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Li X, Yu X, Bi J, Jiang X, Zhang L, Li Z, Shao M. Integrating single-cell and spatial transcriptomes reveals COL4A1/2 facilitates the spatial organisation of stromal cells differentiation in breast phyllodes tumours. Clin Transl Med 2024; 14:e1611. [PMID: 38481388 PMCID: PMC10938066 DOI: 10.1002/ctm2.1611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 03/17/2024] Open
Abstract
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.
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Affiliation(s)
- Xia Li
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Xuewen Yu
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Jiaxin Bi
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Xu Jiang
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Lu Zhang
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Zhixin Li
- Department of SurgeryShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of SurgeryThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
| | - Mumin Shao
- Department of PathologyShenzhen Traditional Chinese Medicine HospitalShenzhenP.R. China
- Department of PathologyThe Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhenP.R. China
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Verma VK, Beevi SS, Nair RA, Kumar A, Kiran R, Alexander LE, Dinesh Kumar L. MicroRNA signatures differentiate types, grades, and stages of breast invasive ductal carcinoma (IDC): miRNA-target interacting signaling pathways. Cell Commun Signal 2024; 22:100. [PMID: 38326829 PMCID: PMC10851529 DOI: 10.1186/s12964-023-01452-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Invasive ductal carcinoma (IDC) is the most common form of breast cancer which accounts for 85% of all breast cancer diagnoses. Non-invasive and early stages have a better prognosis than late-stage invasive cancer that has spread to lymph nodes. The involvement of microRNAs (miRNAs) in the initiation and progression of breast cancer holds great promise for the development of molecular tools for early diagnosis and prognosis. Therefore, developing a cost effective, quick and robust early detection protocol using miRNAs for breast cancer diagnosis is an imminent need that could strengthen the health care system to tackle this disease around the world. METHODS We have analyzed putative miRNAs signatures in 100 breast cancer samples using two independent high fidelity array systems. Unique and common miRNA signatures from both array systems were validated using stringent double-blind individual TaqMan assays and their expression pattern was confirmed with tissue microarrays and northern analysis. In silico analysis were carried out to find miRNA targets and were validated with q-PCR and immunoblotting. In addition, functional validation using antibody arrays was also carried out to confirm the oncotargets and their networking in different pathways. Similar profiling was carried out in Brca2/p53 double knock out mice models using rodent miRNA microarrays that revealed common signatures with human arrays which could be used for future in vivo functional validation. RESULTS Expression profile revealed 85% downregulated and 15% upregulated microRNAs in the patient samples of IDC. Among them, 439 miRNAs were associated with breast cancer, out of which 107 miRNAs qualified to be potential biomarkers for the stratification of different types, grades and stages of IDC after stringent validation. Functional validation of their putative targets revealed extensive miRNA network in different oncogenic pathways thus contributing to epithelial-mesenchymal transition (EMT) and cellular plasticity. CONCLUSION This study revealed potential biomarkers for the robust classification as well as rapid, cost effective and early detection of IDC of breast cancer. It not only confirmed the role of these miRNAs in cancer development but also revealed the oncogenic pathways involved in different progressive grades and stages thus suggesting a role in EMT and cellular plasticity during breast tumorigenesis per se and IDC in particular. Thus, our findings have provided newer insights into the miRNA signatures for the classification and early detection of IDC.
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Affiliation(s)
- Vinod Kumar Verma
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, (CSIR-CCMB) Uppal Road, Hyderabad, Telangana, 500007, India
| | - Syed Sultan Beevi
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, (CSIR-CCMB) Uppal Road, Hyderabad, Telangana, 500007, India
| | - Rekha A Nair
- Department of Pathology, Regional Cancer Centre (RCC), Medical College Campus, Trivandrum, 695011, India
| | - Aviral Kumar
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, (CSIR-CCMB) Uppal Road, Hyderabad, Telangana, 500007, India
| | - Ravi Kiran
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, (CSIR-CCMB) Uppal Road, Hyderabad, Telangana, 500007, India
| | - Liza Esther Alexander
- Department of Pathology, Regional Cancer Centre (RCC), Medical College Campus, Trivandrum, 695011, India
| | - Lekha Dinesh Kumar
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, (CSIR-CCMB) Uppal Road, Hyderabad, Telangana, 500007, India.
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Akrida I, Mulita F, Plachouri KM, Benetatos N, Maroulis I, Papadaki H. Epithelial to mesenchymal transition (EMT) in metaplastic breast cancer and phyllodes breast tumors. Med Oncol 2023; 41:20. [PMID: 38104042 DOI: 10.1007/s12032-023-02259-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
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.
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Affiliation(s)
- Ioanna Akrida
- Department of General Surgery, University General Hospital of Patras, Rion, Greece.
- Department of Anatomy-Histology-Embryology, University of Patras Medical School, Rion, Greece.
- Department of Surgery, Department of Anatomy-Histology-Embryology, School of Medicine, University of Patras, 26504, Rion, Greece.
| | - Francesk Mulita
- Department of General Surgery, University General Hospital of Patras, Rion, Greece
| | | | - Nikolaos Benetatos
- Department of General Surgery, University General Hospital of Patras, Rion, Greece
| | - Ioannis Maroulis
- Department of General Surgery, University General Hospital of Patras, Rion, Greece
| | - Helen Papadaki
- Department of Anatomy-Histology-Embryology, University of Patras Medical School, Rion, Greece
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Zhang L, Bi J, Yu X, Li X, Liu X, Weng X, Shao M. Versican core protein aids in the diagnosis and grading of breast phyllodes tumor. Ann Diagn Pathol 2023; 66:152176. [PMID: 37423116 DOI: 10.1016/j.anndiagpath.2023.152176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023]
Abstract
Phyllodes tumors (PTs) are biphasic fibroepithelial lesions that occur in the breast. Diagnosing and grading PTs remains a challenge in a small proportion of cases, due to the lack of reliable specific biomarkers. We screened a potential marker versican core protein (VCAN) through microproteomics analysis, validated its role for the grading of PTs by immunohistochemistry, and analyzed the correlation between VCAN expression and clinicopathological characteristics. Cytoplasmic immunoreactivity for VCAN was identified in all benign PT samples, among which 40 (93.0 %) showed VCAN-positive staining in ≥50 % of tumor cells. Eight (21.6 %) borderline PT samples showed VCAN-positive staining in ≥50 % of the cells with weak to moderate staining intensity, whereas 29 samples (78.4 %) showed VCAN-positive staining in <50 % of the cells. In malignant PTs, 16 (84.2 %) and three (15.8 %) samples showed VCAN-positive staining in <5 % and 5-25 % of stromal cells, respectively. Fibroadenomas showed a similar expression pattern to benign PTs. Fisher's exact test showed that the percentages of positive cells (P < .001) and staining intensities (P < .001) of tumor cells were significantly different between the five groups. VCAN positivity was associated with tumor categories (P < .0001) and CD34 expression (P < .0001). The expression of VCAN gradually decreases as the tumor categories increases, following recurrence. To the best of our knowledge, our results are the first in the literature to reveal that VCAN is useful for diagnosing and grading PTs. The expression level of VCAN appeared to be negatively associated with PT categories, suggesting that dysregulation of VCAN may be involved in the tumor progression of PTs.
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Affiliation(s)
- Lu Zhang
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, 518033 Shenzhen, China
| | - Jiaxin Bi
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, 518033 Shenzhen, China
| | - Xuewen Yu
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, 518033 Shenzhen, China
| | - Xia Li
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, 518033 Shenzhen, China
| | - Xia Liu
- Department of Pathology, The Second People's Hospital of Shenzhen, 518000 Shenzhen, China
| | - Xin Weng
- Department of Pathology, The Second People's Hospital of Shenzhen, 518000 Shenzhen, China
| | - Mumin Shao
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, 518033 Shenzhen, China.
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Li X, Vail E, Maluf H, Chaum M, Leong M, Lownik J, Che M, Giuliano A, Cao D, Dadmanesh F. Gene Expression Profiling of Fibroepithelial Lesions of the Breast. Int J Mol Sci 2023; 24:ijms24109041. [PMID: 37240386 DOI: 10.3390/ijms24109041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
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.
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Affiliation(s)
- Xiaomo Li
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Eric Vail
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Horacio Maluf
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Manita Chaum
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Leong
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joseph Lownik
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mingtian Che
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Armando Giuliano
- Saul and Joyce Brandman Breast Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Duoyao Cao
- Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Farnaz Dadmanesh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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George IA, Sathe G, Ghose V, Chougule A, Chandrani P, Patil V, Noronha V, Venkataramanan R, Limaye S, Pandey A, Prabhash K, Kumar P. Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Front Cell Dev Biol 2022; 10:957983. [PMID: 36393868 PMCID: PMC9651967 DOI: 10.3389/fcell.2022.957983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/04/2022] [Indexed: 03/27/2024] Open
Abstract
Tongue squamous cell carcinoma is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. Most of the oral cavity cancer patients present in clinics with locally advanced unresectable tumors. Neoadjuvant treatment is beneficial for these individuals as it reduces the tumor size aiding complete resection. However, patients develop therapy resistance to the drug regimen. In this study, we explored the differential expression of proteins and altered phosphorylation in the neoadjuvant chemotherapy resistant tongue cancer patients. We integrated the proteomic and phosphoproteomic profiles of resistant (n = 4) and sensitive cohorts (n = 4) and demonstrated the differential expression and phosphorylation of proteins in the primary tissue of the respective subject groups. We observed differential and extensive phosphorylation of keratins such as KRT10 and KRT1 between the two cohorts. Furthermore, our study revealed a kinase signature associated with neoadjuvant chemotherapy resistance. Kinases such as MAPK1, AKT1, and MAPK3 are predicted to regulate the resistance in non-responders. Pathway analysis showed enrichment of Rho GTPase signaling and hyperphosphosphorylation of proteins involved in cell motility, invasion, and drug resistance. Targeting the kinases could help with the clinical management of neoadjuvant chemotherapy-resistant tongue cancer.
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Affiliation(s)
- Irene A. George
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, Bangalore, India
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vivek Ghose
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | | | | | | | | | - Sewanti Limaye
- Sir H.N. Reliance Foundation Hospital and Research Centre, Mumbai, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Prashant Kumar
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Karkinos Healthcare Pvt Ltd., Mumbai, India
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