Prevalence and mutational determinants of high tumor mutation burden in breast cancer

Immunotherapy in breast cancer: current landscape and emerging trends

Breast cancer remains one of the most prevalent malignancies worldwide, underscoring an urgent need for innovative therapeutic strategies. Immunotherapy has emerged as a transformative frontier in this context. In triple-negative breast cancer (TNBC), the combination of immunotherapy based on PD-1/PD-L1 immune checkpoint inhibitors (ICIs) with chemotherapy has proven efficacious in both early and advanced clinical trials. These encouraging results have led to the approval of ICIs for TNBC, opening up new therapeutic avenues for challenging-to-treat patient populations. Furthermore, a multitude of ongoing trials are actively investigating the efficacy of immunotherapy-based combinations, including ICIs in conjunction with chemotherapy, targeted therapy and radiation therapy, as well as other novel strategies such as bispecific antibodies, CAR-T cells and cancer vaccines across all breast cancer subtypes, including HR-positive/HER2-negative and HER2-positive disease. This review provides a comprehensive overview of current immunotherapeutic approaches in breast cancer, highlighting pivotal findings from recent clinical trials and the potential impact of these advancements on patient outcomes.

The application of compressed sensing on tumor mutation burden calculation from overlapped pooling sequencing data

BACKGROUND

Tumor Mutation Burden (TMB) is commonly characterized as the number of non-synonymous somatic SNVs per megabase within the gene region identified through whole exon sequencing or targeted sequencing in a tumor sample. It has been statistically demonstrated that TMB was related to the ability of neoantigen production and used to predict the efficacy of immunotherapy for various types of cancers. However, screening for TMB in patients poses challenges due to the extensive labor and financial resources required for the preparation of large quantities of parallel sequencing libraries.

RESULTS

In this study, we employed compressed sensing (CS) to calculate TMB from overlapped pooling sequencing data, aiming to reduce the sequencing cost by minimizing the number of library builds. Over 90% SNPs could still be detected without a significant loss of mutation information even when the data is pooled from ten different samples. Based on this, the orthogonal matching pursuit (OMP) algorithm and the basic pursuit (BP) algorithm were used to reconstruct TMB from pooling sequencing data. The performance of these two algorithms was evaluated. The BP algorithm consistently performed well across all cases, albeit necessitating extended computational time. The OMP algorithm has been proved to be suitable for scenarios where the original matrix was sparse but it showed low overall performance. Based on an accurate calculation of TMB, we determined that the number of sequencing runs could be reduced to 0.6 times the total number of samples, resulting in a 40% reduction in sequencing cost.

CONCLUSIONS

In conclusion, we calculated TMB from overlapped pooling sequencing data utilizing compressed sensing strategy to reduce sequencing cost. Our findings confirm that the SNP calling from ten samples' pooling sequencing data is feasible. Additionally, we performed an assessment of the reconstruction efficiency of both the BP model and the OMP model.

APOBEC3 mutagenesis drives therapy resistance in breast cancer

Acquired genetic alterations drive resistance to endocrine and targeted therapies in metastatic breast cancer; however, the underlying processes engendering these alterations are largely uncharacterized. To identify the underlying mutational processes, we utilized a clinically annotated cohort of 3,880 patient samples with tumor-normal sequencing. Mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were prevalent and enriched in post-treatment hormone receptor-positive cancers. These signatures correlated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor therapy in hormone receptor-positive metastatic breast cancer. Whole-genome sequencing of breast cancer models and paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted therapy resistance through characteristic alterations such as RB1 loss. Evidence of APOBEC3 activity in pretreatment samples illustrated its pervasive role in breast cancer evolution. These studies reveal APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlight its potential as a biomarker and target for overcoming resistance.

Nivolumab plus low-dose ipilimumab in hypermutated HER2-negative metastatic breast cancer: a phase II trial (NIMBUS)

In the phase II NIMBUS trial, patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) and high tumor mutational burden (TMB ≥ 9 mut/Mb) received nivolumab (3 mg/kg biweekly) and low-dose ipilimumab (1 mg/kg every 6 weeks) for 2 years or until progression. The primary endpoint was objective response rate (ORR) per RECIST 1.1 criteria. Among 30 patients enrolled, the median TMB was 10.9 mut/Mb (range: 9-110) and the confirmed objective response rate was 20%. Secondary endpoints included progression-free survival, overall survival, clinical benefit rate, and safety and tolerability, including immune-related adverse events (irAEs). A prespecified correlative outcome was to evaluate the ORR in patients with a TMB ≥ 14 mut/Mb. Patients with TMB ≥ 14 mut/Mb (n = 6) experienced higher response rates (60% vs 12%; p = 0.041) and showed a trend towards improved progression-free survival and overall survival compared to patients with TMB < 14 mut/Mb. Exploratory genomic analyses suggested that ESR1 and PTEN mutations may be associated with poor response, while clinical benefit was associated with a decrease or no change in tumor fraction by serial circulating tumor DNA during treatment. Stool microbiome analysis revealed that baseline blood TMB, PD-L1 positivity, and immune-related diarrhea are associated with distinct taxonomic profiles. In summary, some patients with hypermutated HER2-negative MBC experience extended clinical benefit with a dual immunotherapy regimen; a higher TMB, and additional genomic and microbiome biomarkers may optimize patient selection for therapy with nivolumab plus low-dose ipilimumab. (Funded by Bristol Myers Squibb; ClinicalTrials.gov identifier, NCT03789110).

The interplay between the immune response and neoadjuvant therapy in breast cancer

Treatment of early breast cancer is currently experiencing a rapid evolution because of important insight into tumor subtypes and continuous development and improvement of novel therapeutics. Historically considered non-immunogenic, breast cancer has seen a paradigm shift with increased understanding of immune microenvironment, which have revealed extensive heterogeneity in tumor-associated inflammation. Notably, the more aggressive breast cancer subtypes, including triple-negative and HER2-positive, have exhibited favorable responses to combined chemo-immunotherapy protocols. Neoadjuvant therapy has emerged as the standard of care for these tumors, with pathological complete response used as a surrogate endpoint for long-term clinical outcomes and coincidently expediting new drug approval. The neoadjuvant setting affords a unique opportunity for in vivo treatment response evaluation and effects on the tumor microenvironment. In this review, the predictive and prognostic value of the tumor immune microenvironment before, during, and after treatment across various therapeutic regimens, tailored to distinct breast cancer subtypes, is carefully examined.

Knowledge, attitude, and practice toward genetic testing in breast cancer patients in China

Genetic testing is widely recommended in the diagnosis and management of breast cancer. This study aimed to investigate the knowledge, attitude, and practice (KAP) toward genetic testing in Chinese patients with breast cancer. This multicenter cross-sectional study enrolled breast cancer patients in seven public hospitals in Shanghai, China, between November 2022 and January 2023. A self-administered web-based questionnaire was used to collect the participants' demographic information and their KAP regarding genetic testing. A total of 592 valid questionnaires were collected in this study; 145 (24.49%) patients underwent genetic testing, and 20.61% of the patients never learned about genetic testing. The knowledge, attitude, and practice scores were 4.59 ± 4.49 (22.95%, possible range: 0-20), 16.72 ± 2.92 (83.60%, possible range: 0-20), and 23.67 ± 5.18 (73.97%, possible range: 0-32), respectively. Multivariable logistic regression showed that knowledge (OR = 1.21, 95%CI: 1.51-1.28, P < 0.001), attitude (OR = 1.10, 95%CI: 1.01-1.19, P = 0.027), Jiangsu Province (OR = 0.40, 95%CI: 0.19-0.84, P = 0.016), monthly income of 5000-10,000 CNY (OR = 0.46, 95%CI: 0.25-0.86, P = 0.015), disease duration of 5-10 years (OR = 0.50, 95%CI: 0.27-0.94, P = 0.030) and disease duration of ≥ 10 years (OR = 0.26, 95%CI: 0.11-0.60, P = 0.002), triple-negative subtype (OR = 3.45, 95%CI: 1.51-7.85, P = 0.003) were independently associated with patients' behavior of undergoing genetic testing. The structural equation modeling showed that knowledge directly positively influenced attitude (β = 0.343, P < 0.001), while attitude directly positively influenced practice (β = 0.942, P < 0.001). Chinese patients with breast cancer demonstrated poor knowledge, positive attitude, and suboptimal practice toward genetic testing. More education and counseling on genetic testing for patients are necessary.

Advancing breast cancer therapy in the era of molecular diagnostics

Advances in cancer biology and drug development now enable treatments tailored to individual tumor profile. Targeting specific molecular alterations marked a significant step forward in cancer care, including breast cancer. Access to these therapies is improving thanks to the implementation of molecular tumor boards and efforts to provide molecular diagnostics at sustainable costs for all. In this context, we highlight recent progress in breast cancer therapy, focusing on biomarker-driven approaches, immunotherapy, and precision medicine paving the way for increasingly personalized and effective options.

Tumor mutational burden status and clinical characteristics of invasive lobular carcinoma of the breast

BACKGROUND

High tumor mutational burden (TMB-H) is an established biomarker for a favorable response to immune checkpoint inhibitors. However, tumor mutational burden (TMB) in invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) has not been sufficiently investigated.

METHODS

We collected data of patients with ILC or IDC from the Center for Cancer Genomics and Advanced Therapeutics database between June 2019 and August 2023. Furthermore, we examined the clinicopathological factors and TMB status.

RESULTS

Patients with ILC (n = 170) had a median TMB score of 4.00 mut/Mb (interquartile range, 2.00-7.14 mut/Mb), whereas those with IDC (n = 2598) had a score of 3.90 mut/Mb (2.00-6.00 mut/Mb). TMB-H was more common in patients with ILC than in those with IDC (18.2% vs. 10.1%, P < 0.001), particularly in the ER+ /HER2- subtype. Multivariate analysis revealed that the pathological diagnosis of ILC (P = 0.006), tissue samples collected from metastatic sites (P < 0.001), and older age (50 years, P < 0.001) were independent factors for TMB-H.

CONCLUSIONS

Patients with ILC were more likely to have TMB-H than those with IDC. The findings of this study would be invaluable in selecting treatment strategies for patients with ILC.

Current Status of Immune Checkpoint Inhibitors and Treatment Responsive Biomarkers for Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC), accounting for about 10%-20% of all breast cancer cases, is characterized by its aggressive nature, high recurrence rates, and poor prognosis. Unlike other breast cancer subtypes, TNBC lacks hormone receptors and specific molecular targets, limiting therapeutic options. In recent years, immune checkpoint inhibitors (ICIs) have shown promise in treating TNBC by targeting immune evasion mechanisms. Despite these advancements, several issues remain unresolved, including low response rates in programmed cell death ligand 1 (PD-L1) negative TNBC subtypes and the challenge of predicting which patients will benefit from ICIs. Consequently, there is growing interest in identifying reliable biomarkers beyond PD-L1 expression. This review synthesizes recent studies to provide a comprehensive perspective on ICI therapy in TNBC, clarifying the status of single-agent ICI therapies and combination strategies, emphasizing the need for further research into biomarkers. These insights provide clues for more personalized and effective treatment approaches, ultimately aiming to improve clinical outcomes for patients with TNBC.

Comprehensive mapping elucidates high risk genotypes in primary metastatic breast cancer

Among women with primary metastatic breast cancer (pMBC), around 5 % of women with primary invasive breast cancer, high-risk mutations associated with disease progression and poor prognosis is shown. The heterogeneity and clinical implications of these genomic alterations remains to be fully elucidated. We performed comprehensive gene mapping on 211 tumors of women diagnosed with pMBC at Rigshospitalet 2014-2021. After DNA purification 203 tumor samples were eligible for analysis. Median age in our cohort was 69 years, 68 % were ER-positive/HER2-negative, 23 % HER2-positive and 9 % triple-negative. A high tumor mutational burden (TMB), shown in 10 %, was in univariable analysis associated with a poor prognosis and a median overall survival of 5.3 months (95 % CI, 2.5-51.3) but no significant association after adjusting for subtype and age. 65 % of tumors had an actionable biomarker, including a PIK3CA mutation in 39 %. TP53 mutations were found in 33 % of tumors and were associated with an increased risk of death (adjusted HR: 1.60, 95 % CI; 1.07-2.40). We have found that for women with pMBC, the disease is driven by several targetable genetic mutations across subtypes, however our results suggest a reduced prognostic value of TMB for this complex patient group. Taken together, our findings substantiate the value of early genomic profiling to actively identify women that may be eligible for a more individualized treatment scheme.

APOBEC in breast cancer: a dual player in tumor evolution and therapeutic response

The APOBEC (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like) family of cytidine deaminases has emerged as pivotal a contributor to genomic instability and adaptive immunity through DNA/RNA editing. Accumulating evidence underscores their dual role in breast carcinogenesis-driving tumor heterogeneity via mutagenesis while simultaneously shaping immunogenic landscapes. This review synthesizes current insights into APOBEC-mediated molecular mechanisms, focusing on their clinical implications across breast cancer subtypes. Notably, APOBEC-driven mutagenesis correlates with elevated tumor mutational burden (TMB), replication stress vulnerability, and immune checkpoint inhibitor (ICI) responsiveness. Paradoxically, these mutations also accelerate endocrine therapy resistance and subclonal diversification. We propose APOBEC mutational signatures as predictive biomarkers for ICI efficacy and discuss therapeutic strategies leveraging APOBEC activity, including ATR inhibition and hypermutagenic immunotherapy. Harnessing APOBEC's duality-balancing its pro-immunogenic effects against genomic chaos-may redefine precision oncology in breast cancer.

Progress of PD-1/PD-L1 immune checkpoint inhibitors in the treatment of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a highly heterogeneous cancer with substantial recurrence potential. Currently, surgery and chemotherapy are the main treatments for this disease. However, chemotherapy is often limited by several factors, including low bioavailability, significant systemic toxicity, inadequate targeting, and multidrug resistance. Immune checkpoint inhibitors (ICIs), including those targeting programmed death protein-1 (PD-1) and its ligand (PD-L1), have been proven effective in the treatment of various tumours. In particular, in the treatment of TNBC with PD-1/PD-L1 inhibitors, both monotherapy and combination chemotherapy, as well as targeted drugs and other therapeutic strategies, have broad therapeutic prospects. In addition, these inhibitors can participate in the tumour immune microenvironment (TIME) through blocking PD-1/PD-L1 binding, which can improve immune efficacy. This article provides an overview of the use of PD-1/PD-L1 inhibitors in the treatment of TNBC and the progress of multiple therapeutic studies. To increase the survival of TNBC patients, relevant biomarkers for predicting the efficacy of PD-1/PD-L1 inhibitor therapy have been explored to identify new strategies for the treatment of TNBC.

APOBEC-Driven Hypermutation in the Lymphocyte-Predominant Group of Triple-Negative Breast Cancer

This study aimed to evaluate the clinicopathologic and genomic characteristics of triple-negative breast cancer subclassification. Triple-negative breast cancer was classified into the luminal androgen receptor (LAR) subtype and the tumor-infiltrating lymphocytes (TILs) groups of the non-LAR subtype-lymphocyte predominant (LP), lymphocyte intermediate, and lymphocyte depleted-based on androgen receptor immunohistochemistry and TILs. Clinicopathologic and genomic characteristics were evaluated for these triple-negative breast cancer subclasses. The LP group was associated with a histologic type of carcinoma with medullary features, a higher tumor mutation burden, and increased APOBEC activity, indicative of APOBEC-driven hypermutation. The LAR subtype was characterized by a higher prevalence of PIK3CA mutations, lower homologous recombination deficiency scores, and associations with histologic types of invasive lobular carcinoma, and carcinoma with apocrine differentiation. This study demonstrated the distinct clinicopathologic and genomic characteristics of triple-negative breast cancer subclassifications. APOBEC activity-related hypermutation is a defining characteristic of the LP group.

Comprehensive genomic profiling can predict response to neoadjuvant chemotherapy in triple-negative breast cancer

BACKGROUND

The rate of pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC) varies, and adjuvant therapy treatment for residual cancer remains a challenge. The aim of our study was to assess the added value of FoundationOne®CDx (F1CDx) testing in the non-metastatic TNBC in predicting responses to NACT and disease outcomes.

METHODS

Ninety-three eligible patients with stage II-III TNBC were treated with NACT without immunotherapy. Response to NACT was evaluated postoperatively. Comprehensive genomic profiling with NGS-based molecular test F1CDx was performed on diagnostic biopsies (N = 93). Hierarchical clustering and logistic regression were applied for data analysis.

RESULTS

Genomic profiling and data clustering revealed heterogeneous genetic landscapes of TNBC with subsets displaying multilayered co-amplifications of oncogenes and overlapping changes in crucial signaling pathways. TP53 mutations were detected in 95 % of all TNBCs. BRCA1/BRCA2 mutations were significant molecular factors in predicting favorable responses to NACT (OR = 0.09, p = 0.002), while CCNDs co-mutations with FGFs (OR = 13.4, p = 0.016) and PI3Ks family mutations in AR-positive cases (OR = 6.1, p = 0.008) - poor responses. Low tumor mutational burden (TMB) ≤ 3 (OR = 9.4, p = 0.009) was a significant factor for the disease progression after NACT.

CONCLUSIONS

This study suggests that comprehensive CDx testing can be explored as a prognostic tool in early-stage TNBC to predict responses to NACT and disease progression. Based on these results, genomic analysis should be performed early in the patient journey, possibly guiding adjuvant treatment choices and participation in randomized clinical trials, mainly when pCR is not achieved, as the ultimate goal is improving patient outcomes.

Future directions in the evaluation and management of newly diagnosed metastatic cancer

There is much debate regarding optimal selection in patients with metastatic cancer who should undergo local treatment (surgery or radiation treatment) to the primary tumor and/or metastases. Additionally, the optimal treatment of newly diagnosed metastatic cancer is largely unclear. Current prognostication systems to best inform these clinical scenarios are limited, as all metastatic patients are grouped together as having Stage IV disease without further incorporation of patient and disease-specific covariates that significantly impact patient outcomes. Therefore, improving current prognostic scoring systems and incorporation of these covariates is essential to best individualize treatment for patients with metastatic cancer. In this narrative review article, we provide a detailed review of prognostication systems that can be used for both the site of metastasis and primary site to best tailor treatment in these patients. Additionally, we discuss the incorporation and ongoing developments in radiographic, genomic, and biostatistical techniques that can be used as prognostication tools.

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.

Genetic Alterations in HER2-Positive and Equivocal Breast Cancer by Immunohistochemistry

Purpose

We aimed to identify genetic alterations in groups with different HER2 immunohistochemical (IHC) scores.

Patients and Methods

A total of 120 patients with HER2-positive breast cancers, including 89 cases with IHC 3+ tumors and 31 cases with IHC 2+ and positive for in situ hybridization (ISH) were enrolled. Molecular profiles were determined using Thermo Fisher TMO comprehensive assay on surgically removed tissues. All called variants were compared between IHC3+ and IHC2+/ISH+ groups by Fisher exact test.

Results

There was a significantly higher sample frequency 94.4% (84/89) of ERBB2 amplification in IHC3+ group than that in IHC2+/ISH+ group 45.2% (14/31). By contrast, there was a significantly lower sample frequency of MYC_AMP_CNA 10.1% (9/89) and CCND3_AMP_CNA 0% (0/89) in IHC3+ group than those in IHC2+/ISH+ group with sample frequency 25.8% (8/31), and 9.7% (3/31), respectively.

Conclusion

We conclude that HER2 IHC3+ tumors have higher frequency of ERBB2_ AMP_CNA and lower frequency of CCND3_ AMP_CNA and MYC_AMP_CNA than IHC2+/ISH+ tumors. These results provide therapeutic strategies in treatment of HER2-positive breast cancer.

Clinico-pathological factors predicting pathological response in early triple-negative breast cancer

Pathological complete response (pCR) after neoadjuvant chemoimmunotherapy (NACi) is associated with improved patient outcomes in early triple-negative breast cancer (TNBC). This study aimed to identify factors associated with pCR after NACi. This cohort included all patients with stage II-III TNBC treated with NACi who underwent surgery at Institut Curie hospitals between 08/2021-06/2023. Among 208 patients, the overall pCR rate was 70% and was similar in ER < 1% (69%) and ER-low TNBC (73%, p = 0.6). In a multivariate model, Ki-67 ≥ 30% (OR 5.19 [1.73-17.3]), centralized TILs ≥ 30% (OR = 3.08 [1.42-7.04]), absence of DCIS at initial biopsy (OR = 2.56 [1.08-6.25]) and germline mutations in homologous recombination genes (OR = 9.50 [2.37-67.7]) remained strong independent predictors of pCR. These findings may guide treatment decisions in patients with TNBC undergoing NACi. Almost all patients with germline mutations in HR genes achieved pCR, supporting de-escalation trials. We suggest that ER-low tumors should be managed as TNBC tumors.

Hormone therapy enhances anti-PD1 efficacy in premenopausal estrogen receptor-positive and HER2-negative advanced breast cancer

The efficacy of immunotherapy for estrogen receptor-positive/HER2-negative (ER+/HER2-) metastatic breast cancer (MBC) has not been proven. We conduct a phase 1b/2 trial to assess the efficacy of combining pembrolizumab (anti-PD1 antibody), exemestane (nonsteroidal aromatase inhibitor), and leuprolide (gonadotropin-releasing hormone agonist) for 15 patients with premenopausal ER+/HER2- MBC who had failed one to two lines of hormone therapy (HT) without chemotherapy. The primary endpoint of progression-free survival rate at 8 months (i.e., 64.3%) is achieved. Moreover, 5 of the 14 evaluable subjects exhibited partial responses (overall response rate = 35.7%). The combination of anti-PD1 antibody and anti-hormone therapy is associated with an enhanced immunoreactive microenvironment influencing treatment efficacy, as observed in pre- and post-treatment tumor samples through NanoString analysis. Post-treatment tumors are associated with increased immune response and immune cells. The findings indicate that combining HT with anti-PD1 antibody is a promising treatment strategy for patients with premenopausal ER+/HER2- MBC. This study was registered at ClinicalTrials.gov (NCT02990845).

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.

Neoadjuvant atezolizumab in combination with dual HER2 blockade plus epirubicin in women with early HER2-positive breast cancer: the randomized phase 2 ABCSG-52/ATHENE trial

The role of anthracyclines in the treatment of early breast cancer (EBC) is increasingly being challenged, especially in de-escalation strategies. However, owing to their immunogenic effects, anthracyclines are promising combination partners with immunotherapies. In the randomized phase 2 trial ABCSG-52 (EudraCT no. 2019-002364-27), we investigated epirubicin plus immunotherapy in women with human epidermal growth factor receptor 2 (HER2)-positive EBC. A total of 58 patients were randomized 1:1 to two cycles of a chemotherapy-free induction phase (part 1) of dual HER2 blockade with trastuzumab and pertuzumab (TP) plus the anti-programmed death ligand 1 antibody atezolizumab (TP-A) or TP alone. Thereafter, all patients received four cycles of TP-A in combination with epirubicin (part 2). The primary endpoint, pathological complete response (pCR), was met in 35 patients (60.3%; 95% confidence interval (CI) 47.5% to 71.9%), 19 patients (65.5%) in the TP-A group and 16 patients (55.2%) in the TP group. The residual cancer burden 0/I rate and objective response rate (secondary endpoints) in all patients with evaluable data were 80.0% (n = 44/55; 95% CI 67.6% to 88.4%) and 89.3% (n = 50/56; 95% CI 78.5% to 95.0%), respectively. Grade ≥3 adverse events were reported in 17 patients (29.3%). Based on our findings, we conclude that a neoadjuvant chemotherapy de-escalation immunotherapy regimen with trastuzumab, pertuzumab, atezolizumab and epirubicin is effective and safe in patients with HER2-positive EBC.

The cytokine profile correlates with less tumor-infiltrating lymphocytes in luminal A breast cancer

PURPOSE

Tumor-infiltrating lymphocyte (TIL) levels are prognostic and predictive factors for breast cancer. Unlike other subtypes, most luminal A breast cancers are immune deserts; however, the underlying mechanisms are poorly understood.

METHODS

Immune-related cytokines, chemokines, and growth factors were measured in the sera of 103 patients with breast cancer using a multiplex panel. The TILs were evaluated for hotspot lesions.

RESULTS

Circulating interleukin 1 receptor antagonist (IL-1ra), IL-8, IL-12, IL-17, macrophage inflammatory protein-1β (MIP-1b), and platelet-derived growth factor B homodimer (PDGF-bb) concentrations were significantly associated with TIL levels. Cluster analysis using these six variables identified six clusters related to TIL levels. Breast cancers with high TILs (≥ 50%) were most frequent in cluster 3 (9 out of 15 cases, 60.0%), followed by cluster 1 (8 out of 34 cases, 23.5%), and the fewest in cluster 6 (1 out of 21 cases, 4.8%), whereas only one or three cases were present in clusters 2, 4, and 5 (p = 0.0064). Cluster 6, consisting mostly of luminal A (19 out of 21 cases, 90.5%), showed high levels of IL-12, IL-17, and PDGF-bb, and low levels of MIP-1b.

CONCLUSION

We identified a luminal A-associated immunosuppressive cytokine signature in circulation. These results suggest that a tumor microenvironment with high levels of IL-17 and PDGF-bb, and low levels of MIP-1b in luminal A breast cancers results in low induction of TILs. Our data may partially explain the low TIL levels observed in the patients with luminal A breast cancer.

Identification of BRCA new prognostic targets and neoantigen candidates from fusion genes

Cancer-associated gene fusions serve as a potential source of highly immunogenic neoantigens. In this study, we identified fusion proteins from fusion genes and extracted fusion peptides to accurately predict Breast cancer (BRCA) neo-antigen candidates by high-throughput artificial intelligence computation. Firstly, Deepsurv was used to evaluate the prognosis of patients, providing a landscape of prognostic fusion genes in BRCA. Next, AGFusion was utilized to generate full-length fusion protein sequences and annotate functional domains. Advanced neural networks and Transformer-based analyses were implemented to predict the binding of fusion peptides to 112 types of HLA, thereby forming a new immunotherapy candidates' library of BRCA neo-antigens (n = 7791, covering 88.41% of patients). Among them, 15 neo-antigens were validated and factually translated into mass spectrometry data of BRCA patients. Finally, AlphaFold2 was applied to predict the binding sites of these neo-antigens to MHC (HLA) molecules. Notably, we identified a prognostic neoantigen from the TBC1D4-COMMD6 fusion that significantly improves patient prognosis and extensively binds to 16 types of HLA alleles. These highly immunogenic and tumor-specific neoantigens offer emerging targets for personalized cancer immunotherapies and act as prospective predictors for tumor survival prognosis and responses to immune checkpoint therapies.

Integrative analysis of homologous recombination repair patterns unveils prognostic signatures and immunotherapeutic insights in breast cancer

Globally, breast cancer (BC) is the leading cause of female death and morbidity. Homologous recombination repair (HRR) is critical in BC. However, the prognostic role and immunotherapy response of HRR in BC remains to be clarified. Firstly, we identified HRR types in BC samples from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset (GSE42568) based on 65 HRR genes (HRRGs). A differentially expressed gene (DEG) list for different HRR types was generated. Then, the influences of gene sets composed of these DEGs on biological pathways and BC prognosis were explored. Next, we identified gene clusters based on gene sets composed of DEGs. Genes associated with prognosis for DEGs were identified using univariate Cox regression. Finally, the HRR score was constructed based on genes associated with prognosis. We analyzed how HRR score correlates with tumor mutation burden (TMB), immune cell infiltration (ICI), and immunotherapy response. Three HRR clusters were discovered. HRR subtype A demonstrated decreased infiltration and a high number of immunosuppressive cells with a poor prognosis. DEGs among various HRR types were predominantly enriched in cell cycle and genomic stability-related pathways. The prognostic model based on sixteen DEGs accurately predicted BC prognosis. The HRRGs were differentially expressed in three DEG clusters. TMB, ICI, and immunotherapy responses differed significantly between the high and low HRR groups (HSG, LSG). The HSG was distinguished by a high degree of ICI and low TMB. LSG had a better response to anti-PD-1 or anti-PD-1 and anti-CTLA4 combination therapy. This work revealed that HRR patterns would contribute to predicting prognosis and immunotherapy response in BC, which may benefit patients.

PD-1/PD-L1 immune checkpoint blockade in breast cancer: research insights and sensitization strategies

Immunotherapy targeting programmed cell death-1 (PD-1) and PD-L1 immune checkpoints has reshaped treatment paradigms across several cancers, including breast cancer. Combining PD-1/PD-L1 immune checkpoint blockade (ICB) with chemotherapy has shown promising efficacy in both early and metastatic triple-negative breast cancer, although only a subset of patients experiences durable responses. Identifying responders and optimizing immune drug selection are therefore critical. The effectiveness of PD-1/PD-L1 immunotherapy depends on both tumor-intrinsic factors and the extrinsic cell-cell interactions within the tumor microenvironment (TME). This review systematically summarizes the key findings from clinical trials of ICBs in breast cancer and examines the mechanisms underlying PD-L1 expression regulation. We also highlight recent advances in identifying potential biomarkers for PD-1/PD-L1 therapy and emerging evidence of TME alterations following treatment. Among these, the quantity, immunophenotype, and spatial distribution of tumor-infiltrating lymphocytes stand out as promising biomarkers. Additionally, we explore strategies to enhance the effectiveness of ICBs in breast cancer, aiming to support the development of personalized treatment approaches tailored to the unique characteristics of each patient's tumor.

An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer

T cells are generally sparse in hormone receptor-positive (HR+) breast cancer, potentially due to limited antigen presentation, but the driving mechanisms of low T cell abundance remains unclear. Therefore, we defined and investigated programs ('gene modules'), related to estrogen receptor signaling (ERS) and immune signaling using bulk and single-cell transcriptome and multiplexed immunofluorescence of breast cancer tissues from multiple clinical sources and human cell lines. The ERS gene module, dominantly expressed in cancer cells, was negatively associated with immune-related gene modules TNFα/NF-κB signaling and type-I interferon (IFN-I) response, which were expressed in distinct stromal and immune cell types, but also, in part, expressed and preserved as a cancer cell-intrinsic mechanisms. Spatial analysis revealed that ERS strongly correlated with reduced T cell infiltration, potentially due to its association with suppression of TNFα/NF-κB-induced angiogenesis and IFN-I-induced HLA expression in macrophages. Preoperative endocrine therapy in ER+/HER2-breast cancer patients produced better responses in ERS-high patients, with TNFα/NF-κB expression associated with reduced ERS. Targeting these pathways may enhance T cell infiltration in HR+ breast cancer patients.

Statement of Significance

This study elucidates the immunosuppressive role of ER signaling in breast cancer, highlighting a complex interplay between cancer, stromal, and immune cells and reveals potential approaches to enhance immunogenicity in HR+ breast cancer. These findings offer crucial insights into immune evasion in breast cancer and identify strategies to enhance T cell abundance.

Single-cell sequencing unveils mitophagy-related prognostic model for triple-negative breast cancer

Background

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer lacking hormone receptors and HER2 expression, leading to limited treatment options and poor prognosis. Mitophagy, a selective autophagy process targeting damaged mitochondria, plays a complex role in cancer progression, yet its prognostic significance in TNBC is not well understood.

Methods

This study utilized single-cell RNA sequencing data from the TCGA and GEO databases to identify mitophagy-related genes (MRGs) associated with TNBC. A prognostic model was developed using univariate Cox analysis and LASSO regression. The model was validated across multiple independent cohorts, and correlations between MRG expression, immune infiltration, and drug sensitivity were explored.

Results

Nine key MRGs were identified and used to stratify TNBC patients into high-risk and low-risk groups, with the high-risk group showing significantly worse survival outcomes. The model demonstrated strong predictive accuracy across various datasets. Additionally, the study revealed a correlation between higher MRG expression levels and increased immune cell infiltration, as well as potential responsiveness to specific chemotherapeutic agents.

Conclusion

The mitophagy-related prognostic model offers a novel method for predicting outcomes in TNBC patients and highlights the role of mitophagy in influencing the tumor microenvironment, with potential applications in personalized treatment strategies.

Construction of a prognostic model based on cuproptosis-related patterns for predicting survival, immune infiltration, and immunotherapy efficacy in breast cancer: Cuproptosis-based prognostic modeling in breast cancer

Breast cancer is the most common and lethal malignancy among women worldwide. Cuproptosis, a newly identified copper-dependent cell death, is closely associated with cancer development. However, its regulatory mechanisms in breast cancer are not well studied. This study aims to establish a prognostic model for breast cancer to improve risk stratification. The mRNA expression data was downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. Consensus clustering identified patterns based on cuproptosis-related genes. Key genes were screened using Weighted Gene Co-Expression Network Analysis and differentially expressed gene analysis. A prognostic model was constructed using Cox regression and evaluated with time-dependent receiver operating characteristic and Kaplan-Meier analyses. Functional pathways, immune cell infiltration, and other tumor characteristics were also analyzed. Two distinct cuproptosis patterns were identified. The top 21 differentially expressed genes, significantly associated with survival, were used to construct the prognostic model. The risk score has a negative correlation with survival. Enrichment analysis showed immune-related pathways enriched in the low-risk group, which also had more immune cell infiltration, higher stromal component, lower tumor purity, and lower tumor heterogeneity. Finally, significant differences of half maximal inhibitory concentration were also observed between patients in high- and low-risk groups who received chemotherapy and targeted therapy drugs. These findings in our study may provide evidence for further research and individualized management of breast cancer.

Triple-Negative Breast Cancer: Tumor Immunogenicity and Beyond

Triple-negative breast cancer (TNBC) is a breast malignancy with a poor prognosis and limited therapeutic options. Many studies show that TNBC exhibits heterogeneity across clinical, histopathological, and molecular levels. In this review, we discuss the immunogenic features of TNBC with a focus on immunotherapy and the current standard of care in the neoadjuvant, adjuvant, and metastatic setting. In addition, we address the ongoing research on immunotherapy, antibody-drug conjugates (ADCs), poly ADP-ribose polymerase (PARP) inhibitors, and future challenges in the treatment of this entity.

Liquid biopsy in triple-negative breast cancer: unlocking the potential of precision oncology

In the era of precision oncology, the management of triple-negative breast cancer (TNBC) is rapidly changing and becoming more complicated with a variety of chemotherapy, immunotherapy, and targeted treatment options. Currently, TNBC treatment is based on prognostic and predictive factors including immunohistochemical biomarkers [e.g. programmed death-ligand 1 (PD-L1)] and germline BRCA mutations. Given the current limitation of existing biomarkers, liquid biopsies may serve as clinically useful tools to determine treatment efficacy and response in both the (neo)adjuvant and metastatic settings, for detecting early relapse, and for monitoring clonal evolution during treatment. In this review, we comprehensively summarize current and future liquid biopsy applications. Specifically, we highlight the role of circulating tumor cell characterization, circulating tumor DNA, and other preclinical liquid biopsy technologies including circulating exosomes, RNA liquid biopsy, and circulating immune-based biomarkers. In the near future, these biomarkers may serve to identify early disease relapse, therapeutic targets, and disease clonality for patients with TNBC in the clinical setting.

DNA damage response in breast cancer and its significant role in guiding novel precise therapies

DNA damage response (DDR) deficiency has been one of the emerging targets in treating breast cancer in recent years. On the one hand, DDR coordinates cell cycle and signal transduction, whose dysfunction may lead to cell apoptosis, genomic instability, and tumor development. Conversely, DDR deficiency is an intrinsic feature of tumors that underlies their response to treatments that inflict DNA damage. In this review, we systematically explore various mechanisms of DDR, the rationale and research advances in DDR-targeted drugs in breast cancer, and discuss the challenges in its clinical applications. Notably, poly (ADP-ribose) polymerase (PARP) inhibitors have demonstrated favorable efficacy and safety in breast cancer with high homogenous recombination deficiency (HRD) status in a series of clinical trials. Moreover, several studies on novel DDR-related molecules are actively exploring to target tumors that become resistant to PARP inhibition. Before further clinical application of new regimens or drugs, novel and standardized biomarkers are needed to develop for accurately characterizing the benefit population and predicting efficacy. Despite the promising efficacy of DDR-related treatments, challenges of off-target toxicity and drug resistance need to be addressed. Strategies to overcome drug resistance await further exploration on DDR mechanisms, and combined targeted drugs or immunotherapy will hopefully provide more precise or combined strategies and expand potential responsive populations.

Exploring the multifaceted role of key lncRNA in glioma: From genetic expression to clinical implications and immunotherapy potential

Background

Long non-coding RNAs (lncRNAs) are implicated in a variety of regulatory functions within tumors, yet their specific roles in glioma remain underexplored.

Methods

We extracted glioma patient data from The Cancer Genome Atlas and UCSC Xena database for analysis using R, focusing on genomic characterization, biological enrichment, immune evaluation, and the development of a predictive model employing machine learning techniques. Additionally, we conducted cell culture and proliferation assays.

Results

Our analysis revealed that the lncRNA SLC16A1-AS1 plays a pivotal role in glioma pathogenesis and prognosis. We observed that abnormal expression of SLC16A1-AS1 varied with tumor grade, IDH mutation status, and histological type, correlating with worse survival outcomes. Genomically, SLC16A1-AS1 was associated with Tumor Mutational Burden and other prognostic biomarkers. The expression of this lncRNA was also linked to the activation of critical biological pathways and appeared to modulate the immune microenvironment, enhancing the presence of immune cells and checkpoints, which may be predictive of immunotherapy outcomes. Our predictive model, constructed from genes associated with SLC16A1-AS1, accurately forecasted glioma prognosis, strongly correlating with survival and treatment responses. In vitro experiments further demonstrated that SLC16A1-AS1 significantly influences glioma cell proliferation, invasion, and migration, underscoring its role in tumor aggression and its potential as a therapeutic target.

Conclusions

This study underscores the significant influence of SLC16A1-AS1 on glioma progression and prognosis, with its expression correlating with tumor traits and immune responses. The findings highlight the potential of targeting SLC16A1-AS1 in therapeutic strategies aimed at mitigating glioma aggressiveness.

Advancing Cancer Care in Colombia: Results of the First In Situ Implementation of Comprehensive Genomic Profiling

BACKGROUND

Comprehensive genomic profiling (CGP) identifies genetic alterations and patterns that are crucial for therapy selection and precise treatment development. In Colombia, limited access to CGP tests underscores the necessity of documenting the prevalence of treatable genetic alterations. This study aimed to describe the somatic genetic profile of specific cancer types in Colombian patients and assess its impact on treatment selection.

METHODS

A retrospective cohort study was conducted at Clínica Colsanitas S.A. from March 2023 to June 2024. Sequencing was performed on the NextSeq2000 platform with the TruSight Oncology 500 (TSO500) assay, which simultaneously evaluates 523 genes for DNA analysis and 55 for RNA; additionally, analyses were performed with the SOPHiA DDM software. The tumor mutational burden (TMB), microsatellite instability (MSI), and programmed cell death ligand 1 (PDL1) were assessed.

RESULTS

Among 111 patients, 103 were evaluated, with gastrointestinal (27.93%), respiratory (13.51%), and central nervous system cancers (10.81%) being the most prevalent. TP53 (37%), KMT2C (28%), and KRAS (21%) were frequent mutations. Actionable findings were detected in 76.7% of cases, notably in digestive (20 patients) and lung cancers (8 patients). MSI was stable at 82.52% and high at 2.91%, whilst TMB was predominantly low (91.26%).

CONCLUSIONS

The test has facilitated access to targeted therapies, improving clinical outcomes in Colombian patients. This profiling test is expected to increase opportunities for personalized medicine in Colombia.

Identification of lysine lactylation (kla)-related lncRNA signatures using XGBoost to predict prognosis and immune microenvironment in breast cancer patients

Breast cancer (BC) stands as a predominant global malignancy, significantly contributing to female mortality. Recently uncovered, histone lysine lactylation (kla) has assumed a crucial role in cancer progression. However, the correlation with lncRNAs remains ambiguous. Scrutinizing lncRNAs associated with Kla not only improves clinical breast cancer management but also establishes a groundwork for antitumor drug development. We procured breast tissue samples, encompassing both normal and cancerous specimens, from The Cancer Genome Atlas (TCGA) database. Utilizing Cox regression and XGBoost methods, we developed a prognostic model using identified kla-related lncRNAs. The model's predictive efficacy underwent validation across training, testing, and the overall cohort. Functional analysis concerning kla-related lncRNAs ensued. We identified and screened 8 kla-related lncRNAs to formulate the risk model. Pathway analysis disclosed the connection between immune-related pathways and the risk model of kla-related lncRNAs. Significantly, the risk scores exhibited a correlation with both immune cell infiltration and immune function, indicating a clear association. Noteworthy is the observation that patients with elevated risk scores demonstrated an increased tumor mutation burden (TMB) and decreased tumor immune dysfunction and exclusion (TIDE) scores, suggesting heightened responses to immune checkpoint blockade. Our study uncovers a potential link between Kla-related lncRNAs and BC, providing innovative therapeutic guidelines for BC management.

Comprehensive Assessment of Immune Phenotype and Its Effects on Survival Outcomes in HER2-Low versus HER2-Zero Breast Cancer

Background

The understanding of molecular characteristics of HER2-low breast cancer is evolving since the establishment of trastuzumab deruxtecan. Here, we explore the differences in expression patterns of immune-related genes in the tumor immune microenvironment (TME) and survival between HER2-low and HER2-zero breast cancers.

Methods

Comprehensive genomic and immune profiling, including RNA-seq gene expression assessment of 395 immune genes, was performed on FFPE samples from 129 patients with advanced HER2-negative (immunohistochemistry (IHC) 0, 1+ or 2+ with negative ERBB2 amplification by in-situ hybridization) breast cancer. Both estrogen receptor (ER) and HER2 statuses were obtained from available pathology reports. mRNA expressions of immune biomarkers, except for PD-L1 IHC and TMB, were derived from RNA-seq. Statistical comparisons were performed using the Kruskal-Wallis or Wilcoxon Rank-Sum test or the two-sample test for equality of proportions with continuity correction (p≤0.05 for significance). Survival differences were calculated using Kaplan-Meier analysis (p≤0.05 for significance).

Results

There were no significant differences in mRNA expressions of immune-related genes between HER2-low and HER2-zero breast cancers. However, HER2-low breast cancers were associated with a higher proportion of ER-positivity. When ER was analyzed along with HER2, we observed a significantly higher tumor immunogenic signature (TIGS) expression in HER2-zero/ER-negative tumors than in HER2-low/ER-positive tumors (p=0.0088). Similarly, lower expression of PD-L1 and T cell immunoglobulin and ITIM domain (TIGIT) mRNA was observed in HER2-low/ER-positive tumors when compared to HER2-zero/ER-negative tumors (p=0.014 and 0.012, respectively). Patients with HER2-low tumors had a longer median OS than those with HER2-zero tumors (94 months vs 42 months, p=0.0044).

Conclusion

Patients with HER2-low breast cancer have longer survivals yet display no differences in immune-related gene expression when compared to those with HER2-zero cancers. The differences in survival can be attributed to the higher rate of ER-positivity seen in HER2-low breast cancers, compared to HER2-zero tumors.

Insights into E-Cadherin Impairment in CDH1-Unaltered Invasive Lobular Carcinoma: A Comprehensive Bioinformatic Study

Invasive lobular carcinoma exhibits unique morphological features frequently associated with alterations in CDH1. Although some studies have identified abnormalities in adhesion factors other than E-cadherin, the molecular mechanisms underlying E-cadherin abnormalities in CDH1-unaltered invasive lobular carcinoma remain poorly understood. In this study, we investigated the molecular underpinnings of E-cadherin dysregulation in invasive lobular carcinoma in the absence of CDH1 gene alterations, using comprehensive bioinformatic analyses. We conducted a comparative study of CDH1-mutated and non-mutated invasive lobular carcinoma and evaluated the differences in mRNA levels, reverse-phase protein array, methylation, and miRNAs. We observed that invasive lobular carcinoma cases without CDH1 alterations exhibited a significantly higher incidence of the Claudin-low subtype (p < 0.01). The results of the reverse-phase protein array indicate no significant difference in E-cadherin expression between CDH1-mutated and non-mutated cases. Therefore, abnormalities in E-cadherin production also exist in CDH1 non-mutated invasive lobular carcinoma. Considering that there are no differences in mRNA levels and methylation status, post-translational modifications are the most plausible explanation for the same. Hence, future studies should focus on elucidating the mechanism underlying E-cadherin inactivation via post-translational modifications in CDH1 non-mutated invasive lobular carcinoma.

Pan-cancer analysis of COL15A1: an immunological and prognostic biomarker

Collagen, type XV, alpha 1 (COL15A1) belongs to the collagen superfamily, which can influence disease progression by modulating immune pathways. Although the growing number of investigations demonstrating the indispensable role of COL15A1 in the progression of certain tumors, no pan-cancer assessment of COL15A1 is accessible to date. Therefore, the available data was used to explore the role of COL15A1 in 33 types of tumors and to investigate their potential immune function. Numerous bioinformatics approaches were used to research the potential oncogenic role of COL15A1, including analysis of tumor prognosis, microsatellite instability (MSI), tumor mutational burden (TMB), single nucleotide polymorphism (SNP), drug sensitivity, immune cell infiltration, and the correlation between cancer stem cells (CSCs) and COL15A1 expression. The outcome implies that most tumors had a high expression of COL15A1, and COL15A1 manifested different relationships with prognosis in different tumors, including both positive and negative correlations. COL15A1 was also found to have a significant correlation with MSI, TMB, and immune infiltrating cells. Our study suggests that COL15A1 may serve as a prognostic marker for malignancy because of its differential expression in tissues and their function in tumor immunity.

Towards targeting the breast cancer immune microenvironment

The tumour immune microenvironment is shaped by the crosstalk between cancer cells, immune cells, fibroblasts, endothelial cells and other stromal components. Although the immune tumour microenvironment (TME) serves as a source of therapeutic targets, it is also considered a friend or foe to tumour-directed therapies. This is readily illustrated by the importance of T cells in triple-negative breast cancer (TNBC), culminating in the advent of immune checkpoint therapy in combination with cytotoxic chemotherapy as standard of care for both early and advanced-stage TNBC, as well as recent promising signs of efficacy in a subset of hormone receptor-positive disease. In this Review, we discuss the various components of the immune TME in breast cancer and therapies that target or impact the immune TME, as well as the complexity of host physiology.

Identification of N6-Methyladenosine-Associated lncRNAs and Analysis of Prognostic Signature in Breast Cancer

Breast cancer represents the predominant malignant neoplasm in women, posing significant threats to both life and health. N6-methyladenosine (m6A) methylation, the most prevalent RNA modification, plays a crucial role in cancer development. This study aims to delineate the prognostic implications of m6A-associated long non-coding RNAs (m6AlncRNAs) and identify potential m6AlncRNA candidates as novel therapeutic targets for breast cancer. Through univariate Cox, Least Absolute Shrinkage and Selection Operator and multiple Cox regression analysis, m6AlncRNA was analyzed and a risk-prognosis model was constructed. Kaplan-Meier analysis, principal component analysis and nomogram were used to evaluate the risk model. Finally, we screened candidate lncRNAs and validated them in breast cancer cell lines. m6AlncRNAs were stratified into three subtypes, and their associations with survival outcomes and immune infiltrating capacities were systematically analyzed. Subsequently, breast cancer patients were stratified into high and low-risk groups based on median risk scores, revealing distinct clinical characteristics, tumor immunoinvasive profiles, tumor mutation burden, and survival probabilities. Additionally, a prognostic model was established, highlighting three promising candidate lncRNAs: ECE1-AS1, NDUFA6-DT, and COL4A2-AS1. This study investigated the prognostic implications of m6A-associated long non-coding RNAs (m6AlncRNAs) and developed a prognostic risk model to identify three potential m6AlncRNA candidates. These findings provide valuable insights into the potential application of these m6AlncRNAs in guiding immunotherapeutic strategies for breast cancer.

Immunotherapy in Breast Cancer

Breast cancer is a disease encompassing a spectrum of molecular subtypes and clinical presentations, each with distinct prognostic implications and treatment responses. Breast cancer has traditionally been considered an immunologically "cold" tumor, unresponsive to immunotherapy. However, clinical trials in recent years have found immunotherapy to be an efficacious therapeutic option for select patients. Breast cancer is categorized into different subtypes ranging from the most common positive hormone receptor (HR+), human epidermal growth factor receptor 2 (HER2)-negative type, to less frequent HER2- positive breast cancer and triple-negative breast cancer (TNBC), highlighting the necessity for tailored treatment strategies aimed at maximizing patient outcomes. Despite notable progress in early detection and new therapeutic modalities, breast cancer remains the second leading cause of cancer death in the USA. Moreover, in recent decades, breast cancer incidence rates have been increasing, especially in women younger than the age of 50. This has prompted the exploration of new therapeutic approaches to address this trend, offering new therapeutic prospects for breast cancer patients. Immunotherapy is a class of therapeutic agents that has revolutionized the treatment landscape of many cancers, namely melanoma, lung cancer, and gastroesophageal cancers, amongst others. Though belatedly, immunotherapy has entered the treatment armamentarium of breast cancer, with the approval of pembrolizumab in combination with chemotherapy in triple-negative breast cancer (TNBC) in the neoadjuvant and advanced settings, thereby paving the path for further research and integration of immune checkpoint inhibitors in other subtypes of breast cancer. Trials exploring various combination therapies to harness the power of immunotherapy in symbiosis with various chemotherapeutic agents are ongoing in hopes of improving response rates and prolonging survival for breast cancer patients. Biomarkers and precise patient selection for the utilization of immunotherapy remain cardinal and are currently under investigation, with some biomarkers showing promise, such as Program Death Lignat-1 (PDL-1) Combined Positive Score, Tumor Mutation Burden (TMB), and Tumor Infiltrating Lymphocytes (TILs). This review will present the current landscape of immunotherapy, particularly checkpoint inhibitors, in different types of breast cancer.

Evolving Management of Breast Cancer in the Era of Predictive Biomarkers and Precision Medicine

Breast cancer is the most common cancer among women in the world as well as in the United States. Molecular and histological differentiation have helped clinicians optimize treatments with various therapeutics, including hormonal therapy, chemotherapy, immunotherapy, and radiation therapy. Recently, immunotherapy has become the standard of care in locally advanced triple-negative breast cancer and an option across molecular subtypes for tumors with a high tumor mutation burden. Despite the advancements in personalized medicine directing the management of localized and advanced breast cancers, the emergence of resistance to these therapies is the leading cause of death among breast cancer patients. Therefore, there is a critical need to identify and validate predictive biomarkers to direct treatment selection, identify potential responders, and detect emerging resistance to standard therapies. Areas of active scientific and clinical research include novel personalized and predictive biomarkers incorporating tumor microenvironment, tumor immune profiling, molecular characterization, and histopathological differentiation to predict response and the potential emergence of resistance.

Breast Cancer Immune Landscape: Interplay Between Systemic and Local Immunity

Breast cancer (BC) is one of the most common malignancies in women worldwide. Numerous studies in immuno-oncology and successful trials of immunotherapy have demonstrated the causal role of the immune system in cancer pathogenesis. The interaction between the tumor and the immune system is known to have a dual nature. Despite cytotoxic lymphocyte activity against transformed cells, a tumor can escape immune surveillance and leverage chronic inflammation to maintain its own development. Research on antitumor immunity primarily focuses on the role of the tumor microenvironment, whereas the systemic immune response beyond the tumor site is described less thoroughly. Here, a comprehensive review of the formation of the immune profile in breast cancer patients is offered. The interplay between systemic and local immune reactions as self-sustaining mechanism of tumor progression is described and the functional activity of the main cell populations related to innate and adaptive immunity is discussed. Additionally, the interaction between different functional levels of the immune system and their contribution to the development of the pro- or anti-tumor immune response in BC is highlighted. The presented data can potentially inform the development of new immunotherapy strategies in the treatment of patients with BC.

Public neoantigens in breast cancer immunotherapy (Review)

Among women globally, breast cancer is the most prevalent cancer and the leading cause of cancer‑related death. Interestingly, though genetic mutations contribute to the disease, <15% of women diagnosed with breast cancer have a family history of the disease, suggesting a prevalence of sporadic genetic mutations in breast cancer development. In the rapidly rising field of cancer genomics, neoantigen‑based immunotherapy has come to the fore. The investigation of novel proteins arising from unique somatic mutations or neoantigens have opened a new pathway for both individualized and public cancer treatments. Because they are shared among individuals with similar genetic changes, public neoantigens provide an opportunity for 'off‑the‑shelf' anticancer therapies, potentially extending the benefits to a wider patient group. The present review aimed to highlight the role of shared or public neoantigens as therapeutic targets for patients with breast cancer, emphasizing common hotspot mutations of certain genes identified in breast cancer. The clinical utilization of public neoantigen‑based therapies for breast cancer treatment were also discussed.

Dynamic change of cancer genome profiling in metachronous bilateral breast cancer with BRCA pathogenic variant

A 61-year-old woman with BRCA2 pathogenic variant had been treated for 20 years and showed dynamic changes in the genomic profile of her metachronous bilateral breast cancer and metastases. She underwent right breast conservation surgery at age 42-Genome 1, lung metastasis and left axillary lymph node metastasis at age 51, partial excision under local anesthesia for left breast cancer at age 53-Genome 2, left axillary lymph node dissection was added 6 month later-Genome 3. Then, olaparib was administered, and subsequently, left mastectomy was performed for the recurrence of left breast cancer at age 59-Genome 4. Genomic profile of the tumor was analyzed at four points (Genome 1-3 were analyzed by in house breast cancer panel, and Genome 4 was analyzed by Foundation One CDx). Two interesting findings emerged from these analyses. First, the genomic profile revealed that the left axillary lymph node metastasis, considered histologically from right breast cancer, was a metastasis from the left breast cancer. The second finding is that as the disease progressed, mutation profile became more diverse. The profile of the left breast cancer removed after olaparib and other treatments showed reversion mutation of BRCA2 and was diagnosed as tumor mutation burden high. Subsequent response to pembrolizumab was favorable.

Construction of a prognostic model for breast cancer based on moonlighting genes

Breast cancer (BRCA) is a highly heterogeneous disease, with significant differences in prognosis among patients. Existing biomarkers and prognostic models have limited ability to predict BRCA prognosis. Moonlighting genes regulate tumor progression and are associated with cancer prognosis. This study aimed to construct a moonlighting gene-based prognostic model for BRCA. We obtained differentially expressed genes (DEGs) in BRCA from The Cancer Genome Atlas and intersected them with moonlighting genes from MoonProt to acquire differential moonlighting genes. GO and KEGG results showed main enrichment of these genes in the response of BRCA cells to environmental stimuli and pentose phosphate pathway. Based on moonlighting genes, we conducted drug prediction and validated results through cellular experiments. After ABCB1 knockdown, viability and proliferation of BRCA cells were significantly enhanced. Based on differential moonlighting genes, BRCA was divided into three subgroups, among which cluster2 had the highest survival rate and immunophenoscore and relatively low tumor mutation burden. TP53 had the highest mutation frequency in cluster2 and cluster3, while PIK3CA had a higher mutation frequency in cluster1, with the majority being missense mutations. Subsequently, we established an 11-gene prognostic model in the training set based on DEGs among subgroups using univariate Cox regression, LASSO regression, and multivariable Cox regression analyses. Model prognostic performance was verified in GEO, METABRIC and ICGC validation sets. In summary, this study obtained three BRCA moonlighting gene-related subtypes and constructed an 11-gene prognostic model. The 11-gene BRCA prognostic model has good predictive performance, guiding BRCA prognosis for clinical doctors.

Resonance of fatty acid metabolism and immune infiltration in anti-PD-1 monotherapy for breast cancer

The interaction between tumor fatty acid metabolism and immune microenvironment is a novel topic in oncology research, and the relationship of lipid-derived factors with immune editing in tumor is unclear. The breast cancer samples from the TCGA database were used as the training set, and samples from GSE42568 were employed as the validation set for constructing a model to identify a signature associated with fatty acid metabolism through Lasso Cox regression. And the changes in immune related signatures and risk score before and after anti-PD-1 monotherapy were caught by the differential analysis in GSE225078. A 14-gene prognostic risk scoring model identifying by fatty acid metabolism relevant signature was conducted, and the high risk group had shorter overall survival and progression free survival than low risk group. Many metabolism-related pathways were enriched in the high risk group, and many immune-related pathways were enriched in low risk group. The crucial differentially expressed genes between the high/low risk groups, CYP4F8 and CD52, were found to be strongly associated with SUCLA2 and ACOT4 of 14-gene model, and strongly related to immune infiltration. Immune related signatures, fatty acid metabolism-risk score and the expression level of ALDH1A1 (in 14-gene-model) changed after anti-PD-1 monotherapy. And the mice model results also showed anti-PD-1 mAb could significantly reduce the expression level of ALDH1A1 (p < 0.01). These results brought up the crosstalk between immune components and fatty acid metabolism in breast cancer microenvironment, which provided a new possibility of targeting fatty acid metabolism for combination therapy in breast cancer immunotherapy.

Engineered Immunologic Niche Monitors Checkpoint Blockade Response and Probes Mechanisms of Resistance

Antibodies to programmed cell death protein1 (anti-PD-1) have become a promising immunotherapy for triple negative breast cancer (TNBC), blocking PD-L1 signaling from pro-tumor cells through T cell PD-1 receptor binding. Nevertheless, only 10-20% of PD-L1+ metastatic TNBC patients who meet criteria benefit from ICB, and biomarkers to predict patient response have been elusive. We have previously developed an immunological niche, consisting of a microporous implant in the subcutaneous space, that supports tissue formation whose immune composition is consistent with that within vital organs. Herein, we investigated dynamic gene expression within this immunological niche to provide biomarkers of response to anti-PD-1. In a 4T1 model of metastatic TNBC, we observed sensitivity and resistance to anti-PD-1 based on primary tumor growth and survival. The niche was biopsied before, during, and after anti-PD-1 therapy, and analyzed for cell types and gene expression indicative of treatment refractivity. Myeloid cell-to-lymphocyte ratios were altered between ICB-sensitivity and resistance. Longitudinal analysis of gene expression implicated dynamic myeloid cell function that stratified sensitivity from resistance. A niche-derived gene signature predicted sensitivity or resistance prior to therapy. Analysis of the niche to monitor immunotherapy response presents a new opportunity to personalize care and investigate mechanisms underlying treatment resistance.

Comprehensive genomic profiling and therapeutic implications for Taiwanese patients with treatment-naïve breast cancer

BACKGROUND

Breast cancer is a heterogeneous disease categorized based on molecular characteristics, including hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) expression levels. The emergence of profiling technology has revealed multiple driver genomic alterations within each breast cancer subtype, serving as biomarkers to predict treatment outcomes. This study aimed to explore the genomic landscape of breast cancer in the Taiwanese population through comprehensive genomic profiling (CGP) and identify diagnostic and predictive biomarkers.

METHODS

Targeted next-generation sequencing-based CGP was performed on 116 archived Taiwanese breast cancer specimens, assessing genomic alterations (GAs), including single nucleotide variants, copy number variants, fusion genes, tumor mutation burden (TMB), and microsatellite instability (MSI) status. Predictive variants for FDA-approved therapies were evaluated within each subtype.

RESULTS

In the cohort, frequent mutations included PIK3CA (39.7%), TP53 (36.2%), KMT2C (9.5%), GATA3 (8.6%), and SF3B1 (6.9%). All subtypes had low TMB, with no MSI-H tumors. Among HR + HER2- patients, 42% (27/65) harbored activating PIK3CA mutations, implying potential sensitivity to PI3K inhibitors and resistance to endocrine therapies. HR + HER2- patients exhibited intrinsic hormonal resistance via FGFR1 gene gain/amplification (15%), exclusive of PI3K/AKT pathway alterations. Aberrations in the PI3K/AKT/mTOR and FGFR pathways were implicated in chemoresistance, with a 52.9% involvement in triple-negative breast cancer. In HER2+ tumors, 50% harbored GAs potentially conferring resistance to anti-HER2 therapies, including PIK3CA mutations (32%), MAP3K1 (2.9%), NF1 (2.9%), and copy number gain/amplification of FGFR1 (18%), FGFR3 (2.9%), EGFR (2.9%), and AKT2 (2.9%).

CONCLUSION

This study presents CGP findings for treatment-naïve Taiwanese breast cancer, emphasizing its value in routine breast cancer management, disease classification, and treatment selection.

Entinostat, nivolumab and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial

We report the results of 24 women, 50% (N = 12) with hormone receptor-positive breast cancer and 50% (N = 12) with advanced triple-negative breast cancer, treated with entinostat + nivolumab + ipilimumab from the dose escalation (N = 6) and expansion cohort (N = 18) of ETCTN-9844 ( NCT02453620 ). The primary endpoint was safety. Secondary endpoints were overall response rate, clinical benefit rate, progression-free survival and change in tumor CD8:FoxP3 ratio. There were no dose-limiting toxicities. Among evaluable participants (N = 20), the overall response rate was 25% (N = 5), with 40% (N = 4) in triple-negative breast cancer and 10% (N = 1) in hormone receptor-positive breast cancer. The clinical benefit rate was 40% (N = 8), and progression-free survival at 6 months was 50%. Exploratory analyses revealed that changes in myeloid cells may contribute to responses; however, no correlation was noted between changes in CD8:FoxP3 ratio, PD-L1 status and tumor mutational burden and response. These findings support further investigation of this treatment in a phase II trial.

The anti-cancer immune response in breast cancer: current and emerging biomarkers and treatments

Triple-negative breast cancers (TNBCs) exhibit heightened T cell infiltration, contributing to an enhanced response to immune checkpoint blockade (ICB) compared with other subtypes. An immune-rich immune microenvironment correlates with improved prognosis in early and advanced TNBC. Combination chemotherapy and ICB is now the standard of care in early- and late-stage TNBC. Although programmed death ligand-1 (PD-L1) positivity predicts ICB response in advanced stages, its role in early-stage disease remains uncertain. Despite neoadjuvant ICB becoming common in early-stage TNBC, the necessity of adjuvant ICB after surgery remains unclear. Understanding the molecular basis of the immune response in breast cancer is vital for precise biomarkers for ICB and effective combination therapy strategies.