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Wang L, Li J, Mei N, Chen H, Niu L, He J, Wang R. Identifying subtypes and developing prognostic models based on N6-methyladenosine and immune microenvironment related genes in breast cancer. Sci Rep 2024; 14:16586. [PMID: 39020010 PMCID: PMC11255230 DOI: 10.1038/s41598-024-67477-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024] Open
Abstract
Breast cancer (BC) is the most prevalent cancer in women globally. The tumor microenvironment (TME), comprising epithelial tumor cells and stromal elements, is vital for breast tumor development. N6-methyladenosine (m6A) modification plays a key role in RNA metabolism, influencing its various aspects such as stability and translation. There is a notable link between m6A methylation and immune cells in the TME, although this relationship is complex and not fully deciphered. In this research, BC expression and clinicopathological data from TCGA were scrutinized to assess expression profiles, mutations, and CNVs of 31 m6A genes and immune microenvironment-related genes, examining their correlations, functions, and prognostic impacts. Lasso and Cox regression identified prognostic genes for constructing a nomogram. Single-cell analyses mapped the distribution and patterns of these genes in BC cell development. We investigated associations between gene-derived risk scores and factors like immune infiltration, TME, checkpoints, TMB, CSC indices, and drug response. As a complement to computational analyses, in vitro experiments were conducted to confirm these expression patterns. We included 31 m6A regulatory genes and discovered a correlation between these genes and the extent of immune cell infiltration. Subsequently, a 7-gene risk score was generated, encompassing HSPA2, TAP1, ULBP2, CXCL1, RBP1, STC2, and FLT3. It was observed that the low-risk group exhibited better overall survival (OS) in BC, with higher immune scores but lower tumor mutational burden (TMB) and cancer stem cell (CSC) indices, as well as lower IC50 values for commonly used drugs. To enhance clinical applicability, age and stage were incorporated into the risk score, and a more comprehensive nomogram was constructed to predict OS. This nomogram was validated and demonstrated good predictive performance, with area under the curve (AUC) values for 1-year, 3-year, and 5-year OS being 0.848, 0.807, and 0.759, respectively. Our findings highlight the profound impact of prognostic-related genes on BC immune response and prognostic outcomes, suggesting that modulation of the m6A-immune pathway could offer new avenues for personalized BC treatment and potentially improve clinical outcomes.
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Affiliation(s)
- Lizhao Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Jianpeng Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Nan Mei
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Heyan Chen
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Ligang Niu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.
| | - Ru Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.
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Nakamura H, Watanabe M, Takada K, Sato T, Hikage F, Umetsu A, Muramatsu J, Furuhashi M, Ohguro H. Modulation of Epithelial-Mesenchymal Transition Is a Possible Underlying Mechanism for Inducing Chemoresistance in MIA PaCa-2 Cells against Gemcitabine and Paclitaxel. Biomedicines 2024; 12:1011. [PMID: 38790973 PMCID: PMC11118094 DOI: 10.3390/biomedicines12051011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
To elucidate the currently unknown molecular mechanisms responsible for the similarity and difference during the acquirement of resistance against gemcitabine (GEM) and paclitaxel (PTX) in patients with pancreatic carcinoma, we examined two-dimensional (2D) and three-dimensional (3D) cultures of parent MIA PaCa-2 cells (MIA PaCa-2-PA) and their GEM resistance cell line (MIA PaCa-2-GR) and PTX resistance (MIA PaCa-2-PR). Using these cells, we examined 3D spheroid configurations and cellular metabolism, including mitochondrial and glycolytic functions, with a Seahorse bio-analyzer and RNA sequencing analysis. Compared to the MIA PaCa-2-PA, (1) the formation of the 3D spheroids of MIA PaCa-2-GR or -PR was much slower, and (2) their mitochondrial and glycolytic functions were greatly modulated in MIA PaCa-2-GR or -PR, and such metabolic changes were also different between their 2D and 3D culture conditions. RNA sequencing and bioinformatic analyses of the differentially expressed genes (DEGs) using an ingenuity pathway analysis (IPA) suggested that various modulatory factors related to epithelial -mesenchymal transition (EMT) including STAT3, GLI1, ZNF367, NKX3-2, ZIC2, IFIT2, HEY1 and FBLX, may be the possible upstream regulators and/or causal network master regulators responsible for the acquirement of drug resistance in MIA PaCa-2-GR and -PR. In addition, among the prominently altered DEGs (Log2 fold changes more than 6 or less than -6), FABP5, IQSEC3, and GASK1B were identified as unique genes associated with their antisense RNA or pseudogenes, and among these, FABP5 and GASK1B are known to function as modulators of cancerous EMT. Therefore, the observations reported herein suggest that modulations of cancerous EMT may be key molecular mechanisms that are responsible for inducing chemoresistance against GEM or PTX in MIA PaCa-2 cells.
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Affiliation(s)
- Hajime Nakamura
- Departments of Medical Oncology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (H.N.); (K.T.); (J.M.)
| | - Megumi Watanabe
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (M.W.); (F.H.); (A.U.)
| | - Kohichi Takada
- Departments of Medical Oncology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (H.N.); (K.T.); (J.M.)
| | - Tatsuya Sato
- Departments of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (T.S.); (M.F.)
- Departments of Cellular Physiology and Signal Transduction, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan
| | - Fumihito Hikage
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (M.W.); (F.H.); (A.U.)
| | - Araya Umetsu
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (M.W.); (F.H.); (A.U.)
| | - Joji Muramatsu
- Departments of Medical Oncology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (H.N.); (K.T.); (J.M.)
| | - Masato Furuhashi
- Departments of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (T.S.); (M.F.)
| | - Hiroshi Ohguro
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, S1W17, Chuo-ku, Sapporo 060-8556, Japan; (M.W.); (F.H.); (A.U.)
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Wu H, Fu Z, Li H, Fang F, He B, Ye Y, Wu H, Xu D, Zheng H, Zhang Q. TRIB3, as a robust prognostic biomarker for HNSC, is associated with poor immune infiltration and cancer cell immune evasion. Front Immunol 2024; 14:1290839. [PMID: 38235126 PMCID: PMC10791810 DOI: 10.3389/fimmu.2023.1290839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Objective As a pseudokinase, Tribbles Pseudokinase 3 (TRIB3) is implicated in a wide array of biological processes, including cell signal transduction, metabolic regulation, stress responses, and immune regulation. While its significant role in the immune regulation of certain cancers is well-established, the specific functions and impact of TRIB3 in head and neck squamous cell carcinoma (HNSC) remain unclear. Methods The data of RNA-sequence was acquired from the TCGA database to analyze the expression patterns of TRIB3 and elucidate its prognostic value in HNSC patients. Furthermore, the correlation between TRIB3 and tumor mutation burden, clinical data, immune checkpoint genes, and immune cell infiltration was explored. Moreover, the TRIB3 location in tumor tissues and subcellular structures was identified via Tisch in the HPA database, and the potential protein interaction molecules for TRIB3 were elucidated in the STRING database. The potential TRIB3 gene function was assessed using gene set enrichment analysis (GSEA), whereas the TRIB3 expression levels in clinical HNSC samples were verified by RT-qPCR and immunohistochemistry. the role of TRIB3 in enhancing the malignant behavior of HNSC cells was validated in vitro through a series of methods including RT-qPCR, CCK8 assay, wound healing assay, and transwell assay. Results It was revealed that TRIB3 was significantly overexpressed in the nucleus and cytoplasm of HNSC. Furthermore, this overexpression markedly enhanced the migration ability of tumor cells. As an independent prognostic factor, TRIB3 was associated with advanced tumor T stage and was significantly involved with tumor mutation burden and immune cell infiltration in HNSC. Moreover, it was observed that TRIB3 was not a predicted factor for PD1/PDL1 and ATL4 inhibitor treatment; however, it was substantially correlated with various immune evasion-related genes in HNSC. Conclusion TRIB3 could serve as a potential prognostic marker for HNSC and might be a key gene mediating HNSC immune evasion.
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Affiliation(s)
- Huadong Wu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
- Department of Otolaryngology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Zhenzhen Fu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Hong Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Feifei Fang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Bin He
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Yujie Ye
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Heyong Wu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Dong Xu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Haoran Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Zhang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
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Cervenkova L, Palek R, Moulisova V, Liska V, Daum O, Mohelnikova-Duchonova B, Soucek P. Protein expression and localization of ABC transporters in pancreatic adenocarcinoma: Prognostic role of ABCC8. Pancreatology 2023; 23:978-987. [PMID: 37839922 DOI: 10.1016/j.pan.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/03/2023] [Accepted: 10/08/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND ATP-binding cassette (ABC) transporters translocate various substances across cellular membranes. Their deregulation may cause cancer drug resistance or perturbations in the supply of building blocks for cancer cells and modify patients' prognosis. This study investigated protein expression and cellular localization of the previously suggested putative prognostic biomarkers - ABCB2/TAP1, ABCC7/CFTR, ABCC8/SUR1, and ABCD4 in patients with pancreatic ductal adenocarcinoma (PDAC). METHODS Protein expression and localization were assessed by immunohistochemistry in formalin-fixed paraffin-embedded primary tumor tissue blocks of 61 PDAC patients and associated with clinical data and the survival of patients. RESULTS No CFTR protein expression was observed in PDAC, while TAP1 and ABCC8 were expressed predominantly in the cytoplasm of tumor cells. Most samples (81 %) had detectable both membranous and cytoplasmic ABCD4 staining and 42 % had ABCD4 expressed in the apical orientation. Negative membranous ABCD4 staining was significantly more frequent in advanced stage III or IV tumors (p = 0.022). Small or medium counts of individual ABCC8-positive cells in the stroma surrounding tumor tubules were also more often found in stage III or IV (p = 0.044). Patients with moderate or strong ABCC8 cytoplasmic staining intensity in tumor cells had a 3.5-fold higher risk of disease progression than those with weak staining (p = 0.002). CONCLUSIONS The study shows for the first time that the cytoplasmic ABCC8 protein expression has prognostic value in PDAC.
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Affiliation(s)
- Lenka Cervenkova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Third Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Richard Palek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Surgery, Faculty Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Vladimira Moulisova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Vaclav Liska
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Surgery, Faculty Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Ondrej Daum
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Pathology, Faculty Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Pavel Soucek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
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