategies.

Metabolic Reprogramming and Adaption in Breast Cancer Progression and Metastasis

Recent evidence has revealed that cancer is not solely driven by genetic abnormalities but also by significant metabolic dysregulation. Cancer cells exhibit altered metabolic demands and rewiring of cellular metabolism to sustain their malignant characteristics. Metabolic reprogramming has emerged as a hallmark of cancer, playing a complex role in breast cancer initiation, progression, and metastasis. The different molecular subtypes of breast cancer exhibit distinct metabolic genotypes and phenotypes, offering opportunities for subtype-specific therapeutic approaches. Cancer-associated metabolic phenotypes encompass dysregulated nutrient uptake, opportunistic nutrient acquisition strategies, altered utilization of glycolysis and TCA cycle intermediates, increased nitrogen demand, metabolite-driven gene regulation, and metabolic interactions with the microenvironment. The tumor microenvironment, consisting of stromal cells, immune cells, blood vessels, and extracellular matrix components, influences metabolic adaptations through modulating nutrient availability, oxygen levels, and signaling pathways. Metastasis, the process of cancer spread, involves intricate steps that present unique metabolic challenges at each stage. Successful metastasis requires cancer cells to navigate varying nutrient and oxygen availability, endure oxidative stress, and adapt their metabolic processes accordingly. The metabolic reprogramming observed in breast cancer is regulated by oncogenes, tumor suppressor genes, and signaling pathways that integrate cellular signaling with metabolic processes. Understanding the metabolic adaptations associated with metastasis holds promise for identifying therapeutic targets to disrupt the metastatic process and improve patient outcomes. This chapter explores the metabolic alterations linked to breast cancer metastasis and highlights the potential for targeted interventions in this context.

Pan-cancer genomic analysis reveals FOXA1 amplification is associated with adverse outcomes in non-small cell lung, prostate, and breast cancers

BACKGROUND

Alterations in forkhead box A1 (FOXA1), a pioneer transcription factor, are associated with poor prognosis in breast cancer and prostate cancer. We characterized FOXA1 genomic alterations and their clinical impacts in a large pan-cancer cohort from the American Association for Cancer Research Genomics, Evidence, Neoplasia, Information, Exchange database.

METHODS

FOXA1 alterations were characterized across more than 87 000 samples from more than 30 cancer types for primary and metastatic tumors alongside patient characteristics and clinical outcomes. FOXA1 alterations were queried in the Memorial Sloan Kettering - Metastatic Events and Tropisms (MSK-MET) cohort (a GENIE subset), allowing definition of hazard ratios (HRs) and survival estimates based on Cox proportional hazard models.

RESULTS

FOXA1 was altered in 1869 (2.1%) samples, with distinct patterns across different cancers: prostate cancer enriched with indel-inframe alterations, breast cancer with missense mutations, and lung cancers with copy number amplifications. Of 74 715 samples with FOXA1 copy number profiles, amplification was detected in 834 (1.1%). Amplification was most common in non-small cell lung cancer (NSCLC; 3% in primary; 6% in metastatic) and small cell lung cancer (4.1% primary; 3.5% metastatic), followed by breast cancer (2% primary; 1.6% metastatic) and prostate cancer (2.2% primary; 1.6% metastatic). Copy number amplifications were associated with decreased overall survival in NSCLC (HR = 1.45, 95% confidence interval [CI] = 1.06 to 1.99; P = .02), breast cancer (HR = 3.04, 95% CI = 1.89 to 4.89; P = 4e-6), and prostate cancer (HR = 1.94, 95% CI = 1.03 to 3.68; P = .04). Amplifications were associated with widespread metastases in NSCLC, breast cancer, and prostate cancer.

CONCLUSIONS

FOXA1 demonstrates distinct alteration profiles across cancer sites. Our findings suggest an association between FOXA1 amplification and enhanced metastatic potential and decreased survival, highlighting prognostic and therapeutic potential in breast cancer, prostate cancer, and NSCLC.

HER2-Positive Breast Cancer Treatment and Resistance

HER2-positive (+) breast cancer is an aggressive disease with poor prognosis, a narrative that changed drastically with the advent and approval of trastuzumab, the first humanized monoclonal antibody targeting HER2. In addition to another monoclonal antibody, more classes of HER2-targeted agents, including tyrosine kinase inhibitors, and antibody-drug conjugates were developed in the years that followed. While these potent therapies have substantially improved the outcome of patients with HER2+ breast cancer, resistance has prevailed as a clinical challenge ever since the arrival of targeted agents. Efforts to develop new treatment regimens to treat/overcome resistance is futile without a primary understanding of the mechanistic underpinnings of resistance. Resistance could be attributed to mechanisms that are either specific to the tumor epithelial cells or those that emerge through changes in the tumor microenvironment. Reactivation of the HER receptor layer due to incomplete blockade of the HER receptor layer or due to alterations in the HER receptors is one of the major mechanisms. In other instances, resistance may occur due to deregulations in key downstream signaling such as the PI3K/AKT or RAS/MEK/ERK pathways or due to the emergence of compensatory pathways such as ER, other RTKs, or metabolic pathways. Potent new targeted agents and approaches to target key actionable drivers of resistance have already been identified, many of which are in early clinical development or under preclinical evaluation. Ongoing and future translational research will continue to uncover additional therapeutic vulnerabilities, as well as new targeted agents and approaches to treat and/or overcome anti-HER2 treatment resistance.

Human Epidermal Growth Factor Receptor 2 Alterations and Prognostic Implications in All Subtypes of Breast Cancers

PURPOSE

Alterations in human epidermal growth factor receptor 2 (HER2; ERBB2 gene) may be clinically relevant when considering HER2-targeted therapies. We have characterized the breadth of ERBB2 alterations (mutation, fusion, and copy number amplification) in breast cancer and explored the relationship between ERBB2 alterations and prognosis.

METHODS

DNA next-generation sequencing (592-gene panel and whole-exome sequencing) and RNA whole-transcriptome sequencing data from 12,153 breast samples were retrospectively reviewed for ERBB2 alterations. Clinicopathologic features were described, including breast cancer subtype, age, and biopsy site. HER2 status was determined according to ASCO guideline recommendations, including HER2-low. Overall survival (OS) data were obtained from insurance claims, and Kaplan-Meier estimates were calculated for defined patient cohorts. Statistical significance was determined using chi-square and Wilcoxon rank-sum tests.

RESULTS

Pathogenic ERBB2 mutations (ERBB2-mut) were identified in 3.2% (N = 388) of tumors overall, most common in liver metastases (113/1,972, 5.7%). ERBB2-mut was more common among breast lobular than ductal (10% v 2.1%; P < .001) and HER2-positive (HER2+)/low tumors (≥3.8% v 1.5% TNBC; P < .05). The most common variant was ERBB2-L755S (1.0% prevalence), enriched in metastatic tumors (1.2% v 0.6% in primary; P < .001). ERBB2 fusions were rare (0.3% prevalence). Coalterations associated with ERBB2-mutated tumors compared with ERBB2 wildtype (WT) included CDH1 (40.0% v 10.2%; P < .001) and ERBB3 (10.6% v 0.8%; P < .001). Of the 10,115 tumor samples with outcome data, ERBB2-mut was associated with worse OS compared with WT.

CONCLUSION

ERBB2-mut and fusions were observed in all breast cancer subtypes-more commonly in HER2+/low, metastatic, and lobular histology tumors-and associated with poorer prognosis.

Characterization of breast cancer tumors in older patients who show de novo resistance to endocrine therapy

The standard treatment for hormone receptor-positive breast cancer in good general condition is curative surgery followed by endocrine therapy. However, for older patients, endocrine therapy alone is sometimes chosen instead of curative surgery due to health conditions or personal preference, though this is not yet a standard approach. It is crucial to develop elderly-specific treatment strategies, potentially establishing endocrine therapy alone as a standard option. While endocrine therapy is generally effective, some patients show disease progression from the beginning due to de novo resistance. Hence, identifying such tumors is essential to determine who may benefit from endocrine therapy alone. Fifty-one patients aged over 70 years with estrogen receptor-positive and human epidermal growth factor receptor 2-negative invasive breast cancer who were treated with endocrine therapy instead of curative surgery were retrospectively investigated. Genes possibly related to de novo resistance to endocrine therapy were analyzed using a gene expression panel. Of the 51 patients, three patients showed progressive disease (PD) within 6 months of starting endocrine therapy. Gene expression analysis revealed that some genes, including those related to the cell cycle, such as CDKN3, were expressed at higher levels in the PD group compared with the non-PD group. Among these, CDKN3 retained significantly high expression in the PD group, even after analyzing more samples (log2 fold change, 1.99; P = 0.005). Public mRNA microarray data analysis revealed that patients with high CDKN3 tumors had worse outcomes. We identified several genes possibly involved in the de novo resistance to endocrine therapy. Our data indicate CDKN3 to be a predictive marker for de novo endocrine therapy resistance in older patients with breast cancer. We hope that our data will contribute to further research to establish tailored treatments for elderly breast cancer patients.

Breast cancer brain metastases genomic profiling identifies alterations targetable by immune-checkpoint and PARP inhibitors

Understanding the genomic landscape of breast cancer brain metastases (BCBMs) is key to developing targeted treatments. In this study, targetable genomic profiling was performed on 822 BCBMs, 11,988 local breast cancer (BC) biopsies and 15,516 non-central nervous system (N-CNS) metastases (all unpaired samples) collected during the course of routine clinical care by Foundation Medicine Inc (Boston, MA). Clinically relevant genomic alterations were significantly enriched in BCBMs compared to local BCs and N-CNS metastases. Homologous recombination deficiency as measured by BRCA1/2 alteration prevalence and loss-of-heterozygosity and immune checkpoint inhibitor (ICI) biomarkers [Tumor mutation burden (TMB)-High, Microsatellite instability (MSI)-High, PD-L1/L2)] were significantly more prevalent in BCBM than local BC and N-CNS. High PD-L1 protein expression was observed in ER-negative/HER2-negative BCBMs (48.3% vs 50.0% in local BCs, 21.4% in N-CNS). Our data highlights that a high proportion of BCBMs are potentially amenable to treatment with targeted therapeutic agents including PARP inhibitors and ICIs.

Recent advancements in biomarkers and molecular diagnostics in hormonal receptor-positive breast cancer

Molecular applications have limited use in breast cancer compared to other cancer types. In recent years, with an improving appreciation of the molecular genetics of breast cancer and innovative novel targeted and immune-mediated therapeutics, opportunities have arisen for more biomarker analysis and molecular applications in the diagnosis and treatment of both locally advanced and metastatic breast cancers. In hormone receptor-positive, HER2-negative breast cancers, a growing number of revolutionized personalized therapies are in clinical use or on trials, such as CDK4/6 inhibitors and immune checkpoint inhibitors in adjuvant and neoadjuvant settings, and PIK3CA inhibitors in metastatic disease. In this review, we focus on biomarkers associated with those new therapeutic targets and molecular applications for genetic alterations associated with drug resistance or interaction from a pathology perspective for selecting and optimizing breast cancer treatment.

Induction of the TEAD Coactivator VGLL1 by Estrogen Receptor-Targeted Therapy Drives Resistance in Breast Cancer

Resistance to endocrine therapies (ET) is common in estrogen receptor (ER)-positive breast cancer, and most relapsed patients die with ET-resistant disease. Although genetic mutations provide explanations for some relapses, mechanisms of resistance remain undefined in many cases. Drug-induced epigenetic reprogramming has been shown to provide possible routes to resistance. By analyzing histone H3 lysine 27 acetylation profiles and transcriptional reprogramming in models of ET resistance, we discovered that selective ER degraders, such as fulvestrant, promote expression of vestigial-like 1 (VGLL1), a coactivator for TEF-1 and AbaA domain (TEAD) transcription factors. VGLL1, acting via TEADs, promoted the expression of genes that drive the growth of fulvestrant-resistant breast cancer cells. Pharmacological disruption of VGLL1-TEAD4 interaction inhibited VGLL1/TEAD-induced transcriptional programs to prevent the growth of resistant cells. EGFR was among the VGLL1/TEAD-regulated genes, and VGLL1-directed EGFR upregulation sensitized fulvestrant-resistant breast cancer cells to EGFR inhibitors. Taken together, these findings identify VGLL1 as a transcriptional driver in ET resistance and advance therapeutic possibilities for relapsed ER+ breast cancer patients. Significance: Transcriptional reprogramming mediated by the upregulation of the TEAD coactivator VGLL1 confers resistance to estrogen receptor degraders in breast cancer but provides alternative therapeutic options for this clinically important patient group.

The Biological Roles and Clinical Applications of the PI3K/AKT Pathway in Targeted Therapy Resistance in HER2-Positive Breast Cancer: A Comprehensive Review

Epidermal growth factor receptor 2-positive breast cancer (HER2+ BC) is a highly invasive and malignant type of tumor. Due to its resistance to HER2-targeted therapy, HER2+ BC has a poor prognosis and a tendency for metastasis. Understanding the mechanisms underlying this resistance and developing effective treatments for HER2+ BC are major research challenges. The phosphatidylinositol-3-kinase/protein kinase B (PI3K/AKT) pathway, which is frequently altered in cancers, plays a critical role in cellular proliferation and drug resistance. This signaling pathway activates various downstream pathways and exhibits complex interactions with other signaling networks. Given the significance of the PI3K/AKT pathway in HER2+ BC, several targeted drugs are currently in development. Multiple drugs have entered clinical trials or gained market approval, bringing new hope for HER2+ BC therapy. However, new drugs and therapies raise concerns related to safety, regulation, and ethics. Populations of different races and disease statuses exhibit varying responses to treatments. Therefore, in this review, we summarize current knowledge on the alteration and biological roles of the PI3K/AKT pathway, as well as its clinical applications and perspectives, providing new insights for advancing targeted therapies in HER2+ BC.

Polypharmacy and drug-drug interactions in metastatic breast cancer patients receiving cyclin-dependent kinase (CDK) 4/6 inhibitors

INTRODUCTION

Cyclin-dependent kinase (CDK) 4/6 inhibitors have significantly changed the treatment strategy for patients with locally advanced or metastatic hormone receptor positive (HR+), human epidermal growth factor 2 negative (HER2) breast cancer. The purpose of the study was to determine the prevalence of drug-drug interactions (DDI) in breast cancer patients using CDK 4/6 inhibitors and the extent of DDI reflected in the clinic and to increase clinical awareness among physicians.

METHOD

The data of 115 metastatic breast cancer patients using CDK 4/6 inhibitors who were admitted to the Medical Oncology outpatient clinic between July 2021 and July 2023 were retrospectively reviewed. The Drugs.com® Drug Interaction Checker application was used for the interaction between the CDK 4/6 inhibitor and other drugs.

RESULTS

Among patients included in the study, 97.3% had at least one additional drug use. We have identified a total of 170 potential DDI risks in 63.5 % of patients. Among these, 50.5% had a major potential DDI. In our study, there was a potential risk of QT prolongation in 45.2% of 170 DDI, an increase in the potential toxicity of the additional drug in 44.1%, an increase in the potential toxicity of the CDK 4/6 inhibitor in 5.3%, a decrease in the potential efficacy of the CDK 4/6 inhibitor in 2.9%, a decrease in the potential efficacy of the additional drug in 1.1%, and a serious potential infection risk in 1.1%. Most of the drug interactions were QT prolongation and increased toxicity of the additional drug. In terms of cardiovascular events, grade-2 and grade-3 QTc prolongation was found in 4.3% and 1.7% of these interactions, respectively. When evaluated in terms of CDK 4/6 inhibitor subtype, there was a potential risk of DDI at major level with Ribocilib and at moderate level with Palbociclib.

CONCLUSION

If CDK 4/6 inhibitors interact with concomitant drugs, they may cause an increase in the incidence of cardiac side effects and a decrease in the effect of the CDK 4/6 inhibitor or additional drug or an increase in toxicity. Increasing awareness of this issue will help to reduce the rates of side effects or toxicity and provide effective antitumour therapy.

Practical treatment strategies and novel therapies in the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway in hormone receptor-positive/human epidermal growth factor receptor 2 (HER2)-negative (HR+/HER2-) advanced breast cancer

Mutations in the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway occur in 30%-40% of patients with advanced hormone receptor-positive/human epidermal growth factor receptor 2 (HER2)-negative (HR+/HER2-) breast cancer. For most patients, endocrine therapy with a cyclin-dependent kinase 4/6 (CDK4/6) inhibitor is the first-line treatment. Recent studies indicate that adding inavolisib, a PI3Kα inhibitor, to palbociclib/fulvestrant benefits patients with endocrine-resistant HR+/HER2- metastatic breast cancer with a PIK3CA mutation. Alpelisib and capivasertib are both US Food and Drug Administration (FDA) approved in combination with fulvestrant in patients with endocrine-resistant HR+/HER2-, PIK3CA-mutant metastatic breast cancer, both with activity in the post-CDK4/6 setting. Capivasertib added to fulvestrant is the first AKT inhibitor to show a significant progression-free survival benefit with a trend for overall survival benefit and the only approved option for patients with phosphate and tensin homolog (PTEN) or AKT alterations. Toxicity profiles of all agents necessitate careful patient selection. Several mutant-selective and pan-mutant-selective novel inhibitors are under investigation with the potential to improve tolerability and efficacy.

Pyrimidine-triazole-tethered tert-butyl-piperazine-carboxylate suppresses breast cancer by targeting estrogen receptor signaling and β-catenin activation

Several chemotherapeutics against breast cancer are constrained by their adverse effects and chemoresistance. The development of novel chemotherapeutics to target metastatic breast cancer can bring effective clinical outcomes. Many breast cancer patients present with tumors that are positive for estrogen receptors (ERs), highlighting the importance of targeting the ER pathway in this particular subtype. Although selective estrogen receptor modulators (SERMs) are commonly used, their side effects and resistance issues necessitate the development of new ER-targeting agents. In this study, we report that a newly synthesized compound, TTP-5, a hybrid of pyrimidine, triazole, and tert-butyl-piperazine-carboxylate, effectively binds to estrogen receptor alpha (ERα) and suppresses breast cancer cell growth. We assessed the impact of TTP-5 on cell proliferation using MTT and colony formation assays and evaluated its effect on cell motility through wound healing and invasion assays. We further explored the mechanism of action of this novel compound by detecting protein expression changes using Western blotting. Molecular docking was used to confirm the interaction of TTP-5 with ERα. The results indicated that TTP-5 significantly reduced the proliferation of MCF-7 cells by blocking the ERα signaling pathway. Conversely, although it did not influence the growth of MDA-MB-231 cells, TTP-5 hindered their motility by modulating the expression of proteins associated with epithelial-mesenchymal transition (EMT), possibly via the Wnt/β-catenin pathway.

Automated real-world data integration improves cancer outcome prediction

The digitization of health records and growing availability of tumour DNA sequencing provide an opportunity to study the determinants of cancer outcomes with unprecedented richness. Patient data are often stored in unstructured text and siloed datasets. Here we combine natural language processing annotations1,2 with structured medication, patient-reported demographic, tumour registry and tumour genomic data from 24,950 patients at Memorial Sloan Kettering Cancer Center to generate a clinicogenomic, harmonized oncologic real-world dataset (MSK-CHORD). MSK-CHORD includes data for non-small-cell lung (n = 7,809), breast (n = 5,368), colorectal (n = 5,543), prostate (n = 3,211) and pancreatic (n = 3,109) cancers and enables discovery of clinicogenomic relationships not apparent in smaller datasets. Leveraging MSK-CHORD to train machine learning models to predict overall survival, we find that models including features derived from natural language processing, such as sites of disease, outperform those based on genomic data or stage alone as tested by cross-validation and an external, multi-institution dataset. By annotating 705,241 radiology reports, MSK-CHORD also uncovers predictors of metastasis to specific organ sites, including a relationship between SETD2 mutation and lower metastatic potential in immunotherapy-treated lung adenocarcinoma corroborated in independent datasets. We demonstrate the feasibility of automated annotation from unstructured notes and its utility in predicting patient outcomes. The resulting data are provided as a public resource for real-world oncologic research.