Molecular portraits of human breast tumours

Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression

Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.

Pharmacological modulation of cellular senescence: Implications for breast cancer progression and therapeutic strategies

Senescence, defined by the cessation of cell proliferation, plays a critical and multifaceted role in breast cancer progression and treatment. Senescent cells produce senescence-associated secretory phenotypes (SASP) comprising inflammatory cytokines, chemokines, and small molecules, which actively shape the tumor microenvironment, influencing cancer development, progression, and metastasis. This review provides a comprehensive analysis of the types and origins of senescent cells in breast cancer, alongside their markers and detection methods. Special focus is placed on pharmacological strategies targeting senescence, including drugs that induce or inhibit senescence, their molecular mechanisms, and their roles in therapeutic outcomes when combined with chemotherapy and radiotherapy. By exploring these pharmacological interventions and their impact on breast cancer treatment, this review underscores the potential of senescence-targeting therapies to revolutionize breast cancer management.

Landscape of lncRNAs expressed in Mexican patients with triple‑negative breast cancer

Long non‑coding RNAs (lncRNAs) are key regulators of gene expression, that can regulate a range of carcinogenic processes. Moreover, they exhibit stability in biological fluids, with some displaying tissue specificity. As their expression depends on specific conditions or is linked to the regulation of particular signaling pathways, lncRNAs are promising candidates for providing insights into the likely progression of the disease. This allows for the stratification of patients based on their risk of progression, making them potential prognostic biomarkers in various types of cancer. In addition, the tissue‑specific expression profile of lncRNAs renders them ideal candidates for detection, prognosis and monitoring of cancer progression. The present study aims to provide an overview of differentially expressed lncRNAs in Mexican patients with triple‑negative breast cancer (TNBC), a subtype of breast cancer. The aim was to identify potential prognostic biomarkers that can be applied to improve the clinical management of Mexican patients with TNBC. Human Transcriptome Array 2.0 microarrays were used to analyze the transcriptome of TNBC and luminal tumors, which are reported to have a good prognosis amongst aggressive tumor types. Subsequently, results from these microarrays were validated in a cohort from The Cancer Genome Atlas, an independent cohort of Mexican patients and in breast cancer cell lines (MCF7, ZR75, T47D, MDA‑MB‑231, MDA‑MB‑468 and BT20). A total of 746 differentially expressed transcripts were identified, including 102 lncRNAs in TNBC compared with luminal tumors. Among the lncRNAs with the most significant changes in expression levels, SOX9‑AS was highly expressed in TNBC, whereas the expression of Lnc‑peroxidasin‑3:1 (Lnc‑PXDN‑3:1), Lnc‑RNA Synapse Defective Rho GTPase Homolog (Lnc‑SYDE) and long intergenic non‑coding RNA (LINC)01087 were decreased. In addition, the low expression of lncRNA LINC01087, LINC02568, ACO22196, and lncRNA eosinophil granule ontogeny transcript (Lnc‑EGOT) was associated with poor overall survival (OS). Further analysis revealed that the high expression levels of Lnc‑PXDN‑3:1, Lnc RNA fibrous sheath interacting protein 1‑6:3 and (LINC)00182 were associated with reduced survival in patients with the luminal subtype of breast cancer. Similarly, low expression levels of lncRNAs such as GATA binding protein 3‑1 (Lnc‑GATA‑3‑1), LINC01087, and BX679671.1 in luminal subtypes of breast cancer, as well as LINC00504 and LncRNA rho guanine nucleotide exchange factor 38 intronic transcript 1 (Lnc‑ARHGEF38‑IT1) in basal subtypes have been linked to poorer survival. The interactions and functions of LINC01087 were then investigated, revealing the interaction of LINC01087 with RNAs and transcription factors, highlighting their potential involvement in the estrogen receptor pathway. The present study provided a detailed analysis of the expression of lncRNAs in TNBC, which highlights the role of lncRNAs as a biomarker in the survival outcomes of patients with breast cancer to improve the understanding of transcriptional regulation in TNBC.

Awareness of genomic testing among patients with breast cancer in Europe

PURPOSE

Genomic testing, involving expression profiling of tumour tissue, is a powerful tool for determining appropriate treatments for certain cancer patients. This study aimed to evaluate awareness of genomic testing in breast cancer patients in five European countries.

METHODS

The survey was initiated by Cancer Patients Europe and developed with patient associations, oncologists, and a psycho-oncologist. Participants were recruited via email and social media and completed a 42-question internet survey.

RESULTS

Of 1383 participants in eligible countries completing the survey, 566 women with current or previous HR+/HER2- breast cancer, potentially eligible for genomic testing, were analysed. 245 (43.3 %) were aged 50-59 years and 381 (67.3 %) had received higher education. 238 participants (42.1 %) had heard about genomic testing; 122 (21.6 %) were informed of their eligibility for testing, and 104 (18.4 %) were given reasons for the test. The majority (N = 479; 84.6 %) felt they lacked sufficient information to decide, and only 139 (24.6 %) opted for testing. Overall, 246 (43.5 %) wanted more information on additional testing and 234 (41.3 %) wanted more information on treatment options. The main information sources were medical professionals (N = 363; 64.1 %) and the internet (N = 351; 62.0 %). However, 398 participants (70.3 %) indicated that their healthcare professionals did not advise them on where to find more information.

CONCLUSIONS

This study highlights insufficient awareness of, and access to, genomic testing in breast cancer. Healthcare professionals need to improve communication with patients regarding genomic testing and involve them in shared decision-making. Likewise, patient associations have a role in providing clear information to patients.

FGFR4 in endocrine resistance: overexpression and estrogen regulation without direct causative role

PURPOSE

Endocrine therapy resistance is the major challenge of managing patients with estrogen receptor positive (ER+) breast cancer. We previously reported frequent overexpression of FGFR4 in endocrine-resistant cell lines and breast cancers that recurred and metastasized following endocrine therapy, suggesting FGFR4 as a potential driver of endocrine resistance. In this study, we investigated the role of FGFR4 in mediating endocrine resistance and explored the therapeutic potential of targeting FGFR4 in advanced breast cancer.

METHODS

A gene expression signature of FGFR4 activity was examined in ER+breast cancer pre- and post-neoadjuvant endocrine therapy and the association between FGFR4 expression and patient survival was examined. A correlation analysis was used to uncover potential regulators of FGFR4 overexpression. To investigate if FGFR4 is necessary to drive endocrine resistance, we tested response to FGFR4 inhibition in long-term estrogen-deprived (LTED) cells and their paired parental cells. Doxycycline inducible FGFR4 overexpression and knockdown cell models were generated to examine if FGFR4 was sufficient to confer endocrine resistance. Finally, we examined response to FGFR4 monotherapy or combination therapy with fulvestrant in breast cancer cell lines to explore the potential of FGFR4 targeted therapy for advanced breast cancer and assessed the importance of PAM50 subtype in response to FGFR4 inhibition.

RESULTS

A FGFR4 activity gene signature was significantly upregulated post-neoadjuvant aromatase inhibitor treatment, and high FGFR4 expression predicted poorer survival in patients with ER+breast cancer. Gene expression association analysis using TCGA, METABRIC, and SCAN-B datasets uncovered ER as the most significant gene negatively correlated with FGFR4 expression. ER negatively regulates FGFR4 expression at both the mRNA and protein level across multiple ER+breast cancer cell lines. Despite robust overexpression of FGFR4, LTED cells did not show enhanced responses to FGFR4 inhibition compared to parental cells. Similarly, FGFR4 overexpression and knockdown did not substantially alter response to endocrine treatment in ER+cell lines, nor did FGFR4 and fulvestrant combination treatment show synergistic effects. The HER2-like subtype of breast cancer showed elevated expression of FGFR4 and an increased response to FGFR4 inhibition relative to other breast cancer subtypes.

CONCLUSIONS

Despite ER-mediated upregulation of FGFR4 post-endocrine therapy, our study does not support a general role of FGFR4 in mediating endocrine resistance in ER+breast cancer. The significant upregulation of FGFR4 expression in treatment-resistant clinical samples and models following endocrine therapy does not necessarily establish a causal link between the gene and treatment response. Our data suggest that specific genomic backgrounds such as HER2 expression may be required for FGFR4 function in breast cancer and should be further explored.

Molecular mechanisms of the anticancer action of fustin isolated from Cotinus coggygria Scop. in MDA-MB-231 triple-negative breast cancer cell line

The aim of the present work was to investigate some of the molecular mechanisms and targets of the anticancer action of the bioflavonoid fustin isolated from the heartwood of Cotinus coggygria Scop. in the triple-negative breast cancer cell line MDA-MB-231. For this purpose, we applied fluorescence microscopy analysis to evaluate apoptosis, necrosis, and mitochondrial integrity, wound healing assay to study fustin antimigratory potential and quantitative reverse transcription-polymerase chain reaction to analyze the expression of genes associated with cell cycle control, programmed cell death, metastasis, and epigenetic alterations. A complex network-based bioinformatic analysis was also employed for protein-protein network construction, hub genes identification, and functional enrichment. The results revealed a significant induction of early and late apoptotic and necrotic events, a slight alteration of the mitochondria-related fluorescence, and marked antimotility effect after fustin treatment. Of 34 analyzed genes, seven fustin targets were identified, of which CDKN1A, ATM, and MYC were significantly enriched in pathways such as cell cycle, intrinsic apoptotic signaling pathway in response to DNA damage and generic transcription pathway. Our findings outline some molecular mechanisms of the anticancer action of fustin pointing it out as a potential oncotherapeutic agent and provide directions for future in vivo research.

FGFR2-RUNX2 activation: An unexplored therapeutic pathway in luminal breast cancer related to tumor progression

Overcoming luminal breast cancer (BrCa) progression remains a critical challenge for improved overall patient survival. RUNX2 has emerged as a protein related to aggressiveness in triple-negative BrCa, however its role in luminal tumors remains elusive. We have previously shown that active FGFR2 (FGFR2-CA) contributes to increased tumor growth and that RUNX2 expression was high in hormone-independent mouse mammary carcinomas. To elucidate the interaction between FGFR2 and RUNX2 in human BrCa, we investigated their roles in tumor progression and treatment responsiveness. Increased FGFR2 activity resulted in higher RUNX2 expression, cell proliferation, and metastasis. In contrast, silencing FGFR2 reduced these parameters. Overexpression of RUNX2 in FGFR2-silenced cells rescued the inhibitory effects, promoting a more aggressive phenotype, even if compared with the wt RUNX2-transfected cells, which also had increased aggressiveness compared with naïve-transfected cells. RUNX2-overexpressing tumors were insensitive to endocrine- or FGFR inhibitor treatments. Notably, the CBFβ-RUNX complex inhibitor, AI-14-91, demonstrated great effectiveness in vitro. In a small cohort of luminal BrCa patients, nuclear RUNX2 expression was associated with tumor recurrence. Transcriptomic analysis strongly supported these data showing that patients with luminal carcinomas with high RUNX2 activity score have a worse progression-free interval than those with low RUNX2 activity. Our findings suggest a complex interplay between FGFR2 and RUNX2 in regulating tumor aggressiveness. This study underscores the significance of RUNX2 in luminal BrCa progression and posits RUNX2 as a promising therapeutic target and as a potential prognostic biomarker in luminal BrCa patients.

OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer Cells

Triple-negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resistant to chemotherapy. Therefore, there is an urgent need to identify novel therapeutic targets for the treatment of TNBC. Advances in massively parallel sequencing technology have enabled the identification of cancer cell-specific gene expression patterns and epigenetic alterations that regulate their expression. Cancer cell-specific super-enhancers (SEs) have been identified as effective therapeutic targets for cancer. In this study, we identified the functional roles of epigenetic changes and their regulatory mechanisms in TNBC cells. TNBC cell-specific SEs were formed near several genes that contribute to malignant cancer cell acquisition. We found that the transcription factor OCT-2 (encoded by POU2F2) was responsible for the formation of SEs and the expression of genes encoded in the vicinity of the SE regions. Overexpression of POU2F2 enhances the metastasis of TNBC cells in mice, and its expression is highly correlated to poor prognosis of TNBC patients. Our findings provide a new insight into cancer cell-specific epigenetic changes induced by OCT-2, which trigger the progression of TNBC, and suggest possible candidates that could be targeted for the treatment of TNBC.

Recurring cycles of deprivation of serum and migration in confined spaces augments ganglioside SSEA-4 expression, boosting clonogenicity and cisplatin resistance in TNBC cell line

The remarkable biophysical properties of metastatic migrating cells, such as their exceptional motility and deformability, enable them to migrate through physical confinements created by neighboring cells or extracellular matrix. This study explores the adaptive responses of breast cancer (BC) cell sublines derived from the highly aggressive, metastatic triple-negative MDA-MB-231 and the non-metastatic MCF7 human BC cell lines, after undergoing three rounds of confined migration (CM) stress. Our findings demonstrate that CM elicits common and cell-type specific adaptive responses in BC cell sublines. In particular, both cell sublines exhibit a similar enhancement of clonogenicity and nanoparticle (NP) uptake activity, indicating tumorigenic potential. We have, for the first time, shown that stimulation with CM induces a hybrid epithelial-to-mesenchymal transition (EMT) phenotype of MDA-MB-231 cells. This transition is characterized by a significant rise in the expression of stage-specific embryonic antigen-4 (SSEA4), alongside a substantial decline in the population of CD133+ cells and a marked reduction in Ki67 expression in the MDA-MB-231-derived subline following Cis-Platin treatment. These changes are likely associated with heightened resistance of this subline to cisplatin. In contrast, CM induces far fewer such alterations in the MCF7-derived counterpart with a notable increase of CD133+ population, which seems to be insufficient to change cell susceptibility to cisplatin exposure. This study contributes to our understanding of the adaptive mechanisms underlying metastasis and drug resistance in breast cancer, emphasizing the need for personalized approaches in cancer treatment that consider the heterogeneous responses of different cancer subtypes to environmental stresses.

Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

BACKGROUND

Transcriptomic features of breast cancer locoregional recurrence (LRR) remain poorly understood. We therefore sought to investigate transcriptomic features associated with LRR in newly diagnosed invasive breast tumors from our institutional dataset.

METHODS

Transcriptomic profiling was performed on 632 tumors from consecutive patients treated within our health system for newly diagnosed non-metastatic breast cancer. Univariable Cox models identified genes whose expression was associated with LRR (q-value < 0.05). Up-regulated (UR) genes were defined as hazard ratio (HR) > 1 and down-regulated (DR) genes were defined as HR < 1. Gene set enrichment analyses were performed for UR and DR gene sets and validated within two external cohorts of ER- tumors.

RESULTS

With a median follow-up of 7.6 years, we observed 38 LRRs: 28/481 (5.8%) in ER + and 10/151 (6.6%) in ER-. There were 43 UR and 7 DR genes associated with LRR in ER + tumors, while 417 UR and 1150 DR genes were associated with LRR in ER- tumors. UR genes in ER + tumors were enriched for roles in cell proliferation (q < 0.05). In contrast, LRR in ER- tumors was most strongly associated with DR genes enriched for MHC-II-mediated antigen presentation and T cell activation (q < 0.05). In external cohorts of ER- tumors, 97 significant DR genes (p < 0.05) were enriched for 18 pathways, including 5 pathways involved in MHC-II signaling, antigen presentation and T-cell activation.

CONCLUSIONS

Transcriptomic patterns associated with LRR appear distinct between ER + and ER- tumors. In ER + tumors, LRR appears predominantly associated with proliferation, whereas ER- LRR suggests a robust pattern of suppressed antigen presentation via MHC-II.

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations

BACKGROUND

The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors.

RESULTS

We generate epigenomics, transcriptomics, and Hi-C datastreams in healthy and tumor endometrial tissues, identifying robust ERα reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with endometrial cancer risk single-nucleotide polymorphisms and whole-genome sequencing data from primary tumors and metastatic samples reveals a striking enrichment of risk variants and non-coding somatic mutations at tumor-enriched ERα sites. Through machine learning-based predictions and interaction proteomics analyses, we identify an enhancer mutation which alters 3D genome conformation, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC.

CONCLUSIONS

In summary, we identify a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

Reversing the immunosuppressive tumor microenvironment via "Kynurenine starvation therapy" for postsurgical triple-negative breast cancer treatment

Immunotherapy is a potential strategy to suppress the postoperative recurrence and metastasis of triple-negative breast cancer (TNBC). However, the excessive accumulation of kynurenine (Kyn) leads to immunosuppressive tumor microenvironment (TME) and impedes immunotherapeutic efficacy. Herein, a two-pronged approach through "Kynurenine Starvation Therapy" is proposed based on the in-situ hydrogel implantation for postsurgical treatment of TNBC. The hydrogel is constructed via Schiff base reaction between oxidized dextran (ODEX) and 8-arm poly(ethylene glycol) amine (8-arm PEG-NH2), which exhibits excellent biocompatibility and gradual biodegradability. The indoleamine 2,3-dioxygenase 1 (IDO1) inhibitor NLG919 and kynureninase (KYNase) are noncovalently loaded into the hydrogel to prepare NLG919 + KYNase@Gel. The obtained hydrogel can sustainably release NLG919 and KYNase to synergistically deplete Kyn, thereby reversing immunosuppression to enhance the antitumor immunity within TME through "Kynurenine Starvation Therapy". Moreover, a single implantation of NLG919 + KYNase@Gel not only effectively inhibits the postoperative recurrence and metastasis in 4 T1 tumor-bearing mice, but also restrains the growth in an orthotopic TNBC mouse model. These findings highlight an innovative strategy to reinforce the antitumor immune response for the treatment of postsurgical TNBC.

Animal models in preclinical metastatic breast cancer immunotherapy research: A systematic review and meta-analysis of efficacy outcomes

Breast cancer, particularly metastatic breast cancer (MBC), presents aggressive clinical challenges with limited treatment success. Immunotherapy has emerged as a promising approach, however, discrepancies between preclinical animal models and human cancers complicate translation to clinical outcomes. This systematic review and meta-analysis evaluated the effect of immunotherapy on primary and metastatic tumor regression in animal models of MBC and assessed the models' appropriateness and reproducibility to improve future preclinical study design. Following a preregistered protocol in PROSPERO (CRD42021207033), we conducted searches in MEDLINE, Embase, and Web of Science databases, yielding 2255 studies for title/abstract screening and 108 studies included after full-text screening. All included studies used mouse models, assessing primary outcomes through tumor volume or weight and metastatic outcomes via nodule count or bioluminescence. Only 14% of studies fully reported experimental animal characteristics, and 43% provided detailed experimental procedures. Of 105 articles (293 comparisons) included in the meta-analysis, pooled effect sizes indicated significant reductions in both primary and metastatic tumors. However, high heterogeneity across studies and wide prediction intervals suggested substantial variability in model responses to immunotherapy. Univariable and multivariable meta-regressions failed to significantly explain this heterogeneity, suggesting additional factors may influence outcomes. Trim-and-fill and Egger's regression tests indicated funnel plot asymmetry, implying potential publication bias and small study effects. While our analysis demonstrated positive effects of immunotherapy on MBC and highlighted variability in animal tumor models, addressing model-related heterogeneity and enhancing methodological transparency are essential to improve reproducibility and clinical translatability.

Understanding the Molecular Mechanisms of SORBS2 in TNBC Lung Metastasis

Metastasis is the leading cause of recurrence and mortality in triple-negative breast cancer (TNBC), an aggressive subtype that predominantly spreads to the lungs, brain, bones, and liver, with lung metastasis being particularly prevalent. Despite the clinical significance of TNBC metastasis, the molecular mechanisms that drive lung-specific metastasis remain poorly understood. RNA-binding proteins (RBPs) are crucial regulators of post-transcriptional gene expression and are frequently dysregulated in cancers. This study identifies SORBS2 as a critical RBP implicated in TNBC lung metastasis. Using RNA sequencing (RNA-seq) and LACE-seq, we demonstrate that SORBS2 regulates a specific set of genes through direct binding to coding sequences (CDS), introns, and 3' untranslated regions (UTRs), and its binding targets are linked to various pathways, including a possible association with Wnt/β-catenin signaling, among others. Functional assays confirm that SORBS2 knockdown inhibits proliferation, migration, and invasion in TNBC cells. These findings highlight SORBS2 as a key regulator of TNBC lung metastasis, with a context-dependent role that promotes metastatic behavior in highly metastatic TNBC cells, providing potential avenues for novel therapeutic strategies.

A highly resolved integrated transcriptomic atlas of human breast cancers

In this study, we developed an integrated single cell transcriptomic (scRNAseq) atlas of human breast cancer (BC), the largest resource of its kind, totaling > 600,000 cells across 138 patients. Rigorous integration and annotation of publicly available scRNAseq data enabled a highly resolved characterization of epithelial, immune, and stromal heterogeneity within the tumor microenvironment (TME). Within the immune compartment we were able to characterize heterogeneity of CD4, CD8 T cells and macrophage subpopulations. Within the stromal compartment, subpopulations of endothelial cells (ECs) and cancer associated fibroblasts (CAFs) were resolved. Within the cancer epithelial compartment, we characterized the functional heterogeneity of cells across the axes of stemness, epithelial-mesenchymal plasticity, and canonical cancer pathways. Across all subpopulations observed in the TME, we performed a multi-resolution survival analysis to identify epithelial cell states and immune cell types which conferred a survival advantage in both The Cancer Genome Atlas (TCGA) and METABRIC. We also identified robust associations between TME composition and clinical phenotypes such as tumor subtype and grade that were not discernible when the analysis was limited to individual datasets, highlighting the need for atlas-based analyses. This atlas represents a valuable resource for further high-resolution analyses of TME heterogeneity within BC.

Exploiting YES1-Driven EGFR Expression Improves the Efficacy of EGFR Inhibitors

EGFR is a highly expressed driver of many cancers, yet the utility of EGFR inhibitors (EGFRi) is limited to cancers that harbor sensitizing mutations in the EGFR gene because of dose-limiting toxicities. Rather than conventionally blocking the kinase activity of EGFR, we sought to reduce its transcription as an alternative approach to broaden the therapeutic window for EGFR inhibitors targeting wild-type (WT) or mutant EGFR. We found that YES1 is highly expressed in triple-negative breast cancer (TNBC) and drives cell growth by elevating EGFR levels. Mechanistically, YES1 stimulates EGFR expression by signaling to JNK and stabilizing the AP-1 transcription factor c-Jun. This effect extends beyond TNBC as YES1 also sustains EGFR expression in non-small cell lung cancer cells, including those that harbor the EGFR gatekeeper mutation T790M. The novel ability of YES1 to regulate the expression of WT and mutant EGFR mRNA and protein provides a potential therapeutic opportunity of utilizing YES1 blockade to broadly increase the efficacy of EGFR inhibitors. Indeed, we observed synergy within in vitro and in vivo models of TNBC and non-small cell lung cancer, even in the absence of EGFR-activating mutations. Together, these data provide a rationale for blocking YES1 activity as an approach for improving the efficacy of EGFR-targeting drugs in cancers that have generally been refractory to such inhibitors. Implications: YES1 sustains EGFR expression, revealing a therapeutic vulnerability for increasing the efficacy of EGFR inhibitors by lowering the threshold for efficacy in tumors driven by the WT or mutant receptor.

Kindlin-2-Mediated Hematopoiesis Remodeling Regulates Triple-Negative Breast Cancer Immune Evasion

Triple-negative breast cancer (TNBC) presents significant clinical challenges because of its limited treatment options and aggressive behavior, often associated with poor prognosis. This study focuses on kindlin-2, an adapter protein, and its role in TNBC progression, particularly in hematopoiesis-mediated immune evasion. TNBC tumors expressing high levels of kindlin-2 induce a notable reshaping of hematopoiesis, promoting the expansion of myeloid cells in the bone marrow and spleen. This shift correlated with increased levels of neutrophils and monocytes in tumor-bearing mice over time. Conversely, genetic knockout (KO) of kindlin-2 mitigated this myeloid bias and fostered T-cell infiltration within the tumor microenvironment, indicating the pivotal role of kindlin-2 in immune modulation. Further investigations revealed that kindlin-2 deficiency led to reduced expression of PD-L1, a critical immune checkpoint inhibitor, in TNBC tumors. This molecular change sensitized kindlin-2-deficient tumors to host antitumor immune responses, resulting in enhanced tumor suppression in immunocompetent mouse models. Single-cell RNA sequencing, bulk RNA sequencing, and IHC data supported these findings by highlighting enriched immune-related pathways and increased infiltration of immune cells in kindlin-2-deficient tumors. Therapeutically, targeting PD-L1 in kindlin-2-expressing TNBC tumors effectively inhibited tumor growth, akin to the effects observed with genetic kindlin-2 KO or PD-L1 KO. Our data underscore kindlin-2 as a promising therapeutic target in combination with immune checkpoint blockade to bolster antitumor immunity and counteract resistance mechanisms typical of TNBC and other immune-evasive solid tumors. Implications: Kindlin-2 regulates tumor immune evasion through the systemic modulation of hematopoiesis and PD-L1 expression, which warrants therapeutic targeting of kindlin-2 in patients with TNBC.

Cyclin-dependent kinase 4 and 6 inhibitors in breast cancer treatment

Breast cancer is the second largest cancer in the world, and it has highest mortality rate in women worldwide. The aberrant activation of the cyclin-dependent kinase 4 and 6 (CDK4/6) pathway plays an important role in uncontrolled breast cancer cell proliferation. Therefore, targeting CDK4/6 to improve overall survival rates has been a strong interest in breast cancer therapeutics. Till date, four CDK4/6 inhibitors have been developed and approved for hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer therapies with great success. However, acquired resistance to CDK4/6 inhibitors has emerged and limits their effectiveness in breast cancer. In this review, we systematically discussed the mechanisms of resistance to CDK4/6 inhibitors including the cell cycle-specific and cell cycle-nonspecific mechanisms. Also, we analyzed combination strategies with other signaling inhibitors in clinical and preclinical settings that further expand the clinical application of CDK4/6 inhibitors in future breast cancer therapies.

Multi-omic profiling in breast cancer: utility for advancing diagnostics and clinical care

INTRODUCTION

Breast cancer remains a major global health challenge. While advances in precision oncology have contributed to improvements in patient outcomes and provided a deeper understanding of the biological mechanisms that drive the disease, historically, research and patients' allocation to treatment have heavily relied on single-omic approaches, analyzing individual molecular dimensions such as genomics, transcriptomics, or proteomics. While these have provided deep insights into breast cancer biology, they often fail to offer a complete understanding of the disease's complex molecular landscape.

AREAS COVERED

In this review, the authors explore the recent advancements in multi-omic research in the realm of breast cancer and use clinical data to show how multi-omic integration can offer a more holistic understanding of the molecular alterations and their functional consequences underlying breast cancer.

EXPERT OPINION

The overall developments in multi-omic research and AI are expected to complement precision diagnostics through potentially refining prognostic models, and treatment selection. Overcoming challenges such as cost, data complexity, and lack of standardization is crucial for unlocking the full potential of multi-omics and AI in breast cancer patient care to enable the advancement of personalized treatments and improve patient outcomes.

The American Joint Committee on Cancer (AJCC) Breast Cancer Staging, Eighth Edition, is more Reflective of Cancer Biology than the Seventh Edition

BACKGROUND

The American Joint Committee on Cancer (AJCC) eighth-edition breast cancer staging system incorporating tumor grade, hormone/human epidermal growth factor receptor 2 (HER2) receptor status, and genomic assays has demonstrated better prognostic value than the seventh edition. Given the crucial role of cancer biology in prognosis, the authors hypothesized that the AJCC eighth-edition criteria offer better biologic differentiation between stages than the seventh edition.

METHODS

This study analyzed 696 breast cancer patients from The Cancer Genome Atlas (TCGA) and Text Information Extraction System (TIES) database, with complete information available for staging according to both the AJCC seventh- and eighth-edition criteria.

RESULTS

The study indicated an increase in the number of patients classified as stage I in the eighth edition compared with the seventh edition, particularly in hormone-positive breast cancers. Furthermore, the eighth edition demonstrated improved discrimination in overall survival between stages I and II cancers. The eighth edition was able to distinguish significant differences in cell proliferation, intratumor heterogeneity, homologous recombination deficiency, and neoantigen load between stages I and II cancers. Moreover, the eighth edition more clearly differentiated immune cell infiltration between stages II and I cancer than the seventh edition. Finally, immune activity and gene expression of immune checkpoints such as PDCD1, PDL1, CTLA4, LAG3, TIGIT, and IDO1 and 2 showed a more pronounced difference between stages I and II cancers in the eighth edition than in the seventh edition.

CONCLUSION

The AJCC eighth edition breast cancer staging system better distinguishes cancers with more aggressive biology than the seventh edition.

Real-World Outcomes of Combination Anthracycline and Taxane Adjuvant Therapies in Early Triple-Negative Breast Cancer: A Moroccan Retrospective Analysis

PURPOSE

Neoadjuvant chemoimmunotherapy followed by adjuvant immunotherapy is the gold standard for treating patients with higher risk early triple-negative breast cancer (TNBC); however, in some cases, these patients undergo surgery followed by chemotherapy-based anthracyclines and taxanes without adhering to the guidelines.

METHODS

Patients with previously untreated stage I, II, and III TNBC who received adjuvant therapy with either doxorubicin and cyclophosphamide (AC) + docetaxel (AC-D), AC + weekly paclitaxel (AC-WP), epirubicin and cyclophosphamide (EC) + docetaxel (EC-D), or EC + WP (EC-WP); older than 18 years; and diagnosed between January 1st, 2011, and December 31st, 2022, were eligible for the study. Disease-free survival (DFS) is the primary reported end point. Overall survival (OS) and safety were the secondary end points.

RESULTS

We included 272 female patients. At a prespecified event-driven data cutoff, with a median follow-up of 26.3 months, the 5-year DFS was 49% (95% CI, 38 to 63) in the AC-D group, 45% (95% CI, 29 to 70) in the AC-WP group, 73% (95% CI, 61 to 100) in the EC-D group, and 72% (95% CI, 44 to 100) in the EC-WP group (hazard ratio [HR], 0.2 [95% CI, 0.06 to 0.67]; P = .08). The 7-year OS was 52% (95% CI, 32 to 83) in the AC-D group, 88% (95% CI, 78 to 99) in the AC-WP group, 95% (95% CI, 88 to 100) in the EC-D group, and 83% (95% CI, 58 to 100) in the EC-WP group (HR, 0.19 [95% CI, 0.06 to 0.66]; P = .03). Most of the grade 3-4 adverse events occurred in the AC-D group, primarily neutropenia, nausea-vomiting, and alopecia.

CONCLUSION

EC-D was linked to a slightly longer survival free of invasive, noninvasive, or distant disease and a significantly longer OS with fewer adverse events. Further studies are needed to confirm and establish long-term clinical benefits.

Evaluation and Comparison of Prognostic Multigene Tests in Early-Stage Breast Cancer: Which Is the Most Effective? A Literature Review Exploring Clinical Utility to Enhance Therapeutic Management in Luminal Patients

Breast cancer is the most common malignancy affecting women, marked by significant complexity and heterogeneity. This disease includes multiple subtypes, each with unique biological features and treatment responses. Despite significant advancements in detection and therapy, challenges remain, particularly in managing aggressive forms like triple-negative breast cancer and overcoming drug resistance. Breast cancer classification and subtype determination are typically performed by immunohistochemistry (IHC) method, which assesses four key markers (ER, PR, HER2, KI67); however, due to the recognized issues with this approach-especially regarding the evaluation of Ki67-there is a risk of misclassification. Patients who may be suitable for chemotherapy could miss possible advantages and only experience needless toxicity as a result of improper treatment decisions. Molecular profiling has improved breast cancer management, enabling the creation of multigene prognostic tests (MPTs) like Oncotype Dx, MammaPrint, Prosigna, Endopredict, and Breast Cancer Index which assess gene expression profiles to more accurately predict recurrence risks. These tools help personalize treatment, identifying patients who can avoid chemotherapy and/or extended endocrine therapy. While many MPTs are available, only Oncotype Dx and MammaPrint have prospective validation, with Prosigna providing additional prognostic insights by incorporating clinical variables. Molecular tests are especially usefull in the "gray zone," which includes tumors measuring between 1 and 3 cm with 0-3 positive lymph nodes and an intermediate proliferation index. However, their clinical utility has not been definitively established, and significant differences exist between them. This article provides an in-depth analysis of established genomic assays, including testing procedures, clinical validity, utility, diagnostic frameworks, and methodologies. Our comparison aims to improve early breast cancer management by guiding pathologists and oncologists in optimizing the use of genomic assays in clinical practice. By presenting this information, we aim to enhance understanding of the clinical utility and effectiveness of these assays, supporting the development of personalized treatment strategies for early breast cancer patients. Genomic assays offer important insights that can support treatment decisions in early-stage breast cancer, especially when used alongside other clinical evaluations, predictive tools, and management guidelines. While multiple gene expression profiling tests are available, they classify patients differently and are not interchangeable; therefore, their application should be at the clinician's discretion during the decision-making process. It is essential that these tests are not the sole factor in determining the best treatment plan: other clinical considerations and patient preferences should also play a significant role in guiding treatment decisions.

Comparison of mTOR inhibitors combined with endocrine therapy versus that alone in breast cancer: a meta-analysis

BACKGROUND

This meta-analysis aims to evaluate the efficacy and safety of rapamycin (mTOR) inhibitors with endocrine therapy versus endocrine therapy alone in treating advanced or metastatic estrogen receptor/progesterone receptor (ER/PR) + breast cancer.

METHODS

We conducted a comprehensive search in PubMed, Web of Science, Embase, and the Cochrane Library for randomized controlled trials (RCTs) comparing mTOR inhibitors plus endocrine therapy with endocrine therapy alone up to September 2024.

RESULTS

This analysis included 10 RCTs comprising 3,337 patients. Relative to endocrine therapy alone, the combination of mTOR inhibitors and endocrine therapy significantly improved the clinical benefit rate (RR = 1.41, p < 0.001), overall response rate (RR = 1.40, p = 0.006), progression-free survival (PFS; HR = 0.67, p < 0.001), and overall survival (OS; HR = 0.86, p = 0.056), although the improvement in OS was not statistically significant. Subgroup analyses indicated a more pronounced PFS advantage in patients under 65 years of age (HR = 0.55, p = 0.013) and those who had previously received chemotherapy (HR = 0.51, p = 0.001). However, the incidence of adverse events was higher in the combination therapy group, notably stomatitis (p < 0.001), elevated aspartate aminotransferase/alanine aminotransferase (p = 0.04), and diarrhea (p = 0.01).

CONCLUSIONS

The combination of mTOR inhibitors with endocrine therapy offers superior efficacy with manageable toxicities in patients with advanced or metastatic ER/PR+ breast cancer.

Using prognostic signatures and machine learning to identify core features associated with response to CDK4/6 inhibitor-based therapy in metastatic breast cancer

CDK4/6 inhibitors in combination with endocrine therapy are widely used to treat HR+/HER2- metastatic breast cancer leading to improved progression-free survival (PFS) compared to single agent endocrine therapy. Over 300 patients receiving standard-of-care CDK4/6 inhibitor combination therapy for metastatic disease were enrolled at a single institution. Clinical, pathological, and gene expression data were employed to define determinants for PFS duration. Visceral disease (HR 1.55, p = 0.0013), prior endocrine therapy (HR 2.34, p < 0.001), and the type of endocrine therapy (HR 2.16, p < 0.001) were highly associated with PFS duration. Multiple pre-defined gene expression signatures were employed to determine association with response to CDK4/6 inhibitor-based therapy. Random survival forest was applied to define key gene expression and clinical features associated with PFS and develop a predictive model. The time to progression predicted by this model was related to the median PFS observed in PALOMA-2/3 and PEARL studies. Interrogating genes identified as highly significant across all studies indicated common enrichment of gene networks associated with cell cycle and estrogen receptor signaling. These findings indicate that there are common features from real-world use of CDK4/6 inhibitors that could be used to infer time to progression and better inform treatment.

Gene Expression Signatures for Guiding Initial Therapy in ER+/HER2- Early Breast Cancer

In triple-negative (TNBC) and human epidermal growth factor receptor 2-positive (HER2+) breast cancer patients, neoadjuvant systemic therapy is the standard recommendation for tumors larger than 2 cm. Monitoring the response to primary systemic therapy allows for the assessment of treatment effects, the need for breast-conserving surgery (BCS), and the achievement of pathological complete responses (pCRs). In estrogen receptor-positive/HER2-negative (ER+/HER2-) breast cancer, the benefit of neoadjuvant strategies is controversial, as they have shown lower tumor downstaging and pCR rates compared to other breast cancers. In recent decades, several gene expression assays have been developed to tailor adjuvant treatments in ER+/HER2- early breast cancer (EBC) to identify the patients that will benefit the most from adjuvant chemotherapy (CT) and those at low risk who could be spared from undergoing CT. It is still a challenge to identify patients who will benefit from neoadjuvant systemic treatment (CT or endocrine therapy (ET)). Here, we review the published data on the most common gene expression signatures (MammaPrint (MP), BluePrint (BP), Oncotype Dx, PAM50, the Breast Cancer Index (BCI), and EndoPredict (EP)) and their ability to predict the response to neoadjuvant treatment, as well as the possibility of using them on core needle biopsies. Additionally, we review the changes in the gene expression signatures after neoadjuvant treatment, and the ongoing clinical trials related to the utility of gene expression signatures in the neoadjuvant setting.

Leucine rich repeat containing 15 promotes triple-negative breast cancer proliferation and invasion via the ITGB1/FAK/PI3K signalling pathway

Leucine rich repeat containing 15 (LRRC15) is recognized for its intimate association with the extracellular matrix, where it modulates fibroblast function and shapes the immune landscape within the tumour microenvironment. The specific expression patterns and molecular contributions of LRRC15 in triple-negative breast cancer(TNBC) have not been fully elucidated. This study aimed to delineate the clinical relevance and biological implications of LRRC15 in TNBC, and to assess its potential as a novel therapeutic target for this disease. Our findings revealed robust overexpression of LRRC15 in TNBC tumour tissues and cell lines, which was inversely correlated with patient survival outcomes. Notably, the suppression of LRRC15 expression led to pronounced inhibition of TNBC cell proliferation, invasion, and migration both in vitro and in vivo. Mechanistically, we established that LRRC15 interacts with Integrin Beta 1(ITGB1), facilitating the phosphorylation of the T788/T789 residues on ITGB1 and recruiting focal adhesion kinase (FAK) to the site of integrin aggregation. This recruitment promotes the downstream phosphorylation of PI3K and AKT, suggesting that LRRC15 is a key activator of the ITGB1/FAK/PI3K signalling pathway. Collectively, our data indicate that LRRC15 is a critical promoter of TNBC cell proliferation and metastasis through the activation of this signalling pathway, identifying LRRC15 as a promising candidate for therapeutic intervention in TNBC.

tRNA modifications tune m6A-dependent mRNA decay

Chemically modified nucleotides in mRNA are critical regulators of gene expression, primarily through interactions with reader proteins that bind to these modifications. Here, we present a mechanism by which the epitranscriptomic mark N6-methyladenosine (m6A) is read by tRNAs during translation. Codons that are modified with m6A are decoded inefficiently by the ribosome, rendering them "non-optimal" and inducing ribosome collisions on cellular transcripts. This couples mRNA translation to decay. 5-Methoxycarbonylmethyl-2-thiouridine (mcm5s2U) in the tRNA anticodon loop counteracts this effect. This unanticipated link between the mRNA and tRNA epitranscriptomes enables the coordinated decay of mRNA regulons, including those encoding oncogenic signaling pathways. In cancer, dysregulation of the m6A and mcm5s2U biogenesis pathways-marked by a shift toward more mcm5s2U-is associated with more aggressive tumors and poor prognosis. Overall, this pan-epitranscriptomic interaction represents a novel mechanism of post-transcriptional gene regulation with implications for human health.

Novel macromolecule CPD4 suppresses cell proliferation and metastasis of triple-negative breast cancer by targeting ROR1 protein

Breast cancer is the second most common cancer among women in the US, with triple-negative breast cancer (TNBC) accounting for 15-20 % of new diagnoses. TNBC cells lack estrogen and progesterone receptors, and human epidermal growth factor receptor 2, which makes them resistant to standard hormone treatments. Current therapies like chemotherapy and radiation often harm both cancerous and healthy cells, underscoring the need for developing new targeted treatments. ROR1, an oncoprotein that is overexpressed in various cancers, including breast cancer, is minimally present in normal tissues. Targeting ROR1 signaling has been shown to trigger apoptosis and reduce TNBC cell proliferation. A novel macromolecule compound, CPD4, was discovered through in-silico docking for its ability to bind and inhibit the pseudokinase domain of ROR1. In vitro evidence revealed that CPD4 decreases cell viability and induces apoptosis in TNBC cell lines at concentrations of 2-10 μM, while leaving normal breast cells unharmed. CPD4 also blocks migration, invasion, and causes G2/M-phase arrest in TNBC cells. Its mechanism of action involves reducing key downstream markers of ROR1 signaling, particularly the phosphorylation of AKT/GSK3β. In 3D spheroid cultures, CPD4 reduces the size of TNBC spheroids. Moreover, the combination treatment of CPD4 and the standard chemotherapy docetaxel exhibits synergistic efficacy against different TNBC cell lines with a combination index below 0.01. These results suggest that CPD4 holds promise as a therapeutic option for TNBC and could potentially benefit other cancers with ROR1 overexpression.

Targeting the Hippo Pathway in Breast Cancer: A Proteomic Analysis of Yes-Associated Protein Inhibition

The dysregulation of the Hippo signaling pathway leads to the aberrant activation of oncogenic YAP and TAZ, driving tumor progression. In breast cancer, this disruption promotes proliferation and metastasis. This study investigates the effects of CA3, a selective YAP inhibitor, on the proteome of triple-negative breast cancer MDA-MB-231 and luminal-A-like MCF7 cells. Proteomic changes were analyzed via nano-LC-MS/MS, while cytotoxicity, apoptosis, and autophagy were assessed through WST-1 assays, flow cytometry, and Western blot analyses. Bioinformatics tools were employed to identify enriched pathways. MDA-MB-231 cells exhibited an increased expression of DNA repair proteins (p < 0.05), indicating a compensatory response to maintain genomic stability. In contrast, MCF7 cells showed a downregulation of DNA repair factors (p < 0.005). Additionally, metabolic reprogramming was apparent in MCF7 cells (p < 0.001). Apoptosis assays revealed a rise in cell death, while cell cycle analysis indicated pronounced G1-phase arrest in MDA-MB-231 cells (p < 0.01). Moreover, autophagic suppression was particularly evident in MCF7 cells. This study, for the first time, provides evidence that breast cancer subtypes exhibit distinct dependencies on YAP-driven pathways, revealing potential therapeutic vulnerabilities. Targeting Hippo signaling alongside DNA repair in triple-negative breast cancer or combining YAP inhibition with metabolic blockade in luminal breast cancer holds significant potential to enhance treatment efficacy.

Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue

The limitations of Hi-C (high-throughput chromosome conformation capture) profiling in in vitro cell culture include failing to recapitulate disease-specific physiological properties and lacking a clinically relevant disease microenvironment. In this study, we conduct Hi-C profiling in a pilot cohort of 12 breast tissues comprising two normal tissues, five ER+ breast primary tumors, and five tamoxifen-treated recurrent tumors. We demonstrate 3D chromatin-regulated breast tumor heterogeneity and identify a looping-mediated target gene, CA2, which might play a role in driving tamoxifen resistance. The inhibition of CA2 impedes tumor growth both in vitro and in vivo and reverses chromatin looping. The disruption of CA2 looping reduces tamoxifen-resistant cancer cell proliferation, decreases CA2 mRNA and protein expression, and weakens the looping interaction. Our study thus provides mechanistic and functional insights into the role of 3D chromatin architecture in regulating breast tumor heterogeneity and informs a new looping-mediated therapeutic avenue for treating breast cancer.

Biological profile of breast cancer brain metastasis

Breast cancer is one of the leading causes of death worldwide. The aggressive behaviour of breast tumor results from their metastasis. Notably, the brain tissue is one of the common regions of metastasis, thereby reducing the overall survival of patients. Moreover, the metastatic tumors demonstrate poor response or resistance to therapies. In addition, breast cancer brain metastasis provides the poor prognosis of patients. Therefore, it is of importance to understand the mechanisms in breast cancer brain metastasis. Both cell lines and animal models have been developed for the evaluation of breast cancer brain metastasis. Moreover, different tumor microenvironment components and other factors such as lymphocytes and astrocytes can affect brain metastasis. The breast cancer cells can disrupt the blood-brain barrier (BBB) during their metastasis into brain, developing blood-tumor barrier to enhance carcinogenesis. The breast cancer brain metastasis can be increased by the dysregulation of chemokines, STAT3, Wnt, Notch and PI3K/Akt. On the other hand, the effective therapeutics have been developed for the brain metastasis such as introduction of nanoparticles. Moreover, the disruption of BBB by ultrasound can increase the entrance of bioactive compounds to the brain tissue. In order to improve specificity and selectivity, the nanoparticles for the delivery of therapeutics and crossing over BBB have been developed to suppress breast cancer brain metastasis.

SNHG family lncRNAs: Key players in the breast cancer progression and immune cell's modulation

Breast cancer, a highly prevalent form of cancer worldwide, has observed a steady increase in its prevalence over the past few decades. This rise can be attributed to the complex nature of the disease, characterized by its heterogeneity, ability to metastasize, and resistance to various treatment. In the field of cancer research, long non-coding RNAs (lncRNAs) are of special interest, which play an important role in the development and progression of various tumors, including breast cancer. LncRNAs affect the tumor microenvironment by attracting diverse immunosuppressive factors and controlling the differentiation of immune cells, often referred to as myeloid and lymphoid cells, which contributes to immune escape of tumor cells. Among the lncRNA families, the small nucleolar RNA host gene (SNHG) family has been found to be dysregulated in breast cancer. These SNHGs have been implicated in crucial cellular processes such as cell proliferation, invasion, migration, resistance to therapies, apoptosis, as well as immune cell regulation and differentiation. Consequently, they have great potential as diagnostic and prognostic biomarkers as well as potential therapeutic targets for breast cancer. In this comprehensive review, we aim to summarize the recent advances in the study of SNHGs in breast cancer pathogenesis and their role in regulating the activity of immune cells in the tumor microenvironment through affecting SNHGs/miRNA/mRNA pathways, with the aim of providing new insights into the treatment of breast cancer.

Lineage Tracing and Single-Cell RNA Sequencing Reveal a Common Transcriptional State in Breast Cancer Tumor-Initiating Cells Characterized by IFN/STAT1 Activity

A tumor cell subpopulation of tumor-initiating cells (TIC) or "cancer stem cells" is associated with therapeutic resistance, as well as both local and distant recurrences. Signal transducer and activator of transcription (STAT) activity is elevated in TICs in claudin-low models of human triple-negative breast cancer, which enables enrichment of TICs using a STAT-responsive reporter. Lineage tracing of TICs as they undergo cell state changes could enable a better understanding of the molecular phenotypes of TIC and uncover strategies to selectively target TICs. In this study, we developed a STAT-responsive lineage-tracing system and used it in conjunction with the original reporter to enrich for cells with enhanced mammosphere-forming potential. This approach was able to detect TICs in some, but not all, basal-like triple-negative breast cancer xenograft models, indicating that STAT signaling has both TIC-related and TIC-independent functions. Single-cell RNA sequencing (RNA-seq) of reporter-tagged xenografts and clinical samples identified a common IFN/STAT1-associated transcriptional state in TICs that was previously linked to inflammation and macrophage differentiation. Surprisingly, most of the identified genes were not present in previously published TIC signatures derived using bulk RNA-seq. Finally, bone marrow stromal cell antigen-2 was identified as a cell surface marker of this state that functionally regulated TIC frequency. These results suggest that TICs may exploit the IFN/STAT1 signaling axis to promote their activity and that targeting this pathway may help eliminate TICs. Significance: Coupling single-cell transcriptomics with tumor-initiating cell enrichment identified IFN response gene expression not previously reported in bulk RNA-sequencing-derived signatures and proposed IFN/STAT1 signaling as a candidate therapeutic target in breast cancer.

Cost-effectiveness of Prosigna for Adjuvant Treatment Decisions in Early Breast Cancer: Healthcare Sector and Societal Perspectives

BACKGROUND

Gene expression profiling tests such as the Prosigna-assay are used to aid adjuvant treatment decisions in hormone receptor positive (HR+) HER2 negative (HER2-) early breast cancer (EBC). In this evaluation, the cost-effectiveness of Prosigna against immunohistochemical (IHC) markers including Ki-67, was evaluated from the Norwegian healthcare- and societal perspective.

MATERIALS AND METHODS

The treatment decision impact of Prosigna was tested in the prospective, observational EMIT-1 trial. Using individual data collected the first 12 months post-surgery, a decision model was built to project the economic consequences of using the Prosigna compared to IHC-markers for the adjuvant treatment decisions. Health benefits were measured by cost per quality-adjusted life-years (QALYs) and data on income and welfare benefit was obtained from Statistics Norway.

RESULTS

Of 2,178 HR+/HER2- pN0 EBC patients in the EMIT-1 trial, 1,985 had available health economic data and 1,850 had complete income and welfare benefit records. Including all pN0 patients in the Prosigna-test strategy, the test was above the cost-effective threshold (€26,000; incremental cost-per QALY gained (ICER) €255,622) in a healthcare sector perspective. Incorporating also productivity costs, Prosigna was cost-saving (ICER €-435,677). Restricting Prosigna-testing to patients assessed as clear/uncertain chemotherapy candidates, the strategy was cost-effective in both the healthcare and societal perspective (ICER €8884 and €-620170, respectively).

CONCLUSIONS

Using the Prosigna-assay for all HR+/HER2- pN0 EBC patients was not cost-effective from a healthcare perspective, but from the societal perspective it was cost-saving. Selecting patients who are clear/uncertain candidates for chemotherapy based on IHC-classification, Prosigna is cost-effective from both perspectives.

Unraveling the hidden complexity of cancer through long-read sequencing

Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the genome, transcriptome, and epigenome, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long-read sequencing for both germline and somatic cancer analysis. We provide an overview of the computational methodologies tailored to long-read data and highlight key discoveries and resources within cancer genomics that were previously inaccessible with prior technologies. We also address future opportunities and persistent challenges, including the experimental and computational requirements needed to scale to larger sample sizes, the hurdles in sequencing and analyzing complex cancer genomes, and opportunities for leveraging machine learning and artificial intelligence technologies for cancer informatics. We further discuss how the telomere-to-telomere genome and the emerging human pangenome could enhance the resolution of cancer genome analysis, potentially revolutionizing early detection and disease monitoring in patients. Finally, we outline strategies for transitioning long-read sequencing from research applications to routine clinical practice.

Metformin Inhibits Cell Motility and Proliferation of Triple-Negative Breast Cancer Cells by Blocking HMGB1/RAGE Signaling

High-mobility group box 1 (HMGB1) is a nuclear chromatin protein overexpressed in various cancers and linked to tumor progression. Outside the cell, HMGB1 binds to receptors such as the receptor for advanced glycation end products (RAGE), promoting metastasis. Targeting this signaling pathway may provide a new therapeutic strategy for aggressive cancers. Metformin, a well-established antidiabetic drug, directly interacts with HMGB1, inhibiting its pro-inflammatory functions. This study investigates metformin's effects on the HMGB1/RAGE signaling pathway in triple-negative breast cancer (TNBC) cells. Using wound-healing and colony formation assays, we demonstrate that metformin reduces HMGB1-induced cell migration and proliferation. Immunoblotting and immunofluorescence analyses reveal that metformin decreases RAGE stabilization on the cell membrane, disrupts NF-κB signaling, and reverses the epithelial-to-mesenchymal transition (EMT) by increasing E-cadherin, reducing vimentin, and stabilizing β-catenin at the cell membrane. Furthermore, metformin lowers HMGB1 and RAGE protein levels, disrupting the positive feedback loop that promotes cancer aggressiveness. These findings highlight metformin's potential as a therapeutic agent in TNBC by inhibiting HMGB1/RAGE-driven metastasis.

Engineered anti-HER2 drug delivery nanosystems for the treatment of breast cancer

Breast cancer stands as the primary cancer affecting women and the second most prevalent cause of cancer-related fatalities in developed nations. Consequently, there is a pressing demand for the advancement of therapeutic strategies that can be seamlessly integrated into clinical applications. We investigated the effectiveness of an encapsulation and decoration strategy employing biodegradable and biocompatible carriers together with 3D collagen-based culture models. Envisioning the use of nano delivery systems for localized regional release, we explored the feasibility of a light-controlled drug release, assisted by optical fibers. PLGA nanoparticles loaded or decorated with trastuzumab (TZ) were synthesized via a double emulsion protocol and characterized by dynamic light scattering, surface plasmon resonance, transmission electron microscopy, atomic force microscopy, and Fourier transform infrared spectroscopy. In vitro biological evaluation was then performed on HER2-positive breast cancer cell line BT-474, examining the effect of nanoformulations on cell viability in 2D and 3D collagen scaffold culture models. Cell cycle, apoptosis, cell morphology and distribution and protein expression were analyzed. Finally, a core-offset optical fiber was fabricated and particles release was studied in vitro using light in batch and microfluidic tests. The nanoparticles displayed uniform and spherical shape, maintaining stability in DMEM for up to seven days. The successful immobilization of TZ was verified. In vitro trials with BT-474 cells in 2D and 3D models revealed that poly(lactic-co-glycolic acid) (PLGA) nanoparticles encapsulated with TZ demonstrated similar or superior biological activity compared to free TZ. Notably, PLGA functionalized with TZ both internally and on the surface exhibited the highest effectiveness in terms of cell viability, increase of apoptosis markers, and inducing cell quiescence. This affirms the pivotal role of PLGA nanoparticles in preserving the integrity of TZ and enhancing its targeted delivery. Furthermore, we propose a breakthrough fiber-optic technology for the less invasive local delivery of PLGA-based nanocarriers that can be effectively used in clinical practice. In conclusion our studies lay the foundation for future advancements in alternative therapeutic tools for localized breast cancer treatment. The integration of advanced carriers, optical fibers, and microfluidics opens up new possibilities for innovative and targeted therapeutic approaches.

Treating ER-positive breast cancer: a review of the current FDA-approved SERMs and SERDs and their mechanisms of action

Breast cancer is one of the most significant causes of mortality among women and the second most prevalent cancer worldwide. Estrogen receptor (ER)-positive breast cancers are the most common molecular subtype of breast cancer, comprising about 70% of breast carcinoma diagnoses worldwide. Endocrine therapy is the foremost strategy for the treatment of ER-positive breast cancer. In the United States, the Food and Drug Administration (FDA) has approved endocrine therapies for ER-positive breast cancers that include selective estrogen receptor modulators (SERMs), selective estrogen receptor downregulators/degraders (SERDs) and aromatase inhibitors (AIs). The approved SERMS, tamoxifen, toremifene and raloxifene, are the gold-standard treatments. The only FDA-approved SERD available for treating ER and hormone-positive breast cancers is fulvestrant, and various generations of AIs, including exemestane, letrozole, and anastrozole, have also received FDA approval. Herein, we review the major FDA-approved SERMs and SERDs for treating ER-positive breast cancer, focusing on their mechanisms of action. We also explore molecular events that contribute to the resistance of these drugs to endocrine therapies and combinational strategies with drugs such as cyclin-dependant kinases 4/6 (CDK4/6) inhibitors in clinical trials to combat endocrine drug resistance.

Pharmacovigilance study of adverse reactions of anti-HER-2 drugs for the treatment of HER-2-positive breast cancer based on the FAERS database

OBJECTIVE

There are three categories of drugs that treat human epidermal growth factor receptor type 2 (HER-2) positive breast cancer: monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs), and tyrosine kinase inhibitors (TKIs). The purpose of this study is to analyze and compare the adverse reactions of three classes of anti-HER-2 drugs to various body systems in patients based on the FDA Adverse Event Reporting System (FAERS).

METHODS

All data reports were extracted from the FAERS between 2004 and 2024. Data mining of adverse events associated with anti-HER-2 drugs was carried out using disproportionality analysis. A multivariate logistic regression analysis was conducted to explore the risk factors associated with AEs leading to hospitalization.

RESULTS

A total of 47,799 patients were screened for the three classes of drugs, among which ADC drugs caused the largest proportion of deaths. MAb has the strongest ADR signals associated with "cardiac disorders". Moreover, trastuzumab was associated with a greater risk of cardiotoxicity. Logistic regression analysis revealed that the treatment with mAbs should be wary of serious adverse reactions in "infections and infestations" and "metabolism and nutrition disorders". Moreover, "endocrine disorders" were the factor associated with the highest risk of prolonged hospitalization due to trastuzumab deruxtecan (T-DXd). The safety of tucatinib among TKI drugs is greater than that of other drugs.

CONCLUSION

In general, from the perspective of the effects of the three classes of drugs on the various body systems of patients, we should focus on mAb-associated "cardiac disorders", ADC-associated "hepatobiliary disorders", "respiratory, thoracic and mediastinal disorders", and TKI-associated "gastrointestinal disorders.

MicroRNAs as Endocrine Modulators of Breast Cancer

Breast cancer is an aggressive disease of multiple subtypes with varying phenotypic, hormonal, and clinicopathological features, offering enhanced resistance to conventional therapeutic regimens. There is an unmet need for reliable molecular biomarkers capable of detecting the malignant transformation from the early stages of the disease to enhance diagnosis and treatment outcomes. A subset of small non-coding nucleic acid molecules, micro ribonucleic acids (microRNAs/miRNAs), have emerged as promising biomarkers due to their role in gene regulation and cancer pathogenesis. This review discusses, in detail, the different origins and hormone-like regulatory functionalities of miRNAs localized in tumor tissue and in the circulation, as well as their inherent stability and turnover that determines the utility of miRNAs as biomarkers for disease detection, monitoring, prognosis, and therapeutic targets.

Single-cell sequencing exposes mast cell-derived CD52's anti-tumor action in breast cancer through the IL-6/JAK/STAT3 axis

The aggressive nature and rapid progression of triple-negative breast cancer (TNBC), coupled with a high likelihood of recurrence and mortality, underscore the critical need for effective treatments. While immunotherapy presents promising advantages for those with triple-negative breast cancer (TNBC), its efficacy is not universal. This disparity highlights the importance of investigating survival outcomes and prognostic factors for those TNBC patients who don't respond well to immunotherapy. Our study leverages both bulk and single-cell RNA sequencing data to conduct an in-depth analysis, revealing that genes associated with mast cells (PCMT1, VDAC1, YWHAB, BRD4, BTG1, and CD52) are pivotal in prognostication for TNBC patients. Laboratory experiments have further substantiated our findings, demonstrating that the overexpression of CD52 in mast cells impedes the proliferation, invasion, and metastasis of breast cancer cells. Further anti-CD52 treatment inhibiting breast tumor growth in vivo. Additionally, we have discovered that CD52 elicits its antitumor effects by meditating the IL-6/JAK/STAT3 signaling pathway. These insights not only enhance the prognostic significance of mast cells in TNBC but also pave the way for the development of novel targeted immunotherapy strategies.

Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences

PURPOSE

Understanding the impact of gene expression in pathological processes, such as carcinogenesis, is crucial for understanding the biology of cancer and advancing personalised medicine. Yet, current methods lack biologically-informed-omics approaches to stratify cancer patients effectively, limiting our ability to dissect the underlying molecular mechanisms.

RESULTS

To address this gap, we present a novel workflow for the stratification and further analysis of multi-omics samples with matched RNA-Seq data that relies on MSigDB curated gene sets, graph machine learning and ensemble clustering. We compared the performance of our workflow in the top 8 TCGA datasets and showed its clear superiority in separating samples for the study of biological differences. We also applied our workflow to analyse nearly a thousand prostate cancer samples, focusing on the varying expression of the FOLH1 gene, and identified specific pathways such as the PI3K-AKT-mTOR gene sets as well as signatures linked to prostate tumour aggressiveness.

CONCLUSION

Our comprehensive approach provides a novel tool to identify disease-relevant functions of genes of interest (GOI) in large datasets. This integrated approach offers a valuable framework for understanding the role of the expression variation of a GOI in complex diseases and for informing on targeted therapeutic strategies.

Low versus null HER2 tumour expression in "HER2-negative" breast cancer: long-term outcomes based on phenotypes

BACKGROUND

Two new categories of breast cancer (BC) have been proposed among HER2-negative patients: HER2 0 + and HER2-low breast cancer. We combined these two categories with Perou's classification. We aimed to identify potential differences in clinicopathological features and prognosis using a new, unofficial classification: Luminal A HER2 0 + , Luminal A HER2-Low, Luminal B HER2 0 + , Luminal B HER2- Low, Triple Negative HER2 0 + , and Triple Negative HER2-Low.

PATIENTS AND METHODS

We conducted a retrospective analysis of our database from January 1, 2005, to December 31, 2018. Cox Regression served as the basis for our study.

RESULTS

We identified 1704 BC tumor cases from 1,639 HER2-negative patients (65 had bilateral BC). Among these, 608 cases were HER2 0 + , and 1096 were HER2-Low (aggregate). The median follow-up period was 120 months after surgery. None of the patients received anti-HER2 therapy. Case distribution was as follows: Luminal A HER2 0 + : 259. Luminal A HER2-low: 501. Luminal B HER2 0 + : 219. Luminal B HER2-low: 499. Triple-Negative HER2 0 + : 130. Triple-Negative HER2-low: 96. There was a 12.2% excess in the Triple Negative rate in the HER2 0 + group, compared with the HER2 Low group (aggregate), which was highly significant (Chisquare, p < 0.01). Although the HER2 0 + versus HER2 Low Hazard Ratio (HR) for Specific Mortality was of borderline significance:1.39 (IC 1.00-1.92, p = 0.049), the TN imbalance complicated a direct comparison between the two groups. After stratification using the noncanonical classification, the HR was highly significant, but only for the Luminal A subtype: 2.28 (IC 1.09-4.36, p = 0.028).

COMMENTS

In the noncanonical classification, the effect of the unbalanced Triple-Negative proportions disappeared, and a significant finding emerged: HER2 0 + status had a negative prognostic influence exclusively in Luminal A patients.

Molecular shifts in breast cancer following neoadjuvant chemotherapy: a prospective study and review of literature

BACKGROUND

Standard clinical guidelines recommend evaluating Estrogen & progesterone Receptor (ER, PR), Human epidermal growth factor receptor-2 (HER-2), and Ki-67 in breast cancer biopsy samples. This study investigates the changes in molecular subtype following neoadjuvant chemotherapy (NACT) in breast cancer patients.

METHODS

Patients aged 18 to 65 years who underwent core needle biopsy before NACT and received at least four chemotherapy cycles were included in the study. Patients with inflammatory breast cancer, de novo metastatic or bilateral breast cancer, pregnancy, lactation, prior endocrine/radiation therapy, or achieved pathological complete response (pCR) were excluded. Molecular profiles (ER, PR, HER-2, Ki-67) were analyzed pre- and post-NACT.

RESULTS

The study involved 100 breast cancer patients with a median age of 51.78 years. 47% of patients underwent breast-conserving surgery (BCS), while 53% underwent modified radical mastectomy (MRM). Seventy-six percent of patients had tumors larger than 5 cm, and 72% presented with axillary lymph node metastasis. Initially, 90% and 89% of patients were ER, and PR positive, respectively, which decreased to 81% and 75% post-surgery. Ki67 expression showed a significant reduction following chemotherapy. Larger tumors and lymph node-positivity had significant changes in molecular subtypes.

CONCLUSION

The study revealed significant alterations in ER, PR, HER-2, and Ki-67 levels post-NACT, prompting reassessment for tailored therapy.

Characterisation of HER2-Driven Morphometric Signature in Breast Cancer and Prediction of Risk of Recurrence

INTRODUCTION

Human epidermal growth factor receptor 2-positive (HER2-positive) breast cancer (BC) is a heterogeneous disease. In this study, we hypothesised that the degree of HER2 oncogenic activity, and hence response to anti-HER2 therapy is translated into a morphological signature that can be of prognostic/predictive value.

METHODS

We developed a HER2-driven signature based on a set of morphometric features identified through digital image analysis and visual assessment in a sizable cohort of BC patients. HER2-enriched molecular sub-type (HER2-E) was used for validation, and pathway enrichment analysis was performed to assess HER2 pathway activity in the signature-positive cases. The predictive utility of this signature was evaluated in post-adjuvant HER2-positive BC patients.

RESULTS

A total of 57 morphometric features were evaluated; of them, 22 features were significantly associated with HER2 positivity. HER2 IHC score 3+/oestrogen receptor-negative tumours were significantly associated with HER2-related morphometric features compared to other HER2 classes including HER2 IHC 2+ with gene amplification, and they showed the least intra-tumour morphological heterogeneity. Tumours displaying HER2-driven morphometric signature showed the strongest association with PAM50 HER2-E sub-type and were enriched with ERBB signalling pathway compared to signature-negative cases. BC patients with positive HER2 morphometric signature showed prolonged distant metastasis-free survival post-adjuvant anti-HER2 therapy (p = 0.007). The clinico-morphometric prognostic index demonstrated an 87% accuracy in predicting recurrence risk.

CONCLUSION

Our findings underscore the strong prognostic and predictive correlation between HER2 histo-morphometric features and response to targeted anti-HER2 therapy.

Potentiated Effects of Photobiomodulation and Celecoxib on the Epithelial-Mesenchymal Transition Signaling of E-Cadherin, N-Cadherin, α-SMA in Breast Cancer Cells, MCF7, and MDA-MB-231

Background and Objective: Breast cancer (BC) is one of the most common cancers among women, with a high potential for metastasis. The epithelial-mesenchymal transition (EMT) is crucial in the invasion and metastasis of cancer cells. This research was designed to examine the efficacy of photobiomodulation therapy in combination with celecoxib in inhibiting the EMT process. We also analyzed the changes in the expression of E-cadherin, N-cadherin, and α-SMA genes in BC cell lines MCF-7 and MDA-MB-231. Material and Methods: In this study, the IC50 of celecoxib was first determined using the 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyltetrazolium bromide assay for both cell lines. The cells were then treated with celecoxib, laser irradiation, and their combination. A migration assay was performed to evaluate the cell migration. Real-time polymerase chain reaction also assessed the changes in the expression of the abovementioned genes. Results: A combination of celecoxib and laser therapy significantly reduced the migration of cancer cells. Additionally, the potentiated effect of the combined therapy altered the expression levels of the aforementioned genes, indicating the potential role of the combination treatment in regulating EMT. Conclusions: Our research discloses that combining laser therapy with celecoxib could serve as an effective therapeutic approach to inhibit BC invasion and metastasis by targeting the EMT process and decelerating disease progression. Further investigations are essential to validate these results in clinical environments.

Serous-like breast carcinomas: immunophenotypic, genetic, and clinicopathologic characterization of a morphologically distinct group of tumours

AIMS

Unusual morphologic patterns of breast carcinomas can raise diagnostic consideration for metastasis or special breast cancer subtypes with management implications. We describe rare invasive breast cancers that mimic serous carcinoma of the gynaecologic tract (serous-like breast carcinomas, SLBC) and characterize their clinicopathologic, immunophenotypic, and genetic features.

METHODS AND RESULTS

All patients were female (n = 15, median age 49 years) without a history of gynaecologic malignancy. SLBC were characterized histologically by angulated, branched, sometimes anastomosing glands with micropapillary and/or pseudopapillary luminal projections in desmoplastic stroma. Most SLBC were triple-negative (TN, n = 10) or HER2-positive (n = 2) and grade 2 or 3, while some were oestrogen receptor (ER) low-positive/HER2-negative and low-grade (n = 3). CK5/6 was positive irrespective of grade or receptor status (10/10). All SLBC expressed GATA3 (14/15), TRPS1 (7/7), and/or mammaglobin (4/13). SOX10 was positive in most TN (9/10) and all ER low-positive (3/3) cases, but negative in HER2-positive tumours. WT1 was universally negative, and PAX8 was focal in one mammaglobin-positive tumour. All ER-negative SLBC were p53-aberrant and 9/11 were p16-aberrant, whereas ER-positive tumours were wildtype for both markers (3/3). TP53 was the only frequently mutated gene, altered in all ER-negative (10/10) but no ER-positive (0/4) tumours. Clinical behaviour was variable. Only 1/6 patients achieved pathologic complete response to neoadjuvant chemotherapy.

CONCLUSION

SLBC is a rare morphologic pattern of invasive breast carcinoma that mimics metastatic serous gynaecologic carcinoma, a potential diagnostic pitfall. SLBC are heterogeneous with respect to grade, receptor profile, and oncogenic driver alterations, without specific genetic underpinnings identified. Additional studies are warranted to further evaluate the clinical behaviour of these tumours.

Classifying the molecular subtype of breast cancer using vision transformer and convolutional neural network features

PURPOSE

Identification of the molecular subtypes in breast cancer allows to optimize treatment strategies, but usually requires invasive needle biopsy. Recently, non-invasive imaging has emerged as promising means to classify them. Magnetic resonance imaging is often used for this purpose because it is three-dimensional and highly informative. Instead, only a few reports have documented the use of mammograms. Given that mammography is the first choice for breast cancer screening, using it to classify molecular subtypes would allow for early intervention on a much wider scale. Here, we aimed to evaluate the effectiveness of combining global and local mammographic features by using Vision Transformer (ViT) and Convolutional Neural Network (CNN) to classify molecular subtypes in breast cancer.

METHODS

The feature values for binary classification were calculated using the ViT and EfficientnetV2 feature extractors, followed by dimensional compression via principal component analysis. LightGBM was used to perform binary classification of each molecular subtype: triple-negative, HER2-enriched, luminal A, and luminal B.

RESULTS

The combination of ViT and CNN achieved higher accuracy than ViT or CNN alone. The sensitivity for triple-negative subtypes was very high (0.900, with F-value = 0.818); whereas F-value and sensitivity were 0.720 and 0.750 for HER2-enriched, 0.765 and 0.867 for luminal A, and 0.614 and 0.711 for luminal B subtypes, respectively.

CONCLUSION

Features obtained from mammograms by combining ViT and CNN allow the classification of molecular subtypes with high accuracy. This approach could streamline early treatment workflows and triage, especially for poor prognosis subtypes such as triple-negative breast cancer.

Circadian clock features define novel subtypes among breast cancer cells and shape drug sensitivity

The circadian clock regulates key physiological processes, including cellular responses to DNA damage. Circadian-based therapeutic strategies optimize treatment timing to enhance drug efficacy and minimize side effects, offering potential for precision cancer treatment. However, applying these strategies in cancer remains limited due to a lack of understanding of the clock's function across cancer types and incomplete insights into how the circadian clock affects drug responses. To address this, we conducted deep circadian phenotyping across a panel of breast cancer cell lines. Observing diverse circadian dynamics, we characterized metrics to assess circadian rhythm strength and stability in vitro. This led to the identification of four distinct circadian-based phenotypes among 14 breast cancer cell models: functional, weak, unstable, and dysfunctional clocks. Furthermore, we demonstrate that the circadian clock plays a critical role in shaping pharmacological responses to various anti-cancer drugs and we identify circadian features descriptive of drug sensitivity. Collectively, our findings establish a foundation for implementing circadian-based treatment strategies in breast cancer, leveraging clock phenotypes and drug sensitivity patterns to optimize therapeutic outcomes.

KRT14 is a promising prognostic biomarker of breast cancer related to immune infiltration

BACKGROUND

Breast cancer (BC) is the leading cancer among women globally, which has the highest incidence and mortality rate in over a hundred countries. This study was intended to discover a new prognostic biomarker, facilitating personalized treatment approaches.

METHODS

RNA sequencing data from The Cancer Genome Atlas database and Gene Expression Omnibus database were utilized to download to evaluate expression levels and prognostic significance of Keratin 14 (KRT14). Methylation of KRT14 was also assessed. The CIBERSORT and single-sample gene set enrichment analysis algorithms were applied to explore the connection between KRT14 and the tumor microenvironment. Primary drugs' sensitivity and potential small molecule therapeutic compounds were analyzed through the "pRRophetic" R package and the Connectivity Map. The prognostic value of KRT14 was additionally corroborated through a comparison of protein levels in peritumoral and cancerous tissues via immunohistochemistry. Moreover, an immune-related prognostic model based on KRT14 was designed to enhance the prediction accuracy for the prognosis of BC patients.

RESULTS

The study found that KRT14 expression was generally downregulated in BC, correlating strongly with poor prognosis. Compared to normal tissues, the methylation level of KRT14 was higher in BC tissues. Lower expression of KRT14 was linked to decreased anti-tumoral immune cells infiltration and increased immunosuppressive cells infiltration. Sensitivity to various key therapeutic drugs was lower in groups with diminished KRT14 expression. In addition, several potential anti-BC small molecule compounds were identified. The model designed in this study significantly enhanced the predictive capability for BC patients compared to predictions based solely on KRT14 expression levels.

CONCLUSION

Overall, KRT14 was closely correlated with the prognosis in BC, making it a reliable biomarker.