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Liu G, Yang X, Li N. Towards key genes identification for breast cancer survival risk with neural network models. Comput Biol Chem 2024; 112:108143. [PMID: 39142146 DOI: 10.1016/j.compbiolchem.2024.108143] [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: 02/28/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 08/16/2024]
Abstract
Breast cancer, one common malignant tumor all over the world, has a considerably high rate of recurrence, which endangers the health and life of patients. While more and more data have been available, how to leverage the gene expression data to predict the survival risk of cancer patients and identify key genes has become a hot topic for cancer research. Therefore, in this work, we investigate the gene expression and clinical data of breast cancer patients, specifically a novel framework is proposed focusing on the survival risk classification and key gene identification task. We firstly combine the differential expression and univariate Cox regression analysis to achieve dimensional reduction of gene expression data. The median survival time is subsequently proposed as the risk classification threshold and a learning model based on neural network is trained to classify the survival risk of patients. Innovatively, in this work, the activation region visualization technology is selected as the identification tool, which identify 20 key genes related to the survival risk of breast cancer patients. We further analyze the gene function of these 20 key genes based on STRING database. It is critical to learn that, the genetic biomarkers identified in this paper may possess value for the following clinical treatment of breast cancer according to the literature findings. Importantly, the genetic biomarkers identified in this paper may possess value for the following clinical treatment of breast cancer according to the literature findings. Our work accomplishes the objective of proposing a targeted approach to enhancing the survival analysis and therapeutic strategies in breast cancer through advanced computational techniques and gene analysis.
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Affiliation(s)
- Gang Liu
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu 730000, China.
| | - Xiao Yang
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu 730000, China.
| | - Nan Li
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu 730000, China.
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2
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Zhou L, Bi Y, Wu X, He H. High keratin 15 expression reflects favorable prognosis in early cervical cancer patients. Ir J Med Sci 2024; 193:1755-1761. [PMID: 38639842 DOI: 10.1007/s11845-024-03686-6] [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: 02/01/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
OBJECTIVE Keratin 15 (KRT15) exhibits inconsistent prognostic roles in different cancers, and its prognostic value in early cervical cancer patients who receive tumor resection remains unknown. This study aimed to assess the relationship of KRT15 expression with prognosis in these patients. METHODS Totally, 147 early cervical cancer patients who received tumor resection were reviewed in this retrospective study. KRT15 was detected in formalin-fixed paraffin-embedded tumor tissue by immunohistochemistry (IHC). KRT15 IHC scores were computed by multiplying the percentage of positively stained cells (scored as 0-4) and corresponding staining intensity (scored as 0-3), ranging from 0 to 12. RESULTS Elevated KRT15 IHC score was linked with moderate to well differentiation (P = 0.005), tumor size ≤ 4 cm (P = 0.017), and International Federation of Gynecology and Obstetrics (FIGO) stage Ia/Ib (P < 0.001). KRT15 IHC score was inversely associated with adjuvant radiotherapy (P = 0.025) and adjuvant chemotherapy (P = 0.016). KRT15 IHC score ≥ 1 was linked with increased disease-free survival (DFS) (P = 0.003) and overall survival (OS) (P = 0.049). Meanwhile, KRT15 IHC score ≥ 1 independently predicted increased DFS (hazard ratio = 0.213, P = 0.017), but not OS (P > 0.05). KRT15 IHC score ≥ 3 and KRT15 IHC score ≥ 6 could not predict DFS or OS (all P > 0.05). By subgroup analyses, KRT15 IHC score ≥ 1 forecasted favorable DFS in patients with age > 45 years, human papillomavirus-positive, squamous carcinoma, and tumor size ≤ 4 cm (all P < 0.05). KRT15 IHC score ≥ 1 and KRT15 IHC score ≥ 3 predicted ascended DFS in patients without adjuvant radiotherapy or adjuvant chemotherapy (all P < 0.05). CONCLUSION High KRT15 expression reflects favorable tumor features and longer survival in early cervical cancer patients who receive tumor resection.
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Affiliation(s)
- Li Zhou
- Department of Gynecology and Obstetrics, Jingzhou Central Hospital, Jingzhou, 434020, Hubei, China.
| | - Ying Bi
- Department of Gynaecology and Obstetrics, Wuhan Red Cross Hospital, Wuhan, 430015, Hubei, China
| | - Xiaoling Wu
- Department of Gynecology and Obstetrics, Jingzhou Central Hospital, Jingzhou, 434020, Hubei, China
| | - Hong He
- Department of Gynecology and Obstetrics, Jingzhou Central Hospital, Jingzhou, 434020, Hubei, China
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3
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Geay J, Margaron Y, Gentien D, Reyal F, Puisieux A, Blanchoin L, Guyon L, Théry M. Plakins are involved in the regulation of centrosome position in polarized epithelial cells. Biol Cell 2024; 116:e2400048. [PMID: 38850178 DOI: 10.1111/boc.202400048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND INFORMATION The control of epithelial cell polarity is key to their function. Its dysregulation is a major cause of tissue transformation. In polarized epithelial cells,the centrosome is off-centred toward the apical pole. This asymmetry determines the main orientation of the microtubule network and intra-cellular traffic. However, the mechanism regulating centrosome positioning at the apical pole of polarized epithelial cells is still poorly undertood. RESULTS In this study we used transcriptomic data from breast cancer cells to identify molecular changes associated with the different stages of tumour transformation. We correlated these changes with variations in centrosome position or with cell progression along the epithelial-to-mesenchymal transition (EMT), a process that involves centrosome repositioning. We found that low levels of epiplakin, desmoplakin and periplakin correlated with centrosome mispositioning in cells that had progressed through EMT or tissue transformation. We further tested the causal role of these plakins in the regulation of centrosome position by knocking down their expression in a non-tumorigenic breast epithelial cell line (MCF10A). The downregulation of periplakin reduced the length of intercellular junction, which was not affected by the downregulation of epiplakin or desmoplakin. However, down-regulating any of them disrupted centrosome polarisation towards the junction without affecting microtubule stability. CONCLUSIONS Altogether, these results demonstrated that epiplakin, desmoplakin and periplakin are involved in the maintenance of the peripheral position of the centrosome close to inter-cellular junctions. They also revealed that these plakins are downregulated during EMT and breast cancer progression, which are both associated with centrosome mispositioning. SIGNIFICANCE These results revealed that the down-regulation of plakins and the consequential centrosome mispositioning are key signatures of disorganised cytoskeleton networks, inter-cellular junction weakening, shape deregulation and the loss of polarity in breast cancer cells. These metrics could further be used as a new readouts for early phases of tumoral development.
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Affiliation(s)
- Juliana Geay
- Université de Paris, CEA/INSERM/AP-HP, Institut de Recherche Saint Louis, UMR976, HIPI, CytoMorpho Lab, Hopital Saint Louis, Paris, France
| | - Yoran Margaron
- Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, UMR5168, LPCV, CytoMorpho Lab, Grenoble, France
| | - David Gentien
- Université PSL, Department of Translational Research, Institut Curie, Genomics Platform, Paris, France
| | - Fabien Reyal
- Université Paris Cité, Université PSL, INSERM U932, Breast Gynecological and Reconstructive Surgery, Institut Curie, Paris, France
| | - Alain Puisieux
- Université Claude Bernard Lyon 1, Cancer Research Center of Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Lyon, France
- Université PSL, Institut Curie, Université Versailles Saint-Quentin, CNRS UMR 3666, INSERM U1143, Paris, France
| | - Laurent Blanchoin
- Université de Paris, CEA/INSERM/AP-HP, Institut de Recherche Saint Louis, UMR976, HIPI, CytoMorpho Lab, Hopital Saint Louis, Paris, France
- Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, UMR5168, LPCV, CytoMorpho Lab, Grenoble, France
| | - Laurent Guyon
- Université Grenoble Alpes, CEA/INSERM, Interdisciplinary Research Institute of Grenoble, BioSanté UMR_S 1292, Grenoble, France
| | - Manuel Théry
- Université de Paris, CEA/INSERM/AP-HP, Institut de Recherche Saint Louis, UMR976, HIPI, CytoMorpho Lab, Hopital Saint Louis, Paris, France
- Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, UMR5168, LPCV, CytoMorpho Lab, Grenoble, France
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4
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Li X, Liu X, Yang F, Meng T, Li X, Yan Y, Xiao K. Mechanism of Dahuang Mudan Decotion in the treatment of colorectal cancer based on network pharmacology and experimental validation. Heliyon 2024; 10:e32136. [PMID: 38882337 PMCID: PMC11176830 DOI: 10.1016/j.heliyon.2024.e32136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Objective The objective of this study was to assess the pharmacological activity and therapeutic mechanism of Dahuang Mudan Decotion (DHMDD) for colorectal cancer using ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS), network pharmacology and in vitro experiments. Methods The chemical components of DHMDD were identified by UPLC-MS. Network pharmacological analysis was utilized to screen the active ingredients and targets associated with DHMDD for colorectal cancer. Based on the results of network pharmacology, the potential mechanism of DHMDD on colorectal cancer predicted was experimentally studied and verified in vitro. Results DHMDD primarily exerts its effects on colorectal cancer through 52 active ingredients. AKT1, ESR1, HSP90AA1, JUN, PIK3CA, PIK3CB, PIK3R1, SRC, STAT3, TP53 were the top 10 targets. The top 10 ingredient nodes were Quercetin, Physcione, Pontigenin, Crysophanol, Linolenic acid, Piceatannol, Adenosine, Emodin, Sambunigrin, and Prunasin. The main compounds and the target proteins exhibited strong binding ability in molecular docking studies. The results of cell experiments demonstrated that DHMDD can inhibit the proliferation, invasion and migration of CRC cells through the PI3K/Akt pathway. Conclusion Through network pharmacology analysis and cell experiments, this study suggests that DHMDD can exert its therapeutic effects on colorectal cancer through a combination of multiple components and targets.
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Affiliation(s)
- Xinghua Li
- Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, PR China
| | - Xinyue Liu
- Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, PR China
- The Gynecology Department of Shanxi Provincial People' Hospital, Shanxi Medical University, Taiyuan, 030001, PR China
| | - Fan Yang
- Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, PR China
| | - Tianwei Meng
- Heilongjiang University of Chinese Medicine, Harbin, 150040, PR China
| | - Xiang Li
- Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, PR China
| | - Yan Yan
- The Gynecology Department of Shanxi Provincial People' Hospital, Shanxi Medical University, Taiyuan, 030001, PR China
| | - Keyuan Xiao
- Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, PR China
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Wu Q, Luo Y, Lin N, Zheng S, Xie X. Prognostic Value and Immune Signatures of Anoikis-related Genes in Breast Cancer. J Immunother 2024:00002371-990000000-00110. [PMID: 38864225 DOI: 10.1097/cji.0000000000000523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/03/2024] [Indexed: 06/13/2024]
Abstract
From databases of the Cancer Genome Atlas (TCGA) and GSE42568, transcriptome data of breast cancer patients was obtained. Then, anoikis-related genes (ANRGs) were identified and constructed a risk score system. As a threshold value, the median risk score was used to stratify patients into low-risk and high-risk groups. Kaplan-Meier analysis was then conducted to evaluate the prognostic ability of the risk score system, which was validated using GSE7390. Furthermore, we identified potential enrichment of function and tumor immune infiltration in the model. Finally, the biological functions of a risk gene (EPB41L4B) in breast cancer were investigated through in vitro experiments. We constructed a risk score system via 9 prognosis ANRGs (CXCL2, EPB41L4B, SLC7A5, SFRP1, SDC1, BHLHE41, SPINT1, KRT15, and CD24). The Kaplan-Meier analysis showed that both TCGA-BRCA (training set) and GSE7390 (testing set) patients with high-risk status had significantly worse survival outcomes. In addition, the calibration plots were in good agreement with the prognosis prediction. Breast cancer patients with immunosuppressive microenvironment could be screened using risk groups since risk scores were correlated negatively with ESTIMATE score, tumor-infiltration lymphocytes, immune checkpoints, and chemotactic factors. Furthermore, cellular viability and cell migration of cancerous breast cells were inhibited and apoptosis was promoted by down-regulation of EPB41L4B gene expression. Based on ANRGs, a 9-gene prognostic model could be developed to predict breast cancer prognosis; moreover, patients of the high-risk group were in an immunosuppressed tumor microenvironment.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian Province, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
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6
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Andreou M, Jąkalski M, Duzowska K, Filipowicz N, Kostecka A, Davies H, Horbacz M, Ławrynowicz U, Chojnowska K, Bruhn-Olszewska B, Jankau J, Śrutek E, Las-Jankowska M, Bała D, Hoffman J, Hartman J, Pęksa R, Skokowski J, Jankowski M, Szylberg Ł, Maniewski M, Zegarski W, Nowikiewicz M, Nowikiewicz T, Dumanski JP, Mieczkowski J, Piotrowski A. Prelude to malignancy: A gene expression signature in normal mammary gland from breast cancer patients suggests pre-tumorous alterations and is associated with adverse outcomes. Int J Cancer 2024. [PMID: 38850108 DOI: 10.1002/ijc.35050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 06/09/2024]
Abstract
Despite advances in early detection and treatment strategies, breast cancer recurrence and mortality remain a significant health issue. Recent insights suggest the prognostic potential of microscopically healthy mammary gland, in the vicinity of the breast lesion. Nonetheless, a comprehensive understanding of the gene expression profiles in these tissues and their relationship to patient outcomes remain missing. Furthermore, the increasing trend towards breast-conserving surgery may inadvertently lead to the retention of existing cancer-predisposing mutations within the normal mammary gland. This study assessed the transcriptomic profiles of 242 samples from 83 breast cancer patients with unfavorable outcomes, including paired uninvolved mammary gland samples collected at varying distances from primary lesions. As a reference, control samples from 53 mammoplasty individuals without cancer history were studied. A custom panel of 634 genes linked to breast cancer progression and metastasis was employed for expression profiling, followed by whole-transcriptome verification experiments and statistical analyses to discern molecular signatures and their clinical relevance. A distinct gene expression signature was identified in uninvolved mammary gland samples, featuring key cellular components encoding keratins, CDH1, CDH3, EPCAM cell adhesion proteins, matrix metallopeptidases, oncogenes, tumor suppressors, along with crucial genes (FOXA1, RAB25, NRG1, SPDEF, TRIM29, and GABRP) having dual roles in cancer. Enrichment analyses revealed disruptions in epithelial integrity, cell adhesion, and estrogen signaling. This signature, named KAOS for Keratin-Adhesion-Oncogenes-Suppressors, was significantly associated with reduced tumor size but increased mortality rates. Integrating molecular assessment of non-malignant mammary tissue into disease management could enhance survival prediction and facilitate personalized patient care.
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Affiliation(s)
- Maria Andreou
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | | | - Anna Kostecka
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Monika Horbacz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | | | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jerzy Jankau
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Manuela Las-Jankowska
- Chair of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Clinical Oncology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Dariusz Bała
- Chair of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Surgical Oncology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jacek Hoffman
- Department of Clinical Breast Cancer and Reconstructive Surgery, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Michał Jankowski
- Chair of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Surgical Oncology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Mateusz Maniewski
- Department of Tumor Pathology and Pathomorphology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Chair of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Surgical Oncology, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Magdalena Nowikiewicz
- Department of Hepatobiliary and General Surgery, Antoni Jurasz University Hospital, Bydgoszcz, Poland
| | - Tomasz Nowikiewicz
- Chair of Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Clinical Breast Cancer and Reconstructive Surgery, Oncology Center-Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Mieczkowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
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Lee DHY, Tsang JY, Li JJX, Lau SL, Tam F, Loong TC, Tse GM. Cytokeratin 15 is a novel and independent predictor of poor outcome in luminal B HER2-negative breast carcinomas. Pathology 2024:S0031-3025(24)00137-5. [PMID: 38909003 DOI: 10.1016/j.pathol.2024.03.009] [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: 08/28/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 06/24/2024]
Abstract
Cytokeratin 15 (CK15) has been described as a stem cell marker in human organs and its expression is seen in breast tissue. CK15 expression is associated with aggressive features in endometrial and oesophageal cancers, but data on the breast are lacking. This study aims to investigate the clinicopathological associations and prognostic significance of CK15 in breast carcinomas. A multi-institute cohort of breast carcinomas were retrieved. Clinicopathological and outcome data were obtained and compared with immunohistochemical expression CK15 and a panel of biomarkers. In total, 1,476 cases were included, with an expression rate of 3.5%, preferentially expressed in luminal subtypes (p=0.024), with luminal B carcinomas being the highest (4.7%), as opposed to basal-like (1%) and HER2-overexpressed carcinomas (0%). Except for nodal stage (p=0.013) and nodal metastasis (p=0.048), oestrogen (p=0.035) and progesterone receptor (p=0.001) positivity, there were no associations with other clinicopathological parameters. A trend was observed with shorter breast cancer specific survival (BCSS) in CK15-positive luminal B carcinomas (p=0.062). On further subgroup multivariate analysis of luminal B HER2-negative carcinomas, CK15 expression exhibited robust correlation with shorter BCSS (HR=9.004, p=0.001) and disease-free survival (HR=7.085, p<0.001). Restricted to luminal breast carcinomas, specifically luminal B HER2-negative, CK15 is demonstrated to be a robust independent predictor of higher risk of recurrence and shorter survival, with potential as a clinical prognostic marker and an exclusive stem cell marker for this subgroup of carcinomas.
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Affiliation(s)
- Dennis H Y Lee
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Julia Y Tsang
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Joshua J X Li
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Sin Leung Lau
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Fiona Tam
- Department of Pathology, Kwong Wah Hospital, Hong Kong
| | | | - Gary M Tse
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong.
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8
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Sala-Hamrick KE, Tapaswi A, Polemi KM, Nguyen VK, Colacino JA. High-Throughput Transcriptomics of Nontumorigenic Breast Cells Exposed to Environmentally Relevant Chemicals. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:47002. [PMID: 38568856 PMCID: PMC10990114 DOI: 10.1289/ehp12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND There is a suite of chemicals, including metals, pesticides, and personal care product compounds, which are commonly detected at high levels in US Center for Disease Control's National Health and Nutrition Examination Survey (NHANES) chemical biomarker screens. Whether these chemicals influence development of breast cancer is not well understood. OBJECTIVES The objectives were to perform an unbiased concentration-dependent assessment of these chemicals, to quantify differences in cancer-specific genes and pathways, to describe if these differences occur at human population-relevant concentrations, and to specifically test for differences in markers of stemness and cellular plasticity. METHODS We treated nontumorigenic mammary epithelial cells, MCF10A, with 21 chemicals at four concentrations (25 nM , 250 nM , 2.5 μ M , and 25 μ M ) for 48 h. We conducted RNA-sequencing for these 408 samples, adapting the plexWell plate-based RNA-sequencing method to analyze differences in gene expression. We calculated gene and biological pathway-specific benchmark concentrations (BMCs) using BMDExpress3, identifying differentially expressed genes and generating the best fit benchmark concentration models for each chemical across all genes. We identified enriched biological processes and pathways for each chemical and tested whether chemical exposures change predicted cell type distributions. We contextualized benchmark concentrations relative to human population biomarker concentrations in NHANES. RESULTS We detected chemical concentration-dependent differences in gene expression for thousands of genes. Enrichment and cell type distribution analyses showed benchmark concentration responses correlated with differences in breast cancer-related pathways, including induction of basal-like characteristics for some chemicals, including arsenic, lead, copper, and methyl paraben. Comparison of benchmark data to NHANES chemical biomarker (urine or blood) concentrations indicated an overlap between exposure levels and levels sufficient to cause a gene expression response. DISCUSSION These analyses revealed that many of these 21 chemicals resulted in differences in genes and pathways involved in breast cancer in vitro at human exposure-relevant concentrations. https://doi.org/10.1289/EHP12886.
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Affiliation(s)
| | - Anagha Tapaswi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Katelyn M. Polemi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Vy K. Nguyen
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Program in the Environment, University of Michigan, Ann Arbor, Michigan, USA
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9
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Yang X, Liu Z, Wang X, Han Z, Zhang C, Guo L. Tumor keratin 15 expression links with less extent of invasion and better prognosis in papillary thyroid cancer patients receiving tumor resection. Ir J Med Sci 2024; 193:9-15. [PMID: 37243844 DOI: 10.1007/s11845-023-03413-7] [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: 04/17/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
OBJECTIVE Keratin 15 (KRT15) is identified as a useful biomarker in several solid tumors, while its clinical role in papillary thyroid cancer (PTC) remains unknown. Herein, this study is intended to explore the correlation of tumor KRT15 with clinical features and survival in PTC patients who received tumor resection. METHODS This study retrospectively screened 350 PTC patients who received tumor resection and 50 thyroid benign lesions (TBL) patients. KRT15 in formalin-fixed paraffin-embedded lesion specimens of all subjects was detected by immunohistochemistry (IHC). RESULTS KRT15 was reduced in PTC patients compared to TBL patients (P < 0.001). Furthermore, KRT15 was negatively associated with tumor size (P = 0.017), extrathyroidal invasion (P = 0.007), pathological tumor (pT) stage (P < 0.001), and postoperative radioiodine application (P = 0.008) in PTC patients. Regarding prognostic value, high KRT15 (cut-off by an IHC value of 3) is linked with prolonged accumulating disease-free survival (DFS) (P = 0.008) and overall survival (OS) (P = 0.008) in PTC patients. Also, the multivariate Cox regression model showed that high KRT15 (vs. low) was an independent factor for longer DFS (hazard ratio = 0.433, P = 0.049), but not for OS (P > 0.050) in PTC patients. Subgroup analyses revealed that KRT15 possessed a better prognostic value in PTC patients with age ≥ 55 years, tumor size > 4 cm, pathological node stage 1, or pathological tumor-node-metastasis stage ≤ 2 (all P < 0.050). CONCLUSION Increased tumor KRT15 associates with a lower invasive degree, prolonged DFS, and OS, revealing its prognostic utility in PTC patients undergoing tumor resection.
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Affiliation(s)
- Xianguang Yang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China
| | - Zhonghao Liu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China
| | - Xueqian Wang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China
| | - Zheng Han
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China
| | - Cong Zhang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China
| | - Lunhua Guo
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Harbin, 150080, China.
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10
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Janesick A, Shelansky R, Gottscho AD, Wagner F, Williams SR, Rouault M, Beliakoff G, Morrison CA, Oliveira MF, Sicherman JT, Kohlway A, Abousoud J, Drennon TY, Mohabbat SH, Taylor SEB. High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis. Nat Commun 2023; 14:8353. [PMID: 38114474 PMCID: PMC10730913 DOI: 10.1038/s41467-023-43458-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/09/2023] [Indexed: 12/21/2023] Open
Abstract
Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.
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11
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Wang J, Zhu G. Silencing of keratin 15 impairs viability and mobility while facilitating the doxorubicin chemosensitivity by inactivating the β‑catenin pathway in liver cancer. Oncol Lett 2023; 26:447. [PMID: 37720670 PMCID: PMC10502946 DOI: 10.3892/ol.2023.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/11/2023] [Indexed: 09/19/2023] Open
Abstract
Keratin 15 (KRT15) regulates the invasion as well as the stemness and is associated with tumor size and metastasis of several gastrointestinal cancers apart from liver cancer. The present study aimed to explore the effect of KRT15 knockdown on liver cancer malignant behaviors and its interaction with the β-catenin pathway. Small interfering (si)-KRT15 and si-negative control (NC) were transfected into liver cancer cell lines, followed by the addition or not of CHIR-99021 (a β-catenin agonist). Cell viability, invasion, apoptosis, and the half maximal inhibitory concentration (IC50) value of doxorubicin (Dox) were then assessed. The present study illustrated that KRT15 gene and protein expression levels were upregulated in most liver cancer cell lines (Huh7, PLC, Hep3B and HepG2) compared to the normal liver cell line THLE-2. si-KRT15 reduced cell viability and invasive cell count while promoting the apoptosis rate in Huh7 and HepG2 cells. In addition, si-KRT15 also reduced the IC50 value of Dox. Furthermore, si-KRT15 inactivated the β-catenin pathway as reflected by β-catenin, cyclin D1 and c-Myc expression levels in Huh7 and HepG2 cells. Subsequently, CHIR-99021 treatment increased the cell viability and invasive cell count while reducing the apoptosis rate in Huh7 and HepG2 cells. Concurrently, the IC50 value of Dox was also increased. Notably, CHIR-99021 treatment attenuated the effect of si-KRT15 on mediating the aforementioned Huh7 and HepG2 cell malignant behaviors and Dox chemosensitivity. In conclusion, KRT15 knockdown suppressed viability and mobility but facilitated Dox chemosensitivity via inactivating the β-catenin pathway in liver cancer, suggesting its potential as a target for liver cancer treatment.
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Affiliation(s)
- Junying Wang
- Department of Interventional Radiology and Vascular Surgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Guangyu Zhu
- Department of Interventional Radiology and Vascular Surgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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12
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Lin X, Dong Y, Gu Y, Kapoor A, Peng J, Su Y, Wei F, Wang Y, Yang C, Gill A, Neira SV, Tang D. Taxifolin Inhibits Breast Cancer Growth by Facilitating CD8+ T Cell Infiltration and Inducing a Novel Set of Genes including Potential Tumor Suppressor Genes in 1q21.3. Cancers (Basel) 2023; 15:3203. [PMID: 37370814 DOI: 10.3390/cancers15123203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/27/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Taxifolin inhibits breast cancer (BC) via novel mechanisms. In a syngeneic mouse BC model, taxifolin suppressed 4T-1 cell-derived allografts. RNA-seq of 4T-1 tumors identified 36 differentially expressed genes (DEGs) upregulated by taxifolin. Among their human homologues, 19, 7, and 2 genes were downregulated in BCs, high-proliferative BCs, and BCs with high-fatality risks, respectively. Three genes were established as tumor suppressors and eight were novel to BC, including HNRN, KPRP, CRCT1, and FLG2. These four genes exhibit tumor suppressive actions and reside in 1q21.3, a locus amplified in 70% recurrent BCs, revealing a unique vulnerability of primary and recurrent BCs with 1q21.3 amplification with respect to taxifolin. Furthermore, the 36 DEGs formed a multiple gene panel (DEG36) that effectively stratified the fatality risk in luminal, HER2+, and triple-negative (TN) equivalent BCs in two large cohorts: the METABRIC and TCGA datasets. 4T-1 cells model human TNBC cells. The DEG36 most robustly predicted the poor prognosis of TNBCs and associated it with the infiltration of CD8+ T, NK, macrophages, and Th2 cells. Of note, taxifolin increased the CD8+ T cell content in 4T-1 tumors. The DEG36 is a novel and effective prognostic biomarker of BCs, particularly TNBCs, and can be used to assess the BC-associated immunosuppressive microenvironment.
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Affiliation(s)
- Xiaozeng Lin
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Ying Dong
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yan Gu
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Jingyi Peng
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yingying Su
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital of Shenzhen City, Shenzhen 518174, China
| | - Yanjun Wang
- Jilin Jianwei Songkou Biotechnology Co., Ltd., Changchun 510664, China
| | - Chengzhi Yang
- Benda International INC., Ottawa, ON K1X 0C1, Canada
| | - Armaan Gill
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Sandra Vega Neira
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
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13
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Zhang Z, Wang H, Jin Y, Zhou J, Chu C, Tang F, Zou L, Zou Q. KRT15 in early breast cancer screening and correlation with HER2 positivity, pathological grade and N stage. Biomark Med 2023; 17:553-562. [PMID: 37814985 DOI: 10.2217/bmm-2023-0130] [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] [Indexed: 10/11/2023] Open
Abstract
Objective: This study was designed to explore KRT15 dysregulation and its correlation with clinical characteristics among ductal carcinoma in situ (DCIS), DCIS with microinvasion (DCIS-MI) and invasive breast cancer (IBC) patients. Methods: KRT15 from lesion samples of 50 DCIS patients, 48 DCIS-MI patients and 50 IBC patients was detected by immunohistochemistry. Results: KRT15 discriminated IBC patients from DCIS patients (area under the curve [AUC] = 0.895; 95% CI = 0.836-0.954) and DCIS-MI patients (AUC = 0.707; 95% CI = 0.606-0.808). In DCIS patients, KRT15 was negatively correlated with pathological grade (p = 0.015). In DCIS-MI patients, KRT15 was positively related to estrogen receptor positivity but negatively associated with Ki-67 (both p < 0.05). In IBC patients, KRT15 was negatively linked to HER2 positivity, histological grade, N stage and tumor node metastasis stage (all p < 0.05). Conclusion: KRT15 assessment may help with early breast cancer screening.
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Affiliation(s)
- Zijing Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Hongying Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yiting Jin
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jian Zhou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Chengyu Chu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Feng Tang
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Liping Zou
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qiang Zou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
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14
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Takan I, Karakülah G, Louka A, Pavlopoulou A. "In the light of evolution:" keratins as exceptional tumor biomarkers. PeerJ 2023; 11:e15099. [PMID: 36949761 PMCID: PMC10026720 DOI: 10.7717/peerj.15099] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Keratins (KRTs) are the intermediate filament-forming proteins of epithelial cells, classified, according to their physicochemical properties, into "soft" and "hard" keratins. They have a key role in several aspects of cancer pathophysiology, including cancer cell invasion and metastasis, and several members of the KRT family serve as diagnostic or prognostic markers. The human genome contains both, functional KRT genes and non-functional KRT pseudogenes, arranged in two uninterrupted clusters on chromosomes 12 and 17. This characteristic renders KRTs ideal for evolutionary studies. Herein, comprehensive phylogenetic analyses of KRT homologous proteins in the genomes of major taxonomic divisions were performed, so as to fill a gap in knowledge regarding the functional implications of keratins in cancer biology among tumor-bearing species. The differential expression profiles of KRTs in diverse types of cancers were investigated by analyzing high-throughput data, as well. Several KRT genes, including the phylogenetically conserved ones, were found to be deregulated across several cancer types and to participate in a common protein-protein interaction network. This indicates that, at least in cancer-bearing species, these genes might have been under similar evolutionary pressure, perhaps to support the same important function(s). In addition, semantic relations between KRTs and cancer were detected through extensive text mining. Therefore, by applying an integrative in silico pipeline, the evolutionary history of KRTs was reconstructed in the context of cancer, and the potential of using non-mammalian species as model organisms in functional studies on human cancer-associated KRT genes was uncovered.
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Affiliation(s)
- Işıl Takan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aikaterini Louka
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Athens, Greece
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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15
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Wardale L, Cardenas R, Gnanapragasam VJ, Cooper CS, Clark J, Brewer DS. Combining Molecular Subtypes with Multivariable Clinical Models Has the Potential to Improve Prediction of Treatment Outcomes in Prostate Cancer at Diagnosis. Curr Oncol 2022; 30:157-170. [PMID: 36661662 PMCID: PMC9857957 DOI: 10.3390/curroncol30010013] [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: 11/24/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Clinical management of prostate cancer is challenging because of its highly variable natural history and so there is a need for improved predictors of outcome in non-metastatic men at the time of diagnosis. In this study we calculated the model score from the leading clinical multivariable model, PREDICT prostate, and the poor prognosis DESNT molecular subtype, in a combined expression and clinical dataset that were taken from malignant tissue at prostatectomy (n = 359). Both PREDICT score (p < 0.0001, IQR HR = 1.59) and DESNT score (p < 0.0001, IQR HR = 2.08) were significant predictors for time to biochemical recurrence. A joint model combining the continuous PREDICT and DESNT score (p < 0.0001, IQR HR = 1.53 and 1.79, respectively) produced a significantly improved predictor than either model alone (p < 0.001). An increased probability of mortality after diagnosis, as estimated by PREDICT, was characterised by upregulation of cell-cycle related pathways and the downregulation of metabolism and cholesterol biosynthesis. The DESNT molecular subtype has distinct biological characteristics to those associated with the PREDICT model. We conclude that the inclusion of biological information alongside current clinical prognostic tools has the potential to improve the ability to choose the optimal treatment pathway for a patient.
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Affiliation(s)
- Lewis Wardale
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ryan Cardenas
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vincent J. Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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16
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Yang H, Li A, Li A, Zhao F, Zhang T. Upregulated keratin 15 links to the occurrence of lymphovascular invasion, stromal cervical invasion as well as unfavorable survival profile in endometrial cancer patients. Medicine (Baltimore) 2022; 101:e29686. [PMID: 35866777 PMCID: PMC9302346 DOI: 10.1097/md.0000000000029686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Keratin 15 (KRT15) overexpression links with tumor initiation, metastasis, and poor survival in several solid carcinomas. While its clinical relevance is scarcely reported in endometrial cancer (EC). Therefore, the current study aimed to investigate the abnormal expression of KRT15 and its correlation with clinical characteristics, survival in EC patients. Totally, 135 surgical EC patients were enrolled. KRT15 protein expression in formalin-fixed and paraffin-embedded tumor and adjuvant tissues was detected by immunohistochemical staining; meanwhile, KRT15 mRNA expression in fresh-frozen tumor and adjacent tissues was detected by reverse transcription-quantitative polymerase chain reaction. KRT15 protein and mRNA expressions were higher in tumor tissue compared with adjacent tissue (both P < .001). Elevated KRT15 protein expression was correlated with the occurrence of lymphovascular invasion (P = .010) and more advanced International Federation of Gynecology and Obstetrics stage (P = .018); meanwhile, elevated KRT15 mRNA expression was linked with more advanced International Federation of Gynecology and Obstetrics stage (P = .038) and marginally associated with the occurrence of stromal cervical invasion (P = .052). Besides, KRT15 protein and mRNA expressions were not correlated with other clinical features (all P > .05). KRT15 protein high was marginally correlated with poor accumulating disease-free survival (DFS) (P = .091) and overall survival (OS) (P = .059); meanwhile, the correlation of KRT15 mRNA expression with accumulating DFS (P = .212) and OS (P = .092) was even weaker. However, multivariate Cox's regressions showed that tumor KRT15 protein (high vs low) was independently correlated with poor DFS (P = .045) and OS (P = .043). KRT15 is abnormally increased in EC tissue, meanwhile, its upregulation links to the occurrence of lymphovascular invasion, stromal cervical invasion, and poor prognosis in EC patients.
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Affiliation(s)
- Hongxiang Yang
- Department of Gynaecology, HanDan Central Hospital, Handan, China
| | - Aijing Li
- Department of Gynaecology, RenQiu People Hospital, Cangzhou, China
| | - Aili Li
- Department of Gynaecology, HanDan Central Hospital, Handan, China
- *Correspondence: Aili Li, Department of Gynaecology, HanDan Central Hospital, No. 15 Zhonghua South Street, Hanshan District, Handan 056001, China (e-mail: )
| | - Fei Zhao
- Department of Surgery, HanDan Central Hospital, Handan, China
| | - Tongyan Zhang
- Department of Gynaecology, HanDan Central Hospital, Handan, China
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17
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Chen W, Miao C. KRT15 promotes colorectal cancer cell migration and invasion through β-catenin/MMP-7 signaling pathway. Med Oncol 2022; 39:68. [PMID: 35477819 DOI: 10.1007/s12032-021-01619-2] [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: 07/14/2021] [Accepted: 11/20/2021] [Indexed: 11/30/2022]
Abstract
KRT15 has been reported to act as an oncogene in colorectal cancer. However, whether KRT15 promotes colorectal cancer migration and invasion remain unclear. In this study, western blot and qRT-PCR assay were used to determine the expression of KRT15 in colorectal cancer cells. Wound-healing and transwell migration assay were performed to assess the migration of colorectal cancer cells. Matrigel transwell invasion assay was employed to examine the invasion of colorectal cancer cells. We found that KRT15 was highly expressed in colorectal cancer cells. Ectopic expression of KRT15 dramatically promoted colorectal cancer cell migration and invasion. Conversely, silencing KRT15 remarkably suppressed the migration and invasion of colorectal cancer cells. Importantly, we found that MMP-7 was crucial for KRT15-induced migration and invasion of colorectal cancer cells. Knockdown of MMP-7 significantly diminished the migration and invasion induced by KRT15; overexpression of MMP-7 almost completely rescued the inhibitory effects of KRT15 shRNAs on colorectal cancer cell migration and invasion. In addition, by gain- and loss-of function, we confirmed that β-catenin was responsible for the increased expression of MMP-7 induced by KRT15 colorectal cancer cell lines. In conclusion, KRT15 promotes migration and invasion of colorectal cancer cell at least partly through β-catenin/MMP7 signaling pathway, suggesting KRT15 is a potential therapeutic target for patients with metastatic colorectal cancer.
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Affiliation(s)
- Weida Chen
- Department of Retroperitoneal Tumor Surgery, Peking University International Hospital (PKUIH), Beijing, 102206, People's Republic of China
| | - Chengli Miao
- Department of Retroperitoneal Tumor Surgery, Peking University International Hospital (PKUIH), Beijing, 102206, People's Republic of China.
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18
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Barrón-Gallardo CA, Garcia-Chagollán M, Morán-Mendoza AJ, Delgadillo-Cristerna R, Martínez-Silva MG, Aguilar-Lemarroy A, Jave-Suárez LF. Transcriptomic Analysis of Breast Cancer Patients Sensitive and Resistant to Chemotherapy: Looking for Overall Survival and Drug Resistance Biomarkers. Technol Cancer Res Treat 2022; 21:15330338211068965. [PMID: 34981997 PMCID: PMC8733364 DOI: 10.1177/15330338211068965] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Worldwide breast cancer ranks first in mortality and incidence rates in women over 20 years old. Rather than one disease, breast cancer is a heterogeneous group of diseases that express distinct molecular profiles. Neoadjuvant chemotherapy is an important therapeutic strategy for breast cancer patients independently of their molecular subtype, with the drawback of resistance development. In addition, chemotherapy has adverse effects that combined with resistance could contribute to lower overall survival. Although great efforts have been made to find diagnostic and prognostic biomarkers for breast cancer and for response to targeted and immune therapy for this pathology, little has been explored regarding biomarkers of response to anthracyclines and taxanes based neoadjuvant chemotherapy. This work aimed to evaluate the molecular profile of patients who received neoadjuvant chemotherapy to identify differentially expressed genes (DEGs) that could be used as biomarkers of chemotherapy response and overall survival. Breast cancer patients who were candidates for neoadjuvant chemotherapy were enrolled in this study. After treatment and according to their pathological response, they were assigned as sensitive or resistant. To evaluate DEGs, Gene Ontology, Kyoto Encyclopedia Gene and Genome (KEGG), and protein–protein interactions, RNA-seq information from all patients was obtained by next-generation sequencing. A total of 1985 DEGs were found, and KEGG analysis indicated a great number of DEGs in metabolic pathways, pathways in cancer, cytokine–cytokine receptor interactions, and neuroactive ligand-receptor interactions. A selection of 73 DEGs was used further for an analysis of overall survival using the METABRIC study and the ductal carcinoma dataset of The Cancer Genome Atlas (TCGA) database. Nine DEGs correlated with overall survival, of which the subexpression of C1QTNF3, CTF1, OLFML3, PLA2R1, PODN, KRT15, HLA-A, and the overexpression of TUBB and TCP1 were found in resistant patients and related to patients with lower overall survival.
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Affiliation(s)
- Carlos A Barrón-Gallardo
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Mariel Garcia-Chagollán
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | | | | | | | - Luis F Jave-Suárez
- 37767Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
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19
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Nowak E, Bednarek I. Aspects of the Epigenetic Regulation of EMT Related to Cancer Metastasis. Cells 2021; 10:3435. [PMID: 34943943 PMCID: PMC8700111 DOI: 10.3390/cells10123435] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/28/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) occurs during the pathological process associated with tumor progression and is considered to influence and promote the metastatic cascade. Characterized by loss of cell adhesion and apex base polarity, EMT enhances cell motility and metastasis. The key markers of the epithelial to mesenchymal transition are proteins characteristic of the epithelial phenotype, e.g., E-cadherin, cytokeratins, occludin, or desmoplakin, the concentration and activity of which are reduced during this process. On the other hand, as a result of acquiring the characteristics of mesenchymal cells, an increased amount of N-cadherin, vimentin, fibronectin, or vitronectin is observed. Importantly, epithelial cells undergo partial EMT where some of the cells show both epithelial and mesenchymal characteristics. The significant influence of epigenetic regulatory mechanisms is observed in the gene expression involved in EMT. Among the epigenetic modifications accompanying incorrect genetic reprogramming in cancer are changes in the level of DNA methylation within the CpG islands and posttranslational covalent changes of histone proteins. All observed modifications, which are stable but reversible changes, affect the level of gene expression leading to the development and progression of the disease, and consequently affect the uncontrolled growth of the population of cancer cells.
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Affiliation(s)
- Ewa Nowak
- Department of Biotechnology and Genetic Engineering, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland;
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Abante J, Kambhampati S, Feinberg AP, Goutsias J. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Sci Rep 2021; 11:21619. [PMID: 34732768 PMCID: PMC8566571 DOI: 10.1038/s41598-021-00781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
High-throughput third-generation nanopore sequencing devices have enormous potential for simultaneously observing epigenetic modifications in human cells over large regions of the genome. However, signals generated by these devices are subject to considerable noise that can lead to unsatisfactory detection performance and hamper downstream analysis. Here we develop a statistical method, CpelNano, for the quantification and analysis of 5mC methylation landscapes using nanopore data. CpelNano takes into account nanopore noise by means of a hidden Markov model (HMM) in which the true but unknown (“hidden”) methylation state is modeled through an Ising probability distribution that is consistent with methylation means and pairwise correlations, whereas nanopore current signals constitute the observed state. It then estimates the associated methylation potential energy function by employing the expectation-maximization (EM) algorithm and performs differential methylation analysis via permutation-based hypothesis testing. Using simulations and analysis of published data obtained from three human cell lines (GM12878, MCF-10A, and MDA-MB-231), we show that CpelNano can faithfully estimate DNA methylation potential energy landscapes, substantially improving current methods and leading to a powerful tool for the modeling and analysis of epigenetic landscapes using nanopore sequencing data.
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Affiliation(s)
- Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Sandeep Kambhampati
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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