Association of clinicopathological features and prognosis of TERT alterations in phyllodes tumor of breast

Clinical values of nuclear morphometric analysis in fibroepithelial lesions

BACKGROUND

Fibroepithelial lesions (FELs) of the breast encompass a broad spectrum of lesions, ranging from commonly encountered fibroadenomas (FAs) to rare phyllodes tumors (PTs). Accurately diagnosing and grading these lesions is crucial for making management decisions, but it can be challenging due to their overlapping features and the subjective nature of histological assessment. Here, we evaluated the role of digital nuclear morphometric analysis in FEL diagnosis and prognosis.

METHODS

A digital nuclear morphometric analysis was conducted on 241 PTs and 59 FAs. Immunohistochemical staining for cytokeratin and Leukocyte common antigen (LCA) was used to exclude non-stromal components, and nuclear area, perimeters, calipers, circularity, and eccentricity in the stromal cells were quantified with QuPath software. The correlations of these features with FEL diagnosis and prognosis was assessed.

RESULTS

All nuclear features, including area, perimeter, circularity, maximum caliper, minimum caliper and eccentricity, showed significant differences between FAs and benign PTs (p ≤ 0.002). Only nuclear area, perimeter, minimum caliper and eccentricity correlated significantly with PT grading (p ≤ 0.022). For differentiation of FAs from benign PTs, the model integrating all differential nuclear features demonstrated a specificity of 90% and sensitivity of 70%. For PT grading, the nuclear morphometric score showed a specificity of 78% and sensitivity of 96% for distinguishing benign/borderline from malignant PTs. In addition, a relationship of nuclear circularity was found with PT recurrence. The Kaplan-meier analysis, using the best cutoff determined by ROC curve, showed shorter event free survival in benign PTs with high circularity (chi-square = 4.650, p = 0.031).

CONCLUSIONS

Our data suggested the digital nuclear morphometric analysis could have potentials to objectively differentiate different FELs and predict PT outcome. These findings could provide the evidence-based data to support the development of deep-learning based algorithm on nuclear morphometrics in FEL diagnosis.

Predicting Prognosis of Phyllodes Tumors Using a Mammography- and Magnetic Resonance Imaging-Based Radiomics Model: A Preliminary Study

PURPOSE

To investigate whether a radiomics model based on mammography (MG) and magnetic resonance imaging (MRI) can be used to predict disease-free survival (DFS) after phyllodes tumor (PT) surgery.

METHOD

About 131 PT patients who underwent MG and MRI before surgery between January 2010 and December 2020 were retrospectively enrolled, including 15 patients with recurrence and metastasis and 116 without recurrence. 884 and 3138 radiomic features were extracted from MG and MR images, respectively. Then, multiple radiomics models were established to predict the recurrence risk of the patients by applying a support vector machine classifier. The area under the ROC curve (AUC) was calculated to evaluate model performance. After dividing the patients into high- and low-risk groups based on the predicted radiomics scores, survival analysis was conducted to compare differences between the groups.

RESULTS

In total, 3 MG-related and 5 MRI-related radiomic models were established; the prediction performance of the T1WI feature fusion model was the best, with an AUC value of 0.93. After combining the features of MG and MRI, the AUC increased to 0.95. Furthermore, the MG, MRI and all-image radiomic models had statistically significant differences in survival between the high- and low-risk groups (P < .001). All-image radiomics model showed higher survival performance than the MG and MRI radiomics models alone.

CONCLUSIONS

Radiomics features based on preoperative MG and MR images can predict DFS after PT surgery, and the prediction score of the image radiomics model can be used as a potential indicator of recurrence risk.

Genomic landscape of malignant phyllodes tumors reveals multiple targetable opportunities

BACKGROUND

Malignant phyllodes tumors (MPT) are rare fibroepithelial breast cancers with no known effective systemic therapy; metastatic progression portends a dismal prognosis. We sought to describe the genomic landscape of MPTs through genomic profiling and immunotherapeutic biomarker analysis.

MATERIALS AND METHODS

Cases of sequenced MPT were identified from a Clinical Laboratory Improvement Amendments-certified, College of American Pathologists-accredited laboratory (Foundation Medicine). All cases underwent genomic profiling using adaptor ligation-based, next-generation sequencing assay of 324 genes. Tumor agnostic immunotherapy biomarkers, microsatellite instability, tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression were evaluated. Fisher's Exact Tests and analysis of variance were used to test for differences between groups and for continuous variables as appropriate.

RESULTS

Of 135 MPT cases identified; 94 (69.6%) were localized/locally recurrent and 41 (30.4%) were metastatic. Median age was 54 years (range 14-86). The median TMB was 2.5 mut/Mb and 3 were TMB-high (≥10 mut/Mb). 21.4% were PD-L1+ via Dako 22C3 assay (CPS ≥1). Most commonly altered genes included TERT-promoter (69.7%), CDKN2A (45.9%), TP53 (37.8%), NF1 (35.6%), CDKN2B (33.3%), MED12 (28.9%), MTAP (27.7%), KMT2D (22.2%), PIK3CA (20.0%), PTEN (18.5%), and RB1 (18.5%). Several tumors harboring genomic alterations with US Food and Drug Administration-approved indications in other tumor types were found including NF1, PIK3CA, EGFR Exon 19/20 insertions, and BRAF V600E mutations.

CONCLUSIONS

In the largest genomic evaluation of MPT to date, multiple clinically actionable mutations were found. Routine sequencing of metastatic MPT may provide additional information to guide treatment decisions and clinical trial enrollment.

Integrating single-cell and spatial transcriptomes reveals COL4A1/2 facilitates the spatial organisation of stromal cells differentiation in breast phyllodes tumours

BACKGROUND

Breast phyllodes tumours (PTs) are a unique type of fibroepithelial neoplasms with metastatic potential and recurrence tendency. However, the precise nature of heterogeneity in breast PTs remains poorly understood. This study aimed to elucidate the cell subpopulations composition and spatial structure and investigate diagnostic markers in the pathogenesis of PTs.

METHODS

We applied single-cell RNA sequencing and spatial transcriptomes on tumours and adjacent normal tissues for integration analysis. Immunofluorescence experiments were conducted to verify the tissue distribution of cells. Tumour cells from patients with PTs were cultured to validate the function of genes. To validate the heterogeneity, the epithelial and stromal components of tumour tissues were separated using laser capture microdissection, and microproteomics data were obtained using data-independent acquisition mass spectrometry. The diagnostic value of genes was assessed using immunohistochemistry staining.

RESULTS

Tumour stromal cells harboured seven subpopulations. Among them, a population of widely distributed cancer-associated fibroblast-like stroma cells exhibited strong communications with epithelial progenitors which underwent a mesenchymal transition. We identified two stromal subpopulations sharing epithelial progenitors and mesenchymal markers. They were inferred to further differentiate into transcriptionally active stromal subpopulations continuously expressing COL4A1/2. The binding of COL4A1/2 with ITGA1/B1 facilitated a growth pattern from the stroma towards the surrounding glands. Furthermore, we found consistent transcriptional changes between intratumoural heterogeneity and inter-patient heterogeneity by performing microproteomics studies on 30 samples from 11 PTs. The immunohistochemical assessment of 97 independent cohorts identified that COL4A1/2 and CSRP1 could aid in accurate diagnosis and grading.

CONCLUSIONS

Our study demonstrates that COL4A1/2 shapes the spatial structure of stromal cell differentiation and has important clinical implications for accurate diagnosis of breast PTs.

Periductal Stromal Tumor of the Breast with a TERT Promoter Mutation: First Case Report with Comprehensive Molecular Analysis

The molecular pathogenesis of breast fibroepithelial tumors continues to be elucidated. Recently, highly recurrent MED12 mutations arising in exon 2 at codon 44 were discovered in fibroadenomas and phyllodes tumors. In addition, a high prevalence of TERT promoter mutations in two hotspots (124 and 126 bp upstream from the translation start site) was discovered in up to 65% of phyllodes tumors. Breast periductal stromal tumors are a potentially distinct category of fibroepithelial lesions that are exceptionally rare with controversial classification and pathogenesis. Herein, we report the first comprehensive molecular genetic workup of a breast periductal stromal tumor that harbored a TERT promoter -124C > T mutation, supporting a relation to phyllodes tumors.

The Genetic Landscape of Fibroepithelial Lesions of the Breast

Fibroepithelial lesions of the breast encompass a broad spectrum of lesions from fibroadenomas and their variants to phyllodes tumors, including their clinical range of benign, borderline, and malignant. Classification of this spectrum of neoplasms has historically and currently been based purely on morphology, although the nomenclature has shifted over the years largely due to the significant histologic overlap that exists primarily within the cellular fibroadenomas to borderline malignant phyllodes tumor categories. A review of the current diagnostic challenge, proposed ancillary studied and their value in prognostic significance, is provided. This article highlights the most recent molecular and genetic findings as well as the limitations of the studies, in the context of practical and available applications for the diagnostician and managerial implications for the clinician.

Clinical and pathological characteristics of familial melanoma with germline TERT promoter variants

Around 10% of melanoma occur in patients with a suspected familial predisposition. TERT promoter mutations are the most common somatic hotspot mutations in human cancers. However, only two families with germline mutations have been identified to date. We present detailed histological, clinical and molecular pathologic analyses of affected patients and details of newly identified individuals in one of these previously reported families. TERT (NM_198253.3) Chr.5:1,295,161T>C (c.-57 T>C) promoter variants were detected in all melanoma-affected (n=18) and one non-diseased family member. Median age at diagnosis was 30 years (n=18, range 16-46 years, 2 unknown). While most primary melanoma arose on the upper extremities (n=7, 21%) and were superficial spreading melanoma (SSM, n=8, 24%), many primary melanoma also originated from non UV-exposed mucosal (n=2, 6%) and acral (n=4, 12%) locations. One SSM sample harboured a Chr.5:1,295,228C>T TERT promoter region in addition to the germline Chr.5:1,295,161T>C variant, arguing additional pathway activation can support tumor pathogenesis. Patients treated with BRAF inhibitor and/or immune checkpoint inhibition (ICI) showed responses, although of limited duration. One mucosal melanoma harboured both a KIT copy number gain and an activating c.1727 p.Leu576Pro mutation. Following modest response to ICI, subsequent KIT inhibitor (imatinib) therapy demonstrated an ongoing complete pathological response (currently 7 months).

Analysis of recurrent molecular alterations in phyllodes tumour of breast: insights into prognosis and pathogenesis

Phyllodes tumour (PT) of breast is a rare biphasic neoplasm. Recent next generation sequencing analyses had revealed novel genetic alterations in PT but lacked a further characterisation of their relationship to different PT features and outcome. Here, using targeted sequencing, we examined a panel of 90 recurrently altered or cancer related genes in 88 PT samples (including 49 benign, 25 borderline and 14 malignant PT). Twenty-three genes showed alterations in at least 8.0% of cases. Alterations were significantly higher with an increasing grade of PT (p=0.033), particularly for copy number alterations. The top ten alterations were TERT promoter (58.0%), MED12 (53.4%), RARA (22.8%), FLNA (19.3%), SETD2 (15.9%), SYNE1 (18.2%), PCLO (15.9%), KMT2D (14.3%), CDKN2A (15.9%) and DNAH11 (14.8%). Alterations in CDKN2A/B, EGFR, TP53, PIK3CA, PTEN and ARID1B (p≤0.039) were associated with a higher grade. Analysing alterations based on common pathways indicated a significant correlation of cell cycle pathway and epigenetic alterations with a higher PT grade (p=0.036 and 0.075 respectively). Interestingly, recurrences were not correlated with tumour grade, but related to the presence of RARA mutation (p=0.011) and the absence of alterations in epigenetic pathway (p=0.031). Analysis of synchronous pair of PT showed more differences in gene mutations with divergent MED12 mutation. By contrast, the recurrent samples showed similar genetic alterations as the primary tumours. In summary, we characterised genetic alterations in PTs of different grades and confirmed the recurrent alterations observed in earlier studies. In addition, current data implicated the roles of cell cycle, epigenetic and RARA changes in PT recurrence and tumourogenesis.

Prognostic Significance of Three-Tiered World Health Organization Classification of Phyllodes Tumor and Correlation to Singapore General Hospital Nomogram

OBJECTIVES

Phyllodes tumors (PTs) are categorized by the World Health Organization (WHO) as benign, borderline, and malignant. Singapore General Hospital (SGH) nomogram is a recurrence risk assessment tool for PT, which uses cytologic atypia, mitosis, stromal overgrowth, and the surgical margin status. We studied the prognostic significance of WHO classification and its correlation to the SGH nomogram.

METHODS

We identified 270 consecutive cases of PT (195 benign, 49 borderline, 26 malignant). Follow-up was available on 246 cases (mean follow-up of 51 months).

RESULTS

The recurrence rates were 2% (4 of 176) for benign, 4% (2 of 46) for borderline, and 25% (6 of 24) for malignant (log-rank test P < .0001 for recurrence-free survival). Only five patients with malignant PT experienced distant recurrence. Stromal overgrowth was an independent predictor of recurrence-free survival on multivariable analysis. The mean nomogram scores for benign, borderline, and malignant PT were 20, 20.3, and 32, respectively. The higher than expected score for benign PT was due to positive margins in 39% of cases.

CONCLUSIONS

The WHO three-tiered classification of PT is prognostic. Despite positive margin status, most benign PTs do not recur. Other features of the nomogram help in determining recurrence but are also used for WHO classification.

High-Grade Spindle Cell Lesions of the Breast: Key Pathologic and Clinical Updates

Most of the high-grade spindle cell lesions of the breast are malignant phyllodes tumors (MPTs), spindle cell carcinomas (SpCCs), and matrix-producing metaplastic breast carcinomas (MP-MBCs). MPTs have neoplastic spindle stromal cells and a classic leaf-like architecture with subepithelial stromal condensation. MPTs are often positive for CD34, CD117, and bcl-2 and are associated with MED12, TERT, and RARA mutations. SpCCs and MP-MBCs are high-grade metaplastic carcinomas, whereas neoplastic epithelial cells become spindled or show heterologous mesenchymal differentiation, respectively. The expression of epithelial markers must be evaluated to make a diagnosis. SAS, or rare metastatic spindle cell tumors, are seen in the breast, and clinical history is the best supporting evidence. Surgical resection is the standard of care.

Tumorigenic effect of TERT and its potential therapeutic target in NSCLC (Review)

Non‑small cell lung cancer (NSCLC), which accounts for ~85% of all lung cancer cases, is commonly diagnosed at an advanced stage and has a high patient mortality rate. Despite the increasing availability of treatment strategies, the prognosis of patients with NSCLC remains poor, with a low 5‑year survival rate. This poor prognosis may be associated with the tumor heterogeneity of NSCLC, as well as its acquisition and intrinsic resistance to therapeutic drugs. It has been suggested that combination therapy with telomerase inhibition may be an effective strategy for the treatment of drug‑sensitive and drug‑resistant types of cancer. Telomerase is the key enzyme for cell survival, and ~90% of human cancers maintain telomeres by activating telomerase, which is driven by the upregulation of telomerase reverse transcriptase (TERT). Several mechanisms of telomerase reactivation have been described in a variety of cancer types, including TERT promoter mutation, epigenetic modifications via a TERT promoter, TERT amplification, and TERT rearrangement. The aim of the present study was to comprehensively review telomerase activity and its association with the clinical characteristics and prognosis of NSCLC, as well as analyze the potential mechanism via which TERT activates telomerase and determine its potential clinical application in NSCLC. More importantly, current treatment strategies targeting TERT in NSCLC have been summarized with the aim to promote discovery of novel strategies for the future treatment of NSCLC.

CD117/c-KIT Expression in Phyllodes Tumor of the Breast and Its Correlation With Morphology and Clinical Outcome

Introduction

Breast phyllodes tumor’s (PT) clinical behavior is difficult to predict on histology. There is limited amount of data available on the role of biological markers. The objective of this study was to assess the expression of CD117 (c-KIT) in PT of the breast and its relationship with morphology and clinical outcome.

Methods

A total of 78 patients having available clinical records between 2004 and 2014 with breast PT were retrieved from the cancer registry at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore and were followed up. Immunohistochemical studies were performed on all the cases using mono­clonal antibody CD117 (DAKO A4502) using Leica Bond-Max automated biosystem (Leica Biosystems, Melbourne, Australia). Staining proportion and intensity of both epithelial and stromal elements were analyzed. Evaluation of the protein expression was determined and scored.

Results

Patients’ mean age was 45.13 ± 11.4 years. Thirty-nine (50.0%) patients had tumor on right side, 38 (48.7%) had on left and only one (1.3%) was bilateral. Thirty-two (41.0%) patients had benign PT, 21 (26.9%) had borderline and 25 (32.1%) had malignant PT. Negative CD117 expression was observed in 20 (62.5%), eight (38.0%) and 12 (48.0%) of benign, borderline and malignant PTs, respectively. Positive CD117 expression was observed in 12 (37.5%) benign, 13 (61.9%) borderline and 13 (52.0%) malignant PTs. There was insignificant association between CD117 expression with respect to tumor sub-type, patient’s age and clinical behavior (p-value > 0.05).

Conclusion

CD117 expression was not found to be associated with tumor type and was not associated with increased risk of recurrence in this sample of patients. Further work is needed to better understand the prognostic value of CD117 expression in breast PTs.

SETD2 alterations and histone H3K36 trimethylation in phyllodes tumor of breast

PURPOSE

SETD2 is one of the key epigenetic regulatory genes involved in histone modifications. Its alterations were potentially oncogenic and commonly found in cancers. Interestingly, SETD2 is one of the most frequent mutated genes found exclusively in phyllodes tumor of the breast (PT). However, little has been done to further characterize SETD2 alterations in PT.

METHODS

In this study, we examined the alterations of SETD2 gene and protein expression in a large cohort of PTs. Their correlations with SETD2 downstream target, H3K36me3 expression, and clinicopathologic features in PT were also assessed.

RESULTS

SETD2 mutation was found in 15.9% of our cases and was mostly predicted to be damaging mutations. Interestingly, SETD2 mutations were associated with lower H3K36me3 expression, particularly those with damaging mutations (p = .041). Neither SETD2 mutations nor H3K36me3 expression was associated with PT grading and other clinicopathological features. By contrast, the SETD2 protein expression cannot reflect its mutation status and showed a different trend of clinicopathological correlations from H3K36me3.

CONCLUSIONS

Our findings may suggest a potential involvement of epigenetic regulation via SETD2 alterations and downstream H3K36me3 on PT development. SETD2 mutations may occur early in the pathogenic process of PTs and its loss per se may not be sufficient for progression to malignancy. Exclusive alterations of SETD2 in PT can be used as markers for the diagnosis of fibroepithelial lesions. The association of H3K36me3 with SETD2 mutations may also indicate the value of evaluation of H3K36me3 expression in the diagnosis of fibroepithelial lesions.

Expression of lymphoid enhancer-binding factor 1 in breast fibroepithelial lesions

Phyllodes tumors (PTs) are rare epithelial-mesenchymal tumors of the breast with malignant potential. Here, we evaluate the nuclear expression of lymphoid enhancer-binding factor 1 (LEF-1), a transcription factor downstream of Wnt/β-catenin signaling, in fibroepithelial lesions of the breast. Excised fibroepithelial lesions of the breast were retrospectively reviewed, blinded to the original diagnosis, and classified according to World Health Organization (WHO) criteria. A tissue microarray (TMA) was composed with two representative cores from each case, including 24 benign lesions, 11 borderline phyllodes, and 8 malignant PTs. β-Catenin, LEF-1, p120, and E-cadherin immunohistochemistry was performed on the TMA, and staining was quantified. The malignant/borderline PTs showed higher stromal LEF-1 expression than benign tumors (P < 0.001). Stromal cells expressed LEF-1 in 100% (16/16 of core TMA) of malignant phyllodes, compared with 73% (16/22) borderline and 27% (13/48) benign tumors. The average LEF-1 H-score was 24.9, 6.1, and 1.5 for malignant, borderline, and benign tumors, respectively. Nuclear expression of β-catenin in the stromal component was more often seen in malignant than in borderline and benign tumors (44% versus 32% and 23%, respectively). Nine TMA cores of malignant tumors without nuclear β-catenin staining demonstrated LEF-1 expression. Both LEF-1 and nuclear β-catenin showed expression in the majority of borderline/malignant PTs suggesting a biological progression of Wnt/β-catenin pathway activation in the stromal component from benign to malignant tumors. Inhibitors for the Wnt/β-catenin pathway may provide alternative treatment options in the future for malignant or metastatic PTs.

Droplet-digital PCR reveals frequent mutations in TERT promoter region in breast fibroadenomas and phyllodes tumours, irrespective of the presence of MED12 mutations

BACKGROUND

Breast fibroadenoma (FA) and phyllodes tumour (PT) often have variations of gene mediator complex subunit 12 (MED12) and mutations in the telomerase reverse transcriptase promoter region (TERTp). TERTp mutation is usually tested by Sanger sequencing. In this study, we compared Sanger sequencing and droplet-digital PCR (ddPCR) to measure TERTp mutations in FA and PT samples.

METHODS

FA and PT samples were collected from 82 patients who underwent surgery at our institution from 2005 to 2016. MED12 mutations for all cases and TERTp mutations for 17 tumours were detected by Sanger sequencing. ddPCR was performed to analyse TERTp mutation in all cases.

RESULTS

A total of 75 samples were eligible for analysis. Sanger sequencing detected MED12 mutations in 19/44 FA (42%) and 21/31 PT (68%). Among 17 Sanger sequencing-tested samples, 2/17 (12%) were TERTp mutation-positive. In ddPCR analyses, a significantly greater percentage of PT (19/31, 61%) was TERTp mutation-positive than was FA (13/44, 30%; P = 0.0046). The mutation positivity of TERTp and MED12 did not correlate, in either FA or PT.

CONCLUSIONS

ddPCR was more sensitive for detecting TERTp mutation than Sanger sequencing, being able to elucidate tumorigenesis in FA and PT.

Morphologic and genetic heterogeneity in breast fibroepithelial lesions-a comprehensive mapping study

Breast fibroepithelial lesions (FELs) encompass the common fibroadenoma (FA) and relatively rare phyllodes tumour (PT); the latter entity is usually classified as benign, borderline or malignant. Intratumoural heterogeneity is frequently present in these tumours, making accurate histologic evaluation challenging. Despite their rarity, PTs are an important clinical problem due to their propensity for recurrence and, in the case of malignant PT, metastasis. Surgical excision is the mainstay of management. Recent work has uncovered myriad genetic alterations in breast FELs. In this study, exome sequencing was performed on seven cases of morphologically heterogeneous breast FELs, including FAs, PTs of all grades, and a case of metaplastic spindle cell carcinoma arising in PT, in order to elucidate their intratumoural genetic repertoire. Gene mutations identified encompassed cell signalling, tumour suppressor, DNA repair and cell cycle regulating pathways. Mutations common to multiple tumour regions generally showed higher variant allele frequency. Frequent mutations included MED12, TP53, RARA and PIK3CA. Histological observations of increased cellular density and pleomorphism correlated with mutational burden. Phylogenetic analyses revealed disparate pathways of possible tumour progression. In summary, histological heterogeneity correlated with genetic changes in breast FELs.

Core needle biopsy diagnosis of fibroepithelial lesions of the breast: a diagnostic challenge

Fibroepithelial lesions (FEL) of the breast are biphasic neoplasms consisting of proliferative epithelial and stromal components and include fibroadenoma, phyllodes tumour and periductal stromal tumour. Core needle biopsy (CNB) is a commonly used diagnostic modality for investigation of breast lesions. As the accurate diagnosis of FEL requires integrated assessment of both epithelial and stromal components, this may create problems in small biopsies with limited sampling. In this review, common problems encountered in CNB of FEL are discussed, including establishing a diagnosis of borderline/malignant phyllodes tumour in a biopsy consisting of malignant spindle cells, differentiating phyllodes tumour from fibroadenoma on CNB, grading of phyllodes tumour of intermediate histological grade and assessment of periductal stromal tumours. The approaches are detailed systematically based on histology, immunohistochemistry and molecular characterisation. This comprehensive approach may aid in dealing with the overlapping histological appearance of FEL and sampling limitations of CNB.

MED12, TERT and RARA in fibroepithelial tumours of the breast

Fibroepithelial tumours are biphasic neoplasms of the breast comprising the common benign fibroadenomas and the less common phyllodes tumours (PTs), which have recurrent potential. PTs are classified into benign, borderline or malignant, based on five histopathological criteria, with malignant PTs having the highest metastatic capability. Accurate diagnosis can be challenging due to the subjective assessment of histopathological parameters. Fibroadenomas bear morphological similarities to benign PTs, while borderline and malignant PTs can sometimes be difficult to distinguish from other spindle cell tumours of the breast. From clonality studies to whole-genome sequencing, much research has been conducted to elucidate the molecular pathogenesis of fibroepithelial tumours, which, in turn, have allowed leveraging the findings for diagnostic applications, including grading of PTs. The most noteworthy discovery was of recurrent MED12 mutations in both fibroadenomas and PTs. Subsequent studies also uncovered relatively frequent genetic mutations in TERT promoter and RARA. A customised panel of 16 most frequently mutated genes in fibroepithelial tissues has been compiled previously and has contributed to resolving a few diagnostic dilemmas. This review will introduce the 16 genes and focus on the top three that are most frequently mutated in fibroepithelial tumours: MED12, TERT, and RARA.