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Feng S, Ning L, Zhang H, Wang Z, Lu Y. A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer. PeerJ 2024; 12:e17861. [PMID: 39119106 PMCID: PMC11308995 DOI: 10.7717/peerj.17861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/14/2024] [Indexed: 08/10/2024] Open
Abstract
Background As a heterogeneous malignancy, breast cancer (BRCA) shows high incidence and mortality. Discovering novel molecular markers and developing reliable prognostic models may improve the survival of BCRA. Methods The RNA-seq data of BRCA patients were collected from the training set The Cancer Genome Atlas (TCGA)-BRCA and validation set GSE20685 in the Gene Expression Omnibus (GEO) databases. The "GSVA" R package was used to calculate the glycolysis score for each patient, based on which all the patients were divided into different glycolysis groups. The "limma" package was employed to perform differentially expression genes (DEGs) analysis. Key signature genes were selected by performing un/multivariate and least absolute shrinkage and selection operator (LASSO) C regression and used to develop a RiskScore model. The ESTIMATE and MCP-Counter algorithms were used for quantifying immune infiltration level. The functions of the genes were validated using Western blot, colony formation, transwell and wound-healing assay. Results The glycolysis score and prognostic analysis showed that high glycolysis score was related to tumorigenesis pathway and a poor prognosis in BRCA as overactive glycolysis inhibited the normal functions of immune cells. Subsequently, we screened five key prognostic genes using the LASSO Cox regression analysis and used them to establish a RiskScore with a high classification efficiency. Based on the results of the RiskScore, it was found that patients in the high-risk group had significantly unfavorable immune infiltration and prognostic outcomes. A nomogram integrating the RiskScore could well predict the prognosis for BRCA patients. Knockdown of PSCA suppressed cell proliferation, invasion and migration of BRCA cells. Conclusion This study developed a glycolysis-related signature with five genes to distinguish between high-risk and low-risk BRCA patients. A nomogram developed on the basis of the RiskScore was reliable to predict BRCA survival. Our model provided clinical guidance for the treatment of BRCA patients.
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Affiliation(s)
- Sijie Feng
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Linwei Ning
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Huizhen Zhang
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Zhenhui Wang
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Yunkun Lu
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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2
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Xu Z, Ke Y, Feng Q, Tuerdimaimaiti A, Zhang D, Dong L, Liu A. Proteomic characteristics of the aqueous humor in Uyghur patients with pseudoexfoliation syndrome and pseudoexfoliative glaucoma. Exp Eye Res 2024; 243:109903. [PMID: 38642601 DOI: 10.1016/j.exer.2024.109903] [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: 01/05/2024] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Pseudoexfoliation syndrome (PEX) is characterized by the deposition of fibrous pseudoexfoliation material (PEXM) in the eye, and secondary glaucoma associated with this syndrome has a faster and more severe clinical course. The incidence of PEX and pseudoexfoliative glaucoma (PEXG) exhibits ethnic clustering; however, few proteomic studies related to PEX and PEXG have been conducted in Asian populations. Therefore, we aimed to conduct proteomic analysis on the aqueous humor (AH) obtained from Uyghur patients with cataracts, those with PEX and cataracts, and those with PEXG and cataracts to better understand the molecular mechanisms of the disease and identify its potential biomarkers. To this end, AH was collected from patients with cataracts (n = 10, control group), PEX with cataracts (n = 10, PEX group), and PEXG with cataracts (n = 10, PEXG group) during phacoemulsification. Label-free quantitative proteomic techniques combined with bioinformatics were used to identify and analyze differentially expressed proteins (DEPs) in the AH of PEX and PEXG groups. Then, independent AH samples (n = 12, each group) were collected to validate DEPs by enzyme-linked immunosorbent assay (ELISA). The PEX group exhibited 25 DEPs, while the PEXG group showed 44 DEPs, both compared to the control group. Subsequently, we found three newly identified proteins in both PEX and PEXG groups, wherein FRAS1-related extracellular matrix protein 2 (FREM2) and osteoclast-associated receptor (OSCAR) exhibited downregulation, whereas coagulation Factor IX (F9) displayed upregulation. Bioinformatics analysis suggested that extracellular matrix interactions, abnormal blood-derived proteins, and lysosomes were mainly involved in the process of PEX and PEXG, and the PPI network further revealed F9 may serve as a potential biomarker for both PEX and PEXG. In conclusion, this study provides new information for understanding the proteomics of AH in PEX and PEXG.
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Affiliation(s)
- Zhao Xu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yin Ke
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Qiang Feng
- Ophthalmology Department of People's Hospital of Hotan District, Xinjiang, China
| | | | - Dandan Zhang
- Ophthalmology Department of People's Hospital of Hotan District, Xinjiang, China
| | - Lijie Dong
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China.
| | - Aihua Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China.
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3
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Xu Y, Chen B, Guo Z, Chen C, Wang C, Zhou H, Zhang C, Feng Y. Identification of diagnostic markers for moyamoya disease by combining bulk RNA-sequencing analysis and machine learning. Sci Rep 2024; 14:5931. [PMID: 38467737 PMCID: PMC10928210 DOI: 10.1038/s41598-024-56367-w] [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: 09/27/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
Moyamoya disease (MMD) remains a chronic progressive cerebrovascular disease with unknown etiology. A growing number of reports describe the development of MMD relevant to infection or autoimmune diseases. Identifying biomarkers of MMD is to understand the pathogenesis and development of novel targeted therapy and may be the key to improving the patient's outcome. Here, we analyzed gene expression from two GEO databases. To identify the MMD biomarkers, the weighted gene co-expression network analysis (WGCNA) and the differential expression analyses were conducted to identify 266 key genes. The KEGG and GO analyses were then performed to construct the protein interaction (PPI) network. The three machine-learning algorithms of support vector machine-recursive feature elimination (SVM-RFE), random forest and least absolute shrinkage and selection operator (LASSO) were used to analyze the key genes and take intersection to construct MMD diagnosis based on the four core genes found (ACAN, FREM1, TOP2A and UCHL1), with highly accurate AUCs of 0.805, 0.903, 0.815, 0.826. Gene enrichment analysis illustrated that the MMD samples revealed quite a few differences in pathways like one carbon pool by folate, aminoacyl-tRNA biosynthesis, fat digestion and absorption and fructose and mannose metabolism. In addition, the immune infiltration profile demonstrated that ACAN expression was associated with mast cells resting, FREM1 expression was associated with T cells CD4 naive, TOP2A expression was associated with B cells memory, UCHL1 expression was associated with mast cells activated. Ultimately, the four key genes were verified by qPCR. Taken together, our study analyzed the diagnostic biomarkers and immune infiltration characteristics of MMD, which may shed light on the potential intervention targets of moyamoya disease patients.
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Affiliation(s)
- Yifan Xu
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Bing Chen
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Zhongxiang Guo
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Cheng Chen
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Chao Wang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Han Zhou
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Chonghui Zhang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China
| | - Yugong Feng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao City, 266000, China.
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4
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Cai Y, Wang S. Deeply integrating latent consistent representations in high-noise multi-omics data for cancer subtyping. Brief Bioinform 2024; 25:bbae061. [PMID: 38426322 PMCID: PMC10939425 DOI: 10.1093/bib/bbae061] [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: 08/24/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Cancer is a complex and high-mortality disease regulated by multiple factors. Accurate cancer subtyping is crucial for formulating personalized treatment plans and improving patient survival rates. The underlying mechanisms that drive cancer progression can be comprehensively understood by analyzing multi-omics data. However, the high noise levels in omics data often pose challenges in capturing consistent representations and adequately integrating their information. This paper proposed a novel variational autoencoder-based deep learning model, named Deeply Integrating Latent Consistent Representations (DILCR). Firstly, multiple independent variational autoencoders and contrastive loss functions were designed to separate noise from omics data and capture latent consistent representations. Subsequently, an Attention Deep Integration Network was proposed to integrate consistent representations across different omics levels effectively. Additionally, we introduced the Improved Deep Embedded Clustering algorithm to make integrated variable clustering friendly. The effectiveness of DILCR was evaluated using 10 typical cancer datasets from The Cancer Genome Atlas and compared with 14 state-of-the-art integration methods. The results demonstrated that DILCR effectively captures the consistent representations in omics data and outperforms other integration methods in cancer subtyping. In the Kidney Renal Clear Cell Carcinoma case study, cancer subtypes were identified by DILCR with significant biological significance and interpretability.
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Affiliation(s)
- Yueyi Cai
- Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming, 650504, Yunnan, China
| | - Shunfang Wang
- Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming, 650504, Yunnan, China
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Wang L, Liu J, Chen F, Li G, Wang J, Chan DSH, Wong CY, Wang W, Leung CH. A Switch-On Affinity-Based Iridium(III) Conjugate Probe for Imaging Mitochondrial Glutathione S-Transferase in Breast Cancer Cells. Bioconjug Chem 2023; 34:1727-1737. [PMID: 37750807 DOI: 10.1021/acs.bioconjchem.3c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Glutathione S-transferase is heterogeneously expressed in breast cancer cells and is therefore emerging as a potential diagnostic biomarker for studying the heterogeneity of breast cancers. However, available fluorescent probes for GSTs depend heavily on GSTs-catalyzed glutathione (GSH) nucleophilic substitution reactions, making them susceptible to interference by the high concentration of nucleophilic species in the cellular environment. Moreover, the functions of subcellular GSTs are generally overlooked due to the lack of suitable luminescence probes. Herein, we report a highly selective affinity-based luminescence probe 1 for GST in breast cancer cells through tethering a GST inhibitor, ethacrynic acid, to an iridium(III) complex. Compared to activity-based probes which require the use of GSH, this probe could image GST-pi in the mitochondria by directly adducting to GST-pi (or potentially GST-pi/GS) in living cells. Probe 1 possesses desirable photophysical properties including a lifetime of 911 ns, a Stokes shift of 343 nm, and high photostability. The "turn on" luminescence mode of the probe enables highly selective detection of the GST with a limit of detection of 1.01 μM, while its long emission lifetime allows sensitive detection in organic dye-spiked autofluorescence samples by a time-resolved mode. The probe was further applied to specifically and quantitatively visualize MDA-MB-231 cells via specific binding to mitochondrial GST, and could differentiate breast cell lines based on their expression levels of GST. To the best of our knowledge, this probe is the first affinity-based iridium(III) imaging probe for the subcellular GST. Our work provides a valuable tool for unmasking the diverse roles of a subcellular GST in living systems, as well as for studying the heterogeneity of breast cancers.
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Affiliation(s)
- Ling Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Jingqi Liu
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
| | - Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Jing Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
| | | | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Hong Kong, 999077, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, 999078, China
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao, 999078, China
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Capik O, Gundogdu B, Tatar A, Sahin A, Chen F, Creighton CJ, Karatas OF. Oncogenic miR-1825 promotes head and neck carcinogenesis via targeting FREM1. J Cell Biochem 2023; 124:1628-1645. [PMID: 37683055 DOI: 10.1002/jcb.30473] [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: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignant cancer type worldwide. Although the therapeutic modalities currently used for patients with HNSCC improved in recent decades, HNSCC prognosis is still poor. Therefore, it is an urgent necessity to understand the pathogenesis of HNSCC, to develop novel and effective treatment strategies, and to characterize and identify the oncogenes that are responsible for an aggressive HNSCC phenotype. In this study, we aimed to better understand the roles of miR-1825 in the pathogenesis of HNSCC. We examined the impacts of miR-1825 deregulation on the cancer-associated phenotypes using in vitro tests evaluating cell viability, clonogenicity, cell migration, invasion, apoptosis, and stem cell characteristics. In addition, we investigated the effects of miR-1825 overexpression on the tumor formation capacity of head and neck cancer cells in vivo using nude mice. We searched for potential targets of miR-1825 using microarray analysis and luciferase assay. We found that miR-1825 expression is upregulated in head and neck cells and clinical tumor samples in comparison to corresponding controls, where it potentially acts as an oncogene. We, then, showed that ectopic miR-1825 overexpression promotes cellular phenotypes related to head and neck cancer progression in vitro and has a stimulating potential on cancer formation in vivo. We also identified FREM1 as a direct target of miR-1825 and demonstrated its reduced expression in HNSCC samples using immunohistochemistry analysis. Collectively, we suggest that the miR-1825/FREM1 axis serves as an important mediator of HNSCC development, where miR-1825 acts as an oncogene.
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Affiliation(s)
- Ozel Capik
- Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Betul Gundogdu
- Department of Medical Pathology, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Arzu Tatar
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Abdulkadir Sahin
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Fengju Chen
- Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Omer Faruk Karatas
- Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
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Vlajic K, Pennington Kluger H, Bie W, Merrill BJ, Nonn L, Kajdacsy-Balla A, Tyner AL. Appearance of tuft cells during prostate cancer progression. Oncogene 2023; 42:2374-2385. [PMID: 37386128 PMCID: PMC10374444 DOI: 10.1038/s41388-023-02743-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023]
Abstract
Tuft cells are chemosensory epithelial cells that increase in number following infection or injury to robustly activate the innate immune response to alleviate or promote disease. Recent studies of castration resistant prostate cancer and its subtype, neuroendocrine prostate cancer, revealed Pou2f3+ populations in mouse models. The transcription factor Pou2f3 is a master regulator of the tuft cell lineage. We show that tuft cells are upregulated early during prostate cancer development, and their numbers increase with progression. Cancer-associated tuft cells in the mouse prostate express DCLK1, COX1, COX2, while human tuft cells express COX1. Mouse and human tuft cells exhibit strong activation of signaling pathways including EGFR and SRC-family kinases. While DCLK1 is a mouse tuft cell marker, it is not present in human prostate tuft cells. Tuft cells that appear in mouse models of prostate cancer display genotype-specific tuft cell gene expression signatures. Using bioinformatic analysis tools and publicly available datasets, we characterized prostate tuft cells in aggressive disease and highlighted differences between tuft cell populations. Our findings indicate that tuft cells contribute to the prostate cancer microenvironment and may promote development of more advanced disease. Further research is needed to understand contributions of tuft cells to prostate cancer progression.
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Affiliation(s)
- Katarina Vlajic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Hannah Pennington Kluger
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Wenjun Bie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
- The University of Illinois Cancer Center, Chicago, IL, 60607, USA
| | - Larisa Nonn
- The University of Illinois Cancer Center, Chicago, IL, 60607, USA
- The Department of Pathology, at the University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Andre Kajdacsy-Balla
- The University of Illinois Cancer Center, Chicago, IL, 60607, USA
- The Department of Pathology, at the University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Angela L Tyner
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- The University of Illinois Cancer Center, Chicago, IL, 60607, USA.
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Li L, Yang W, Jia D, Zheng S, Gao Y, Wang G. Establishment of a N1-methyladenosine-related risk signature for breast carcinoma by bioinformatics analysis and experimental validation. Breast Cancer 2023:10.1007/s12282-023-01458-1. [PMID: 37178414 DOI: 10.1007/s12282-023-01458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023]
Abstract
OBJECTIVES Breast carcinoma (BRCA) has resulted in a huge health burden globally. N1-methyladenosine (m1A) RNA methylation has been proven to play key roles in tumorigenesis. Nevertheless, the function of m1A RNA methylation-related genes in BRCA is indistinct. METHODS The RNA sequencing (RNA-seq), copy-number variation (CNV), single-nucleotide variant (SNV), and clinical data of BRCA were acquired via The Cancer Genome Atlas (TCGA) database. In addition, the GSE20685 dataset, the external validation set, was acquired from the Gene Expression Omnibus (GEO) database. 10 m1A RNA methylation regulators were obtained from the previous literature, and further analyzed through differential expression analysis by rank-sum test, mutation by SNV data, and mutual correlation by Pearson Correlation Analysis. Furthermore, the differentially expressed m1A-related genes were selected through overlapping m1A-related module genes obtained by weighted gene co-expression network analysis (WGCNA), differentially expressed genes (DEGs) in BRCA and DEGs between high- and low- m1A score subgroups. The m1A-related model genes in the risk signature were derived by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. In addition, a nomogram was built through univariate and multivariate Cox analyses. After that, the immune infiltration between the high- and low-risk groups was investigated through ESTIMATE and CIBERSORT. Finally, the expression trends of model genes in clinical BRCA samples were further confirmed by quantitative real-time PCR (RT‒qPCR). RESULTS Eighty-five differentially expressed m1A-related genes were obtained. Among them, six genes were selected as prognostic biomarkers to build the risk model. The validation results of the risk model showed that its prediction was reliable. In addition, Cox independent prognosis analysis revealed that age, risk score, and stage were independent prognostic factors for BRCA. Moreover, 13 types of immune cells were different between the high- and low-risk groups and the immune checkpoint molecules TIGIT, IDO1, LAG3, ICOS, PDCD1LG2, PDCD1, CD27, and CD274 were significantly different between the two risk groups. Ultimately, RT-qPCR results confirmed that the model genes MEOX1, COL17A1, FREM1, TNN, and SLIT3 were significantly up-regulated in BRCA tissues versus normal tissues. CONCLUSIONS An m1A RNA methylation regulator-related prognostic model was constructed, and a nomogram based on the prognostic model was constructed to provide a theoretical reference for individual counseling and clinical preventive intervention in BRCA.
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Affiliation(s)
- Leilei Li
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Wenhui Yang
- Department of Digestive Oncology, Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, People's Republic of China
| | - Daqi Jia
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Shiqi Zheng
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Yuzhe Gao
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
| | - Guanghui Wang
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
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Wang G, Wang Z, Lu H, Zhao Z, Guo L, Kong F, Wang A, Zhao S. Comprehensive analysis of FRAS1/FREM family as potential biomarkers and therapeutic targets in renal clear cell carcinoma. Front Pharmacol 2022; 13:972934. [PMID: 36249757 PMCID: PMC9558830 DOI: 10.3389/fphar.2022.972934] [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: 06/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: FRAS1 (Fraser syndrome protein 1), together with FREM1 (the Fras1-related extracellular matrix proteins 1) and FREM2, belonging to the FRAS1/FREM extracellular matrix protein family, are considered to play essential roles in renal organogenesis and cancer progression. However, their roles in kidney renal clear cell carcinoma (KIRC) remain to be elucidated.Methods: FRAS1/FREM RNA expression analysis was performed using TCGA/GTEx databases, and valided using GEO databases and real-time PCR. Protein expression was peformed using CPTAC databases. Herein, we employed an array of bioinformatics methods and online databases to explore the potential oncogenic roles of FRAS1/FREM in KIRC.Results: We found that FRAS1, FREM1 and FREM2 genes and proteins expression levels were significantly decreased in KIRC tissues than in normal tissues. Decreased FRAS1/FREM expression levels were significantly associated with advanced clinicopathological parameters (pathological stage, grade and tumor metastasis status). Notably, the patients with decreased FRAS1/FREM2 expression showed a high propensity for metastasis and poor prognosis. FRAS1/FREM were correlated with various immune infiltrating cells, especially CD4+ T cells and its corresponding subsets (Th1, Th2, Tfh and Tregs). FRAS1 and FREM2 had association with DNA methylation and their single CpG methylation levels were associated with prognosis. Moreover, FRAS1/FREM might exert antitumor effects by functioning in key oncogenic signalling pathways and metabolic pathways. Drug sensitivity analysis indicated that high FRAS1 and FREM2 expression can be a reliable predictor of targeted therapeutic drug response, highlighting the potential as anticancer drug targets.Conclusion: Together, our results indicated that FRAS1/FREM family members could be potential therapeutic targets and valuable prognostic biomarkers of KIRC.
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Affiliation(s)
- Ganggang Wang
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- Department of Urology, Maternal and Child Health Care Hospital of Shandong Province, Shandong University, Jinan, Shandong, China
| | - Zheng Wang
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Haiquan Lu
- Advanced Medical Research Institute and Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhiqun Zhao
- Advanced Medical Research Institute and Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Liqiang Guo
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Feng Kong
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Aizhen Wang
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Shengtian Zhao
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- Binzhou Medical University, Binzhou, Shandong, China
- *Correspondence: Shengtian Zhao,
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10
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Zhou T, Chen W, Wu Z, Cai J, Zhou C. A newly defined basement membrane-related gene signature for the prognosis of clear-cell renal cell carcinoma. Front Genet 2022; 13:994208. [PMID: 36186476 PMCID: PMC9520985 DOI: 10.3389/fgene.2022.994208] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Basement membranes (BMs) are associated with cell polarity, differentiation, migration, and survival. Previous studies have shown that BMs play a key role in the progression of cancer, and thus could serve as potential targets for inhibiting the development of cancer. However, the association between basement membrane-related genes (BMRGs) and clear cell renal cell carcinoma (ccRCC) remains unclear. To address that gap, we constructed a novel risk signature utilizing BMRGs to explore the relationship between ccRCC and BMs.Methods: We gathered transcriptome and clinical data from The Cancer Genome Atlas (TCGA) and randomly separated the data into training and test sets to look for new potential biomarkers and create a predictive signature of BMRGs for ccRCC. We applied univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses to establish the model. The risk signature was further verified and evaluated through principal component analysis (PCA), the Kaplan-Meier technique, and time-dependent receiver operating characteristics (ROC). A nomogram was constructed to predict the overall survival (OS). The possible biological pathways were investigated through functional enrichment analysis. In this study, we also determined tumor mutation burden (TMB) and performed immunological analysis and immunotherapeutic drug analysis between the high- and low-risk groups.Results: We identified 33 differentially expressed genes and constructed a risk model of eight BMRGs, including COL4A4, FREM1, CSPG4, COL4A5, ITGB6, ADAMTS14, MMP17, and THBS4. The PCA analysis showed that the signature could distinguish the high- and low-risk groups well. The K-M and ROC analysis demonstrated that the model could predict the prognosis well from the areas under the curves (AUCs), which was 0.731. Moreover, the nomogram showed good predictability. Univariate and multivariate Cox regression analysis validated that the model results supported the hypothesis that BMRGs were independent risk factors for ccRCC. Furthermore, immune cell infiltration, immunological checkpoints, TMB, and the half-inhibitory concentration varied considerably between high- and low-risk groups.Conclusion: Employing eight BMRGs to construct a risk model as a prognostic indicator of ccRCC could provide us with a potential progression trajectory as well as predictions of therapeutic response.
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Affiliation(s)
- Tao Zhou
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weikang Chen
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhigang Wu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Zhigang Wu, ; Jian Cai, ; Chaofeng Zhou,
| | - Jian Cai
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Zhigang Wu, ; Jian Cai, ; Chaofeng Zhou,
| | - Chaofeng Zhou
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Zhigang Wu, ; Jian Cai, ; Chaofeng Zhou,
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11
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Wang C, Zhang L, Ren L, Zhang G, Wan A, Xiong S, Tian H, Peng Z, Zhao T, Gao P, Sun N, Zhang Y, Qi X. A novel pyroptosis-related indicator of immune infiltration features and prognosis in breast cancer. Front Oncol 2022; 12:961500. [PMID: 36158689 PMCID: PMC9491236 DOI: 10.3389/fonc.2022.961500] [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: 06/04/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Breast cancer is the most common malignancy in women, and there is evidence for the dual role of cell pyroptosis in tumor development. However, little is known about the relationship between cell pyroptosis and breast cancer and its prognostic value. We aimed to construct a prognostic model using cell-pyroptosis-related genes to provide innovative insights into the prognosis and treatment of breast cancer. We screened candidate genes for pyroptosis using public databases and identified 10 cell pyroptosis signature genes with the random forest method. Finally, a nomogram for predicting 1-, 3-, and 5-year survival probabilities was constructed. The differences in immune cell distributions between survival periods were similar across the breast cancer datasets. The 10 identified key pyroptosis factors showed a significant correlation with Her2, tumor–node–metastasis (TNM) stage, and survival of breast cancer. The risk scores correlated positively with the infiltration features of naive B cells, CD8+ T cells, atpdelnd mast cells, while they correlated negatively with those of M0 macrophages and dendritic cells. In conclusion, our findings confirm that cell pyroptosis is closely associated with breast cancer. Importantly, the prognostic complex values generated from the 10 cell-pyroptosis-related genes based on various clinical features may provide an important basis for future studies on the prognosis of breast cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Na Sun
- *Correspondence: Na Sun, ; Yi Zhang, ; Xiaowei Qi,
| | - Yi Zhang
- *Correspondence: Na Sun, ; Yi Zhang, ; Xiaowei Qi,
| | - Xiaowei Qi
- *Correspondence: Na Sun, ; Yi Zhang, ; Xiaowei Qi,
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12
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Characterization of Butyrate-Resistant Colorectal Cancer Cell Lines and the Cytotoxicity of Anticancer Drugs against These Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6565300. [PMID: 35909471 PMCID: PMC9325644 DOI: 10.1155/2022/6565300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. The gut microbiota plays a critical role in homeostasis and carcinogenesis. Butyrate, a short-chain fatty acid produced by the gut microbiota, plays a role in intestinal homeostasis and acts as an anticancer agent by inhibiting growth and inducing apoptosis. However, microbiota studies have revealed an abnormally high abundance of butyrate-producing bacteria in patients with CRC and indicated that it leads to chemoresistance. We characterized butyrate resistance in HCT-116 and PMF-K014 CRC cells after treatment with a maximum butyrate concentration of 3.2 mM. The 50% inhibitory concentration of butyrate was increased in butyrate-resistant (BR) cells compared with that in parental (PT) cells. The mechanism of butyrate resistance was initially investigated by determining the expression of butyrate influx- and drug efflux-related genes. We found the increased expression of influx- and efflux-related genes in BR cells compared with that in PT cells. Proteomic data showed both identical and different proteins in PT and BR cells. Further analysis revealed the crossresistance of HCT-116 cells to metformin and oxaliplatin and that of PMF-K014 cells to 5-fluorouracil. Our findings suggest that the acquisition of butyrate resistance induces the development of chemoresistance in CRC cells, which may play an important role in CRC development, treatment, and metastasis.
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13
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Petersson A, Andersson N, Hau SO, Eberhard J, Karlsson J, Chattopadhyay S, Valind A, Elebro J, Nodin B, Leandersson K, Gisselsson D, Jirström K. Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer. Mol Cancer Res 2022; 20:749-761. [PMID: 35149544 PMCID: PMC9381114 DOI: 10.1158/1541-7786.mcr-21-0986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/05/2022] [Accepted: 02/04/2022] [Indexed: 01/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double IHC staining. Copy-number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, an FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated patients with PDAC. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected. IMPLICATIONS Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.
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Affiliation(s)
- Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sofie Olsson Hau
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jakob Eberhard
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Jacob Elebro
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Björn Nodin
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - David Gisselsson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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14
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Wang L, Yang X, Zhou F, Sun X, Li S. Circular RNA UBAP2 facilitates the cisplatin resistance of triple-negative breast cancer via microRNA-300/anti-silencing function 1B histone chaperone/PI3K/AKT/mTOR axis. Bioengineered 2022; 13:7197-7208. [PMID: 35263216 PMCID: PMC8973968 DOI: 10.1080/21655979.2022.2036894] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Circular RNAs (CircRNAs) have attracted increasing attention in the diagnosis and treatment of human cancers. CircUBAP2 has been identified to promote the progression of triple-negative breast cancer (TNBC), but the function of circUBAP2 in the cisplatin (DDP) resistance of TNBC remains obscure. Our investigation showed that circUBAP2 was significantly upregulated in DDP-resistant TNBC and TNBC sensitivity to DDP could be enhanced by silencing of circUBAP2. Moreover, circUBAP2 was revealed to be a ceRNA for miR-300 to upregulate the expression of anti-silencing function 1B histone chaperone (ASF1B). The effect of circUBAP2/miR-300/ASF1B axis on DDP resistance of TNBC was evaluated by rescue experiments, which demonstrated that circUBAP2 inhibited TNBC sensitivity to DDP through miR-300/ASF1B axis. Furthermore, it was discovered that ASF1B activated PI3K/AKT/mTOR signaling to facilitate the DDP resistance of TNBC cells. In summary, this research revealed a novel regulatory mechanism that circUBAP2 functioned as ceRNA of miR-300 to upregulate ASF1B, which further triggered the PI3K/AKT/mTOR (PAM) signaling to enhance the DDP resistance of TNBC.
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Affiliation(s)
- Leiming Wang
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province 223600, China
| | - Xi Yang
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province 223600, China
| | - Fei Zhou
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province 223600, China
| | - Xuesi Sun
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province 223600, China
| | - Shulin Li
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province 223600, China
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15
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Ko CY, Chu TH, Hsu CC, Chen HP, Huang SC, Chang CL, Tzou SJ, Chen TY, Lin CC, Shih PC, Lin CH, Chang CF, Lee YK. Bioinformatics Analyses Identify the Therapeutic Potential of ST8SIA6 for Colon Cancer. J Pers Med 2022; 12:jpm12030401. [PMID: 35330401 PMCID: PMC8953768 DOI: 10.3390/jpm12030401] [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: 01/26/2022] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Sialylation of glycoproteins is modified by distinct sialyltransferases such as ST3Gal, ST6Gal, ST6GalNAc, or ST8SIA with α2,3-, α2,6-, or α2,8-linkages. Alteration of these sialyltransferases causing aberrant sialylation is associated with the progression of colon cancer. However, among the ST8- sialyltransferases, the role of ST8SIA6 in colon cancer remains poorly understood. In this study, we explored the involvement of ST8SIA6 in colon cancer using multiple gene databases. The relationship between ST8SIA6 expression and tumor stages/grades was investigated by UALCAN analysis, and Kaplan–Meier Plotter analysis was used to analyze the expression of ST8SIA6 on the survival outcome of colon cancer patients. Moreover, the biological functions of ST8SIA6 in colon cancer were explored using LinkedOmics and cancer cell metabolism gene DB. Finally, TIMER and TISMO analyses were used to delineate ST8SIA6 levels in tumor immunity and immunotherapy responses, respectively. ST8SIA6 downregulation was associated with an advanced stage and poorly differentiated grade; however, ST8SIA6 expression did not affect the survival outcomes in patients with colon cancer. Gene ontology analysis suggested that ST8SIA6 participates in cell surface adhesion, angiogenesis, and membrane vesicle trafficking. In addition, ST8SIA6 levels affected immunocyte infiltration and immunotherapy responses in colon cancer. Collectively, these results suggest that ST8SIA6 may serve as a novel therapeutic target towards personalized medicine for colon cancer.
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Affiliation(s)
- Chou-Yuan Ko
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (S.-C.H.); (C.-L.C.); (S.-J.T.)
| | - Tian-Huei Chu
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
| | - Ching-Cheng Hsu
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (P.-C.S.); (C.-H.L.)
| | - Hsin-Pao Chen
- Department of Surgery, E-DA Hospital, I-Shou University, Kaohsiung 82445, Taiwan;
| | - Shih-Chung Huang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (S.-C.H.); (C.-L.C.); (S.-J.T.)
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Division of Cardiology, Department of Medicine, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Chen-Lin Chang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (S.-C.H.); (C.-L.C.); (S.-J.T.)
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Department of Psychiatry, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Shiow-Jyu Tzou
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (S.-C.H.); (C.-L.C.); (S.-J.T.)
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Department of Nursing, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Tung-Yuan Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
| | - Chia-Chen Lin
- Clinical Pathology Department, Chi Mei Medical Center, Tainan 71004, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pei-Chun Shih
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (P.-C.S.); (C.-H.L.)
| | - Chung-Hsien Lin
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (P.-C.S.); (C.-H.L.)
| | - Chuan-Fa Chang
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (P.-C.S.); (C.-H.L.)
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Correspondence: (C.-F.C.); (Y.-K.L.); Tel.: +886-6-235-3535 (ext. 5796) (C.-F.C.); +886-7-749-6751 (ext. 726201) (Y.-K.L.)
| | - Yung-Kuo Lee
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Correspondence: (C.-F.C.); (Y.-K.L.); Tel.: +886-6-235-3535 (ext. 5796) (C.-F.C.); +886-7-749-6751 (ext. 726201) (Y.-K.L.)
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16
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Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients. Int J Mol Sci 2022; 23:ijms23052835. [PMID: 35269977 PMCID: PMC8911431 DOI: 10.3390/ijms23052835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.
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17
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Kashem MA, Yuan XY, Li L, Kimani J, Plummer F, Luo M. TILRR (Toll-like Interleukin-1 Receptor Regulator), an Important Modulator of Inflammatory Responsive Genes, is Circulating in the Blood. J Inflamm Res 2021; 14:4927-4943. [PMID: 34594127 PMCID: PMC8478437 DOI: 10.2147/jir.s325553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/24/2021] [Indexed: 01/07/2023] Open
Abstract
Purpose TILRR (Toll-like interleukin-1 receptor regulator), a variant of FREM1 (Fras-related extracellular matrix 1), is a modulator of many genes in NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) signaling and inflammatory responses. It enhanced the expression of multiple genes in the NF-κB signaling pathway and promoted the production of multiple pro-inflammatory cytokines/chemokines. TILRR is an extracellular matrix protein and expressed in cells and tissues, and has never been considered to exist in the blood. The study aimed to identify circulating TILRR protein in human plasma as a biomarker of systemic inflammation. Methods and Results We developed a multiplex bead array method (Bio-Plex) using 4 monoclonal antibodies targeting different protein domains of FREM1/TILRR to investigate whether TILRR can be detected in blood plasma. The results of the multiplex bead array method were validated by Western blot analysis of affinity-purified TILRR from patient plasma samples. We subsequently analyzed 640 plasma samples from women enrolled in the Pumwani Sex Worker cohort (PSWC) (Nairobi, Kenya). Our study showed that TILRR exists in all patient plasma samples, but its quantities vary greatly among the patients, ranging from 2.38 ng/mL to 5196.79 ng/mL. The plasma TILRR below 2.38 ng/mL can only be detected by affinity purification and Western blot analysis. Conclusion Our in-house developed multiplex bead array method can successfully quantify TILRR protein in plasma samples. Because TILRR is an important modulator of many inflammation-responsive genes, it may be an inflammation biomarker in blood and play a role in modulating systemic inflammation.
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Affiliation(s)
- Mohammad Abul Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,JC Wilt Infectious Diseases Research Centre, Winnipeg, Mb, Canada.,Department of Microbiology and Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Xin-Yong Yuan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lin Li
- JC Wilt Infectious Diseases Research Centre, Winnipeg, Mb, Canada
| | - Joshua Kimani
- Institute for Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Francis Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,JC Wilt Infectious Diseases Research Centre, Winnipeg, Mb, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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18
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Zolotovskaia M, Tkachev V, Sorokin M, Garazha A, Kim E, Kantelhardt SR, Bikar SE, Zottel A, Šamec N, Kuzmin D, Sprang B, Moisseev A, Giese A, Efimov V, Jovčevska I, Buzdin A. Algorithmically Deduced FREM2 Molecular Pathway Is a Potent Grade and Survival Biomarker of Human Gliomas. Cancers (Basel) 2021; 13:4117. [PMID: 34439271 PMCID: PMC8394245 DOI: 10.3390/cancers13164117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 01/17/2023] Open
Abstract
Gliomas are the most common malignant brain tumors with high mortality rates. Recently we showed that the FREM2 gene has a role in glioblastoma progression. Here we reconstructed the FREM2 molecular pathway using the human interactome model. We assessed the biomarker capacity of FREM2 expression and its pathway as the overall survival (OS) and progression-free survival (PFS) biomarkers. To this end, we used three literature and one experimental RNA sequencing datasets collectively covering 566 glioblastomas (GBM) and 1097 low-grade gliomas (LGG). The activation level of deduced FREM2 pathway showed strong biomarker characteristics and significantly outperformed the FREM2 expression level itself. For all relevant datasets, it could robustly discriminate GBM and LGG (p < 1.63 × 10-13, AUC > 0.74). High FREM2 pathway activation level was associated with poor OS in LGG (p < 0.001), and low PFS in LGG (p < 0.001) and GBM (p < 0.05). FREM2 pathway activation level was poor prognosis biomarker for OS (p < 0.05) and PFS (p < 0.05) in LGG with IDH mutation, for PFS in LGG with wild type IDH (p < 0.001) and mutant IDH with 1p/19q codeletion(p < 0.05), in GBM with unmethylated MGMT (p < 0.05), and in GBM with wild type IDH (p < 0.05). Thus, we conclude that the activation level of the FREM2 pathway is a potent new-generation diagnostic and prognostic biomarker for multiple molecular subtypes of GBM and LGG.
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Affiliation(s)
- Marianna Zolotovskaia
- Omicsway Corp., Walnut, CA 91789, USA; (M.S.); (A.G.); (A.M.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
- Department of Oncology, Hematology and Radiotherapy, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victor Tkachev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
| | - Maxim Sorokin
- Omicsway Corp., Walnut, CA 91789, USA; (M.S.); (A.G.); (A.M.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
- Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Andrew Garazha
- Omicsway Corp., Walnut, CA 91789, USA; (M.S.); (A.G.); (A.M.)
| | - Ella Kim
- Clinic for Neurosurgery, Laboratory of Experimental Neurooncology, Johannes Gutenberg University Medical Centre, Langenbeckstrasse 1, 55124 Mainz, Germany; (E.K.); (S.R.K.); (B.S.)
| | - Sven Rainer Kantelhardt
- Clinic for Neurosurgery, Laboratory of Experimental Neurooncology, Johannes Gutenberg University Medical Centre, Langenbeckstrasse 1, 55124 Mainz, Germany; (E.K.); (S.R.K.); (B.S.)
| | - Sven-Ernö Bikar
- StarSEQ GmbH, Joh.-Joachim-Becher-Weg 30a, 55128 Mainz, Germany;
| | - Alja Zottel
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Neja Šamec
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Denis Kuzmin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
| | - Bettina Sprang
- Clinic for Neurosurgery, Laboratory of Experimental Neurooncology, Johannes Gutenberg University Medical Centre, Langenbeckstrasse 1, 55124 Mainz, Germany; (E.K.); (S.R.K.); (B.S.)
| | - Alexey Moisseev
- Omicsway Corp., Walnut, CA 91789, USA; (M.S.); (A.G.); (A.M.)
| | - Alf Giese
- Orthocentrum Hamburg, Hansastrasse 1, 20149 Hamburg, Germany;
| | - Victor Efimov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
| | - Ivana Jovčevska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Anton Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; (V.T.); (D.K.); (V.E.); (A.B.)
- Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1200 Brussels, Belgium
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The Potential Role of FREM1 and Its Isoform TILRR in HIV-1 Acquisition through Mediating Inflammation. Int J Mol Sci 2021; 22:ijms22157825. [PMID: 34360591 PMCID: PMC8346017 DOI: 10.3390/ijms22157825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
FREM1 (Fras-related extracellular matrix 1) and its splice variant TILRR (Toll-like interleukin-1 receptor regulator) have been identified as integral components of innate immune systems. The potential involvement of FREM1 in HIV-1 (human immunodeficiency virus 1) acquisition was suggested by a genome-wide SNP (single nucleotide polymorphism) analysis of HIV-1 resistant and susceptible sex workers enrolled in the Pumwani sex worker cohort (PSWC) in Nairobi, Kenya. The studies showed that the minor allele of a FREM1 SNP rs1552896 is highly enriched in the HIV-1 resistant female sex workers. Subsequent studies showed that FREM1 mRNA is highly expressed in tissues relevant to mucosal HIV-1 infection, including cervical epithelial tissues, and TILRR is a major modulator of many genes in the NF-κB signal transduction pathway. In this article, we review the role of FREM1 and TILRR in modulating inflammatory responses and inflammation, and how their influence on inflammatory responses of cervicovaginal tissue could enhance the risk of vaginal HIV-1 acquisition.
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