Genetic differences between benign phyllodes tumors and fibroadenomas revealed through targeted next generation sequencing

Deep learning-assisted distinguishing breast phyllodes tumours from fibroadenomas based on ultrasound images: a diagnostic study

OBJECTIVES

To evaluate the performance of ultrasound-based deep learning (DL) models in distinguishing breast phyllodes tumours (PTs) from fibroadenomas (FAs) and their clinical utility in assisting radiologists with varying diagnostic experiences.

METHODS

We retrospectively collected 1180 ultrasound images from 539 patients (247 PTs and 292 FAs). Five DL network models with different structures were trained and validated using nodule regions annotated by radiologists on breast ultrasound images. DL models were trained using the methods of transfer learning and 3-fold cross-validation. The model demonstrated the best evaluation index in the 3-fold cross-validation was selected for comparison with radiologists' diagnostic decisions. Two-round reader studies were conducted to investigate the value of DL model in assisting 6 radiologists with different levels of experience.

RESULTS

Upon testing, Xception model demonstrated the best diagnostic performance (area under the receiver-operating characteristic curve: 0.87; 95% CI, 0.81-0.92), outperforming all radiologists (all P < .05). Additionally, the DL model enhanced the diagnostic performance of radiologists. Accuracy demonstrated improvements of 4%, 4%, and 3% for senior, intermediate, and junior radiologists, respectively.

CONCLUSIONS

The DL models showed superior predictive abilities compared to experienced radiologists in distinguishing breast PTs from FAs. Utilizing the model led to improved efficiency and diagnostic performance for radiologists with different levels of experience (6-25 years of work).

ADVANCES IN KNOWLEDGE

We developed and validated a DL model based on the largest available dataset to assist in diagnosing PTs. This model has the potential to allow radiologists to discriminate 2 types of breast tumours which are challenging to identify with precision and accuracy, and subsequently to make more informed decisions about surgical plans.

Salivary Metabolites in Breast Cancer and Fibroadenomas: Focus on Menopausal Status and BMI

This study of the features of the biochemical composition of biological fluids in patients with breast cancer, including saliva, allows us to identify some indicators as metabolic predictors of the presence of the disease.

OBJECTIVES

to study the influence of the menopause factor and body mass index (BMI) on the biochemical composition of saliva and to evaluate the applicability of metabolic markers of saliva for the diagnosis of breast cancer.

METHODS

The case-control study involved 1438 people (breast cancer, n = 543; fibroadenomas, n = 597; control, n = 298). A comprehensive study of the biochemical composition of saliva was carried out using 36 parameters.

RESULTS

When comparing the salivary biochemical composition in breast cancer, fibroadenomas, and controls, it is necessary to take into account the menopausal status, as well as BMI (less than 25 or more) for the group of patients with preserved menstrual function. A complex of biochemical parameters has been identified that change in saliva during breast cancer, regardless of menopause and BMI (total protein, urea, uric acid, NO, α-amino acids, GGT), as well as specific parameters that must be taken into account when analyzing individual subgroups (imidazole compounds, LDH, catalase, α-amylase). During the study of a separate group of patients with leaf-shaped (phyllodes) tumors, we found similarities with breast cancer in the changes in some biochemical parameters that can be attributed to metabolites of malignant growth (protein, α-amino acids, calcium, NO, pyruvate, peroxidase, α-amylase).

CONCLUSIONS

We demonstrated changes in a wide range of salivary biochemical parameters depending on the presence of fibroadenomas and breast cancer. From the point of view of clinical practice, this may be useful information for monitoring the condition of patients with fibroadenomas, which are difficult to unambiguously classify based on instrumental diagnostics alone.

Malignant phyllodes tumor with EGFR variant III mutation: A rare case report with immunohistochemical and genomic studies

A female in her 60's presented with a left-sided breast mass. A core needle biopsy specimen showed diffuse proliferation of a round cell tumor, which was positive for vimentin, NKX2.2, BCOR, and focal CD99 on immunohistochemistry (IHC). No fusion genes of the Ewing family sarcomas were detected. With a tentative diagnosis of primary breast sarcoma (PBS), total mastectomy was performed after chemotherapy. The resected tissues showed proliferation of round or spindle-shaped tumor cells with a high nuclear-to-cytoplasmic ratio, exhibiting solid and fascicular arrangements but no epithelial component or organoid pattern. While IHC indicated no particular histological diagnosis, genomic examination revealed gene alterations in MED12 p.G44D, MLL2 (KMT2D) p.T1496fs*27, and EGFR variant III (vIII). Moreover, a retrospective IHC study showed overexpression of EGFRvIII. A malignant phyllodes tumor (PT) with extensive sarcomatous overgrowth was indicated as an integrative diagnosis. This is a rare case of a malignant PT harboring EGFRvIII. The present case provides an importance of accurate diagnosis and genomic analysis of rare breast tumors, as malignant PT and PBS are different in its treatment strategy and prognosis.

Epithelial to mesenchymal transition (EMT) in metaplastic breast cancer and phyllodes breast tumors

Epithelial-mesenchymal transition (EMT), a transdifferentiation program whereby epithelial cells acquire mesenchymal phenotype, is essential during embryonic development. EMT has also been implicated in cancer progression by conferring migratory and metastatic potential, as well as cell plasticity and stem cell like traits, to cancer cells. Metaplastic breast carcinoma (MBC) is a rare aggressive type of breast cancer characterized by the presence of heterologous elements, typically by the existence of epithelial and mesenchymal components. Phyllodes tumors (PTs) are uncommon fibroepithelial neoplasms consisting of epithelial and mesenchymal elements. Although various hypotheses have been proposed on the pathogenesis of these biphasic tumors, there is growing evidence supporting the theory that PTs and MBC could both correlate with cancer related EMT. This review summarizes the existing literature on the emerging role of EMT in the pathogenesis of MBC and PTs. Both malignant PTs and MBC are characterized by poor prognosis. Therefore, several anti-EMT targeting strategies such as blocking upstream signaling pathways, targeting the molecular drivers of EMT and targeting mesenchymal cells and the extracellular matrix, could potentially represent a promising therapeutic approach for patients suffering from these aggressive neoplasms.

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.

Gene Expression Profiling of Fibroepithelial Lesions of the Breast

Fibroepithelial lesions of the breast (FELs) are a heterogeneous group of neoplasms exhibiting a histologic spectrum ranging from fibroadenomas (FAs) to malignant phyllodes tumors (PTs). Despite published histologic criteria for their classification, it is common for such lesions to exhibit overlapping features, leading to subjective interpretation and interobserver disagreements in histologic diagnosis. Therefore, there is a need for a more objective diagnostic modality to aid in the accurate classification of these lesions and to guide appropriate clinical management. In this study, the expression of 750 tumor-related genes was measured in a cohort of 34 FELs (5 FAs, 9 cellular FAs, 9 benign PTs, 7 borderline PTs, and 4 malignant PTs). Differentially expressed gene analysis, gene set analysis, pathway analysis, and cell type analysis were performed. Genes involved in matrix remodeling and metastasis (e.g., MMP9, SPP1, COL11A1), angiogenesis (VEGFA, ITGAV, NFIL3, FDFR1, CCND2), hypoxia (ENO1, HK1, CYBB, HK2), metabolic stress (e.g., UBE2C, CDKN2A, FBP1), cell proliferation (e.g., CENPF, CCNB1), and the PI3K-Akt pathway (e.g., ITGB3, NRAS) were highly expressed in malignant PTs and less expressed in borderline PTs, benign PTs, cellular FAs, and FAs. The overall gene expression profiles of benign PTs, cellular FAs, and FAs were very similar. Although a slight difference was observed between borderline and benign PTs, a higher degree of difference was observed between borderline and malignant PTs. Additionally, the macrophage cell abundance scores and CCL5 were significantly higher in malignant PTs compared with all other groups. Our results suggest that the gene-expression-profiling-based approach could lead to further stratification of FELs and may provide clinically useful biological and pathophysiological information to improve the existing histologic diagnostic algorithm.

Refining the classification of breast phyllodes tumours

Phyllodes tumours of the breast are uncommon fibroepithelial neoplasms that pose recurrent classification challenges, in large part due to the multiple histological parameters of stromal hypercellularity and atypia, stromal mitotic count, stromal overgrowth and tumour borders, that are used for grading. While the World Health Organization (WHO) Classification of Breast Tumours provides recommendations on diagnostic features, defining criteria are not always applied in routine practice. Lack of concordance among pathologists in typing and grading further underscores the classification difficulties, especially in the borderline category. Although there has been significant molecular information on phyllodes tumours in recent years which has been diagnostically helpful, it has not been translated into daily clinical practice. In order to refine the classification of phyllodes tumours into one that is simple yet comprehensive, reproducible and prognostically precise, a multipronged approach is needed that leverages on global contributions of the International Fibroepithelial Consortium, support by the International Collaboration on Cancer Classification and Research (IC³ R) in amalgamating evidence translation, and guidance from the International Collaboration on Cancer Reporting (ICCR) for standardised reporting. It is hoped that the evidence generated can be used towards refining the classification of phyllodes tumours for the future.

Discrimination between phyllodes tumor and fibro-adenoma: Does artificial intelligence-aided mammograms have an impact?

Background

The indulgence of artificial intelligence (AI) has been considered recently in the work up for the detection and diagnosis of breast cancer through algorithms that could supply diagnosis as the radiologist do. The algorithm learns from a supervised and continuous input of large and new data sets unlike the standard programming, which requires clear step-by-step instructions. The aim of this study is to assess the ability of AI scanned mammograms to aid the ultrasound in the discrimination between phyllodes tumors and fibro-adenomas.

Results

This is a retrospective analysis included 374 proven phyllodes tumors (PT) and fibro-adenomas (FA). Digital mammogram and breast ultrasound was performed for all the cases and each breast was given a “Breast Imaging Reporting and Data System” (BI-RADS) score. Included mammograms were scanned by AI with resultant a qualitative heatmap and a quantitative abnormality scoring of suspicion percentage.

The study included 164 PT (43.9%) and 210 FA (56.1%). BI-RADS category 2 was assigned in 40.1%, category 3 in 38.2%, category 4 in 18.5% and category 5 in 3.2% with median value of the AI abnormality scoring of 23%, 44%, 65% and 90% respectively. Sensitivity and specificity of the conventional imaging were 59.2% and 75.8% respectively. The AI abnormality scoring of 49.5% upgraded the sensitivity to 89.6% and specificity to 94.8% in the ability to discriminate PT from FA masses.

Conclusion

Artificial intelligence-aided mammograms could be used as method of distinction between PT from FA detected on sono-mammogram. The color hue and the quantification of the abnormality scoring percentage could be used as a one setting method for specification and so guide clinicians in their decision of conservative management or the choice of the surgical procedure.

A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samples

Introduction: A well-validated diagnostic assay with curated biomarkers complements clinicopathological factors to facilitate early diagnosis and ensure timely treatment delivery. This study focuses on an Asian-centric cancer diagnostic assay designed and thoroughly validated against commercially available standard references and a cohort of over 200 clinical specimens spanning 12 diverse Asian-centric cancer types.

Methods: The assay uses hybrid-capture probes capable of profiling DNA aberrations from 572 cancer-related genes and 91 RNA fusion partners. The panel can detect clinically-tractable biomarkers such as microsatellite instability (MSI) and tumor mutation burden (TMB).

Results: Analytical evaluation demonstrated 100% specificity and 99.9% sensitivity within a ≥5% VAF limit of detection (LoD) for SNV/Indels. RNA-based fusion features an LoD of ≥5 copies per nanogram input when evaluated against commercial references. Excellent linearity and concordance were observed when benchmarking against orthogonal methods in identifying MSI status, TMB scores and RNA fusions. Actionable genetic alterations were identified in 65% of the clinical samples.

Conclusion: These results demonstrate a molecular diagnostic assay that accurately detects genomic alterations and complex biomarkers. The data also supports an excellent performance of this assay for making critical diagnoses and well-informed therapeutic decisions in Asian prevalent cancers.

Surgical management and prognosis of phyllodes tumors of the breast

BACKGROUND

Regardless of histological grade, phyllodes tumors (PTs) exhibit the potential of local recurrence. The National Comprehensive Cancer Network (NCCN) recommends wide local excision (WLE) with a 1 cm margin or more for borderline/malignant PTs but excisional biopsy for benign PTs. However, the treatment of benign PTs remains controversial and the clinicopathologic risk factors for the local recurrence is still unclear.

METHODS

We retrospectively analyzed 238 patients with PTs who underwent surgery at the Chinese PLA General Hospital from January 1, 2006 and April 30, 2020. We stratified our analysis according to histologic grade and explored the clinicopathologic factors to influence local recurrence (LR), including age, histologic grade, history of fibroadenoma, type of surgery [vacuum-assisted biopsy system (VABS), local excision (LE), wide local excision (WLE) and mastectomy].

RESULTS

All 238 cases were categorized as benign (171, 71.8%), borderline (38, 16.0%), or malignant (29, 12.2%). The median follow-up was 50.2 months. In multivariate analysis, histologic grade (P<0.01) and history of fibroadenoma (P<0.01) were independent prognostic factors for LR. No difference existed in the recurrence rate of BPT treated with different surgical procedures (P=0.397), whereas a higher recurrence rate was found in VABS and LE subgroups than in WLE and mastectomy subgroups for borderline/malignant tumors (P<0.01).

CONCLUSIONS

No association found between surgical modalities and LR rate for BPT. We suggested a "wait-and-watch" policy for patients with unexpected benign subtypes, instead of unnecessary re-excision. In addition, VABS or LE can be treated for BPT with small mass, whereas WLE or even mastectomy should be conducted for borderline/malignant PTs with large mass.

Malignant phyllodes tumor of the breast: a systematic review

Phyllodes tumors (PT) are fibroepithelial neoplasms of the breast showing a peculiar leaf-like appearance. They account for 0.3 to 1% of all primary breast tumors and 2.5% of all fibroepithelial breast tumors. PT are classified into benign, borderline and malignant based upon their stromal morphology with a distribution of 60%, 20%, and 20%, respectively. Malignant PT of the breast constitute an uncommon challenging group of fibroepithelial neoplasms. They have a relatively high tendency to recur, although distant metastasis is uncommon, and nearly exclusive to malignant PT. Adequate surgical resection remains the standard approach to achieve maximal local control. Giant malignant PT are rare and a pose a diagnostic dilemma for pathologists, especially when comprised of sarcomatous elements. This review highlights the morphological features of PT detected in cytology and histology specimens and discusses diagnostic pitfalls and differential diagnosis.

Artificial intelligence modelling in differentiating core biopsies of fibroadenoma from phyllodes tumor

Breast fibroepithelial lesions (FEL) are biphasic tumors which consist of benign fibroadenomas (FAs) and the rarer phyllodes tumors (PTs). FAs and PTs have overlapping features, but have different clinical management, which makes correct core biopsy diagnosis important. This study used whole-slide images (WSIs) of 187 FA and 100 PT core biopsies, to investigate the potential role of artificial intelligence (AI) in FEL diagnosis. A total of 9228 FA patches and 6443 PT patches was generated from WSIs of the training subset, with each patch being 224 × 224 pixel in size. Our model employed a two-stage architecture comprising a convolutional neural network (CNN) component for feature extraction from the patches, and a recurrent neural network (RNN) component for whole-slide classification using activation values from the global average pooling layer in the CNN model. It achieved an overall slide-level accuracy of 87.5%, with accuracies of 80% and 95% for FA and PT slides respectively. This affirms the potential role of AI in diagnostic discrimination between FA and PT on core biopsies which may be further refined for use in routine practice.

Large borderline phyllodes breast tumor related to histopathology, diagnosis, and treatment management - case report

Breast phyllodes tumors (PTs) are uncommon tumors with a biphasic fibroepithelial component, characterized by rapid development in middle-aged women. A correct preoperative diagnosis after Tru-Cut biopsy allows for proper surgical planning. The treatment of choice remains surgery (wide local excision or mastectomy) with or without breast reconstruction, depending on the size and histopathological (HP) nature of the tumor. We reported a case of a 50-year-old woman with a large PT in her left breast, measuring 11/10 cm. Preoperative HP examination revealed biphasic proliferation, with the appearance of benign PT. The patient underwent a left mastectomy, with a favorable postoperative evolution. The final HP diagnosis was borderline PT, with areas of lipomatous metaplasia. After three months, breast reconstruction was performed. The therapeutic management of large PTs continues to be a challenge for pathologists and surgeons. Due to the increased frequency of local recurrence and HP progression to malignancies, the treatment of choice for these patients is mastectomy, without lymphadenectomy.

MED12 exon 2 and TERT promoter mutations in primary and recurrent breast fibroepithelial lesions

The genetic alterations in the recurrent breast fibroepithelial tumors are poorly understood. In the present study, we aimed to investigate mediator protein complex subunit 12 (MED12) exon 2 and telomerase reverse transcriptase (TERT) promoter mutations in a series of primary and recurrent fibroepithelial tumors. Sanger sequencing for MED12 exon 2 and TERT promoter was performed in 26 pairs of primary and recurrent fibroepithelial tumors (19 pairs of phyllodes tumors and seven pairs of fibroadenomas). The relationship between the genotypes and clinicopathological variables was also analyzed. MED12 mutation was identified in 19 primary tumors (12 phyllodes tumors and 7 fibroadenomas) and 17 recurrences (14 phyllodes tumors and three fibroadenomas). Most recurrent phyllodes tumors retained the original MED12 variants (17/19). Six recurrent fibroadenomas showed different MED12 variants from their paired primary tumors (6/7). TERT promoter mutation was identified in 13 primary phyllodes tumors (13/19) and 15 recurrent phyllodes tumors (15/19). However, it was only identified in one primary fibroadenoma (1/7). Recurrent phyllodes tumors often retained the original MED12 and TERT promoter mutations, while recurrent fibroadenomas often acquired new MED12 mutations. Our findings suggest that recurrent phyllodes tumors may be "true recurrence," and TERT mutant "benign fibroepithelial tumors" should be treated as phyllodes tumors.

Fibroepithelial tumours of the breast-a review

Fibroepithelial tumours of the breast are biphasic neoplasms composed of both epithelial and stromal elements, including the common fibroadenoma and the infrequent phyllodes tumour. The admixture of epithelium and stroma in the fibroadenoma shows intra- and pericanalicular patterns, and may display a variety of histological changes. Fibroadenoma variants include the cellular, juvenile, myxoid and complex forms. The cellular fibroadenoma may be difficult to distinguish from the benign phyllodes tumour. Stromal mitotic activity can be increased in fibroadenomas in the young and pregnant patients. Phyllodes tumours, neoplasms with the potential for recurrence, show an exaggerated intracanalicular growth pattern with broad stromal fronded architecture and stromal hypercellularity. They are graded into benign, borderline and malignant forms based on histological assessment of stromal features of hypercellularity, atypia, mitotic activity, overgrowth and the nature of the tumour borders. Classification of phyllodes tumours is imperfect, compounded by tumour heterogeneity with overlapping microscopic features among the different grades, especially in the borderline category. Malignant phyllodes tumours can metastasise and cause death. Determining which phyllodes tumours may behave aggressively has been difficult. The discovery of MED12 mutations in the pathogenesis of fibroepithelial tumours, together with other gene abnormalities in the progression pathway, has allowed refinements in diagnosis and prognosis.

Benign myofibroblastic/epithelial lesions of the breast with minimally infiltrative margins

A minority of mixed fibro-epithelial lesions of the breast lacks both fibroadenoma and phyllodes architectural patterns and have been previously labeled with different terms, including "hamartomas", "myoid/muscular hamartomas", "benign fibroadenomatous lesions" or "stromo-epithelial lesions of the breast". This study emphasizes the clinico-pathologic features of 5 cases of mammary benign fibro(stromo)-epithelial lesions sharing as a common morphologic theme the presence of minimally infiltrative margins due to the overgrowth of the stromal component into the surrounding fibro-fatty tissue. Notably the radiological features were suspicious for malignancy in 3 out of 5 cases. The following histologic features were seen in all cases: i) an epithelial component of benign glandular structures exhibiting the morphological spectrum of fibro-cystic disease; ii) a stromal component of bland-looking spindle cell myofibroblasts (vimentin + and α-smooth muscle actin +) set in a variably fibro-myxoid stroma. The present paper contributes to widen the morphological spectrum of the benign fibro-epithelial lesions of the breast, emphasizing the possibility that some cases, exhibiting a predominant myofibroblastic stromal component and minimally infiltrative margins, may be confused with other primary spindle cell mimickers of the breast. Accordingly, we propose the descriptive term "benign myofibroblastic/epithelial lesions of the breast with minimally infiltrative margins" for these previously underrecognized lesions.